Running as unit: rb-build-amd64_31-48025.service ==================================================================================== Sat Jul 5 18:01:10 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_amd64_31) on jenkins, called using "ionos11-amd64 ionos5-amd64" as arguments. Sat Jul 5 18:01:10 UTC 2025 - actually running "reproducible_build.sh" (md5sum 44ec6a3142940d5e9a7ab76543d96029) as "/tmp/jenkins-script-3cZdgF0o" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Sat Jul 5 18:01:10 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos11-amd64.debian.net is marked as down. Sat Jul 5 18:01:10 UTC 2025 - checking via ssh if ionos11-amd64.debian.net is up. removed '/tmp/read-only-fs-test-UvUg6O' Sat Jul 5 18:01:11 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos5-amd64.debian.net is marked as down. Sat Jul 5 18:01:11 UTC 2025 - checking via ssh if ionos5-amd64.debian.net is up. removed '/tmp/read-only-fs-test-RKuTs7' ok, let's check if bcftools is building anywhere yet… ok, bcftools is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of bcftools in unstable on amd64 on jenkins now. 1st build will be done on ionos11-amd64.debian.net. 2nd build will be done on ionos5-amd64.debian.net. ============================================================================= Sat Jul 5 18:01:16 UTC 2025 I: starting to build bcftools/unstable/amd64 on jenkins on '2025-07-05 18:01' Sat Jul 5 18:01:16 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_31/48025/console.log 1751738476 amd64 unstable bcftools Sat Jul 5 18:01:16 UTC 2025 I: Downloading source for unstable/bcftools=1.21-1 --2025-07-05 18:01:16-- http://deb.debian.org/debian/pool/main/b/bcftools/bcftools_1.21-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2267 (2.2K) [text/prs.lines.tag] Saving to: ‘bcftools_1.21-1.dsc’ 0K .. 100% 250M=0s 2025-07-05 18:01:16 (250 MB/s) - ‘bcftools_1.21-1.dsc’ saved [2267/2267] --2025-07-05 18:01:16-- http://deb.debian.org/debian/pool/main/b/bcftools/bcftools_1.21-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2267 (2.2K) [text/prs.lines.tag] Saving to: ‘bcftools_1.21-1.dsc’ 0K .. 100% 250M=0s 2025-07-05 18:01:16 (250 MB/s) - ‘bcftools_1.21-1.dsc’ saved [2267/2267] Sat Jul 5 18:01:16 UTC 2025 I: bcftools_1.21-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: bcftools Binary: bcftools Architecture: any Version: 1.21-1 Maintainer: Debian Med Packaging Team Uploaders: Michael R. Crusoe , Étienne Mollier Homepage: https://samtools.github.io/bcftools/ Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/bcftools Vcs-Git: https://salsa.debian.org/med-team/bcftools.git Testsuite: autopkgtest Testsuite-Triggers: perl, tabix Build-Depends: debhelper-compat (= 13), zlib1g-dev, libbz2-dev, liblzma-dev, libhts-dev (>= 1.14), libgsl-dev, tabix , libio-pty-perl Package-List: bcftools deb science optional arch=any Checksums-Sha1: 7f367e0f03d4f56ca88d5f3a79435f196591fbce 3665160 bcftools_1.21.orig.tar.gz 5b3b3f9251d64665efa2c5ed61c6e2aef032cde1 7504 bcftools_1.21-1.debian.tar.xz Checksums-Sha256: 7484695c5d833fb1a89c2b886ec302db0514ba3c8e5ef7397b9302fa8bd37f8d 3665160 bcftools_1.21.orig.tar.gz d1332716453f270248afa7476a5a824b0289150a7829442f691559209dcc38cf 7504 bcftools_1.21-1.debian.tar.xz Files: e144a5777c606c69eb643ae8ff613dbb 3665160 bcftools_1.21.orig.tar.gz 756abc1b4df76e455bd705ddf6ef5c9e 7504 bcftools_1.21-1.debian.tar.xz Dgit: 1cbbbd21cccc5d95d73df54271b167d9e450842a debian archive/debian/1.21-1 https://git.dgit.debian.org/bcftools -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmeuYIEUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdpyzRAAlczvukE0/A+j5esHHalBAeaq8nnO SC4BULLNsaVcn31OlRTGS1RXt1zU6u3ise+jLfRMAbhM4Qx57Ek9S+2+uvX2M5lh 6Wlz3M6DvyTEXN0MZTztIinmdxODYf/IiD8d4qDf8KYZNBeKE+spfINNeRiWyl6e /QXwVTUB0jRc5ZBqsOONR4uOliMKk3LWUy3xwM3YzUKhVlFQpf2OJXk5bQSew6NM PIwjBLcHdDE42tplpMuRjT0FdWk4i8EeZlR8oIdBwoVc1ffNqRpWbz77OJouDhe8 dz7kPHok/2DEBod4k3yeIZH0deK+G47sycXhhSOA7IS+43opAYIHFscpHZMdnoaA lQjIMES546gBHagarHdb5dbHKcvWuq2aQdsuyc0Z2kOnS4Kaop/YugT14ba0pu73 50x5eyPJL2LgnFDb+36HygKNL0CCA6v6EOC7qEU5zzqkmXYXBWEKGxht4KvXbdtc NAvxqxbw2AtQF1kRH6dur00lo9ZCjVq+wa5NnQHZh+BILAIrdo8lpM5Gm6yCifwE 9HU+bY2IaF3LMMgTxvRVyT8yeu65YtA6FbZjnYW6Y0ZeVlQLFvn+830b4L4fWlt3 waTPrdRQcvexseaLFmxuZY2igfMRPtzyf3UXQaomDkitd4jC0WhH+Tg6OoTD88Fa IFTp1pvu+xmgjw4= =1qOu -----END PGP SIGNATURE----- Sat Jul 5 18:01:16 UTC 2025 I: Checking whether the package is not for us Sat Jul 5 18:01:16 UTC 2025 I: Starting 1st build on remote node ionos11-amd64.debian.net. Sat Jul 5 18:01:16 UTC 2025 I: Preparing to do remote build '1' on ionos11-amd64.debian.net. Sat Jul 5 18:01:16 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos11-amd64.debian.net is marked as down. Sat Jul 5 18:01:16 UTC 2025 - checking via ssh if ionos11-amd64.debian.net is up. removed '/tmp/read-only-fs-test-M9V26y' ==================================================================================== Sat Jul 5 18:01:17 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos11-amd64, called using "1 bcftools unstable /srv/reproducible-results/rbuild-debian/r-b-build.k066tCUN 1.21-1" as arguments. Sat Jul 5 18:01:17 UTC 2025 - actually running "reproducible_build.sh" (md5sum 44ec6a3142940d5e9a7ab76543d96029) as "/tmp/jenkins-script-iZU2XO2z" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Sat Jul 5 18:01:17 UTC 2025 I: Downloading source for unstable/bcftools=1.21-1 Reading package lists... NOTICE: 'bcftools' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/bcftools.git Please use: git clone https://salsa.debian.org/med-team/bcftools.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 3675 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main bcftools 1.21-1 (dsc) [2267 B] Get:2 http://deb.debian.org/debian unstable/main bcftools 1.21-1 (tar) [3665 kB] Get:3 http://deb.debian.org/debian unstable/main bcftools 1.21-1 (diff) [7504 B] Fetched 3675 kB in 0s (51.1 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'bcftools' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/bcftools.git Please use: git clone https://salsa.debian.org/med-team/bcftools.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 3675 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main bcftools 1.21-1 (dsc) [2267 B] Get:2 http://deb.debian.org/debian unstable/main bcftools 1.21-1 (tar) [3665 kB] Get:3 http://deb.debian.org/debian unstable/main bcftools 1.21-1 (diff) [7504 B] Fetched 3675 kB in 0s (51.1 MB/s) Download complete and in download only mode ============================================================================= Building bcftools in unstable on amd64 on ionos11-amd64 now. Date: Sat Jul 5 18:01:17 UTC 2025 Date UTC: Sat Jul 5 18:01:17 UTC 2025 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Sat Jul 5 06:01:17 -12 2025 I: pbuilder-time-stamp: 1751738477 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [bcftools_1.21-1.dsc] I: copying [./bcftools_1.21.orig.tar.gz] I: copying [./bcftools_1.21-1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./bcftools_1.21-1.dsc: no acceptable signature found dpkg-source: info: extracting bcftools in bcftools-1.21 dpkg-source: info: unpacking bcftools_1.21.orig.tar.gz dpkg-source: info: unpacking bcftools_1.21-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying skip_new_test_failing_on_32bit.patch dpkg-source: info: applying 2to3.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/712482/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='9646257e45ef4c9dafc0d245b5209d67' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='712482' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.k066tCUN/pbuilderrc_K5ta --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.k066tCUN/b1 --logfile b1/build.log bcftools_1.21-1.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos11-amd64 6.1.0-37-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.140-1 (2025-05-22) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 12 19:25 /bin -> usr/bin I: user script /srv/workspace/pbuilder/712482/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), zlib1g-dev, libbz2-dev, liblzma-dev, libhts-dev (>= 1.14), libgsl-dev, tabix, libio-pty-perl dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19849 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. pbuilder-satisfydepends-dummy depends on liblzma-dev; however: Package liblzma-dev is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev (>= 1.14); however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on libgsl-dev; however: Package libgsl-dev is not installed. pbuilder-satisfydepends-dummy depends on tabix; however: Package tabix is not installed. pbuilder-satisfydepends-dummy depends on libio-pty-perl; however: Package libio-pty-perl is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} comerr-dev{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} krb5-multidev{a} libarchive-zip-perl{a} libbrotli-dev{a} libbrotli1{a} libbz2-dev{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1t64{a} libevent-2.1-7t64{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgnutls30t64{a} libgsl-dev{a} libgsl28{a} libgslcblas0{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libidn2-0{a} libidn2-dev{a} libio-pty-perl{a} libk5crypto3{a} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} libldap-dev{a} libldap2{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp2-dev{a} libnghttp3-9{a} libnghttp3-dev{a} libngtcp2-16{a} libngtcp2-crypto-gnutls-dev{a} libngtcp2-crypto-gnutls8{a} libngtcp2-dev{a} libp11-kit-dev{a} libp11-kit0{a} libpipeline1{a} libpkgconf3{a} libpsl-dev{a} libpsl5t64{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libtasn1-6{a} libtasn1-6-dev{a} libtool{a} libuchardet0{a} libunbound8{a} libunistring5{a} libxml2{a} libzstd-dev{a} m4{a} man-db{a} nettle-dev{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} sensible-utils{a} tabix{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc ca-certificates curl krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules libtasn1-doc lynx publicsuffix wget 0 packages upgraded, 98 newly installed, 0 to remove and 0 not upgraded. Need to get 33.8 MB of archives. After unpacking 124 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.25 [25.0 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2 [243 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41-5 [94.6 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-8 [294 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-3+b1 [25.0 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 comerr-dev amd64 2.1-1.47.2-3+b1 [56.7 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-4 [539 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 24 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-1 [698 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2 [1680 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.2 [919 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get: 35 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 libgssrpc4t64 amd64 1.21.3-5 [60.0 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 libkadm5clnt-mit12 amd64 1.21.3-5 [42.5 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libkdb5-10t64 amd64 1.21.3-5 [42.6 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 libkadm5srv-mit12 amd64 1.21.3-5 [54.2 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 krb5-multidev amd64 1.21.3-5 [126 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 libbrotli-dev amd64 1.1.0-2+b7 [316 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.8-2 [109 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.4.8-2 [24.1 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libgnutls30t64 amd64 3.8.9-2 [1464 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 libldap2 amd64 2.6.10+dfsg-1 [194 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1.1 [76.0 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.8.0-1 [67.7 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.11.0-1 [131 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.11.0-1 [29.3 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.14.1-2 [384 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libunbound8 amd64 1.22.0-1+b1 [598 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 libgnutls-dane0t64 amd64 3.8.9-2 [455 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 libgnutls-openssl27t64 amd64 3.8.9-2 [455 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 libidn2-dev amd64 2.3.8-2 [103 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 libp11-kit-dev amd64 0.25.5-3 [208 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 libtasn1-6-dev amd64 4.20.0-2 [99.2 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-3 [329 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-3 [642 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 nettle-dev amd64 3.10.1-1 [1318 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 libgnutls28-dev amd64 3.8.9-2 [1401 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 libkrb5-dev amd64 1.21.3-5 [16.1 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 libldap-dev amd64 2.6.10+dfsg-1 [312 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 libnghttp2-dev amd64 1.64.0-1.1 [116 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 libnghttp3-dev amd64 1.8.0-1 [91.3 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.11.0-1 [34.0 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 libngtcp2-dev amd64 1.11.0-1 [179 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 libpsl-dev amd64 0.21.2-1.1+b1 [77.6 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-2+b5 [68.0 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 libssl-dev amd64 3.5.0-2 [2950 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 libssh2-1-dev amd64 1.11.1-1 [393 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.7+dfsg-1 [371 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls-dev amd64 8.14.1-2 [503 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.23-2 [47.3 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 libdeflate-dev amd64 1.23-2 [55.9 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 libgslcblas0 amd64 2.8+dfsg-5 [116 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 libgsl28 amd64 2.8+dfsg-5 [994 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 libgsl-dev amd64 2.8+dfsg-5 [1222 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.1-2 [95.8 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.21+ds-1 [463 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.8.1-1 [348 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 libhts-dev amd64 1.21+ds-1 [1733 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 libio-pty-perl amd64 1:1.20-1+b3 [34.3 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 tabix amd64 1.21+ds-1 [496 kB] Fetched 33.8 MB in 3s (12.8 MB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19849 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.25_all.deb ... Unpacking sensible-utils (0.0.25) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.46-5_amd64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-2_amd64.deb ... Unpacking gettext-base (0.23.1-2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-9_amd64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.41-5_amd64.deb ... Unpacking bsdextrautils (2.41-5) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.1-1_amd64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-8_amd64.deb ... Unpacking m4 (1.4.19-8) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.23.1-2_all.deb ... Unpacking autopoint (0.23.1-2) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../15-libcom-err2_1.47.2-3+b1_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.2-3+b1) ... Selecting previously unselected package comerr-dev:amd64. Preparing to unpack .../16-comerr-dev_2.1-1.47.2-3+b1_amd64.deb ... Unpacking comerr-dev:amd64 (2.1-1.47.2-3+b1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../17-libdebhelper-perl_13.24.2_all.deb ... Unpacking libdebhelper-perl (13.24.2) ... Selecting previously unselected package libtool. Preparing to unpack .../18-libtool_2.5.4-4_all.deb ... Unpacking libtool (2.5.4-4) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../19-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../20-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../21-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../22-dh-strip-nondeterminism_1.14.1-2_all.deb ... Unpacking dh-strip-nondeterminism (1.14.1-2) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../23-libelf1t64_0.192-4_amd64.deb ... Unpacking libelf1t64:amd64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../24-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libunistring5:amd64. Preparing to unpack .../25-libunistring5_1.3-2_amd64.deb ... Unpacking libunistring5:amd64 (1.3-2) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../26-libxml2_2.12.7+dfsg+really2.9.14-1_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-1) ... Selecting previously unselected package gettext. Preparing to unpack .../27-gettext_0.23.1-2_amd64.deb ... Unpacking gettext (0.23.1-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../28-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../29-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../30-debhelper_13.24.2_all.deb ... Unpacking debhelper (13.24.2) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../31-libkrb5support0_1.21.3-5_amd64.deb ... Unpacking libkrb5support0:amd64 (1.21.3-5) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../32-libk5crypto3_1.21.3-5_amd64.deb ... Unpacking libk5crypto3:amd64 (1.21.3-5) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../33-libkeyutils1_1.6.3-6_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-6) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../34-libkrb5-3_1.21.3-5_amd64.deb ... Unpacking libkrb5-3:amd64 (1.21.3-5) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../35-libgssapi-krb5-2_1.21.3-5_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.21.3-5) ... Selecting previously unselected package libgssrpc4t64:amd64. Preparing to unpack .../36-libgssrpc4t64_1.21.3-5_amd64.deb ... Unpacking libgssrpc4t64:amd64 (1.21.3-5) ... Selecting previously unselected package libkadm5clnt-mit12:amd64. Preparing to unpack .../37-libkadm5clnt-mit12_1.21.3-5_amd64.deb ... Unpacking libkadm5clnt-mit12:amd64 (1.21.3-5) ... Selecting previously unselected package libkdb5-10t64:amd64. Preparing to unpack .../38-libkdb5-10t64_1.21.3-5_amd64.deb ... Unpacking libkdb5-10t64:amd64 (1.21.3-5) ... Selecting previously unselected package libkadm5srv-mit12:amd64. Preparing to unpack .../39-libkadm5srv-mit12_1.21.3-5_amd64.deb ... Unpacking libkadm5srv-mit12:amd64 (1.21.3-5) ... Selecting previously unselected package krb5-multidev:amd64. Preparing to unpack .../40-krb5-multidev_1.21.3-5_amd64.deb ... Unpacking krb5-multidev:amd64 (1.21.3-5) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../41-libbrotli1_1.1.0-2+b7_amd64.deb ... Unpacking libbrotli1:amd64 (1.1.0-2+b7) ... Selecting previously unselected package libbrotli-dev:amd64. Preparing to unpack .../42-libbrotli-dev_1.1.0-2+b7_amd64.deb ... Unpacking libbrotli-dev:amd64 (1.1.0-2+b7) ... Selecting previously unselected package libbz2-dev:amd64. Preparing to unpack .../43-libbz2-dev_1.0.8-6_amd64.deb ... Unpacking libbz2-dev:amd64 (1.0.8-6) ... Selecting previously unselected package libidn2-0:amd64. Preparing to unpack .../44-libidn2-0_2.3.8-2_amd64.deb ... Unpacking libidn2-0:amd64 (2.3.8-2) ... Selecting previously unselected package libffi8:amd64. Preparing to unpack .../45-libffi8_3.4.8-2_amd64.deb ... Unpacking libffi8:amd64 (3.4.8-2) ... Selecting previously unselected package libp11-kit0:amd64. Preparing to unpack .../46-libp11-kit0_0.25.5-3_amd64.deb ... Unpacking libp11-kit0:amd64 (0.25.5-3) ... Selecting previously unselected package libtasn1-6:amd64. Preparing to unpack .../47-libtasn1-6_4.20.0-2_amd64.deb ... Unpacking libtasn1-6:amd64 (4.20.0-2) ... Selecting previously unselected package libgnutls30t64:amd64. Preparing to unpack .../48-libgnutls30t64_3.8.9-2_amd64.deb ... Unpacking libgnutls30t64:amd64 (3.8.9-2) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../49-libsasl2-modules-db_2.1.28+dfsg1-9_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg1-9) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../50-libsasl2-2_2.1.28+dfsg1-9_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg1-9) ... Selecting previously unselected package libldap2:amd64. Preparing to unpack .../51-libldap2_2.6.10+dfsg-1_amd64.deb ... Unpacking libldap2:amd64 (2.6.10+dfsg-1) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../52-libnghttp2-14_1.64.0-1.1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.64.0-1.1) ... Selecting previously unselected package libnghttp3-9:amd64. Preparing to unpack .../53-libnghttp3-9_1.8.0-1_amd64.deb ... Unpacking libnghttp3-9:amd64 (1.8.0-1) ... Selecting previously unselected package libngtcp2-16:amd64. Preparing to unpack .../54-libngtcp2-16_1.11.0-1_amd64.deb ... Unpacking libngtcp2-16:amd64 (1.11.0-1) ... Selecting previously unselected package libngtcp2-crypto-gnutls8:amd64. Preparing to unpack .../55-libngtcp2-crypto-gnutls8_1.11.0-1_amd64.deb ... Unpacking libngtcp2-crypto-gnutls8:amd64 (1.11.0-1) ... Selecting previously unselected package libpsl5t64:amd64. Preparing to unpack .../56-libpsl5t64_0.21.2-1.1+b1_amd64.deb ... Unpacking libpsl5t64:amd64 (0.21.2-1.1+b1) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../57-librtmp1_2.4+20151223.gitfa8646d.1-2+b5_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Selecting previously unselected package libssh2-1t64:amd64. Preparing to unpack .../58-libssh2-1t64_1.11.1-1_amd64.deb ... Unpacking libssh2-1t64:amd64 (1.11.1-1) ... Selecting previously unselected package libcurl3t64-gnutls:amd64. Preparing to unpack .../59-libcurl3t64-gnutls_8.14.1-2_amd64.deb ... Unpacking libcurl3t64-gnutls:amd64 (8.14.1-2) ... Selecting previously unselected package libevent-2.1-7t64:amd64. Preparing to unpack .../60-libevent-2.1-7t64_2.1.12-stable-10+b1_amd64.deb ... Unpacking libevent-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Selecting previously unselected package libunbound8:amd64. Preparing to unpack .../61-libunbound8_1.22.0-1+b1_amd64.deb ... Unpacking libunbound8:amd64 (1.22.0-1+b1) ... Selecting previously unselected package libgnutls-dane0t64:amd64. Preparing to unpack .../62-libgnutls-dane0t64_3.8.9-2_amd64.deb ... Unpacking libgnutls-dane0t64:amd64 (3.8.9-2) ... Selecting previously unselected package libgnutls-openssl27t64:amd64. Preparing to unpack .../63-libgnutls-openssl27t64_3.8.9-2_amd64.deb ... Unpacking libgnutls-openssl27t64:amd64 (3.8.9-2) ... Selecting previously unselected package libidn2-dev:amd64. Preparing to unpack .../64-libidn2-dev_2.3.8-2_amd64.deb ... Unpacking libidn2-dev:amd64 (2.3.8-2) ... Selecting previously unselected package libp11-kit-dev:amd64. Preparing to unpack .../65-libp11-kit-dev_0.25.5-3_amd64.deb ... Unpacking libp11-kit-dev:amd64 (0.25.5-3) ... Selecting previously unselected package libtasn1-6-dev:amd64. Preparing to unpack .../66-libtasn1-6-dev_4.20.0-2_amd64.deb ... Unpacking libtasn1-6-dev:amd64 (4.20.0-2) ... Selecting previously unselected package libgmpxx4ldbl:amd64. Preparing to unpack .../67-libgmpxx4ldbl_2%3a6.3.0+dfsg-3_amd64.deb ... Unpacking libgmpxx4ldbl:amd64 (2:6.3.0+dfsg-3) ... Selecting previously unselected package libgmp-dev:amd64. Preparing to unpack .../68-libgmp-dev_2%3a6.3.0+dfsg-3_amd64.deb ... Unpacking libgmp-dev:amd64 (2:6.3.0+dfsg-3) ... Selecting previously unselected package nettle-dev:amd64. Preparing to unpack .../69-nettle-dev_3.10.1-1_amd64.deb ... Unpacking nettle-dev:amd64 (3.10.1-1) ... Selecting previously unselected package libgnutls28-dev:amd64. Preparing to unpack .../70-libgnutls28-dev_3.8.9-2_amd64.deb ... Unpacking libgnutls28-dev:amd64 (3.8.9-2) ... Selecting previously unselected package libkrb5-dev:amd64. Preparing to unpack .../71-libkrb5-dev_1.21.3-5_amd64.deb ... Unpacking libkrb5-dev:amd64 (1.21.3-5) ... Selecting previously unselected package libldap-dev:amd64. Preparing to unpack .../72-libldap-dev_2.6.10+dfsg-1_amd64.deb ... Unpacking libldap-dev:amd64 (2.6.10+dfsg-1) ... Selecting previously unselected package libpkgconf3:amd64. Preparing to unpack .../73-libpkgconf3_1.8.1-4_amd64.deb ... Unpacking libpkgconf3:amd64 (1.8.1-4) ... Selecting previously unselected package pkgconf-bin. Preparing to unpack .../74-pkgconf-bin_1.8.1-4_amd64.deb ... Unpacking pkgconf-bin (1.8.1-4) ... Selecting previously unselected package pkgconf:amd64. Preparing to unpack .../75-pkgconf_1.8.1-4_amd64.deb ... Unpacking pkgconf:amd64 (1.8.1-4) ... Selecting previously unselected package libnghttp2-dev:amd64. Preparing to unpack .../76-libnghttp2-dev_1.64.0-1.1_amd64.deb ... Unpacking libnghttp2-dev:amd64 (1.64.0-1.1) ... Selecting previously unselected package libnghttp3-dev:amd64. Preparing to unpack .../77-libnghttp3-dev_1.8.0-1_amd64.deb ... Unpacking libnghttp3-dev:amd64 (1.8.0-1) ... 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Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up gettext (0.23.1-2) ... Setting up libgsl-dev (2.8+dfsg-5) ... Setting up libgmp-dev:amd64 (2:6.3.0+dfsg-3) ... Setting up nettle-dev:amd64 (3.10.1-1) ... Setting up libtool (2.5.4-4) ... Setting up libidn2-0:amd64 (2.3.8-2) ... Setting up libngtcp2-dev:amd64 (1.11.0-1) ... Setting up pkgconf:amd64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libldap-dev:amd64 (2.6.10+dfsg-1) ... Setting up libp11-kit0:amd64 (0.25.5-3) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-5) ... Setting up libssh2-1-dev:amd64 (1.11.1-1) ... Setting up libidn2-dev:amd64 (2.3.8-2) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-9) ... Setting up libp11-kit-dev:amd64 (0.25.5-3) ... Setting up libgnutls30t64:amd64 (3.8.9-2) ... Setting up libgnutls-openssl27t64:amd64 (3.8.9-2) ... Setting up libnghttp2-dev:amd64 (1.64.0-1.1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libpsl-dev:amd64 (0.21.2-1.1+b1) ... Setting up libgnutls-dane0t64:amd64 (3.8.9-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libgssrpc4t64:amd64 (1.21.3-5) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.11.0-1) ... Setting up libkadm5clnt-mit12:amd64 (1.21.3-5) ... Setting up libgnutls28-dev:amd64 (3.8.9-2) ... Setting up libkdb5-10t64:amd64 (1.21.3-5) ... Setting up libcurl3t64-gnutls:amd64 (8.14.1-2) ... Setting up debhelper (13.24.2) ... Setting up libngtcp2-crypto-gnutls-dev:amd64 (1.11.0-1) ... Setting up librtmp-dev:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libkadm5srv-mit12:amd64 (1.21.3-5) ... Setting up libhts3t64:amd64 (1.21+ds-1) ... Setting up krb5-multidev:amd64 (1.21.3-5) ... Setting up libkrb5-dev:amd64 (1.21.3-5) ... Setting up libcurl4-gnutls-dev:amd64 (8.14.1-2) ... Setting up libhts-dev:amd64 (1.21+ds-1) ... Processing triggers for libc-bin (2.41-9) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/bcftools-1.21/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../bcftools_1.21-1_source.changes dpkg-buildpackage: info: source package bcftools dpkg-buildpackage: info: source version 1.21-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean rm -f config.mk && touch config.mk dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/bcftools-1.21' dh_auto_clean make -j40 distclean make[2]: Entering directory '/build/reproducible-path/bcftools-1.21' rm -f test/*.o test/*.fa.fai test/*~ test/test-rbuf test/test-regidx rm -f plugins/*.so plugins/*.P rm -rf plugins/*.dSYM rm -f test/*.unsorted.hex test/*.unsorted.tsv rm -f gmon.out *.o *.a *~ bcftools version.h rm -rf *.dSYM test/*.dSYM rm -f config.cache config.h config.log config.mk config.status rm -rf autom4te.cache rm -f TAGS make[2]: Leaving directory '/build/reproducible-path/bcftools-1.21' rm -f test/mpileup/indel-AD.1.out.new test/view-t.1.out.new test/view-t.2.out.new make[1]: Leaving directory '/build/reproducible-path/bcftools-1.21' dh_clean debian/rules binary dh binary dh_update_autotools_config debian/rules override_dh_autoreconf make[1]: Entering directory '/build/reproducible-path/bcftools-1.21' rm -f config.mk && touch config.mk export MAKEFLAGS="-s"; dh_autoreconf configure.ac:94: warning: _AC_CONFIG_SUBDIRS: you should use literals ./lib/autoconf/status.m4:1096: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:94: the top level make[1]: Leaving directory '/build/reproducible-path/bcftools-1.21' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/bcftools-1.21' dh_auto_configure -- \ --with-htslib=system \ --enable-gsl \ --with-cblas=gslcblas \ --with-bcf-plugin-dir=/usr/lib/x86_64-linux-gnu/bcftools ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system --enable-gsl --with-cblas=gslcblas --with-bcf-plugin-dir=/usr/lib/x86_64-linux-gnu/bcftools checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking for -Wdate-time -D_FORTIFY_SOURCE=2 option for large files... none needed checking for htslib/sam.h... yes checking for hts_version in -lhts... yes checking shared library type... plain .so checking for library containing dlopen... none required checking if the compiler accepts -rdynamic... yes checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing regcomp... none required configure: creating ./config.status config.status: creating config.mk config.status: creating config.h make[1]: Leaving directory '/build/reproducible-path/bcftools-1.21' dh_auto_build make -j40 make[1]: Entering directory '/build/reproducible-path/bcftools-1.21' echo '#define BCFTOOLS_VERSION "1.21"' > version.h gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfindex.o vcfindex.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tabix.o tabix.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfstats.o vcfstats.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfisec.o vcfisec.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfmerge.o vcfmerge.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfquery.o vcfquery.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcffilter.o vcffilter.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o filter.o filter.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfsom.o vcfsom.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfnorm.o vcfnorm.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfgtcheck.o vcfgtcheck.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfview.o vcfview.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfannotate.o vcfannotate.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfroh.o vcfroh.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfconcat.o vcfconcat.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcall.o vcfcall.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mcall.o mcall.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcmp.o vcmp.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gvcf.o gvcf.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o reheader.o reheader.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o convert.o convert.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfconvert.o vcfconvert.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tsv2vcf.o tsv2vcf.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcnv.o vcfcnv.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfhead.o vcfhead.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o HMM.o HMM.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o consensus.o consensus.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ploidy.o ploidy.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bin.o bin.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hclust.o hclust.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o version.o version.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o regidx.o regidx.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o smpl_ilist.o smpl_ilist.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o csq.o csq.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfbuf.o vcfbuf.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mpileup.o mpileup.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_iaux.o bam2bcf_iaux.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_edlib.o bam2bcf_edlib.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o read_consensus.o read_consensus.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sample.o bam_sample.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfsort.o vcfsort.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cols.o cols.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o extsort.o extsort.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dist.o dist.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o abuf.o abuf.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ccall.o ccall.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o em.o em.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o prob1.o prob1.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kmin.o kmin.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o str_finder.o str_finder.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gff.o gff.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o edlib.o edlib.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DPLUGINPATH='"/usr/lib/x86_64-linux-gnu/bcftools"' -c -o vcfplugin.o vcfplugin.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-rbuf.o test/test-rbuf.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-regidx.o test/test-regidx.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/GTisec.so version.c plugins/GTisec.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/GTsubset.so version.c plugins/GTsubset.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/ad-bias.so convert.c version.c plugins/ad-bias.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/add-variantkey.so version.c plugins/add-variantkey.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/af-dist.so bin.c version.c plugins/af-dist.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/allele-length.so version.c plugins/allele-length.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/check-ploidy.so version.c plugins/check-ploidy.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/check-sparsity.so version.c plugins/check-sparsity.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/color-chrs.so HMM.c version.c plugins/color-chrs.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/contrast.so version.c plugins/contrast.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/counts.so version.c plugins/counts.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/dosage.so version.c plugins/dosage.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/fill-AN-AC.so version.c plugins/fill-AN-AC.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/fill-from-fasta.so filter.c version.c plugins/fill-from-fasta.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/fill-tags.so version.c plugins/fill-tags.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/fixploidy.so ploidy.c regidx.c version.c plugins/fixploidy.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/fixref.so version.c plugins/fixref.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/frameshifts.so version.c plugins/frameshifts.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/guess-ploidy.so version.c plugins/guess-ploidy.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/gvcfz.so version.c plugins/gvcfz.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/impute-info.so version.c plugins/impute-info.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/indel-stats.so version.c plugins/indel-stats.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/isecGT.so smpl_ilist.c version.c plugins/isecGT.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/mendelian2.so version.c plugins/mendelian2.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/missing2ref.so version.c plugins/missing2ref.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/parental-origin.so version.c plugins/parental-origin.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/prune.so version.c plugins/prune.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/remove-overlaps.so version.c plugins/remove-overlaps.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/scatter.so version.c plugins/scatter.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/setGT.so version.c plugins/setGT.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/smpl-stats.so version.c plugins/smpl-stats.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/split-vep.so version.c plugins/split-vep.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/split.so version.c plugins/split.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/tag2tag.so version.c plugins/tag2tag.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/trio-dnm2.so version.c plugins/trio-dnm2.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/trio-stats.so version.c plugins/trio-stats.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/trio-switch-rate.so version.c plugins/trio-switch-rate.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/variant-distance.so version.c plugins/variant-distance.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/variantkey-hex.so version.c plugins/variantkey-hex.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o main.o main.c gcc -Wl,-z,relro -Wl,-z,now -o test/test-rbuf test/test-rbuf.o -lz gcc -Wl,-z,relro -Wl,-z,now -o test/test-regidx test/test-regidx.o regidx.o -lhts -lpthread -lz gcc -rdynamic -Wl,-z,relro -Wl,-z,now -o bcftools main.o vcfindex.o tabix.o vcfstats.o vcfisec.o vcfmerge.o vcfquery.o vcffilter.o filter.o vcfsom.o vcfnorm.o vcfgtcheck.o vcfview.o vcfannotate.o vcfroh.o vcfconcat.o vcfcall.o mcall.o vcmp.o gvcf.o reheader.o convert.o vcfconvert.o tsv2vcf.o vcfcnv.o vcfhead.o HMM.o consensus.o ploidy.o bin.o hclust.o version.o regidx.o smpl_ilist.o csq.o vcfbuf.o mpileup.o bam2bcf.o bam2bcf_indel.o bam2bcf_iaux.o bam2bcf_edlib.o read_consensus.o bam_sample.o vcfsort.o cols.o extsort.o dist.o abuf.o ccall.o em.o prob1.o kmin.o str_finder.o gff.o edlib.o vcfplugin.o -lhts -lm -lz -lpthread make[1]: Leaving directory '/build/reproducible-path/bcftools-1.21' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/bcftools-1.21' make test-no-plugins VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/bcftools-1.21' ./test/test-rbuf Inserted 1-9 starting at offset 5: 5 6 7 8 9 0 1 2 3 1 2 3 4 5 6 7 8 9 4th is 4 Deleting 1-2: 7 8 9 0 1 2 3 3 4 5 6 7 8 9 Prepending 0-8: 8 9 0 1 2 3 4 5 6 7 8 7 6 5 4 3 2 1 0 3 Expanding: 8 9 10 11 12 13 14 15 16 17 8 7 6 5 4 3 2 1 0 3 ./test/test-regidx REF_PATH=: ./test/test.pl --exec bgzip= --exec tabix= --htsdir= ${TEST_OPTS:-} test_usage: bcftools .. ok test_usage_subcommand: bcftools index .. ok test_usage_subcommand: bcftools annotate .. ok test_usage_subcommand: bcftools concat .. ok test_usage_subcommand: bcftools convert .. ok test_usage_subcommand: bcftools head .. ok test_usage_subcommand: bcftools isec .. ok test_usage_subcommand: bcftools merge .. ok test_usage_subcommand: bcftools norm .. ok test_usage_subcommand: bcftools plugin .. ok test_usage_subcommand: bcftools query .. ok test_usage_subcommand: bcftools reheader .. ok test_usage_subcommand: bcftools sort .. ok test_usage_subcommand: bcftools view .. ok test_usage_subcommand: bcftools call .. ok test_usage_subcommand: bcftools consensus .. ok test_usage_subcommand: bcftools cnv .. ok test_usage_subcommand: bcftools csq .. ok test_usage_subcommand: bcftools filter .. ok test_usage_subcommand: bcftools gtcheck .. ok test_usage_subcommand: bcftools mpileup .. ok test_usage_subcommand: bcftools roh .. ok test_usage_subcommand: bcftools stats .. ok test_tabix: tabix /tmp/wj8A4a3te7/merge.a.vcf.gz 2:3199812-3199812 .. ok test_tabix: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/wj8A4a3te7/merge.a.bcf 2:3199812-3199812 .. ok test_tabix: tabix /tmp/wj8A4a3te7/merge.a.vcf.gz 1:3000151-3000151 .. ok test_tabix: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/wj8A4a3te7/merge.a.bcf 1:3000151-3000151 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/wj8A4a3te7/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/wj8A4a3te7/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/wj8A4a3te7/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/wj8A4a3te7/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/wj8A4a3te7/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/wj8A4a3te7/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/wj8A4a3te7/large_chrom_csi_limit.bcf chr20 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/wj8A4a3te7/large_chrom_csi_limit.bcf chr20 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/wj8A4a3te7/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/wj8A4a3te7/large_chrom_csi_limit.bcf chr20 .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -s /tmp/wj8A4a3te7/idx.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -s /tmp/wj8A4a3te7/idx.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -s /tmp/wj8A4a3te7/idx.bcf .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/wj8A4a3te7/idx.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/wj8A4a3te7/idx.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/wj8A4a3te7/idx.vcf.gz.csi .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/wj8A4a3te7/idx.bcf .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/wj8A4a3te7/idx.bcf.csi .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -s /tmp/wj8A4a3te7/empty.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -s /tmp/wj8A4a3te7/empty.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -s /tmp/wj8A4a3te7/empty.bcf .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/wj8A4a3te7/empty.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/wj8A4a3te7/empty.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/wj8A4a3te7/empty.vcf.gz.csi .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/wj8A4a3te7/empty.bcf .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/wj8A4a3te7/empty.bcf.csi .. ok test_vcf_check: /build/reproducible-path/bcftools-1.21/bcftools stats -s - /tmp/wj8A4a3te7/check.vcf.gz | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/check.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools stats -s - | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check_merge: /build/reproducible-path/bcftools-1.21/misc/plot-vcfstats -m /tmp/wj8A4a3te7/check.1.chk /tmp/wj8A4a3te7/check.2.chk /tmp/wj8A4a3te7/check.3.chk /tmp/wj8A4a3te7/check.4.chk | grep -v 'plot-vcfstats' | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_stats: /build/reproducible-path/bcftools-1.21/bcftools stats -s - /tmp/wj8A4a3te7/stats.a.vcf.gz /tmp/wj8A4a3te7/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/reproducible-path/bcftools-1.21/bcftools stats -s B /tmp/wj8A4a3te7/stats.a.vcf.gz /tmp/wj8A4a3te7/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/reproducible-path/bcftools-1.21/bcftools stats -s - /tmp/wj8A4a3te7/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/reproducible-path/bcftools-1.21/bcftools stats -s - -i 'type="snp"' /tmp/wj8A4a3te7/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/reproducible-path/bcftools-1.21/bcftools stats -s - /tmp/wj8A4a3te7/stats.vaf.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -n =2 /tmp/wj8A4a3te7/isec.a.vcf.gz /tmp/wj8A4a3te7/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -n =2 /tmp/wj8A4a3te7/isec.a.vcf.gz /tmp/wj8A4a3te7/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/wj8A4a3te7/isec.a.vcf.gz /tmp/wj8A4a3te7/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -n =2 -i"STRLEN(REF)==2" /tmp/wj8A4a3te7/isec.a.vcf.gz /tmp/wj8A4a3te7/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -n =2 -c both /tmp/wj8A4a3te7/isec.a.vcf.gz /tmp/wj8A4a3te7/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -n =2 -c both /tmp/wj8A4a3te7/isec.a.vcf.gz /tmp/wj8A4a3te7/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -n =2 -c any /tmp/wj8A4a3te7/isec.a.vcf.gz /tmp/wj8A4a3te7/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -n =2 -c any /tmp/wj8A4a3te7/isec.a.vcf.gz /tmp/wj8A4a3te7/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -C -c any /tmp/wj8A4a3te7/isec.a.vcf.gz /tmp/wj8A4a3te7/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -C -c any /tmp/wj8A4a3te7/isec.a.vcf.gz /tmp/wj8A4a3te7/isec.b.vcf.gz .. ok test_vcf_isec2: /build/reproducible-path/bcftools-1.21/bcftools isec --no-version -T /tmp/wj8A4a3te7/isec.tab.gz /tmp/wj8A4a3te7/isec.a.vcf.gz .. ok test_vcf_isec2: /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -T /tmp/wj8A4a3te7/isec.tab.gz /tmp/wj8A4a3te7/isec.a.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/wj8A4a3te7/isec-miss.1.1.vcf.gz /tmp/wj8A4a3te7/isec-miss.1.2.vcf.gz /tmp/wj8A4a3te7/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/wj8A4a3te7/isec-miss.1.1.vcf.gz /tmp/wj8A4a3te7/isec-miss.1.2.vcf.gz /tmp/wj8A4a3te7/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -R /build/reproducible-path/bcftools-1.21/test/isec-miss.1.regs.txt -n +1 /tmp/wj8A4a3te7/isec-miss.1.1.vcf.gz /tmp/wj8A4a3te7/isec-miss.1.2.vcf.gz /tmp/wj8A4a3te7/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -R /build/reproducible-path/bcftools-1.21/test/isec-miss.1.regs.txt -n +1 /tmp/wj8A4a3te7/isec-miss.1.1.vcf.gz /tmp/wj8A4a3te7/isec-miss.1.2.vcf.gz /tmp/wj8A4a3te7/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/wj8A4a3te7/isec-miss.2.1.vcf.gz /tmp/wj8A4a3te7/isec-miss.2.2.vcf.gz /tmp/wj8A4a3te7/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/wj8A4a3te7/isec-miss.2.1.vcf.gz /tmp/wj8A4a3te7/isec-miss.2.2.vcf.gz /tmp/wj8A4a3te7/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -R /build/reproducible-path/bcftools-1.21/test/isec-miss.1.regs.txt -n +1 /tmp/wj8A4a3te7/isec-miss.2.1.vcf.gz /tmp/wj8A4a3te7/isec-miss.2.2.vcf.gz /tmp/wj8A4a3te7/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -R /build/reproducible-path/bcftools-1.21/test/isec-miss.1.regs.txt -n +1 /tmp/wj8A4a3te7/isec-miss.2.1.vcf.gz /tmp/wj8A4a3te7/isec-miss.2.2.vcf.gz /tmp/wj8A4a3te7/isec-miss.2.3.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/wj8A4a3te7/merge.11.a.vcf.gz /tmp/wj8A4a3te7/merge.11.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/wj8A4a3te7/merge.11.a.vcf.gz /tmp/wj8A4a3te7/merge.11.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/wj8A4a3te7/merge.11.a.bcf /tmp/wj8A4a3te7/merge.11.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/wj8A4a3te7/merge.11.a.bcf /tmp/wj8A4a3te7/merge.11.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -i AF:join /tmp/wj8A4a3te7/merge.join.a.vcf.gz /tmp/wj8A4a3te7/merge.join.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -i AF:join /tmp/wj8A4a3te7/merge.join.a.vcf.gz /tmp/wj8A4a3te7/merge.join.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -i AF:join /tmp/wj8A4a3te7/merge.join.a.bcf /tmp/wj8A4a3te7/merge.join.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -i AF:join /tmp/wj8A4a3te7/merge.join.a.bcf /tmp/wj8A4a3te7/merge.join.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-single /tmp/wj8A4a3te7/merge.LPL.a.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-single /tmp/wj8A4a3te7/merge.LPL.a.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-single /tmp/wj8A4a3te7/merge.LPL.a.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-single /tmp/wj8A4a3te7/merge.LPL.a.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples /tmp/wj8A4a3te7/merge.LPL.a.vcf.gz /tmp/wj8A4a3te7/merge.LPL.b.vcf.gz /tmp/wj8A4a3te7/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/wj8A4a3te7/merge.LPL.a.vcf.gz /tmp/wj8A4a3te7/merge.LPL.b.vcf.gz /tmp/wj8A4a3te7/merge.LPL.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples /tmp/wj8A4a3te7/merge.LPL.a.bcf /tmp/wj8A4a3te7/merge.LPL.b.bcf /tmp/wj8A4a3te7/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/wj8A4a3te7/merge.LPL.a.bcf /tmp/wj8A4a3te7/merge.LPL.b.bcf /tmp/wj8A4a3te7/merge.LPL.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -L 1 /tmp/wj8A4a3te7/merge.LPL.a.vcf.gz /tmp/wj8A4a3te7/merge.LPL.b.vcf.gz /tmp/wj8A4a3te7/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 1 /tmp/wj8A4a3te7/merge.LPL.a.vcf.gz /tmp/wj8A4a3te7/merge.LPL.b.vcf.gz /tmp/wj8A4a3te7/merge.LPL.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -L 1 /tmp/wj8A4a3te7/merge.LPL.a.bcf /tmp/wj8A4a3te7/merge.LPL.b.bcf /tmp/wj8A4a3te7/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 1 /tmp/wj8A4a3te7/merge.LPL.a.bcf /tmp/wj8A4a3te7/merge.LPL.b.bcf /tmp/wj8A4a3te7/merge.LPL.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -L 2 /tmp/wj8A4a3te7/merge.LPL.a.vcf.gz /tmp/wj8A4a3te7/merge.LPL.b.vcf.gz /tmp/wj8A4a3te7/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 2 /tmp/wj8A4a3te7/merge.LPL.a.vcf.gz /tmp/wj8A4a3te7/merge.LPL.b.vcf.gz /tmp/wj8A4a3te7/merge.LPL.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -L 2 /tmp/wj8A4a3te7/merge.LPL.a.bcf /tmp/wj8A4a3te7/merge.LPL.b.bcf /tmp/wj8A4a3te7/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 2 /tmp/wj8A4a3te7/merge.LPL.a.bcf /tmp/wj8A4a3te7/merge.LPL.b.bcf /tmp/wj8A4a3te7/merge.LPL.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -L 3 /tmp/wj8A4a3te7/merge.LPL.a.vcf.gz /tmp/wj8A4a3te7/merge.LPL.b.vcf.gz /tmp/wj8A4a3te7/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 3 /tmp/wj8A4a3te7/merge.LPL.a.vcf.gz /tmp/wj8A4a3te7/merge.LPL.b.vcf.gz /tmp/wj8A4a3te7/merge.LPL.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -L 3 /tmp/wj8A4a3te7/merge.LPL.a.bcf /tmp/wj8A4a3te7/merge.LPL.b.bcf /tmp/wj8A4a3te7/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 3 /tmp/wj8A4a3te7/merge.LPL.a.bcf /tmp/wj8A4a3te7/merge.LPL.b.bcf /tmp/wj8A4a3te7/merge.LPL.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -L 4 /tmp/wj8A4a3te7/merge.LPL.a.vcf.gz /tmp/wj8A4a3te7/merge.LPL.b.vcf.gz /tmp/wj8A4a3te7/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 4 /tmp/wj8A4a3te7/merge.LPL.a.vcf.gz /tmp/wj8A4a3te7/merge.LPL.b.vcf.gz /tmp/wj8A4a3te7/merge.LPL.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -L 4 /tmp/wj8A4a3te7/merge.LPL.a.bcf /tmp/wj8A4a3te7/merge.LPL.b.bcf /tmp/wj8A4a3te7/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 4 /tmp/wj8A4a3te7/merge.LPL.a.bcf /tmp/wj8A4a3te7/merge.LPL.b.bcf /tmp/wj8A4a3te7/merge.LPL.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -L 5 /tmp/wj8A4a3te7/merge.LPL.a.vcf.gz /tmp/wj8A4a3te7/merge.LPL.b.vcf.gz /tmp/wj8A4a3te7/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 5 /tmp/wj8A4a3te7/merge.LPL.a.vcf.gz /tmp/wj8A4a3te7/merge.LPL.b.vcf.gz /tmp/wj8A4a3te7/merge.LPL.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -L 5 /tmp/wj8A4a3te7/merge.LPL.a.bcf /tmp/wj8A4a3te7/merge.LPL.b.bcf /tmp/wj8A4a3te7/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 5 /tmp/wj8A4a3te7/merge.LPL.a.bcf /tmp/wj8A4a3te7/merge.LPL.b.bcf /tmp/wj8A4a3te7/merge.LPL.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples /tmp/wj8A4a3te7/merge.a.vcf.gz /tmp/wj8A4a3te7/merge.b.vcf.gz /tmp/wj8A4a3te7/merge.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/wj8A4a3te7/merge.a.vcf.gz /tmp/wj8A4a3te7/merge.b.vcf.gz /tmp/wj8A4a3te7/merge.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples /tmp/wj8A4a3te7/merge.a.bcf /tmp/wj8A4a3te7/merge.b.bcf /tmp/wj8A4a3te7/merge.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/wj8A4a3te7/merge.a.bcf /tmp/wj8A4a3te7/merge.b.bcf /tmp/wj8A4a3te7/merge.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -Fx /tmp/wj8A4a3te7/merge.a.vcf.gz /tmp/wj8A4a3te7/merge.b.vcf.gz /tmp/wj8A4a3te7/merge.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -Fx /tmp/wj8A4a3te7/merge.a.vcf.gz /tmp/wj8A4a3te7/merge.b.vcf.gz /tmp/wj8A4a3te7/merge.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -Fx /tmp/wj8A4a3te7/merge.a.bcf /tmp/wj8A4a3te7/merge.b.bcf /tmp/wj8A4a3te7/merge.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -Fx /tmp/wj8A4a3te7/merge.a.bcf /tmp/wj8A4a3te7/merge.b.bcf /tmp/wj8A4a3te7/merge.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -0 /tmp/wj8A4a3te7/merge.a.vcf.gz /tmp/wj8A4a3te7/merge.b.vcf.gz /tmp/wj8A4a3te7/merge.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -0 /tmp/wj8A4a3te7/merge.a.vcf.gz /tmp/wj8A4a3te7/merge.b.vcf.gz /tmp/wj8A4a3te7/merge.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -0 /tmp/wj8A4a3te7/merge.a.bcf /tmp/wj8A4a3te7/merge.b.bcf /tmp/wj8A4a3te7/merge.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -0 /tmp/wj8A4a3te7/merge.a.bcf /tmp/wj8A4a3te7/merge.b.bcf /tmp/wj8A4a3te7/merge.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -m none /tmp/wj8A4a3te7/merge.2.a.vcf.gz /tmp/wj8A4a3te7/merge.2.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m none /tmp/wj8A4a3te7/merge.2.a.vcf.gz /tmp/wj8A4a3te7/merge.2.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -m none /tmp/wj8A4a3te7/merge.2.a.bcf /tmp/wj8A4a3te7/merge.2.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m none /tmp/wj8A4a3te7/merge.2.a.bcf /tmp/wj8A4a3te7/merge.2.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -m both /tmp/wj8A4a3te7/merge.2.a.vcf.gz /tmp/wj8A4a3te7/merge.2.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m both /tmp/wj8A4a3te7/merge.2.a.vcf.gz /tmp/wj8A4a3te7/merge.2.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -m both /tmp/wj8A4a3te7/merge.2.a.bcf /tmp/wj8A4a3te7/merge.2.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m both /tmp/wj8A4a3te7/merge.2.a.bcf /tmp/wj8A4a3te7/merge.2.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -m all /tmp/wj8A4a3te7/merge.2.a.vcf.gz /tmp/wj8A4a3te7/merge.2.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m all /tmp/wj8A4a3te7/merge.2.a.vcf.gz /tmp/wj8A4a3te7/merge.2.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -m all /tmp/wj8A4a3te7/merge.2.a.bcf /tmp/wj8A4a3te7/merge.2.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m all /tmp/wj8A4a3te7/merge.2.a.bcf /tmp/wj8A4a3te7/merge.2.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/wj8A4a3te7/merge.3.a.vcf.gz /tmp/wj8A4a3te7/merge.3.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/wj8A4a3te7/merge.3.a.vcf.gz /tmp/wj8A4a3te7/merge.3.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/wj8A4a3te7/merge.3.a.bcf /tmp/wj8A4a3te7/merge.3.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/wj8A4a3te7/merge.3.a.bcf /tmp/wj8A4a3te7/merge.3.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -m id /tmp/wj8A4a3te7/merge.4.a.vcf.gz /tmp/wj8A4a3te7/merge.4.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m id /tmp/wj8A4a3te7/merge.4.a.vcf.gz /tmp/wj8A4a3te7/merge.4.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -m id /tmp/wj8A4a3te7/merge.4.a.bcf /tmp/wj8A4a3te7/merge.4.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m id /tmp/wj8A4a3te7/merge.4.a.bcf /tmp/wj8A4a3te7/merge.4.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/wj8A4a3te7/gvcf.merge.1.vcf.gz /tmp/wj8A4a3te7/gvcf.merge.2.vcf.gz /tmp/wj8A4a3te7/gvcf.merge.3.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/wj8A4a3te7/gvcf.merge.1.vcf.gz /tmp/wj8A4a3te7/gvcf.merge.2.vcf.gz /tmp/wj8A4a3te7/gvcf.merge.3.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/wj8A4a3te7/gvcf.merge.1.bcf /tmp/wj8A4a3te7/gvcf.merge.2.bcf /tmp/wj8A4a3te7/gvcf.merge.3.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/wj8A4a3te7/gvcf.merge.1.bcf /tmp/wj8A4a3te7/gvcf.merge.2.bcf /tmp/wj8A4a3te7/gvcf.merge.3.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/wj8A4a3te7/merge.gvcf.2.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.2.b.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/wj8A4a3te7/merge.gvcf.2.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.2.b.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.2.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - -m both,* /tmp/wj8A4a3te7/merge.gvcf.2.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.2.b.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - -m both,* /tmp/wj8A4a3te7/merge.gvcf.2.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.2.b.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.2.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - -m both,** /tmp/wj8A4a3te7/merge.gvcf.2.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.2.b.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - -m both,** /tmp/wj8A4a3te7/merge.gvcf.2.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.2.b.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.2.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - -i SRC:join /tmp/wj8A4a3te7/merge.gvcf.3.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.3.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - -i SRC:join /tmp/wj8A4a3te7/merge.gvcf.3.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.3.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/wj8A4a3te7/merge.gvcf.4.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.4.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/wj8A4a3te7/merge.gvcf.4.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.4.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/wj8A4a3te7/merge.gvcf.4.a.bcf /tmp/wj8A4a3te7/merge.gvcf.4.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/wj8A4a3te7/merge.gvcf.4.a.bcf /tmp/wj8A4a3te7/merge.gvcf.4.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/wj8A4a3te7/merge.5.a.vcf.gz /tmp/wj8A4a3te7/merge.5.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/wj8A4a3te7/merge.5.a.vcf.gz /tmp/wj8A4a3te7/merge.5.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/wj8A4a3te7/merge.5.a.bcf /tmp/wj8A4a3te7/merge.5.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/wj8A4a3te7/merge.5.a.bcf /tmp/wj8A4a3te7/merge.5.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/wj8A4a3te7/merge.6.a.vcf.gz /tmp/wj8A4a3te7/merge.6.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/wj8A4a3te7/merge.6.a.vcf.gz /tmp/wj8A4a3te7/merge.6.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/wj8A4a3te7/merge.6.a.bcf /tmp/wj8A4a3te7/merge.6.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/wj8A4a3te7/merge.6.a.bcf /tmp/wj8A4a3te7/merge.6.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/wj8A4a3te7/merge.gvcf.7.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.7.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/wj8A4a3te7/merge.gvcf.7.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.7.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/wj8A4a3te7/merge.gvcf.7.a.bcf /tmp/wj8A4a3te7/merge.gvcf.7.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/wj8A4a3te7/merge.gvcf.7.a.bcf /tmp/wj8A4a3te7/merge.gvcf.7.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/wj8A4a3te7/merge.gvcf.8.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.8.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/wj8A4a3te7/merge.gvcf.8.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.8.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/wj8A4a3te7/merge.gvcf.8.a.bcf /tmp/wj8A4a3te7/merge.gvcf.8.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/wj8A4a3te7/merge.gvcf.8.a.bcf /tmp/wj8A4a3te7/merge.gvcf.8.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples /tmp/wj8A4a3te7/merge.7.a.vcf.gz /tmp/wj8A4a3te7/merge.7.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/wj8A4a3te7/merge.7.a.vcf.gz /tmp/wj8A4a3te7/merge.7.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples /tmp/wj8A4a3te7/merge.7.a.bcf /tmp/wj8A4a3te7/merge.7.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/wj8A4a3te7/merge.7.a.bcf /tmp/wj8A4a3te7/merge.7.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa /tmp/wj8A4a3te7/merge.gvcf.9a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9b.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9c.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9d.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa /tmp/wj8A4a3te7/merge.gvcf.9a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9b.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9c.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9d.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa /tmp/wj8A4a3te7/merge.gvcf.9a.bcf /tmp/wj8A4a3te7/merge.gvcf.9b.bcf /tmp/wj8A4a3te7/merge.gvcf.9c.bcf /tmp/wj8A4a3te7/merge.gvcf.9d.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa /tmp/wj8A4a3te7/merge.gvcf.9a.bcf /tmp/wj8A4a3te7/merge.gvcf.9b.bcf /tmp/wj8A4a3te7/merge.gvcf.9c.bcf /tmp/wj8A4a3te7/merge.gvcf.9d.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa -r 22:21-23 /tmp/wj8A4a3te7/merge.gvcf.9a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9b.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9c.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9d.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa -r 22:21-23 /tmp/wj8A4a3te7/merge.gvcf.9a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9b.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9c.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9d.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa -r 22:21-23 /tmp/wj8A4a3te7/merge.gvcf.9a.bcf /tmp/wj8A4a3te7/merge.gvcf.9b.bcf /tmp/wj8A4a3te7/merge.gvcf.9c.bcf /tmp/wj8A4a3te7/merge.gvcf.9d.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa -r 22:21-23 /tmp/wj8A4a3te7/merge.gvcf.9a.bcf /tmp/wj8A4a3te7/merge.gvcf.9b.bcf /tmp/wj8A4a3te7/merge.gvcf.9c.bcf /tmp/wj8A4a3te7/merge.gvcf.9d.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa /tmp/wj8A4a3te7/merge.gvcf.9a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9b.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9c.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9d.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9e.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa /tmp/wj8A4a3te7/merge.gvcf.9a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9b.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9c.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9d.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9e.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa /tmp/wj8A4a3te7/merge.gvcf.9a.bcf /tmp/wj8A4a3te7/merge.gvcf.9b.bcf /tmp/wj8A4a3te7/merge.gvcf.9c.bcf /tmp/wj8A4a3te7/merge.gvcf.9d.bcf /tmp/wj8A4a3te7/merge.gvcf.9e.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa /tmp/wj8A4a3te7/merge.gvcf.9a.bcf /tmp/wj8A4a3te7/merge.gvcf.9b.bcf /tmp/wj8A4a3te7/merge.gvcf.9c.bcf /tmp/wj8A4a3te7/merge.gvcf.9d.bcf /tmp/wj8A4a3te7/merge.gvcf.9e.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa -r 22:21-23 /tmp/wj8A4a3te7/merge.gvcf.9a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9b.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9c.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9d.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9e.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa -r 22:21-23 /tmp/wj8A4a3te7/merge.gvcf.9a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9b.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9c.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9d.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9e.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa -r 22:21-23 /tmp/wj8A4a3te7/merge.gvcf.9a.bcf /tmp/wj8A4a3te7/merge.gvcf.9b.bcf /tmp/wj8A4a3te7/merge.gvcf.9c.bcf /tmp/wj8A4a3te7/merge.gvcf.9d.bcf /tmp/wj8A4a3te7/merge.gvcf.9e.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa -r 22:21-23 /tmp/wj8A4a3te7/merge.gvcf.9a.bcf /tmp/wj8A4a3te7/merge.gvcf.9b.bcf /tmp/wj8A4a3te7/merge.gvcf.9c.bcf /tmp/wj8A4a3te7/merge.gvcf.9d.bcf /tmp/wj8A4a3te7/merge.gvcf.9e.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/wj8A4a3te7/merge.gvcf.10.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/wj8A4a3te7/merge.gvcf.10.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.10.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/wj8A4a3te7/merge.gvcf.10.a.bcf /tmp/wj8A4a3te7/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/wj8A4a3te7/merge.gvcf.10.a.bcf /tmp/wj8A4a3te7/merge.gvcf.10.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -m none /tmp/wj8A4a3te7/merge.gvcf.10.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m none /tmp/wj8A4a3te7/merge.gvcf.10.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.10.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -m none /tmp/wj8A4a3te7/merge.gvcf.10.a.bcf /tmp/wj8A4a3te7/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m none /tmp/wj8A4a3te7/merge.gvcf.10.a.bcf /tmp/wj8A4a3te7/merge.gvcf.10.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -g /build/reproducible-path/bcftools-1.21/test/merge.gvcf.10.fa /tmp/wj8A4a3te7/merge.gvcf.10.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -g /build/reproducible-path/bcftools-1.21/test/merge.gvcf.10.fa /tmp/wj8A4a3te7/merge.gvcf.10.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.10.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -g /build/reproducible-path/bcftools-1.21/test/merge.gvcf.10.fa /tmp/wj8A4a3te7/merge.gvcf.10.a.bcf /tmp/wj8A4a3te7/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -g /build/reproducible-path/bcftools-1.21/test/merge.gvcf.10.fa /tmp/wj8A4a3te7/merge.gvcf.10.a.bcf /tmp/wj8A4a3te7/merge.gvcf.10.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -g /build/reproducible-path/bcftools-1.21/test/merge.gvcf.10.fa -m none /tmp/wj8A4a3te7/merge.gvcf.10.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -g /build/reproducible-path/bcftools-1.21/test/merge.gvcf.10.fa -m none /tmp/wj8A4a3te7/merge.gvcf.10.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.10.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -g /build/reproducible-path/bcftools-1.21/test/merge.gvcf.10.fa -m none /tmp/wj8A4a3te7/merge.gvcf.10.a.bcf /tmp/wj8A4a3te7/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -g /build/reproducible-path/bcftools-1.21/test/merge.gvcf.10.fa -m none /tmp/wj8A4a3te7/merge.gvcf.10.a.bcf /tmp/wj8A4a3te7/merge.gvcf.10.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/wj8A4a3te7/merge.noidx.a.vcf.gz /tmp/wj8A4a3te7/merge.noidx.b.vcf.gz /tmp/wj8A4a3te7/merge.noidx.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/wj8A4a3te7/merge.noidx.a.vcf.gz /tmp/wj8A4a3te7/merge.noidx.b.vcf.gz /tmp/wj8A4a3te7/merge.noidx.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/wj8A4a3te7/merge.noidx.a.bcf /tmp/wj8A4a3te7/merge.noidx.b.bcf /tmp/wj8A4a3te7/merge.noidx.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/wj8A4a3te7/merge.noidx.a.bcf /tmp/wj8A4a3te7/merge.noidx.b.bcf /tmp/wj8A4a3te7/merge.noidx.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --no-index /build/reproducible-path/bcftools-1.21/test/merge.noidx.a.vcf /build/reproducible-path/bcftools-1.21/test/merge.noidx.b.vcf /build/reproducible-path/bcftools-1.21/test/merge.noidx.c.vcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --no-index /build/reproducible-path/bcftools-1.21/test/merge.noidx.a.vcf /build/reproducible-path/bcftools-1.21/test/merge.noidx.b.vcf /build/reproducible-path/bcftools-1.21/test/merge.noidx.c.vcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --no-index /tmp/wj8A4a3te7/merge.noidx.a.bcf /tmp/wj8A4a3te7/merge.noidx.b.bcf /tmp/wj8A4a3te7/merge.noidx.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --no-index /tmp/wj8A4a3te7/merge.noidx.a.bcf /tmp/wj8A4a3te7/merge.noidx.b.bcf /tmp/wj8A4a3te7/merge.noidx.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/wj8A4a3te7/merge.8.a.vcf.gz /tmp/wj8A4a3te7/merge.8.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/wj8A4a3te7/merge.8.a.vcf.gz /tmp/wj8A4a3te7/merge.8.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/wj8A4a3te7/merge.8.a.bcf /tmp/wj8A4a3te7/merge.8.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/wj8A4a3te7/merge.8.a.bcf /tmp/wj8A4a3te7/merge.8.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -i AN:sum,AC:sum /tmp/wj8A4a3te7/merge.8.a.vcf.gz /tmp/wj8A4a3te7/merge.8.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/wj8A4a3te7/merge.8.a.vcf.gz /tmp/wj8A4a3te7/merge.8.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -i AN:sum,AC:sum /tmp/wj8A4a3te7/merge.8.a.bcf /tmp/wj8A4a3te7/merge.8.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/wj8A4a3te7/merge.8.a.bcf /tmp/wj8A4a3te7/merge.8.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/wj8A4a3te7/merge.9.a.vcf.gz /tmp/wj8A4a3te7/merge.9.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/wj8A4a3te7/merge.9.a.vcf.gz /tmp/wj8A4a3te7/merge.9.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/wj8A4a3te7/merge.9.a.bcf /tmp/wj8A4a3te7/merge.9.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/wj8A4a3te7/merge.9.a.bcf /tmp/wj8A4a3te7/merge.9.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -i AN:sum,AC:sum /tmp/wj8A4a3te7/merge.9.a.vcf.gz /tmp/wj8A4a3te7/merge.9.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/wj8A4a3te7/merge.9.a.vcf.gz /tmp/wj8A4a3te7/merge.9.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -i AN:sum,AC:sum /tmp/wj8A4a3te7/merge.9.a.bcf /tmp/wj8A4a3te7/merge.9.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/wj8A4a3te7/merge.9.a.bcf /tmp/wj8A4a3te7/merge.9.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -m none /tmp/wj8A4a3te7/merge.10.a.vcf.gz /tmp/wj8A4a3te7/merge.10.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m none /tmp/wj8A4a3te7/merge.10.a.vcf.gz /tmp/wj8A4a3te7/merge.10.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -m none /tmp/wj8A4a3te7/merge.10.a.bcf /tmp/wj8A4a3te7/merge.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m none /tmp/wj8A4a3te7/merge.10.a.bcf /tmp/wj8A4a3te7/merge.10.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -m both /tmp/wj8A4a3te7/merge.10.a.vcf.gz /tmp/wj8A4a3te7/merge.10.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m both /tmp/wj8A4a3te7/merge.10.a.vcf.gz /tmp/wj8A4a3te7/merge.10.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -m both /tmp/wj8A4a3te7/merge.10.a.bcf /tmp/wj8A4a3te7/merge.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m both /tmp/wj8A4a3te7/merge.10.a.bcf /tmp/wj8A4a3te7/merge.10.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -m snp-ins-del /tmp/wj8A4a3te7/merge.10.a.vcf.gz /tmp/wj8A4a3te7/merge.10.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m snp-ins-del /tmp/wj8A4a3te7/merge.10.a.vcf.gz /tmp/wj8A4a3te7/merge.10.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -m snp-ins-del /tmp/wj8A4a3te7/merge.10.a.bcf /tmp/wj8A4a3te7/merge.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m snp-ins-del /tmp/wj8A4a3te7/merge.10.a.bcf /tmp/wj8A4a3te7/merge.10.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/wj8A4a3te7/merge.mrules.1.a.vcf.gz /tmp/wj8A4a3te7/merge.mrules.1.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/wj8A4a3te7/merge.mrules.1.a.vcf.gz /tmp/wj8A4a3te7/merge.mrules.1.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/wj8A4a3te7/merge.mrules.1.a.bcf /tmp/wj8A4a3te7/merge.mrules.1.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/wj8A4a3te7/merge.mrules.1.a.bcf /tmp/wj8A4a3te7/merge.mrules.1.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - -M AD:.,PL:. /tmp/wj8A4a3te7/merge.mrules.1.a.vcf.gz /tmp/wj8A4a3te7/merge.mrules.1.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - -M AD:.,PL:. /tmp/wj8A4a3te7/merge.mrules.1.a.vcf.gz /tmp/wj8A4a3te7/merge.mrules.1.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - -M AD:.,PL:. /tmp/wj8A4a3te7/merge.mrules.1.a.bcf /tmp/wj8A4a3te7/merge.mrules.1.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - -M AD:.,PL:. /tmp/wj8A4a3te7/merge.mrules.1.a.bcf /tmp/wj8A4a3te7/merge.mrules.1.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/wj8A4a3te7/merge.gvcf.5.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.5.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/wj8A4a3te7/merge.gvcf.5.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.5.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/wj8A4a3te7/merge.gvcf.5.a.bcf /tmp/wj8A4a3te7/merge.gvcf.5.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/wj8A4a3te7/merge.gvcf.5.a.bcf /tmp/wj8A4a3te7/merge.gvcf.5.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - --merge none /tmp/wj8A4a3te7/merge.gvcf.5.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.5.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - --merge none /tmp/wj8A4a3te7/merge.gvcf.5.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.5.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - --merge none /tmp/wj8A4a3te7/merge.gvcf.5.a.bcf /tmp/wj8A4a3te7/merge.gvcf.5.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - --merge none /tmp/wj8A4a3te7/merge.gvcf.5.a.bcf /tmp/wj8A4a3te7/merge.gvcf.5.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/wj8A4a3te7/merge.gvcf.11.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.11.b.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.11.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/wj8A4a3te7/merge.gvcf.11.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.11.b.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.11.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/wj8A4a3te7/merge.gvcf.11.a.bcf /tmp/wj8A4a3te7/merge.gvcf.11.b.bcf /tmp/wj8A4a3te7/merge.gvcf.11.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/wj8A4a3te7/merge.gvcf.11.a.bcf /tmp/wj8A4a3te7/merge.gvcf.11.b.bcf /tmp/wj8A4a3te7/merge.gvcf.11.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided,_conflicting_interpretations"' /tmp/wj8A4a3te7/query.string.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.string.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided,_conflicting_interpretations"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" || CLNREVSTAT="_conflicting_interpretations"' /tmp/wj8A4a3te7/query.string.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.string.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" || CLNREVSTAT="_conflicting_interpretations"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" && CLNREVSTAT="_conflicting_interpretations"' /tmp/wj8A4a3te7/query.string.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.string.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" && CLNREVSTAT="_conflicting_interpretations"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%INFO/STR\n' -i'INFO/STR=@/build/reproducible-path/bcftools-1.21/test/query.string.2.1.txt' /tmp/wj8A4a3te7/query.string.2.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.string.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%INFO/STR\n' -i'INFO/STR=@/build/reproducible-path/bcftools-1.21/test/query.string.2.1.txt' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS[\t%STR]\n' -i'FMT/STR=@/build/reproducible-path/bcftools-1.21/test/query.string.2.2.txt' /tmp/wj8A4a3te7/query.string.2.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.string.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS[\t%STR]\n' -i'FMT/STR=@/build/reproducible-path/bcftools-1.21/test/query.string.2.2.txt' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' /tmp/wj8A4a3te7/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f '%RSX\t%VKX\n' /tmp/wj8A4a3te7/query.variantkey.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.variantkey.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f '%RSX\t%VKX\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%XRI\n' -i'XRI[*]>1111' /tmp/wj8A4a3te7/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%XRI\n' -i'XRI[*]>1111' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' /tmp/wj8A4a3te7/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' /tmp/wj8A4a3te7/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' /tmp/wj8A4a3te7/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' /tmp/wj8A4a3te7/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' /tmp/wj8A4a3te7/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' /tmp/wj8A4a3te7/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' /tmp/wj8A4a3te7/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' /tmp/wj8A4a3te7/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' /tmp/wj8A4a3te7/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' /tmp/wj8A4a3te7/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' /tmp/wj8A4a3te7/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' /tmp/wj8A4a3te7/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' /tmp/wj8A4a3te7/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' /tmp/wj8A4a3te7/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' /tmp/wj8A4a3te7/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'I8=%I8 I16=%I16 I32=%I32 IF=%IF IA8=%IA8 IA16=%IA16 IA32=%IA32 IAF=%IAF IA8=%IA8{1} IA16=%IA16{1} IA32=%IA32{1} IAF=%IAF{1} [ %F8:%F16:%F32:%FF]\n' /tmp/wj8A4a3te7/view.vectors.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.vectors.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'I8=%I8 I16=%I16 I32=%I32 IF=%IF IA8=%IA8 IA16=%IA16 IA32=%IA32 IAF=%IAF IA8=%IA8{1} IA16=%IA16{1} IA32=%IA32{1} IAF=%IAF{1} [ %F8:%F16:%F32:%FF]\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' /tmp/wj8A4a3te7/query.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' /tmp/wj8A4a3te7/query.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' /tmp/wj8A4a3te7/query.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' /tmp/wj8A4a3te7/query.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' /tmp/wj8A4a3te7/query.2.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'IINT="."' -f'%POS %IINT\n' /tmp/wj8A4a3te7/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'IINT!="."' -f'%POS %IINT\n' /tmp/wj8A4a3te7/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -e'IINT!="."' -f'%POS %IINT\n' /tmp/wj8A4a3te7/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -e'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -e'IINT="."' -f'%POS %IINT\n' /tmp/wj8A4a3te7/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -e'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' /tmp/wj8A4a3te7/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' /tmp/wj8A4a3te7/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' /tmp/wj8A4a3te7/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' /tmp/wj8A4a3te7/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' /tmp/wj8A4a3te7/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' /tmp/wj8A4a3te7/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' /tmp/wj8A4a3te7/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' /tmp/wj8A4a3te7/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' /tmp/wj8A4a3te7/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER="A"' -f'%POS %FILTER\n' /tmp/wj8A4a3te7/filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/filter.11.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER="A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER!="A"' -f'%POS %FILTER\n' /tmp/wj8A4a3te7/filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/filter.11.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER!="A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER~"A"' -f'%POS %FILTER\n' /tmp/wj8A4a3te7/filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/filter.11.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER~"A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n' /tmp/wj8A4a3te7/filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/filter.11.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%LINE' /tmp/wj8A4a3te7/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%LINE' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' /tmp/wj8A4a3te7/query.filter-type.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter-type.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' /tmp/wj8A4a3te7/query.filter-type.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter-type.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' /tmp/wj8A4a3te7/query.filter-type.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter-type.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' /tmp/wj8A4a3te7/query.filter-type.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter-type.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'INFO/TYPE="xxx"' /tmp/wj8A4a3te7/query.filter-type.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter-type.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'INFO/TYPE="xxx"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -i'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001' /tmp/wj8A4a3te7/filter-missing-floats.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/filter-missing-floats.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -i'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -e'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001' /tmp/wj8A4a3te7/filter-missing-floats.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/filter-missing-floats.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -e'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' /tmp/wj8A4a3te7/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' /tmp/wj8A4a3te7/query.filter.2.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' /tmp/wj8A4a3te7/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' /tmp/wj8A4a3te7/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' /tmp/wj8A4a3te7/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' /tmp/wj8A4a3te7/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' /tmp/wj8A4a3te7/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' /tmp/wj8A4a3te7/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' /tmp/wj8A4a3te7/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' /tmp/wj8A4a3te7/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' /tmp/wj8A4a3te7/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' /tmp/wj8A4a3te7/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' /tmp/wj8A4a3te7/filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/filter.5.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' /tmp/wj8A4a3te7/filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/filter.5.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' /tmp/wj8A4a3te7/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' /tmp/wj8A4a3te7/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' /tmp/wj8A4a3te7/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' /tmp/wj8A4a3te7/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' /tmp/wj8A4a3te7/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 & FMT/GQ=589' /tmp/wj8A4a3te7/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 & FMT/GQ=589' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' /tmp/wj8A4a3te7/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' /tmp/wj8A4a3te7/query.filter.3.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.3.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"' /tmp/wj8A4a3te7/query.filter.3.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.3.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' /tmp/wj8A4a3te7/query.filter.3.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.3.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %AD\n]\n' -i'AD[:0]+AD[:1] > 12' /tmp/wj8A4a3te7/filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/filter.5.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %AD\n]\n' -i'AD[:0]+AD[:1] > 12' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' /tmp/wj8A4a3te7/query.filter.4.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.4.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i 'ID=@/build/reproducible-path/bcftools-1.21/test/query.56.out' /tmp/wj8A4a3te7/view.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i 'ID=@/build/reproducible-path/bcftools-1.21/test/query.56.out' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD)>0.01' /tmp/wj8A4a3te7/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.5.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD)>0.01' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD[:0],FMT/AD[:1])>0.01' /tmp/wj8A4a3te7/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.5.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD[:0],FMT/AD[:1])>0.01' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%AD\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01' /tmp/wj8A4a3te7/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.5.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%AD\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[GT]==10' /tmp/wj8A4a3te7/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.5.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[GT]==10' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'sSUM(FMT/AD[GT])==210' /tmp/wj8A4a3te7/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.5.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'sSUM(FMT/AD[GT])==210' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[0:GT]==30' /tmp/wj8A4a3te7/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.5.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[0:GT]==30' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TF[:GT]==1 && FMT/TF[:GT]==2' /tmp/wj8A4a3te7/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.gtidx.1.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TF[:GT]==1 && FMT/TF[:GT]==2' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TI[:GT]==1 && FMT/TF[:GT]==2' /tmp/wj8A4a3te7/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.gtidx.1.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TI[:GT]==1 && FMT/TF[:GT]==2' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TS[:GT]=="BB" && FMT/TS[:GT]=="CC"' /tmp/wj8A4a3te7/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.gtidx.1.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TS[:GT]=="BB" && FMT/TS[:GT]=="CC"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TC[:GT]=="B" && FMT/TC[:GT]=="C"' /tmp/wj8A4a3te7/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.gtidx.1.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TC[:GT]=="B" && FMT/TC[:GT]=="C"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%GT %TI\n]' -i'FMT/TI[:GT]=="."' /tmp/wj8A4a3te7/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.gtidx.1.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%GT %TI\n]' -i'FMT/TI[:GT]=="."' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS\n' -i'CHROM="4"' /tmp/wj8A4a3te7/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS\n' -i'CHROM="4"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%TAG1\n' -i'(TAG1>=-129 && TAG1<=-120) || (TAG1>=-32769 && TAG1<=-32760)' /tmp/wj8A4a3te7/query.negative.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.negative.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%TAG1\n' -i'(TAG1>=-129 && TAG1<=-120) || (TAG1>=-32769 && TAG1<=-32760)' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%TAGV1\n' -i'(TAGV1>=-129 && TAGV1<=-120) || (TAGV1>=-32769 && TAGV1<=-32760)' /tmp/wj8A4a3te7/query.negative.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.negative.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%TAGV1\n' -i'(TAGV1>=-129 && TAGV1<=-120) || (TAGV1>=-32769 && TAGV1<=-32760)' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%TAG2\n' -i'(TAG2>=-129 && TAG2<=-120) || (TAG2>=-32769 && TAG2<=-32760)' /tmp/wj8A4a3te7/query.negative.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.negative.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%TAG2\n' -i'(TAG2>=-129 && TAG2<=-120) || (TAG2>=-32769 && TAG2<=-32760)' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%TAGV2\n' -i'(TAGV2>=-129 && TAGV2<=-120) || (TAGV2>=-32769 && TAGV2<=-32760)' /tmp/wj8A4a3te7/query.negative.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.negative.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%TAGV2\n' -i'(TAGV2>=-129 && TAGV2<=-120) || (TAGV2>=-32769 && TAGV2<=-32760)' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GQ\n]' -i'N_PASS(GQ<20)==1' /tmp/wj8A4a3te7/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GQ\n]' -i'N_PASS(GQ<20)==1' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")==1' /tmp/wj8A4a3te7/query.filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.11.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")==1' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")!=1' /tmp/wj8A4a3te7/query.filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.11.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")!=1' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")==1' /tmp/wj8A4a3te7/query.filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.11.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")==1' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")!=1' /tmp/wj8A4a3te7/query.filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.11.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")!=1' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM\t%POS\t%INFO\t%FORMAT\n' -s D,C /tmp/wj8A4a3te7/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM\t%POS\t%INFO\t%FORMAT\n' -s D,C .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\n' -i'POS==16777217 || POS==33554432 || POS=118673904' /tmp/wj8A4a3te7/query.filter.6.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.6.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\n' -i'POS==16777217 || POS==33554432 || POS=118673904' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(II)==6' /tmp/wj8A4a3te7/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(II)==6' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(FORMAT/FI)==7' /tmp/wj8A4a3te7/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(FORMAT/FI)==7' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(II)==2' /tmp/wj8A4a3te7/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(II)==2' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(FORMAT/FI)==1.75' /tmp/wj8A4a3te7/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(FORMAT/FI)==1.75' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(II)==2' /tmp/wj8A4a3te7/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(II)==2' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(FORMAT/FI)==1.75' /tmp/wj8A4a3te7/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(FORMAT/FI)==1.75' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(II)==2' /tmp/wj8A4a3te7/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(II)==2' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(FORMAT/FI)==1.5' /tmp/wj8A4a3te7/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(FORMAT/FI)==1.5' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'%ILEN==1' /tmp/wj8A4a3te7/query.filter.8.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.8.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'%ILEN==1' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'ILEN==1' /tmp/wj8A4a3te7/query.filter.8.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.8.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'ILEN==1' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] < FMT/AD[:1]' /tmp/wj8A4a3te7/query.filter.9.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.9.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] < FMT/AD[:1]' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] > FMT/AD[:1]' /tmp/wj8A4a3te7/query.filter.9.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.9.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] > FMT/AD[:1]' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[ %AD\n]' -i'AD[:1] / sum(AD[*]) > 0.5' /tmp/wj8A4a3te7/query.filter.13.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.13.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[ %AD\n]' -i'AD[:1] / sum(AD[*]) > 0.5' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %NUM_TAG\n' -i'COUNT(INFO/NUM_TAG)=2' /tmp/wj8A4a3te7/query.filter.10.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.10.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %NUM_TAG\n' -i'COUNT(INFO/NUM_TAG)=2' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2' /tmp/wj8A4a3te7/query.filter.10.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.10.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM:%POS\t%N_PASS(GT="alt" & GQ>110)\t[\t%GT]\t[\t%GQ]\n' /tmp/wj8A4a3te7/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM:%POS\t%N_PASS(GT="alt" & GQ>110)\t[\t%GT]\t[\t%GQ]\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 1,3,0 /tmp/wj8A4a3te7/query.filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.12.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 1,3,0 .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 0,1,3 /tmp/wj8A4a3te7/query.filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.12.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 0,1,3 .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f "[%SAMPLE %GT\n]" -S /build/reproducible-path/bcftools-1.21/test/query.smpl.11.txt /tmp/wj8A4a3te7/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.smpl.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f "[%SAMPLE %GT\n]" -S /build/reproducible-path/bcftools-1.21/test/query.smpl.11.txt .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -l -S /build/reproducible-path/bcftools-1.21/test/query.smpl.11.txt /tmp/wj8A4a3te7/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.smpl.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -l -S /build/reproducible-path/bcftools-1.21/test/query.smpl.11.txt .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f "[%SAMPLE %GT\n]" -S ^/build/reproducible-path/bcftools-1.21/test/query.smpl.11.txt /tmp/wj8A4a3te7/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.smpl.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f "[%SAMPLE %GT\n]" -S ^/build/reproducible-path/bcftools-1.21/test/query.smpl.11.txt .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -l -S ^/build/reproducible-path/bcftools-1.21/test/query.smpl.11.txt /tmp/wj8A4a3te7/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.smpl.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -l -S ^/build/reproducible-path/bcftools-1.21/test/query.smpl.11.txt .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f "[%SAMPLE %GT\n]" -S /build/reproducible-path/bcftools-1.21/test/query.smpl.txt /tmp/wj8A4a3te7/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.smpl.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f "[%SAMPLE %GT\n]" -S /build/reproducible-path/bcftools-1.21/test/query.smpl.txt .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -l -S /build/reproducible-path/bcftools-1.21/test/query.smpl.txt /tmp/wj8A4a3te7/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.smpl.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -l -S /build/reproducible-path/bcftools-1.21/test/query.smpl.txt .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID~"s12"' /tmp/wj8A4a3te7/query.filter.id.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.id.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID~"s12"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID="rs123"' /tmp/wj8A4a3te7/query.filter.id.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.id.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID="rs123"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID="abc"' /tmp/wj8A4a3te7/query.filter.id.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.id.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID="abc"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID=@/build/reproducible-path/bcftools-1.21/test/query.filter.id.3.txt' /tmp/wj8A4a3te7/query.filter.id.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.id.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID=@/build/reproducible-path/bcftools-1.21/test/query.filter.id.3.txt' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID!="abc"' /tmp/wj8A4a3te7/query.filter.id.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.id.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID!="abc"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID!=@/build/reproducible-path/bcftools-1.21/test/query.filter.id.3.txt' /tmp/wj8A4a3te7/query.filter.id.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.id.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID!=@/build/reproducible-path/bcftools-1.21/test/query.filter.id.3.txt' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER="A"' -f'%FILTER\n' /tmp/wj8A4a3te7/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/filter.12.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER="A"' -f'%FILTER\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER~"A"' -f'%FILTER\n' /tmp/wj8A4a3te7/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/filter.12.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER~"A"' -f'%FILTER\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER="A;B"' -f'%FILTER\n' /tmp/wj8A4a3te7/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/filter.12.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER="A;B"' -f'%FILTER\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER!="A;B"' -f'%FILTER\n' /tmp/wj8A4a3te7/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/filter.12.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER!="A;B"' -f'%FILTER\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER~"A;B"' -f'%FILTER\n' /tmp/wj8A4a3te7/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/filter.12.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER~"A;B"' -f'%FILTER\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER!~"A;B"' -f'%FILTER\n' /tmp/wj8A4a3te7/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/filter.12.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER!~"A;B"' -f'%FILTER\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'DP%10==2' -f'[ %DP]\n' /tmp/wj8A4a3te7/filter.10.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/filter.10.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'DP%10==2' -f'[ %DP]\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'REF="N"' -f'%CHROM %POS %REF %ALT %QUAL\n' /tmp/wj8A4a3te7/filter.13.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/filter.13.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'REF="N"' -f'%CHROM %POS %REF %ALT %QUAL\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -H -f'[%CHROM %POS %SAMPLE %DP %GT\n]' /tmp/wj8A4a3te7/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.header.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -H -f'[%CHROM %POS %SAMPLE %DP %GT\n]' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -H -f'[%CHROM %POS %SAMPLE %DP %GT\t]\n' /tmp/wj8A4a3te7/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.header.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -H -f'[%CHROM %POS %SAMPLE %DP %GT\t]\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]\n' /tmp/wj8A4a3te7/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.header.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]' /tmp/wj8A4a3te7/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.header.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]\n' /tmp/wj8A4a3te7/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.header.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]' /tmp/wj8A4a3te7/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.header.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -HH -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]' /tmp/wj8A4a3te7/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.header.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -HH -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%SAMPLE %DP\n]' -i'DP=1 || DP=2' /tmp/wj8A4a3te7/query.filter-or.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter-or.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%SAMPLE %DP\n]' -i'DP=1 || DP=2' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%SAMPLE %DP\n]' -i'DP=1 | DP=2' /tmp/wj8A4a3te7/query.filter-or.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter-or.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%SAMPLE %DP\n]' -i'DP=1 | DP=2' .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/wj8A4a3te7/norm.sort.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/wj8A4a3te7/norm.sort.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - -S lex /tmp/wj8A4a3te7/norm.sort.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - -S lex /tmp/wj8A4a3te7/norm.sort.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +both /tmp/wj8A4a3te7/norm.join-missing-ploidy.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +both /tmp/wj8A4a3te7/norm.join-missing-ploidy.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - --multi-overlaps . /tmp/wj8A4a3te7/norm.split.5.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - --multi-overlaps . /tmp/wj8A4a3te7/norm.split.5.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version /tmp/wj8A4a3te7/norm.symbolic.3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.symbolic.3.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version /tmp/wj8A4a3te7/norm.symbolic.3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.symbolic.3.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -cx /tmp/wj8A4a3te7/norm.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -cx /tmp/wj8A4a3te7/norm.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- /tmp/wj8A4a3te7/norm.split.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- /tmp/wj8A4a3te7/norm.split.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- /tmp/wj8A4a3te7/norm.split.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- /tmp/wj8A4a3te7/norm.split.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- --force /tmp/wj8A4a3te7/norm.split.3.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- --force /tmp/wj8A4a3te7/norm.split.3.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- /tmp/wj8A4a3te7/norm.split.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- /tmp/wj8A4a3te7/norm.split.4.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- --keep-sum AD /tmp/wj8A4a3te7/norm.split.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- --keep-sum AD /tmp/wj8A4a3te7/norm.split.4.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- /tmp/wj8A4a3te7/norm.split.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- /tmp/wj8A4a3te7/norm.split.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m+ /tmp/wj8A4a3te7/norm.merge.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m+ /tmp/wj8A4a3te7/norm.merge.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m+ /tmp/wj8A4a3te7/norm.merge.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m+ /tmp/wj8A4a3te7/norm.merge.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m+ /tmp/wj8A4a3te7/norm.merge.3.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m+ /tmp/wj8A4a3te7/norm.merge.3.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m+ -s /tmp/wj8A4a3te7/norm.merge.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m+ -s /tmp/wj8A4a3te7/norm.merge.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -Nc s /tmp/wj8A4a3te7/norm.setref.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -Nc s /tmp/wj8A4a3te7/norm.setref.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version /tmp/wj8A4a3te7/norm.telomere.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version /tmp/wj8A4a3te7/norm.telomere.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d snps /tmp/wj8A4a3te7/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d snps /tmp/wj8A4a3te7/norm.rmdup.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d indels /tmp/wj8A4a3te7/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d indels /tmp/wj8A4a3te7/norm.rmdup.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d both /tmp/wj8A4a3te7/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d both /tmp/wj8A4a3te7/norm.rmdup.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d all /tmp/wj8A4a3te7/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d all /tmp/wj8A4a3te7/norm.rmdup.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d none /tmp/wj8A4a3te7/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d none /tmp/wj8A4a3te7/norm.rmdup.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d exact /tmp/wj8A4a3te7/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d exact /tmp/wj8A4a3te7/norm.rmdup.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d none /tmp/wj8A4a3te7/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d none /tmp/wj8A4a3te7/norm.rmdup.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d exact /tmp/wj8A4a3te7/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d exact /tmp/wj8A4a3te7/norm.rmdup.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d indels /tmp/wj8A4a3te7/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d indels /tmp/wj8A4a3te7/norm.rmdup.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d any /tmp/wj8A4a3te7/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d any /tmp/wj8A4a3te7/norm.rmdup.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d both /tmp/wj8A4a3te7/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d both /tmp/wj8A4a3te7/norm.rmdup.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d snps /tmp/wj8A4a3te7/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d snps /tmp/wj8A4a3te7/norm.rmdup.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d exact /tmp/wj8A4a3te7/norm.rmdup.3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.rmdup.3.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d exact /tmp/wj8A4a3te7/norm.rmdup.3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.rmdup.3.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d all /tmp/wj8A4a3te7/norm.rmdup.3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.rmdup.3.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d all /tmp/wj8A4a3te7/norm.rmdup.3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.rmdup.3.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -c s -a /tmp/wj8A4a3te7/norm.2.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.2.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -c s -a /tmp/wj8A4a3te7/norm.2.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.2.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -c s /tmp/wj8A4a3te7/norm.iupac.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.iupac.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -c s /tmp/wj8A4a3te7/norm.iupac.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.iupac.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -c s /tmp/wj8A4a3te7/norm.3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.3.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -c s /tmp/wj8A4a3te7/norm.3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.3.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -c s -i'alt="N"' /tmp/wj8A4a3te7/norm.3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.3.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -c s -i'alt="N"' /tmp/wj8A4a3te7/norm.3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.3.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -a --old-rec-tag OLD_REC /tmp/wj8A4a3te7/atomize.split.1.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any --force .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -a --old-rec-tag OLD_REC /tmp/wj8A4a3te7/atomize.split.1.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any --force -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any --old-rec-tag OLD_REC --force /tmp/wj8A4a3te7/atomize.split.1.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -a .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any --old-rec-tag OLD_REC --force /tmp/wj8A4a3te7/atomize.split.1.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -a -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any --old-rec-tag OLD_REC --force -a /tmp/wj8A4a3te7/atomize.split.1.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any --old-rec-tag OLD_REC --force -a /tmp/wj8A4a3te7/atomize.split.1.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/wj8A4a3te7/atomize.split.1.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/wj8A4a3te7/atomize.split.1.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/wj8A4a3te7/atomize.split.1.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/wj8A4a3te7/atomize.split.1.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/wj8A4a3te7/atomize.split.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/wj8A4a3te7/atomize.split.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/wj8A4a3te7/atomize.split.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/wj8A4a3te7/atomize.split.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . /tmp/wj8A4a3te7/atomize.split.3.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . /tmp/wj8A4a3te7/atomize.split.3.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/wj8A4a3te7/atomize.split.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/wj8A4a3te7/atomize.split.4.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC -i 'ILEN=0' /tmp/wj8A4a3te7/atomize.split.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC -i 'ILEN=0' /tmp/wj8A4a3te7/atomize.split.4.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --old-rec-tag OLD_REC --atom-overlaps . /tmp/wj8A4a3te7/atomize.split.5.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --old-rec-tag OLD_REC --atom-overlaps . /tmp/wj8A4a3te7/atomize.split.5.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/wj8A4a3te7/atomize.split.5.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/wj8A4a3te7/atomize.split.5.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +both /tmp/wj8A4a3te7/norm.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +both /tmp/wj8A4a3te7/norm.4.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +any /tmp/wj8A4a3te7/norm.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +any /tmp/wj8A4a3te7/norm.4.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - --multi-overlaps 0 /tmp/wj8A4a3te7/norm.5.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - --multi-overlaps 0 /tmp/wj8A4a3te7/norm.5.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - --multi-overlaps . /tmp/wj8A4a3te7/norm.5.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - --multi-overlaps . /tmp/wj8A4a3te7/norm.5.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any /tmp/wj8A4a3te7/norm.m-any.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any /tmp/wj8A4a3te7/norm.m-any.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any /tmp/wj8A4a3te7/norm.phased-split.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any /tmp/wj8A4a3te7/norm.phased-split.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +any /tmp/wj8A4a3te7/norm.phased-join.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +any /tmp/wj8A4a3te7/norm.phased-join.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI /tmp/wj8A4a3te7/norm.symbolic.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.symbolic.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI /tmp/wj8A4a3te7/norm.symbolic.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.symbolic.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI /tmp/wj8A4a3te7/norm.symbolic.2.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.symbolic.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI /tmp/wj8A4a3te7/norm.symbolic.2.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.symbolic.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI /tmp/wj8A4a3te7/norm.right-align.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.right-align.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI /tmp/wj8A4a3te7/norm.right-align.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.right-align.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI -g /build/reproducible-path/bcftools-1.21/test/norm.right-align.gff /tmp/wj8A4a3te7/norm.right-align.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.right-align.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI -g /build/reproducible-path/bcftools-1.21/test/norm.right-align.gff /tmp/wj8A4a3te7/norm.right-align.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.right-align.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI -a -m -any /tmp/wj8A4a3te7/norm.atom-split-norm.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.atom-split-norm.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI -a -m -any /tmp/wj8A4a3te7/norm.atom-split-norm.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.atom-split-norm.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any /tmp/wj8A4a3te7/norm.string-tags.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any /tmp/wj8A4a3te7/norm.string-tags.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/wj8A4a3te7/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +both .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/wj8A4a3te7/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +both -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/wj8A4a3te7/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +indels .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/wj8A4a3te7/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +indels -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/wj8A4a3te7/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +snps .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/wj8A4a3te7/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +snps -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/wj8A4a3te7/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +snps .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/wj8A4a3te7/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +snps -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/wj8A4a3te7/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +any .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/wj8A4a3te7/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +any -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - -i 'type="snp"' /tmp/wj8A4a3te7/norm.split.merge.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - -i 'type="snp"' /tmp/wj8A4a3te7/norm.split.merge.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +any /tmp/wj8A4a3te7/norm.merge.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +any /tmp/wj8A4a3te7/norm.merge.4.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +both /tmp/wj8A4a3te7/norm.merge.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +both /tmp/wj8A4a3te7/norm.merge.4.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -i 'INFO/TAG=@/build/reproducible-path/bcftools-1.21/test/filter.string.1.txt' /tmp/wj8A4a3te7/filter.string.1.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -i 'INFO/TAG=@/build/reproducible-path/bcftools-1.21/test/filter.string.1.txt' /tmp/wj8A4a3te7/filter.string.1.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -i 'FMT/TAG=@/build/reproducible-path/bcftools-1.21/test/filter.string.1.txt' /tmp/wj8A4a3te7/filter.string.1.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -i 'FMT/TAG=@/build/reproducible-path/bcftools-1.21/test/filter.string.1.txt' /tmp/wj8A4a3te7/filter.string.1.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -HA /tmp/wj8A4a3te7/merge.gvcf.2.a.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -HAA /tmp/wj8A4a3te7/merge.gvcf.2.a.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r 1 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r 1 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r 1:1-2 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r 1:1-2 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r 1:1,1:2 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r 1:1,1:2 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r 1:1-1 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r 1:1-1 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r {1:1} .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r {1:1} | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r {1:1}:1-2 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r {1:1}:1-2 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r {1:1}:1,{1:1}:2 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r {1:1}:1,{1:1}:2 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r {1:1}:1-1 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r {1:1}:1-1 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r {1:1-1} .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r {1:1-1} | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r {1:1-1}:1-2 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r {1:1-1}:1-2 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r {1:1-1}:1,{1:1-1}:2 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r {1:1-1}:1,{1:1-1}:2 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r {1:1-1}:1-1 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r {1:1-1}:1-1 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r {1:1-1}-2 .. ok, expected non-zero status test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r {1:1-1}-2 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok, expected non-zero status test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -aUc1 -C1 -s NA00002 -v snps /tmp/wj8A4a3te7/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/wj8A4a3te7/view.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -f PASS -Xks NA00003 /tmp/wj8A4a3te7/view.vcf.gz -r20,Y .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -f PASS -Xks NA00003 /tmp/wj8A4a3te7/view.vcf.gz -r20,Y | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -xs NA00003 /tmp/wj8A4a3te7/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -xs NA00003 /tmp/wj8A4a3te7/view.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/wj8A4a3te7/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/wj8A4a3te7/view.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -p /tmp/wj8A4a3te7/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -p /tmp/wj8A4a3te7/view.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -P /tmp/wj8A4a3te7/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -P /tmp/wj8A4a3te7/view.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -hm2 -M2 -q0.3 -Q0.7 /tmp/wj8A4a3te7/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/wj8A4a3te7/view.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -Hu /tmp/wj8A4a3te7/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -GVsnps /tmp/wj8A4a3te7/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -GVsnps /tmp/wj8A4a3te7/view.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -ne 'INDEL=1 || PV4[0]<0.006' /tmp/wj8A4a3te7/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/wj8A4a3te7/view.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -s ^NA00003 /tmp/wj8A4a3te7/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -s ^NA00003 /tmp/wj8A4a3te7/view.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/wj8A4a3te7/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.omitgenotypes.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -G /tmp/wj8A4a3te7/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -G /tmp/wj8A4a3te7/view.omitgenotypes.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -HG /tmp/wj8A4a3te7/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -a /tmp/wj8A4a3te7/many.alleles.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -a /tmp/wj8A4a3te7/many.alleles.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -asA /tmp/wj8A4a3te7/view.vectors.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -asA /tmp/wj8A4a3te7/view.vectors.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -asB /tmp/wj8A4a3te7/view.vectors.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -asB /tmp/wj8A4a3te7/view.vectors.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -asA /tmp/wj8A4a3te7/view.vectors.2.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -asA /tmp/wj8A4a3te7/view.vectors.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -i'FMT/FGS[*:0]="AAAAAA"' /tmp/wj8A4a3te7/view.filter.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -i'FMT/FGS[*:2]="C"' /tmp/wj8A4a3te7/view.filter.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -i'FMT/FGS[*:4]="EE"' /tmp/wj8A4a3te7/view.filter.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -i'FMT/FRS[*:1]="BB"' /tmp/wj8A4a3te7/view.filter.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -i'TXT0="text"' /tmp/wj8A4a3te7/view.filter.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -T /build/reproducible-path/bcftools-1.21/test/view.chrs.tab /tmp/wj8A4a3te7/view.chrs.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -T /build/reproducible-path/bcftools-1.21/test/view.chrs.tab /tmp/wj8A4a3te7/view.chrs.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -i 'POS>=3062917' /tmp/wj8A4a3te7/filter.2.vcf.gz 1:3062917-3157410 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -i 'POS>=3062917' /tmp/wj8A4a3te7/filter.2.vcf.gz 1:3062917-3157410 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -r 1:10,1:12,1:10 /tmp/wj8A4a3te7/idx.1.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -r 1:1172777-1172804,1:1172806-1172808 /tmp/wj8A4a3te7/idx.2.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -R /build/reproducible-path/bcftools-1.21/test/idx.2.bed /tmp/wj8A4a3te7/idx.2.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -R /build/reproducible-path/bcftools-1.21/test/idx.3.bed /tmp/wj8A4a3te7/idx.3.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -R /build/reproducible-path/bcftools-1.21/test/idx.4.bed /tmp/wj8A4a3te7/idx.4.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -Ht 2 /tmp/wj8A4a3te7/view-t.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -Ht 3 /tmp/wj8A4a3te7/view-t.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 0 /tmp/wj8A4a3te7/overlap.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 1 /tmp/wj8A4a3te7/overlap.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 2 /tmp/wj8A4a3te7/overlap.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 0 /tmp/wj8A4a3te7/overlap.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 1 /tmp/wj8A4a3te7/overlap.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 2 /tmp/wj8A4a3te7/overlap.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 0 /tmp/wj8A4a3te7/overlap.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 1 /tmp/wj8A4a3te7/overlap.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 2 /tmp/wj8A4a3te7/overlap.vcf.gz .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.21/bcftools view /build/reproducible-path/bcftools-1.21/test/view64bit.1.vcf -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.21/bcftools view /build/reproducible-path/bcftools-1.21/test/view64bit.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.21/bcftools view /build/reproducible-path/bcftools-1.21/test/view64bit.1.vcf -Ou | /build/reproducible-path/bcftools-1.21/bcftools view -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.21/bcftools view /build/reproducible-path/bcftools-1.21/test/view64bit.2.vcf -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.21/bcftools view /build/reproducible-path/bcftools-1.21/test/view64bit.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.21/bcftools view /build/reproducible-path/bcftools-1.21/test/view64bit.2.vcf -Ou | /build/reproducible-path/bcftools-1.21/bcftools view -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.21/bcftools view /build/reproducible-path/bcftools-1.21/test/view64bit.3.vcf -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.21/bcftools view /build/reproducible-path/bcftools-1.21/test/view64bit.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.21/bcftools view /build/reproducible-path/bcftools-1.21/test/view64bit.4.vcf -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.21/bcftools view /build/reproducible-path/bcftools-1.21/test/view64bit.4.vcf | /build/reproducible-path/bcftools-1.21/bcftools view -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.21/bcftools view /build/reproducible-path/bcftools-1.21/test/view64bit.4.vcf -Ou | /build/reproducible-path/bcftools-1.21/bcftools view -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.21/bcftools view /build/reproducible-path/bcftools-1.21/test/view64bit.5.vcf -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.21/bcftools view /build/reproducible-path/bcftools-1.21/test/view64bit.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools view -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.21/bcftools view /build/reproducible-path/bcftools-1.21/test/view64bit.5.vcf -Ou | /build/reproducible-path/bcftools-1.21/bcftools view -H .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -C5:nonmajor /tmp/wj8A4a3te7/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -c6:nonmajor /tmp/wj8A4a3te7/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -q0.3:major /tmp/wj8A4a3te7/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/wj8A4a3te7/view.filter.annovar.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -i 'Gene.refGene~"NOD"' /tmp/wj8A4a3te7/view.filter.annovar.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -i 'LJB2_MutationTaster=="0.291000"' /tmp/wj8A4a3te7/view.filter.annovar.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -a /tmp/wj8A4a3te7/view-a.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -T /build/reproducible-path/bcftools-1.21/test/view.sites.txt /tmp/wj8A4a3te7/view.sites.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -T /build/reproducible-path/bcftools-1.21/test/view.sites.txt /tmp/wj8A4a3te7/view.sites.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -T /build/reproducible-path/bcftools-1.21/test/view.sites.txt.gz /tmp/wj8A4a3te7/view.sites.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -T /build/reproducible-path/bcftools-1.21/test/view.sites.txt.gz /tmp/wj8A4a3te7/view.sites.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_head: /build/reproducible-path/bcftools-1.21/bcftools head /build/reproducible-path/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_head: /build/reproducible-path/bcftools-1.21/bcftools head -h 0 /build/reproducible-path/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_head: /build/reproducible-path/bcftools-1.21/bcftools head -h 1 /build/reproducible-path/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_head: /build/reproducible-path/bcftools-1.21/bcftools head -h 5 /build/reproducible-path/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_head: /build/reproducible-path/bcftools-1.21/bcftools head -h 22 /build/reproducible-path/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_head: /build/reproducible-path/bcftools-1.21/bcftools head -h 23 /build/reproducible-path/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_head: /build/reproducible-path/bcftools-1.21/bcftools head -n 0 /build/reproducible-path/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_head: /build/reproducible-path/bcftools-1.21/bcftools head -n 1 /build/reproducible-path/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_head: /build/reproducible-path/bcftools-1.21/bcftools head -n 5 /build/reproducible-path/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_head: /build/reproducible-path/bcftools-1.21/bcftools head -h 5 -n 5 < /build/reproducible-path/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_head2: /build/reproducible-path/bcftools-1.21/bcftools head -s0 /tmp/wj8A4a3te7/mpileup.2.vcf.gz .. ok test_vcf_head2: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -Ob /tmp/wj8A4a3te7/mpileup.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools head -s0 .. ok test_vcf_head2: /build/reproducible-path/bcftools-1.21/bcftools head -s1 /tmp/wj8A4a3te7/mpileup.2.vcf.gz .. ok test_vcf_head2: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -Ob /tmp/wj8A4a3te7/mpileup.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools head -s1 .. ok test_vcf_head2: /build/reproducible-path/bcftools-1.21/bcftools head -s2 -h2 /tmp/wj8A4a3te7/mpileup.2.vcf.gz .. ok test_vcf_head2: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -Ob /tmp/wj8A4a3te7/mpileup.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools head -s2 -h2 .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mv /build/reproducible-path/bcftools-1.21/test/mpileup.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mv /build/reproducible-path/bcftools-1.21/test/mpileup.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mg0 /build/reproducible-path/bcftools-1.21/test/mpileup.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mg0 /build/reproducible-path/bcftools-1.21/test/mpileup.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mv -S /build/reproducible-path/bcftools-1.21/test/mpileup.3.samples /build/reproducible-path/bcftools-1.21/test/mpileup.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mv -S /build/reproducible-path/bcftools-1.21/test/mpileup.3.samples /build/reproducible-path/bcftools-1.21/test/mpileup.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mv -S /build/reproducible-path/bcftools-1.21/test/mpileup.4.samples /build/reproducible-path/bcftools-1.21/test/mpileup.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mv -S /build/reproducible-path/bcftools-1.21/test/mpileup.4.samples /build/reproducible-path/bcftools-1.21/test/mpileup.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mv -S /build/reproducible-path/bcftools-1.21/test/mpileup.5.samples /build/reproducible-path/bcftools-1.21/test/mpileup.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mv -S /build/reproducible-path/bcftools-1.21/test/mpileup.5.samples /build/reproducible-path/bcftools-1.21/test/mpileup.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mv --ploidy-file /build/reproducible-path/bcftools-1.21/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.21/test/mpileup.samples /build/reproducible-path/bcftools-1.21/test/mpileup.X.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mv --ploidy-file /build/reproducible-path/bcftools-1.21/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.21/test/mpileup.samples /build/reproducible-path/bcftools-1.21/test/mpileup.X.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mv --ploidy-file /build/reproducible-path/bcftools-1.21/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.21/test/mpileup.ped /build/reproducible-path/bcftools-1.21/test/mpileup.X.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mv --ploidy-file /build/reproducible-path/bcftools-1.21/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.21/test/mpileup.ped /build/reproducible-path/bcftools-1.21/test/mpileup.X.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mv --ploidy-file /build/reproducible-path/bcftools-1.21/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.21/test/mpileup.2.samples /build/reproducible-path/bcftools-1.21/test/mpileup.X.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mv --ploidy-file /build/reproducible-path/bcftools-1.21/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.21/test/mpileup.2.samples /build/reproducible-path/bcftools-1.21/test/mpileup.X.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mv /build/reproducible-path/bcftools-1.21/test/mpileup.NA19213.NA19129.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mv /build/reproducible-path/bcftools-1.21/test/mpileup.NA19213.NA19129.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mv -G - --group-samples-tag AD /build/reproducible-path/bcftools-1.21/test/mpileup.NA19213.NA19129.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mv -G - --group-samples-tag AD /build/reproducible-path/bcftools-1.21/test/mpileup.NA19213.NA19129.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mv /build/reproducible-path/bcftools-1.21/test/mpileup.hwe.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mv /build/reproducible-path/bcftools-1.21/test/mpileup.hwe.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mv -G - --group-samples-tag AD /build/reproducible-path/bcftools-1.21/test/mpileup.hwe.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mv -G - --group-samples-tag AD /build/reproducible-path/bcftools-1.21/test/mpileup.hwe.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mv -G /build/reproducible-path/bcftools-1.21/test/mpileup.hwe.samples --group-samples-tag AD /build/reproducible-path/bcftools-1.21/test/mpileup.hwe.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mv -G /build/reproducible-path/bcftools-1.21/test/mpileup.hwe.samples --group-samples-tag AD /build/reproducible-path/bcftools-1.21/test/mpileup.hwe.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/wj8A4a3te7/mpileup.tab.gz /build/reproducible-path/bcftools-1.21/test/mpileup.vcf .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/wj8A4a3te7/mpileup.tab.gz /build/reproducible-path/bcftools-1.21/test/mpileup.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/wj8A4a3te7/mpileup.2.tab.gz /build/reproducible-path/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/wj8A4a3te7/mpileup.2.tab.gz /build/reproducible-path/bcftools-1.21/test/mpileup.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/wj8A4a3te7/mpileup.3.tab.gz -i /build/reproducible-path/bcftools-1.21/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/wj8A4a3te7/mpileup.3.tab.gz -i /build/reproducible-path/bcftools-1.21/test/mpileup.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/wj8A4a3te7/mpileup.4.tab.gz -i /build/reproducible-path/bcftools-1.21/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/wj8A4a3te7/mpileup.4.tab.gz -i /build/reproducible-path/bcftools-1.21/test/mpileup.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/wj8A4a3te7/mpileup.5.tab.gz -i /build/reproducible-path/bcftools-1.21/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/wj8A4a3te7/mpileup.5.tab.gz -i /build/reproducible-path/bcftools-1.21/test/mpileup.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/wj8A4a3te7/mpileup.6.tab.gz -i /build/reproducible-path/bcftools-1.21/test/mpileup.4.vcf .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/wj8A4a3te7/mpileup.6.tab.gz -i /build/reproducible-path/bcftools-1.21/test/mpileup.4.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/wj8A4a3te7/mpileup.7.tab.gz -i /build/reproducible-path/bcftools-1.21/test/mpileup.5.vcf .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/wj8A4a3te7/mpileup.7.tab.gz -i /build/reproducible-path/bcftools-1.21/test/mpileup.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/wj8A4a3te7/mpileup.cals.1.tab.gz /build/reproducible-path/bcftools-1.21/test/mpileup.cals.1.vcf .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/wj8A4a3te7/mpileup.cals.1.tab.gz /build/reproducible-path/bcftools-1.21/test/mpileup.cals.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/wj8A4a3te7/mpileup.cals.2.tab.gz /build/reproducible-path/bcftools-1.21/test/mpileup.cals.2.vcf .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/wj8A4a3te7/mpileup.cals.2.tab.gz /build/reproducible-path/bcftools-1.21/test/mpileup.cals.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -cv /build/reproducible-path/bcftools-1.21/test/mpileup.c.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -cv /build/reproducible-path/bcftools-1.21/test/mpileup.c.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -cv --ploidy-file /build/reproducible-path/bcftools-1.21/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.21/test/mpileup.samples /build/reproducible-path/bcftools-1.21/test/mpileup.c.X.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -cv --ploidy-file /build/reproducible-path/bcftools-1.21/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.21/test/mpileup.samples /build/reproducible-path/bcftools-1.21/test/mpileup.c.X.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -cv --ploidy-file /build/reproducible-path/bcftools-1.21/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.21/test/mpileup.ped /build/reproducible-path/bcftools-1.21/test/mpileup.c.X.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -cv --ploidy-file /build/reproducible-path/bcftools-1.21/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.21/test/mpileup.ped /build/reproducible-path/bcftools-1.21/test/mpileup.c.X.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -cv --ploidy-file /build/reproducible-path/bcftools-1.21/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.21/test/mpileup.2.samples /build/reproducible-path/bcftools-1.21/test/mpileup.c.X.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -cv --ploidy-file /build/reproducible-path/bcftools-1.21/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.21/test/mpileup.2.samples /build/reproducible-path/bcftools-1.21/test/mpileup.c.X.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mv /build/reproducible-path/bcftools-1.21/test/call-G.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mv /build/reproducible-path/bcftools-1.21/test/call-G.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mv -G - --group-samples-tag AD /build/reproducible-path/bcftools-1.21/test/call-G.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mv -G - --group-samples-tag AD /build/reproducible-path/bcftools-1.21/test/call-G.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mv -F AN_POP,AC_POP /build/reproducible-path/bcftools-1.21/test/call-G.2.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mv -F AN_POP,AC_POP /build/reproducible-path/bcftools-1.21/test/call-G.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -m /build/reproducible-path/bcftools-1.21/test/call.af-fixation.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -m /build/reproducible-path/bcftools-1.21/test/call.af-fixation.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -m -G /build/reproducible-path/bcftools-1.21/test/call.af-fixation.txt /build/reproducible-path/bcftools-1.21/test/call.af-fixation.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -m -G /build/reproducible-path/bcftools-1.21/test/call.af-fixation.txt /build/reproducible-path/bcftools-1.21/test/call.af-fixation.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -m -G /build/reproducible-path/bcftools-1.21/test/call.af-fixation.txt -a GP,GQ /build/reproducible-path/bcftools-1.21/test/call.af-fixation.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -m -G /build/reproducible-path/bcftools-1.21/test/call.af-fixation.txt -a GP,GQ /build/reproducible-path/bcftools-1.21/test/call.af-fixation.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S. -e'TXT0="text"' /build/reproducible-path/bcftools-1.21/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S. -e'TXT0="text"' /build/reproducible-path/bcftools-1.21/test/view.filter.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S. -e'FMT/FRS[*:1]="BB"' /build/reproducible-path/bcftools-1.21/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S. -e'FMT/FRS[*:1]="BB"' /build/reproducible-path/bcftools-1.21/test/view.filter.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S. -e'FMT/FGS[*:0]="AAAAAA"' /build/reproducible-path/bcftools-1.21/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S. -e'FMT/FGS[*:0]="AAAAAA"' /build/reproducible-path/bcftools-1.21/test/view.filter.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S. -e'FMT/FGS[*:1]="BBB"' /build/reproducible-path/bcftools-1.21/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S. -e'FMT/FGS[*:1]="BBB"' /build/reproducible-path/bcftools-1.21/test/view.filter.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S. -e'FMT/FGS[*:4]="EE"' /build/reproducible-path/bcftools-1.21/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S. -e'FMT/FGS[*:4]="EE"' /build/reproducible-path/bcftools-1.21/test/view.filter.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S. -e'FMT/STR="XX"' /build/reproducible-path/bcftools-1.21/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S. -e'FMT/STR="XX"' /build/reproducible-path/bcftools-1.21/test/view.filter.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S. -e'FMT/FILTER="aaa"' /build/reproducible-path/bcftools-1.21/test/view.filter.2.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S. -e'FMT/FILTER="aaa"' /build/reproducible-path/bcftools-1.21/test/view.filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -mx -g2 -G2 /build/reproducible-path/bcftools-1.21/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -mx -g2 -G2 /build/reproducible-path/bcftools-1.21/test/filter.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -e'INFO/DP=19' /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -e'INFO/DP=19' /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -e'INFO/DP=19' -s XX /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -e'INFO/DP=19' -s XX /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -e'INFO/DP=19' -s XX -m+ /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+ /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -e'INFO/DP=19' -s XX -mx /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -e'INFO/DP=19' -s XX -mx /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -e'INFO/DP=19' -s XX -m+x /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+x /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -e'FMT/GT="0/2"' /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -e'FMT/GT="0/2"' /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -e'FMT/GT="0/2"' -s XX /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -e'FMT/GT="0/2"' -s XX -m+ /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+ /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -e'FMT/GT="0/2"' -s XX -mx /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -mx /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -e'FMT/GT="0/2"' -s XX -m+x /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+x /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'FMT/GT="0/0" && AC[*]=2' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'FMT/GT="0/0" && AC[*]=2' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'AC[*]=2 && FMT/GT="0/0"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'AC[*]=2 && FMT/GT="0/0"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'ALT="."' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'ALT="."' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -i 'FORMAT/TEST3<25' /build/reproducible-path/bcftools-1.21/test/filter.4.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -i 'FORMAT/TEST3<25' /build/reproducible-path/bcftools-1.21/test/filter.4.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -i 'FORMAT/TEST4<25' /build/reproducible-path/bcftools-1.21/test/filter.4.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -i 'FORMAT/TEST4<25' /build/reproducible-path/bcftools-1.21/test/filter.4.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'GT="A"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'GT="A"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'GT="RR"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'GT="RR"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'GT="RA"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'GT="RA"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'GT="AR"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'GT="AR"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'GT="AA"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'GT="AA"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'GT="aA"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'GT="aA"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'GT="Aa"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'GT="Aa"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'GT="HOM"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'GT="HOM"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'GT="HET"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'GT="HET"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'GT="HAP"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'GT="HAP"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'AD[:1]=11' /build/reproducible-path/bcftools-1.21/test/filter.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'AD[:1]=11' /build/reproducible-path/bcftools-1.21/test/filter.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'AD[1:]=11' /build/reproducible-path/bcftools-1.21/test/filter.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'AD[1:]=11' /build/reproducible-path/bcftools-1.21/test/filter.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'FR[0:1]=11' /build/reproducible-path/bcftools-1.21/test/filter.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%FR]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'FR[0:1]=11' /build/reproducible-path/bcftools-1.21/test/filter.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%FR]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'AD[*]="."' /build/reproducible-path/bcftools-1.21/test/filter.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'AD[*]="."' /build/reproducible-path/bcftools-1.21/test/filter.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'AD[0:0]=="."' /build/reproducible-path/bcftools-1.21/test/filter.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'AD[0:0]=="."' /build/reproducible-path/bcftools-1.21/test/filter.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'AD[0:0]!="."' /build/reproducible-path/bcftools-1.21/test/filter.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'AD[0:0]!="."' /build/reproducible-path/bcftools-1.21/test/filter.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'QUAL=="."' /build/reproducible-path/bcftools-1.21/test/filter.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%QUAL\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'QUAL=="."' /build/reproducible-path/bcftools-1.21/test/filter.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%QUAL\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'N_PASS(DP>32)=1' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'N_PASS(DP>32)=1' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'F_PASS(DP>32)=0.5' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'F_PASS(DP>32)=0.5' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'F_MISSING>=1/5' /build/reproducible-path/bcftools-1.21/test/filter.6.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'F_MISSING>=1/5' /build/reproducible-path/bcftools-1.21/test/filter.6.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'F_MISSING>=0.2' /build/reproducible-path/bcftools-1.21/test/filter.6.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'F_MISSING>=0.2' /build/reproducible-path/bcftools-1.21/test/filter.6.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'F_PASS(GT=="mis")>=1/5' /build/reproducible-path/bcftools-1.21/test/filter.6.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'F_PASS(GT=="mis")>=1/5' /build/reproducible-path/bcftools-1.21/test/filter.6.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'F_PASS(GT=="mis")>=0.2' /build/reproducible-path/bcftools-1.21/test/filter.6.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'F_PASS(GT=="mis")>=0.2' /build/reproducible-path/bcftools-1.21/test/filter.6.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -mx -s + -g2:mnp,indel,other /build/reproducible-path/bcftools-1.21/test/filter.7.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -mx -s + -g2:mnp,indel,other /build/reproducible-path/bcftools-1.21/test/filter.7.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'FORMAT/AO==4' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'FORMAT/AO==4' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'MAX(FORMAT/AO[0:])==4' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'MAX(FORMAT/AO[0:])==4' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'MAX(FORMAT/AO)==4' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'MAX(FORMAT/AO)==4' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'MIN(FORMAT/AO[0:])==3' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO[0:])==3' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'MIN(FORMAT/AO)==2' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO)==2' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'MIN(FORMAT/AO[0:])==3' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO[0:])==3' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'AVG(FORMAT/AO[2:])==4' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'AVG(FORMAT/AO[2:])==4' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'MEDIAN(FORMAT/AO[2:])==4' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'MEDIAN(FORMAT/AO[2:])==4' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'STDEV(FORMAT/AO[0:])=0.5' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'STDEV(FORMAT/AO[0:])=0.5' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'SUM(FORMAT/AO[0:])=7' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'SUM(FORMAT/AO[0:])=7' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'SMPL_MAX(FORMAT/AO)==4' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'SMPL_MAX(FORMAT/AO)==4' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'sMIN(FORMAT/AO)==2' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'sMIN(FORMAT/AO)==2' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'ABS(sAVG(FORMAT/AO)-3.66666)<1e-5' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'ABS(sAVG(FORMAT/AO)-3.66666)<1e-5' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'sMEDIAN(FORMAT/AO)==4' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'sMEDIAN(FORMAT/AO)==4' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'ABS(sSTDEV(FORMAT/AO)-1.2472191)<1e-5' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'ABS(sSTDEV(FORMAT/AO)-1.2472191)<1e-5' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'sSUM(FORMAT/AO)==11' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'sSUM(FORMAT/AO)==11' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i 'QUAL/FMT/AD==55' /build/reproducible-path/bcftools-1.21/test/filter.9.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i 'QUAL/FMT/AD==55' /build/reproducible-path/bcftools-1.21/test/filter.9.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i 'QUAL/INFO/AD==10' /build/reproducible-path/bcftools-1.21/test/filter.9.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i 'QUAL/INFO/AD==10' /build/reproducible-path/bcftools-1.21/test/filter.9.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'ABS(SMPL_MAX(FORMAT/AO))=5' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'ABS(SMPL_MAX(FORMAT/AO))=5' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'PHRED(AO[1:])>-4' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'PHRED(AO[1:])>-4' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'ABS(AO[1:])==2' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'ABS(AO[1:])==2' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i 'sum(AD[*]) > FORMAT/DP' /build/reproducible-path/bcftools-1.21/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i 'sum(AD[*]) > FORMAT/DP' /build/reproducible-path/bcftools-1.21/test/filter.10.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i 'FORMAT/DP < sum(AD[*])' /build/reproducible-path/bcftools-1.21/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i 'FORMAT/DP < sum(AD[*])' /build/reproducible-path/bcftools-1.21/test/filter.10.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i 'sum(AD[*]) < FORMAT/DP' /build/reproducible-path/bcftools-1.21/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i 'sum(AD[*]) < FORMAT/DP' /build/reproducible-path/bcftools-1.21/test/filter.10.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i 'FORMAT/DP > sum(AD[*])' /build/reproducible-path/bcftools-1.21/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i 'FORMAT/DP > sum(AD[*])' /build/reproducible-path/bcftools-1.21/test/filter.10.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 0 /build/reproducible-path/bcftools-1.21/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 0 /build/reproducible-path/bcftools-1.21/test/filter.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 1 /build/reproducible-path/bcftools-1.21/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 1 /build/reproducible-path/bcftools-1.21/test/filter.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 2 /build/reproducible-path/bcftools-1.21/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 2 /build/reproducible-path/bcftools-1.21/test/filter.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter --soft-filter xxx --mask ^2:1005-1008 /build/reproducible-path/bcftools-1.21/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob --soft-filter xxx --mask ^2:1005-1008 /build/reproducible-path/bcftools-1.21/test/filter.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_sort: /build/reproducible-path/bcftools-1.21/bcftools sort -m 0 /build/reproducible-path/bcftools-1.21/test/sort.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /build/reproducible-path/bcftools-1.21/bcftools sort -Ob -m 0 /build/reproducible-path/bcftools-1.21/test/sort.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /build/reproducible-path/bcftools-1.21/bcftools sort -m 1000 /build/reproducible-path/bcftools-1.21/test/sort.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /build/reproducible-path/bcftools-1.21/bcftools sort -Ob -m 1000 /build/reproducible-path/bcftools-1.21/test/sort.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /build/reproducible-path/bcftools-1.21/test/regions.tab /tmp/wj8A4a3te7/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/regions.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /build/reproducible-path/bcftools-1.21/test/regions.tab .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /build/reproducible-path/bcftools-1.21/test/regions.tab /tmp/wj8A4a3te7/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/wj8A4a3te7/regions.tab.gz /tmp/wj8A4a3te7/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/regions.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/wj8A4a3te7/regions.tab.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/wj8A4a3te7/regions.tab.gz /tmp/wj8A4a3te7/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/wj8A4a3te7/regions.bed /tmp/wj8A4a3te7/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/regions.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/wj8A4a3te7/regions.bed .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/wj8A4a3te7/regions.bed /tmp/wj8A4a3te7/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/wj8A4a3te7/regions.bed.gz /tmp/wj8A4a3te7/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/regions.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/wj8A4a3te7/regions.bed.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/wj8A4a3te7/regions.bed.gz /tmp/wj8A4a3te7/regions.vcf.gz .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate.escape.1.tab.gz -c CHROM,POS,ISTR,FMT/FSTR /build/reproducible-path/bcftools-1.21/test/annotate.escape.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate.escape.1.tab.gz -c CHROM,POS,ISTR,FMT/FSTR /build/reproducible-path/bcftools-1.21/test/annotate.escape.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate.match.1.tab.gz -c CHROM,POS,-,-,SCORE,~X,-,- -i'STR={X}' /build/reproducible-path/bcftools-1.21/test/annotate.match.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate.match.1.tab.gz -c CHROM,POS,-,-,SCORE,~X,-,- -i'STR={X}' /build/reproducible-path/bcftools-1.21/test/annotate.match.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate.match.1.tab.gz -c CHROM,POS,REF,ALT,SCORE,-,~X,- -i'INT={X}' /build/reproducible-path/bcftools-1.21/test/annotate.match.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate.match.1.tab.gz -c CHROM,POS,REF,ALT,SCORE,-,~X,- -i'INT={X}' /build/reproducible-path/bcftools-1.21/test/annotate.match.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate.match.1.tab.gz -c CHROM,POS,REF,ALT,SCORE,-,-,~X -i'FLT={X}' /build/reproducible-path/bcftools-1.21/test/annotate.match.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate.match.1.tab.gz -c CHROM,POS,REF,ALT,SCORE,-,-,~X -i'FLT={X}' /build/reproducible-path/bcftools-1.21/test/annotate.match.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /build/reproducible-path/bcftools-1.21/test/annotate.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /build/reproducible-path/bcftools-1.21/test/annotate.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate2.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate.hdr -c CHROM,POS,-,T_STR /build/reproducible-path/bcftools-1.21/test/annotate.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate2.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate.hdr -c CHROM,POS,-,T_STR /build/reproducible-path/bcftools-1.21/test/annotate.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate2.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate.hdr -c CHROM,FROM,TO,T_STR /build/reproducible-path/bcftools-1.21/test/annotate.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate2.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate.hdr -c CHROM,FROM,TO,T_STR /build/reproducible-path/bcftools-1.21/test/annotate.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/wj8A4a3te7/annotate.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/wj8A4a3te7/annotate.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /build/reproducible-path/bcftools-1.21/test/annotate3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /build/reproducible-path/bcftools-1.21/test/annotate3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -x FORMAT /build/reproducible-path/bcftools-1.21/test/annotate3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -x FORMAT /build/reproducible-path/bcftools-1.21/test/annotate3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots4.vcf.gz -c +INFO /tmp/wj8A4a3te7/annotate4.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots4.vcf.gz -c +INFO /tmp/wj8A4a3te7/annotate4.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots4.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /build/reproducible-path/bcftools-1.21/test/annotate4.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots4.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /build/reproducible-path/bcftools-1.21/test/annotate4.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots10.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /build/reproducible-path/bcftools-1.21/test/annotate10.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots10.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /build/reproducible-path/bcftools-1.21/test/annotate10.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /build/reproducible-path/bcftools-1.21/test/annotate2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /build/reproducible-path/bcftools-1.21/test/annotate2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots11.vcf.gz -c FMT /tmp/wj8A4a3te7/annotate11.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots11.vcf.gz -c FMT /tmp/wj8A4a3te7/annotate11.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots2.vcf.gz -c FMT/newGT:=GT /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots2.vcf.gz -c FMT/newGT:=GT /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots12.vcf.gz -c FMT/GT:=newGT /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots12.vcf.gz -c FMT/GT:=newGT /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots13.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate13.hdr -c CHROM,BEG,END,ABC /build/reproducible-path/bcftools-1.21/test/annotate13.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots13.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate13.hdr -c CHROM,BEG,END,ABC /build/reproducible-path/bcftools-1.21/test/annotate13.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots13.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:append /build/reproducible-path/bcftools-1.21/test/annotate13.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots13.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:append /build/reproducible-path/bcftools-1.21/test/annotate13.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots13.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:unique /build/reproducible-path/bcftools-1.21/test/annotate13.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots13.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:unique /build/reproducible-path/bcftools-1.21/test/annotate13.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -x FILTER/XX,INFO/XX --force /build/reproducible-path/bcftools-1.21/test/annotate14.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -x FILTER/XX,INFO/XX --force /build/reproducible-path/bcftools-1.21/test/annotate14.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate15.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate15.hdr -s SAMPLE1 -c CHROM,FROM,TO,FMT/FOO,BAR /build/reproducible-path/bcftools-1.21/test/annotate15.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate15.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate15.hdr -s SAMPLE1 -c CHROM,FROM,TO,FMT/FOO,BAR /build/reproducible-path/bcftools-1.21/test/annotate15.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate15.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate15.hdr -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR /build/reproducible-path/bcftools-1.21/test/annotate15.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate15.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate15.hdr -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR /build/reproducible-path/bcftools-1.21/test/annotate15.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate15.tab.gz -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR -H '##FORMAT=' -H '##INFO=' /build/reproducible-path/bcftools-1.21/test/annotate15.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate15.tab.gz -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR -H '##FORMAT=' -H '##INFO=' /build/reproducible-path/bcftools-1.21/test/annotate15.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -x FILTER /build/reproducible-path/bcftools-1.21/test/annotate16.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -x FILTER /build/reproducible-path/bcftools-1.21/test/annotate16.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/reproducible-path/bcftools-1.21/test/annotate17.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/reproducible-path/bcftools-1.21/test/annotate17.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/reproducible-path/bcftools-1.21/test/annotate17.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/reproducible-path/bcftools-1.21/test/annotate17.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate17.3.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/reproducible-path/bcftools-1.21/test/annotate17.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate17.3.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/reproducible-path/bcftools-1.21/test/annotate17.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate18.1.tab.gz -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /build/reproducible-path/bcftools-1.21/test/annotate18.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate18.1.tab.gz -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /build/reproducible-path/bcftools-1.21/test/annotate18.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate18.2.tab.gz -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /build/reproducible-path/bcftools-1.21/test/annotate18.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate18.2.tab.gz -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /build/reproducible-path/bcftools-1.21/test/annotate18.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/wj8A4a3te7/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/wj8A4a3te7/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/wj8A4a3te7/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/wj8A4a3te7/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/wj8A4a3te7/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/wj8A4a3te7/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -c INFO/FILTER:=FILTER /build/reproducible-path/bcftools-1.21/test/annotate19.dst.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -c INFO/FILTER:=FILTER /build/reproducible-path/bcftools-1.21/test/annotate19.dst.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER /tmp/wj8A4a3te7/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER /tmp/wj8A4a3te7/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER /tmp/wj8A4a3te7/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER /tmp/wj8A4a3te7/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER,FILTER /tmp/wj8A4a3te7/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER,FILTER /tmp/wj8A4a3te7/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=./FILTER /tmp/wj8A4a3te7/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=./FILTER /tmp/wj8A4a3te7/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate20.src.vcf.gz -c FMT/GT /tmp/wj8A4a3te7/annotate20.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate20.src.vcf.gz -c FMT/GT /tmp/wj8A4a3te7/annotate20.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate20.src.vcf.gz -c +FMT/GT /tmp/wj8A4a3te7/annotate20.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate20.src.vcf.gz -c +FMT/GT /tmp/wj8A4a3te7/annotate20.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate20.src.vcf.gz -c -FMT/GT /tmp/wj8A4a3te7/annotate20.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate20.src.vcf.gz -c -FMT/GT /tmp/wj8A4a3te7/annotate20.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate.multi.tab.gz -c CHROM,POS,REF,ALT,ANN -l ANN:append /build/reproducible-path/bcftools-1.21/test/annotate.multi.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate.multi.tab.gz -c CHROM,POS,REF,ALT,ANN -l ANN:append /build/reproducible-path/bcftools-1.21/test/annotate.multi.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate.missing-append.tab.gz -c CHROM,POS,REF,ALT,STR,INT,FLT -l STR:append-missing,INT:append-missing,FLT:append-missing /build/reproducible-path/bcftools-1.21/test/annotate.missing-append.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate.missing-append.tab.gz -c CHROM,POS,REF,ALT,STR,INT,FLT -l STR:append-missing,INT:append-missing,FLT:append-missing /build/reproducible-path/bcftools-1.21/test/annotate.missing-append.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /build/reproducible-path/bcftools-1.21/test/annotate9.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /build/reproducible-path/bcftools-1.21/test/annotate9.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate --rename-annots /build/reproducible-path/bcftools-1.21/test/annotate21.txt /build/reproducible-path/bcftools-1.21/test/annotate21.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob --rename-annots /build/reproducible-path/bcftools-1.21/test/annotate21.txt /build/reproducible-path/bcftools-1.21/test/annotate21.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -c XX:=FORMAT/X-X,YY:=FORMAT/Y-Y,AA:=FORMAT/A-A,AA:=INFO/A-A,BB:=INFO/B-B,XX:=INFO/X-X,YY:=INFO/Y-Y,fltA:=FILTER/flt-A,fltB:=FILTER/flt-B,fltX:=FILTER/flt-X,fltY:=FILTER/flt-Y /build/reproducible-path/bcftools-1.21/test/annotate21.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -c XX:=FORMAT/X-X,YY:=FORMAT/Y-Y,AA:=FORMAT/A-A,AA:=INFO/A-A,BB:=INFO/B-B,XX:=INFO/X-X,YY:=INFO/Y-Y,fltA:=FILTER/flt-A,fltB:=FILTER/flt-B,fltX:=FILTER/flt-X,fltY:=FILTER/flt-Y /build/reproducible-path/bcftools-1.21/test/annotate21.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/wj8A4a3te7/annotate22.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/wj8A4a3te7/annotate22.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate23.tab.gz -c CHROM,POS,~ID,REF,ALT,INFO/END /build/reproducible-path/bcftools-1.21/test/annotate23.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate23.tab.gz -c CHROM,POS,~ID,REF,ALT,INFO/END /build/reproducible-path/bcftools-1.21/test/annotate23.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate24.src.vcf.gz -c XX /tmp/wj8A4a3te7/annotate24.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate24.src.vcf.gz -c XX /tmp/wj8A4a3te7/annotate24.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate25.tab.gz -c CHROM,POS,ID,REF,ALT,~INFO/END /build/reproducible-path/bcftools-1.21/test/annotate25.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate25.tab.gz -c CHROM,POS,ID,REF,ALT,~INFO/END /build/reproducible-path/bcftools-1.21/test/annotate25.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate26.tab.gz -c CHROM,POS,-POS /build/reproducible-path/bcftools-1.21/test/annotate26.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate26.tab.gz -c CHROM,POS,-POS /build/reproducible-path/bcftools-1.21/test/annotate26.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,TSTR,TFLT,TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,TSTR,TFLT,TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.TSTR,.TFLT,.TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.TSTR,.TFLT,.TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.+TSTR,.+TFLT,.+TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.+TSTR,.+TFLT,.+TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,+TSTR,+TFLT,+TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,+TSTR,+TFLT,+TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.=TSTR,.=TFLT,.=TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.=TSTR,.=TFLT,.=TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,=TSTR,=TFLT,=TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,=TSTR,=TFLT,=TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique /build/reproducible-path/bcftools-1.21/test/annotate.olap.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique /build/reproducible-path/bcftools-1.21/test/annotate.olap.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique --min-overlap 0.4:0.5 -m XXX /build/reproducible-path/bcftools-1.21/test/annotate.olap.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique --min-overlap 0.4:0.5 -m XXX /build/reproducible-path/bcftools-1.21/test/annotate.olap.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots.id.vcf.gz -c ALT /tmp/wj8A4a3te7/annotate.id.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots.id.vcf.gz -c ALT /tmp/wj8A4a3te7/annotate.id.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots.id.vcf.gz -c +ALT /tmp/wj8A4a3te7/annotate.id.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots.id.vcf.gz -c +ALT /tmp/wj8A4a3te7/annotate.id.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots.id.2.vcf.gz --pair-logic some -c +ID /tmp/wj8A4a3te7/annotate.id.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots.id.2.vcf.gz --pair-logic some -c +ID /tmp/wj8A4a3te7/annotate.id.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots.id.2.vcf.gz --pair-logic any -c +ID /tmp/wj8A4a3te7/annotate.id.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots.id.2.vcf.gz --pair-logic any -c +ID /tmp/wj8A4a3te7/annotate.id.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate27.tab.gz -c CHROM,POS,REF,ALT,EVIDENCE /build/reproducible-path/bcftools-1.21/test/annotate27.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate27.tab.gz -c CHROM,POS,REF,ALT,EVIDENCE /build/reproducible-path/bcftools-1.21/test/annotate27.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1,smpl2 /build/reproducible-path/bcftools-1.21/test/annotate28.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1,smpl2 /build/reproducible-path/bcftools-1.21/test/annotate28.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2,smpl1 /build/reproducible-path/bcftools-1.21/test/annotate28.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2,smpl1 /build/reproducible-path/bcftools-1.21/test/annotate28.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1 /build/reproducible-path/bcftools-1.21/test/annotate28.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1 /build/reproducible-path/bcftools-1.21/test/annotate28.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2 /build/reproducible-path/bcftools-1.21/test/annotate28.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2 /build/reproducible-path/bcftools-1.21/test/annotate28.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -m XXX /build/reproducible-path/bcftools-1.21/test/annotate.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -m XXX /build/reproducible-path/bcftools-1.21/test/annotate.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots34.tab.gz -c CHROM,FROM,TO,INFO/END -H '##INFO=' /build/reproducible-path/bcftools-1.21/test/annotate34.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots34.tab.gz -c CHROM,FROM,TO,INFO/END -H '##INFO=' /build/reproducible-path/bcftools-1.21/test/annotate34.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots-mark.bed.gz -c CHROM,FROM,TO -m TAG /build/reproducible-path/bcftools-1.21/test/annots-mark.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots-mark.bed.gz -c CHROM,FROM,TO -m TAG /build/reproducible-path/bcftools-1.21/test/annots-mark.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --no-version /tmp/wj8A4a3te7/concat.1.a.vcf.gz /tmp/wj8A4a3te7/concat.1.b.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob /tmp/wj8A4a3te7/concat.1.a.vcf.gz /tmp/wj8A4a3te7/concat.1.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --no-version /tmp/wj8A4a3te7/concat.1.a.bcf /tmp/wj8A4a3te7/concat.1.b.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob /tmp/wj8A4a3te7/concat.1.a.bcf /tmp/wj8A4a3te7/concat.1.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -a /tmp/wj8A4a3te7/concat.2.a.vcf.gz /tmp/wj8A4a3te7/concat.2.b.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -a /tmp/wj8A4a3te7/concat.2.a.vcf.gz /tmp/wj8A4a3te7/concat.2.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -a /tmp/wj8A4a3te7/concat.2.a.bcf /tmp/wj8A4a3te7/concat.2.b.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -a /tmp/wj8A4a3te7/concat.2.a.bcf /tmp/wj8A4a3te7/concat.2.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -aD /tmp/wj8A4a3te7/concat.2.a.vcf.gz /tmp/wj8A4a3te7/concat.2.b.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -aD /tmp/wj8A4a3te7/concat.2.a.vcf.gz /tmp/wj8A4a3te7/concat.2.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -aD /tmp/wj8A4a3te7/concat.2.a.bcf /tmp/wj8A4a3te7/concat.2.b.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -aD /tmp/wj8A4a3te7/concat.2.a.bcf /tmp/wj8A4a3te7/concat.2.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -l --ligate-warn /tmp/wj8A4a3te7/concat.3.a.vcf.gz /tmp/wj8A4a3te7/concat.3.b.vcf.gz /tmp/wj8A4a3te7/concat.3.0.vcf.gz /tmp/wj8A4a3te7/concat.3.c.vcf.gz /tmp/wj8A4a3te7/concat.3.d.vcf.gz /tmp/wj8A4a3te7/concat.3.e.vcf.gz /tmp/wj8A4a3te7/concat.3.f.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -l --ligate-warn /tmp/wj8A4a3te7/concat.3.a.vcf.gz /tmp/wj8A4a3te7/concat.3.b.vcf.gz /tmp/wj8A4a3te7/concat.3.0.vcf.gz /tmp/wj8A4a3te7/concat.3.c.vcf.gz /tmp/wj8A4a3te7/concat.3.d.vcf.gz /tmp/wj8A4a3te7/concat.3.e.vcf.gz /tmp/wj8A4a3te7/concat.3.f.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -l --ligate-warn /tmp/wj8A4a3te7/concat.3.a.bcf /tmp/wj8A4a3te7/concat.3.b.bcf /tmp/wj8A4a3te7/concat.3.0.bcf /tmp/wj8A4a3te7/concat.3.c.bcf /tmp/wj8A4a3te7/concat.3.d.bcf /tmp/wj8A4a3te7/concat.3.e.bcf /tmp/wj8A4a3te7/concat.3.f.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -l --ligate-warn /tmp/wj8A4a3te7/concat.3.a.bcf /tmp/wj8A4a3te7/concat.3.b.bcf /tmp/wj8A4a3te7/concat.3.0.bcf /tmp/wj8A4a3te7/concat.3.c.bcf /tmp/wj8A4a3te7/concat.3.d.bcf /tmp/wj8A4a3te7/concat.3.e.bcf /tmp/wj8A4a3te7/concat.3.f.bcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ Random seed for test_naive_concat: 2755974125 .. ok test_naive_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --naive-force /tmp/wj8A4a3te7/naive_concat.0.bcf /tmp/wj8A4a3te7/naive_concat.1.bcf /tmp/wj8A4a3te7/naive_concat.2.bcf /tmp/wj8A4a3te7/naive_concat.3.bcf /tmp/wj8A4a3te7/naive_concat.4.bcf /tmp/wj8A4a3te7/naive_concat.5.bcf /tmp/wj8A4a3te7/naive_concat.6.bcf /tmp/wj8A4a3te7/naive_concat.7.bcf /tmp/wj8A4a3te7/naive_concat.8.bcf /tmp/wj8A4a3te7/naive_concat.9.bcf | /build/reproducible-path/bcftools-1.21/bcftools view -H .. ok test_naive_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --naive /tmp/wj8A4a3te7/naive_concat.0.vcf.gz /tmp/wj8A4a3te7/naive_concat.1.vcf.gz /tmp/wj8A4a3te7/naive_concat.2.vcf.gz /tmp/wj8A4a3te7/naive_concat.3.vcf.gz /tmp/wj8A4a3te7/naive_concat.4.vcf.gz /tmp/wj8A4a3te7/naive_concat.5.vcf.gz /tmp/wj8A4a3te7/naive_concat.6.vcf.gz /tmp/wj8A4a3te7/naive_concat.7.vcf.gz /tmp/wj8A4a3te7/naive_concat.8.vcf.gz /tmp/wj8A4a3te7/naive_concat.9.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view -H .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -l /tmp/wj8A4a3te7/concat.4.a.vcf.gz /tmp/wj8A4a3te7/concat.4.b.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -l /tmp/wj8A4a3te7/concat.4.a.vcf.gz /tmp/wj8A4a3te7/concat.4.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -l /tmp/wj8A4a3te7/concat.4.a.bcf /tmp/wj8A4a3te7/concat.4.b.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -l /tmp/wj8A4a3te7/concat.4.a.bcf /tmp/wj8A4a3te7/concat.4.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -l --ligate-warn /tmp/wj8A4a3te7/concat.5.a.vcf.gz /tmp/wj8A4a3te7/concat.5.b.vcf.gz /tmp/wj8A4a3te7/concat.5.c.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -l --ligate-warn /tmp/wj8A4a3te7/concat.5.a.vcf.gz /tmp/wj8A4a3te7/concat.5.b.vcf.gz /tmp/wj8A4a3te7/concat.5.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -l --ligate-warn /tmp/wj8A4a3te7/concat.5.a.bcf /tmp/wj8A4a3te7/concat.5.b.bcf /tmp/wj8A4a3te7/concat.5.c.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -l --ligate-warn /tmp/wj8A4a3te7/concat.5.a.bcf /tmp/wj8A4a3te7/concat.5.b.bcf /tmp/wj8A4a3te7/concat.5.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -l --ligate-force /tmp/wj8A4a3te7/concat.5.a.bcf /tmp/wj8A4a3te7/concat.5.b.bcf /tmp/wj8A4a3te7/concat.5.c.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -l --ligate-force /tmp/wj8A4a3te7/concat.5.a.bcf /tmp/wj8A4a3te7/concat.5.b.bcf /tmp/wj8A4a3te7/concat.5.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -G -a -D /tmp/wj8A4a3te7/concat.5.a.vcf.gz /tmp/wj8A4a3te7/concat.5.b.vcf.gz /tmp/wj8A4a3te7/concat.5.c.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -G -a -D /tmp/wj8A4a3te7/concat.5.a.vcf.gz /tmp/wj8A4a3te7/concat.5.b.vcf.gz /tmp/wj8A4a3te7/concat.5.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -G -a -D /tmp/wj8A4a3te7/concat.5.a.bcf /tmp/wj8A4a3te7/concat.5.b.bcf /tmp/wj8A4a3te7/concat.5.c.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -G -a -D /tmp/wj8A4a3te7/concat.5.a.bcf /tmp/wj8A4a3te7/concat.5.b.bcf /tmp/wj8A4a3te7/concat.5.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.hdr /build/reproducible-path/bcftools-1.21/test/reheader.vcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /build/reproducible-path/bcftools-1.21/test/reheader.vcf | /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.hdr | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.hdr /tmp/wj8A4a3te7/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/wj8A4a3te7/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.hdr | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.hdr /tmp/wj8A4a3te7/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/wj8A4a3te7/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.hdr | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples /build/reproducible-path/bcftools-1.21/test/reheader.vcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /build/reproducible-path/bcftools-1.21/test/reheader.vcf | /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples /tmp/wj8A4a3te7/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/wj8A4a3te7/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples /tmp/wj8A4a3te7/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/wj8A4a3te7/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples2 /build/reproducible-path/bcftools-1.21/test/reheader.vcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /build/reproducible-path/bcftools-1.21/test/reheader.vcf | /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples2 | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples2 /tmp/wj8A4a3te7/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/wj8A4a3te7/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples2 | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples2 /tmp/wj8A4a3te7/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/wj8A4a3te7/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples2 | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples3 /build/reproducible-path/bcftools-1.21/test/reheader.vcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /build/reproducible-path/bcftools-1.21/test/reheader.vcf | /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples3 | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples3 /tmp/wj8A4a3te7/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/wj8A4a3te7/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples3 | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples3 /tmp/wj8A4a3te7/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/wj8A4a3te7/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples3 | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples4 /build/reproducible-path/bcftools-1.21/test/reheader.vcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /build/reproducible-path/bcftools-1.21/test/reheader.vcf | /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples4 | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples4 /tmp/wj8A4a3te7/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/wj8A4a3te7/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples4 | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples4 /tmp/wj8A4a3te7/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/wj8A4a3te7/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples4 | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.empty.hdr /build/reproducible-path/bcftools-1.21/test/empty.vcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /build/reproducible-path/bcftools-1.21/test/empty.vcf | /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.empty.hdr | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.empty.hdr /tmp/wj8A4a3te7/empty.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/wj8A4a3te7/empty.bcf | /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.empty.hdr | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.empty.hdr /tmp/wj8A4a3te7/empty.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/wj8A4a3te7/empty.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.empty.hdr | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -f /build/reproducible-path/bcftools-1.21/test/reheader.fai /build/reproducible-path/bcftools-1.21/test/reheader.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -f /build/reproducible-path/bcftools-1.21/test/reheader.fai /tmp/wj8A4a3te7/reheader.2.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -f /build/reproducible-path/bcftools-1.21/test/reheader.fai /tmp/wj8A4a3te7/reheader.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.2.hdr -f /build/reproducible-path/bcftools-1.21/test/reheader.fai /build/reproducible-path/bcftools-1.21/test/reheader.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.2.hdr -f /build/reproducible-path/bcftools-1.21/test/reheader.fai /tmp/wj8A4a3te7/reheader.2.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.2.hdr -f /build/reproducible-path/bcftools-1.21/test/reheader.fai /tmp/wj8A4a3te7/reheader.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -f /build/reproducible-path/bcftools-1.21/test/reheader.3.fai /build/reproducible-path/bcftools-1.21/test/reheader.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -f /build/reproducible-path/bcftools-1.21/test/reheader.3.fai /tmp/wj8A4a3te7/reheader.3.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -f /build/reproducible-path/bcftools-1.21/test/reheader.3.fai /tmp/wj8A4a3te7/reheader.3.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_rename_chrs: /build/reproducible-path/bcftools-1.21/bcftools annotate --rename-chrs /tmp/wj8A4a3te7/rename.map -Ov /tmp/wj8A4a3te7/annotate.bcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /build/reproducible-path/bcftools-1.21/bcftools annotate --rename-chrs /tmp/wj8A4a3te7/rename.map -Ob /tmp/wj8A4a3te7/annotate.bcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /build/reproducible-path/bcftools-1.21/bcftools annotate --rename-chrs /tmp/wj8A4a3te7/rename.map -Ov /build/reproducible-path/bcftools-1.21/test/annotate.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /build/reproducible-path/bcftools-1.21/bcftools annotate --rename-chrs /tmp/wj8A4a3te7/rename.map -Ob /build/reproducible-path/bcftools-1.21/test/annotate.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM\t%POS\n' .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. /tmp/wj8A4a3te7/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --vcf-ids /tmp/wj8A4a3te7/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --vcf-ids .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --vcf-ids --3N6 /tmp/wj8A4a3te7/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --vcf-ids --3N6 .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert -g .,- /tmp/wj8A4a3te7/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g .,- .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert --vcf-ids -G /build/reproducible-path/bcftools-1.21/test/convert.gs.gt.ids.gen,/build/reproducible-path/bcftools-1.21/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert --vcf-ids -G /build/reproducible-path/bcftools-1.21/test/convert.gs.gt.ids.gen,/build/reproducible-path/bcftools-1.21/test/convert.gs.gt.samples -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert -G /build/reproducible-path/bcftools-1.21/test/convert.gs.gt.ids.gen,/build/reproducible-path/bcftools-1.21/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert -G /build/reproducible-path/bcftools-1.21/test/convert.gs.gt.ids.gen,/build/reproducible-path/bcftools-1.21/test/convert.gs.gt.samples -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert --3N6 -G /build/reproducible-path/bcftools-1.21/test/convert.gs.gt.ids.3N6.gen,/build/reproducible-path/bcftools-1.21/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert --3N6 -G /build/reproducible-path/bcftools-1.21/test/convert.gs.gt.ids.3N6.gen,/build/reproducible-path/bcftools-1.21/test/convert.gs.gt.samples -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert --vcf-ids -G /build/reproducible-path/bcftools-1.21/test/convert.gs.gt.ids.gen.rev,/build/reproducible-path/bcftools-1.21/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert --vcf-ids -G /build/reproducible-path/bcftools-1.21/test/convert.gs.gt.ids.gen.rev,/build/reproducible-path/bcftools-1.21/test/convert.gs.gt.samples -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert -G /build/reproducible-path/bcftools-1.21/test/convert.gs.gt.ids.gen.rev,/build/reproducible-path/bcftools-1.21/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert -G /build/reproducible-path/bcftools-1.21/test/convert.gs.gt.ids.gen.rev,/build/reproducible-path/bcftools-1.21/test/convert.gs.gt.samples -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^## .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --tag PL /tmp/wj8A4a3te7/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --tag PL .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert -g .,- --tag PL /tmp/wj8A4a3te7/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g .,- --tag PL .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --vcf-ids /tmp/wj8A4a3te7/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/check.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --vcf-ids .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert -g .,- --vcf-ids /tmp/wj8A4a3te7/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/check.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g .,- --vcf-ids .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --3N6 /tmp/wj8A4a3te7/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/check.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --3N6 .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert -g .,- --3N6 /tmp/wj8A4a3te7/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/check.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g .,- --3N6 .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --3N6 --vcf-ids /tmp/wj8A4a3te7/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/check.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --3N6 --vcf-ids .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert -g .,- --3N6 --vcf-ids /tmp/wj8A4a3te7/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/check.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g .,- --3N6 --vcf-ids .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert -h -,.,. /tmp/wj8A4a3te7/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -h -,.,. .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert -h .,-,. /tmp/wj8A4a3te7/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -h .,-,. .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert -h .,-,. --vcf-ids /tmp/wj8A4a3te7/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -h .,-,. --vcf-ids .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert -h .,.,- /tmp/wj8A4a3te7/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -h .,.,- .. ok test_vcf_convert_hls2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert -H /build/reproducible-path/bcftools-1.21/test/convert.hls.gt.hap,/build/reproducible-path/bcftools-1.21/test/convert.hls.gt.legend,/build/reproducible-path/bcftools-1.21/test/convert.hls.gt.samples | grep -v ^## .. ok test_vcf_convert_hls2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert -H /build/reproducible-path/bcftools-1.21/test/convert.hls.gt.hap,/build/reproducible-path/bcftools-1.21/test/convert.hls.gt.legend,/build/reproducible-path/bcftools-1.21/test/convert.hls.gt.samples -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^## .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert --haplegendsample -,.,. /tmp/wj8A4a3te7/convert.hap-missing.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/convert.hap-missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert --haplegendsample -,.,. .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert --hapsample -,. /tmp/wj8A4a3te7/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert --hapsample -,. .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert --hapsample -,. --vcf-ids /tmp/wj8A4a3te7/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert --hapsample -,. --vcf-ids .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert --hapsample .,- /tmp/wj8A4a3te7/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert --hapsample .,- .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert --hapsample2vcf /build/reproducible-path/bcftools-1.21/test/convert.hs.gt.hap,/build/reproducible-path/bcftools-1.21/test/convert.hs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert --hapsample2vcf /build/reproducible-path/bcftools-1.21/test/convert.hs.gt.hap,/build/reproducible-path/bcftools-1.21/test/convert.hs.gt.samples -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert --vcf-ids --hapsample2vcf /build/reproducible-path/bcftools-1.21/test/convert.hs.gt.ids.hap,/build/reproducible-path/bcftools-1.21/test/convert.hs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert --vcf-ids --hapsample2vcf /build/reproducible-path/bcftools-1.21/test/convert.hs.gt.ids.hap,/build/reproducible-path/bcftools-1.21/test/convert.hs.gt.samples -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^## .. ok test_vcf_convert_gvcf: /build/reproducible-path/bcftools-1.21/bcftools convert --no-version --gvcf2vcf -i'FILTER="PASS"' -f /build/reproducible-path/bcftools-1.21/test/gvcf.fa /tmp/wj8A4a3te7/convert.gvcf.vcf.gz .. ok test_vcf_convert_gvcf: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/convert.gvcf.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert --gvcf2vcf -i'FILTER="PASS"' -f /build/reproducible-path/bcftools-1.21/test/gvcf.fa | grep -v ^##bcftools .. ok test_vcf_convert_tsv2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert --no-version -c ID,CHROM,POS,AA -s SAMPLE1 -f /build/reproducible-path/bcftools-1.21/test/23andme.fa --tsv2vcf /build/reproducible-path/bcftools-1.21/test/convert.23andme .. ok test_vcf_convert_tsv2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert -Ou -c ID,CHROM,POS,AA -s SAMPLE1 -f /build/reproducible-path/bcftools-1.21/test/23andme.fa --tsv2vcf /build/reproducible-path/bcftools-1.21/test/convert.23andme | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_convert_tsv2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert --no-version -c -,CHROM,POS,REF,ALT -f /build/reproducible-path/bcftools-1.21/test/23andme.fa --tsv2vcf /build/reproducible-path/bcftools-1.21/test/convert.tsv .. ok test_vcf_convert_tsv2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert -Ou -c -,CHROM,POS,REF,ALT -f /build/reproducible-path/bcftools-1.21/test/23andme.fa --tsv2vcf /build/reproducible-path/bcftools-1.21/test/convert.tsv | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.overlaps.1.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.overlaps.1.fa -s A .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.overlaps.1.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.overlaps.1.fa -s A .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.overlaps.1.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.overlaps.1.fa -s B .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.overlaps.1.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.overlaps.1.fa -s B .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.overlaps.1.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.overlaps.1.fa -s A -a N .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.overlaps.1.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.overlaps.1.fa -s A -a N .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.overlaps.1.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.overlaps.1.fa -s B -a N .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.overlaps.1.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.overlaps.1.fa -s B -a N .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.beyond.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.beyond.fa .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.beyond.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.beyond.fa .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -m /build/reproducible-path/bcftools-1.21/test/consensus.tab .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -m /build/reproducible-path/bcftools-1.21/test/consensus.tab .. ok test_vcf_consensus_chain: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -m /build/reproducible-path/bcftools-1.21/test/consensus.tab -c /tmp/wj8A4a3te7/consensus.1.chain.new >/dev/null; cat /tmp/wj8A4a3te7/consensus.1.chain.new .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -H 1 -m /build/reproducible-path/bcftools-1.21/test/consensus.tab .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -H 1 -m /build/reproducible-path/bcftools-1.21/test/consensus.tab .. ok test_vcf_consensus_chain: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -H 1 -m /build/reproducible-path/bcftools-1.21/test/consensus.tab -c /tmp/wj8A4a3te7/consensus.2.chain.new >/dev/null; cat /tmp/wj8A4a3te7/consensus.2.chain.new .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -I -s - -m /build/reproducible-path/bcftools-1.21/test/consensus.tab .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -I -s - -m /build/reproducible-path/bcftools-1.21/test/consensus.tab .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -I -m /build/reproducible-path/bcftools-1.21/test/consensus.tab --mask-with X -m /build/reproducible-path/bcftools-1.21/test/consensus.tab --mask-with lc .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -I -m /build/reproducible-path/bcftools-1.21/test/consensus.tab --mask-with X -m /build/reproducible-path/bcftools-1.21/test/consensus.tab --mask-with lc .. ok test_vcf_consensus_chain: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -I -m /build/reproducible-path/bcftools-1.21/test/consensus.tab -c /tmp/wj8A4a3te7/consensus.3.chain.new >/dev/null; cat /tmp/wj8A4a3te7/consensus.3.chain.new .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -H 1 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -H 1 .. ok test_vcf_consensus_chain: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -H 1 -c /tmp/wj8A4a3te7/consensus.4.chain.new >/dev/null; cat /tmp/wj8A4a3te7/consensus.4.chain.new .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus2.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -H 1 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus2.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -H 1 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus2.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -H 2 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus2.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -H 2 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/empty.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/empty.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -H 2 -M "?" .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus3.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -H 2 -M "?" .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -H 2 -M "?" -p xx_ .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus3.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -H 2 -M "?" -p xx_ .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus4.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus4.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus5.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus5.fa --haplotype LA .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus5.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus5.fa --haplotype LA .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus6.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus6.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus6.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus6.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus7.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 2 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus7.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 2 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus7.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 4 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus7.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 4 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus7.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 2pIu .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus7.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 2pIu .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus7.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 4pIu .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus7.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 4pIu .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus7.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 1 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus7.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 1 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus7.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 3 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus7.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 3 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus7.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 1pIu .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus7.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 1pIu .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus7.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 3pIu .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus7.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 3pIu .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus8.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus8.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus8.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -a . .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus8.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -a . .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus8.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -a . -i 'type="snp" || type="ref"' .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus8.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -a . -i 'type="snp" || type="ref"' .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus8.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -a . -i 'ALT!=""' .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus8.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -a . -i 'ALT!=""' .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus8.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -a . -e 'MinDP>15' .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus8.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -a . -e 'MinDP>15' .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus8.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -a . -e 'MinDP<15' .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus8.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -a . -e 'MinDP<15' .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.9.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.9.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.9.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.9.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.10.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.10.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.10.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.10.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.11.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.11.fa -s smpl .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.11.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.11.fa -s smpl .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.11.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.11.fa -s smpl -a N .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.11.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.11.fa -s smpl -a N .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.12.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.12.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.12.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.12.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.13.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.13.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.13.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.13.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.14.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.14.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.14.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.14.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.12.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.12.fa -s - --mark-del - --mark-ins uc --mark-snv uc .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.12.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.12.fa -s - --mark-del - --mark-ins uc --mark-snv uc .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.12.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.12.fa -s - --mark-del - --mark-ins + --mark-snv : .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.12.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.12.fa -s - --mark-del - --mark-ins + --mark-snv : .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.15.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.15.fa -H I --mark-ins lc --mark-snv lc .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.15.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.15.fa -H I --mark-ins lc --mark-snv lc .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.16.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -I .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.16.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -I .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.16.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -H I .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.16.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -H I .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.17.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -s - -M N -m /build/reproducible-path/bcftools-1.21/test/consensus.17.bed .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.17.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -s - -M N -m /build/reproducible-path/bcftools-1.21/test/consensus.17.bed .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.18.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.18.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.18.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.18.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.19.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.19.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.19.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.19.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.20.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.20.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.20.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.20.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.20.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.20.fa .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.20.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.20.fa .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.20.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.20.fa -M . -s b .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.20.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.20.fa -M . -s b .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.20.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.20.fa -M . -s a .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.20.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.20.fa -M . -s a .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.21.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.21.fa .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.21.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.21.fa .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.22.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 0 --mark-del . .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.22.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 0 --mark-del . .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.22.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 1 --mark-del . .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.22.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 1 --mark-del . .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.22.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 2 --mark-del . .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.22.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 2 --mark-del . .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.22.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 0 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.22.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 0 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.22.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 1 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.22.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 1 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.22.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 2 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.22.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 2 .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -r17:100-150 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -r17:100-150 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -r17:100-150 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -b /tmp/wj8A4a3te7/mpileup.bam.list --no-version | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -r17:100-150 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob -b /tmp/wj8A4a3te7/mpileup.bam.urllist | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -r17:100-150 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -r17:100-150 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -r17:100-150 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -b /tmp/wj8A4a3te7/mpileup.cram.list --no-version | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -r17:100-150 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob -b /tmp/wj8A4a3te7/mpileup.cram.urllist | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DV -r17:100-600 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DV -r17:100-600 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DV -r17:100-600 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DV -r17:100-600 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP,-AD -r17:100-600 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP,-AD -r17:100-600 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP,-AD -r17:100-600 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP,-AD -r17:100-600 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DV,-AD -r17:100-600 --gvcf 0,2,5 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DV,-AD -r17:100-600 --gvcf 0,2,5 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DV,-AD -r17:100-600 --gvcf 0,2,5 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DV,-AD -r17:100-600 --gvcf 0,2,5 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DV,-AD -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DV,-AD -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DV,-AD -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DV,-AD -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -s HG00101,HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -s HG00101,HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -s HG00101,HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -s HG00101,HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -S /build/reproducible-path/bcftools-1.21/test/mplp.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -S /build/reproducible-path/bcftools-1.21/test/mplp.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -S /build/reproducible-path/bcftools-1.21/test/mplp.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -S /build/reproducible-path/bcftools-1.21/test/mplp.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -s ^HG00101,HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -s ^HG00101,HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -s ^HG00101,HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -s ^HG00101,HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -S ^/build/reproducible-path/bcftools-1.21/test/mplp.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -S ^/build/reproducible-path/bcftools-1.21/test/mplp.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -S ^/build/reproducible-path/bcftools-1.21/test/mplp.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -S ^/build/reproducible-path/bcftools-1.21/test/mplp.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -S /build/reproducible-path/bcftools-1.21/test/mplp.9.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -S /build/reproducible-path/bcftools-1.21/test/mplp.9.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -S /build/reproducible-path/bcftools-1.21/test/mplp.9.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -S /build/reproducible-path/bcftools-1.21/test/mplp.9.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -S /build/reproducible-path/bcftools-1.21/test/mplp.9.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -S /build/reproducible-path/bcftools-1.21/test/mplp.9.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -G /build/reproducible-path/bcftools-1.21/test/mplp.10.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -G /build/reproducible-path/bcftools-1.21/test/mplp.10.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -G /build/reproducible-path/bcftools-1.21/test/mplp.10.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -G /build/reproducible-path/bcftools-1.21/test/mplp.10.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -G /build/reproducible-path/bcftools-1.21/test/mplp.10.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -G /build/reproducible-path/bcftools-1.21/test/mplp.10.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -s HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -s HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.sam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -s HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -s HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -s HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -s HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -s ^HG99999 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -s ^HG99999 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.sam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -s ^HG99999 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -s ^HG99999 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -s ^HG99999 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -s ^HG99999 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -G /build/reproducible-path/bcftools-1.21/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -G /build/reproducible-path/bcftools-1.21/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.sam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -G /build/reproducible-path/bcftools-1.21/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -G /build/reproducible-path/bcftools-1.21/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -G /build/reproducible-path/bcftools-1.21/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -G /build/reproducible-path/bcftools-1.21/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -G /build/reproducible-path/bcftools-1.21/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -G /build/reproducible-path/bcftools-1.21/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.sam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -G /build/reproducible-path/bcftools-1.21/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -G /build/reproducible-path/bcftools-1.21/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -G /build/reproducible-path/bcftools-1.21/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -G /build/reproducible-path/bcftools-1.21/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.fa /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.sam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.fa /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.fa /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD --indels-cns -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.fa /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD --indels-cns -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.sam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD --indels-cns -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.fa /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD --indels-cns -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD --indels-cns -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.fa /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD --indels-cns -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -r 11:75 -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.fa /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -r 11:75 -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -r 11:75 -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.fa /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -r 11:75 -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.fa /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.fa /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.fa /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.fa /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD,INFO/SCR,FMT/SCR -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD,INFO/SCR,FMT/SCR -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD,INFO/SCR,FMT/SCR -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD,INFO/SCR,FMT/SCR -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t 1:100 --skip-all-set PAIRED,PROPER_PAIR,MREVERSE -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t 1:100 --skip-all-set PAIRED,PROPER_PAIR,MREVERSE -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-filter.sam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t 1:100 --skip-any-set READ1 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t 1:100 --skip-any-set READ1 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-filter.sam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t 1:100 --skip-all-unset READ1 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t 1:100 --skip-all-unset READ1 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-filter.sam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t 1:100 --skip-any-unset READ1 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t 1:100 --skip-any-unset READ1 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-filter.sam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD,INFO/NMBZ -r chr19:69-99 -f /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.1.fa /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD,INFO/NMBZ -r chr19:69-99 -f /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.1.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.1.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD,INFO/NMBZ -r chr6:75 -f /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.2.fa /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD,INFO/NMBZ -r chr6:75 -f /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.2.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.2.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD,INFO/NMBZ -r chr16:75 -f /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.3.fa /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.3.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.3.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD,INFO/NMBZ -r chr16:75 -f /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.3.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.3.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.3.2.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_csq: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq.fa -g /build/reproducible-path/bcftools-1.21/test/csq.gff3 /build/reproducible-path/bcftools-1.21/test/csq.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq.fa -g /build/reproducible-path/bcftools-1.21/test/csq.chr.gff3 /build/reproducible-path/bcftools-1.21/test/csq.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq.fa -g /build/reproducible-path/bcftools-1.21/test/csq.2.gff /build/reproducible-path/bcftools-1.21/test/csq.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq.fa -g /build/reproducible-path/bcftools-1.21/test/csq.2.gff --ncsq 64 /build/reproducible-path/bcftools-1.21/test/csq.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq.nchr.fa -g /build/reproducible-path/bcftools-1.21/test/csq.nchr.gff /build/reproducible-path/bcftools-1.21/test/csq.nchr.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq.ychr.fa -g /build/reproducible-path/bcftools-1.21/test/csq.nchr.gff /build/reproducible-path/bcftools-1.21/test/csq.nchr.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq.nchr.fa -g /build/reproducible-path/bcftools-1.21/test/csq.ychr.gff /build/reproducible-path/bcftools-1.21/test/csq.nchr.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq.ychr.fa -g /build/reproducible-path/bcftools-1.21/test/csq.ychr.gff /build/reproducible-path/bcftools-1.21/test/csq.nchr.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq.ychr.fa -g /build/reproducible-path/bcftools-1.21/test/csq.ychr.gff /build/reproducible-path/bcftools-1.21/test/csq.ychr.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq.ychr.fa -g /build/reproducible-path/bcftools-1.21/test/csq.nchr.gff /build/reproducible-path/bcftools-1.21/test/csq.ychr.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq.nchr.fa -g /build/reproducible-path/bcftools-1.21/test/csq.ychr.gff /build/reproducible-path/bcftools-1.21/test/csq.ychr.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq.nchr.fa -g /build/reproducible-path/bcftools-1.21/test/csq.nchr.gff /build/reproducible-path/bcftools-1.21/test/csq.ychr.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.21/test/csq/ENST00000410009 && /build/reproducible-path/bcftools-1.21/bcftools csq -lb -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.21/test/csq/ENST00000410009 && /build/reproducible-path/bcftools-1.21/bcftools csq -B 5 -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000410009/ENST00000410009.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000410009/ENST00000410009.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000410009/frameshift.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.21/test/csq/ENST00000410009 && /build/reproducible-path/bcftools-1.21/bcftools csq -b -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000557788/ENST00000557788.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000557788/ENST00000557788.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000557788/long-overlap-del.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.21/test/csq/ENSMUST00000133836 && /build/reproducible-path/bcftools-1.21/bcftools csq -f ENSMUST00000133836.fa -g ENSMUST00000133836.gff filter-problem.vcf -i 'FILTER="PASS"' --phase m | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000420190/ENST00000420190.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000420190/ENST00000420190.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000420190/abort-in-csq-push.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000448695/ENST00000448695.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000448695/ENST00000448695.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000448695/syn-and-splice-reg.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000520868/ENST00000520868.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000520868/ENST00000520868.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000520868/long-deletion.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000373833/ENST00000373833.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000373833/ENST00000373833.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000373833/boundary-insertion.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000373833/ENST00000373833.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000373833/ENST00000373833.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000373833/boundary-insertion.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000518414/ENST00000518414.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000518414/ENST00000518414.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000518414/incorrect-inframe-del.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000571540/ENST00000571540.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000571540/ENST00000571540.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000571540/nmd.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000318249/ENST00000318249.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000318249/ENST00000318249.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000318249/start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000318249/ENST00000318249.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000318249/ENST00000318249.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000318249/start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000218032/ENST00000218032.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000218032/ENST00000218032.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000218032/start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000218032/ENST00000218032.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000218032/ENST00000218032.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000218032/start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000218032/ENST00000218032.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000218032/ENST00000218032.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000218032/start-lost-del.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000329454/ENST00000329454.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000329454/ENST00000329454.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000329454/boundary-deletion.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000329454/ENST00000329454.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000329454/ENST00000329454.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000329454/boundary-deletion.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0002/EDUMMY0002.fa -g /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0002/EDUMMY0002.gff /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0002/boundaries.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0001/EDUMMY0001.fa -g /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0001/EDUMMY0001.gff /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0001/starts-with-1.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0001/EDUMMY0001.fa -g /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0001/EDUMMY0001.gff /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0001/starts-with-1.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/frame2.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/frame2.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/frame1.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/frame1.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/frame3.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/frame3.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000382647/ENST00000382647.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000382647/ENST00000382647.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000382647/synon-splice-region-insert.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000303039/ENST00000303039.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000303039/ENST00000303039.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000303039/not-a-stop.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000303039/ENST00000303039.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000303039/ENST00000303039.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000303039/not-a-stop.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000409523/ENST00000409523.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000409523/ENST00000409523.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000409523/long-overlapping-del.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000573314/ENST00000573314.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000573314/ENST00000573314.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000573314/ENST00000573314.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000573314/ENST00000573314.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000230048/ENST00000230048.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000230048/ENST00000230048.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000230048/start-del.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/snps.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/snps.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/insert3.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/insert3.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0003/EDUMMY0003.fa -g /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0003/EDUMMY0003.gff /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0003/long-del.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000375992/ENST00000375992.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000375992/ENST00000375992.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000375992/incorrect-synon-del-not-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000263103-INS/ENST00000263103-INS.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000263103-INS/ENST00000263103-INS.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000263103-INS/insertions.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000413103/ENST00000413103.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000413103/ENST00000413103.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000413103/long-deletion.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000295641/ENST00000295641.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000295641/ENST00000295641.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000295641/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000295641/ENST00000295641.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000295641/ENST00000295641.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000295641/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000378322/ENST00000378322.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000378322/ENST00000378322.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000378322/end-overlap-tscript.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000378322/ENST00000378322.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000378322/ENST00000378322.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000378322/end-overlap-tscript.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000542803/ENST00000542803.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000542803/ENST00000542803.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000542803/splice-region.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000542803/ENST00000542803.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000542803/ENST00000542803.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000542803/splice-region.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000271583/ENST00000271583.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000271583/ENST00000271583.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000271583/splice-acceptor.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000294661/ENST00000294661.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000294661/ENST00000294661.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000294661/non-coding-boundary.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000294661/ENST00000294661.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000294661/ENST00000294661.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000294661/non-coding-boundary.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000360372/ENST00000360372.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000360372/ENST00000360372.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000360372/mnp.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.21/test/csq/ENST00000422159 && /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000422159.fa -g ENST00000422159.gff multiallelic.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%REF\t%ALT\t%GT\t%TBCSQ\n]' | ../sort-csq -q ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000422159.fa -g short.gff multiallelic.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%REF\t%ALT\t%GT\t%TBCSQ\n]' | ../sort-csq -q .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000518414-ENST00000521270/valgrind.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000528237/ENST00000528237.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000528237/ENST00000528237.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000528237/retained-stop-incomplete-cds.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.21/test/csq/ENST00000379416 && /build/reproducible-path/bcftools-1.21/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.del-snp.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-del.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-ins.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-snp.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff single.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000536784/ENST00000536784.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000536784/ENST00000536784.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000536784/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000536784/ENST00000536784.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000536784/ENST00000536784.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000536784/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000436063/ENST00000436063.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000436063/ENST00000436063.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000436063/insert-before-utr.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.21/test/csq/EMN908947 && /build/reproducible-path/bcftools-1.21/bcftools csq -f EMN908947.fa -g ribosomal-slippage.gff ribosomal-slippage.vcf --force | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.21/test/csq/EMN908947 && /build/reproducible-path/bcftools-1.21/bcftools csq -f EMN908947.fa -g simple.gff simple.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000357367/ENST00000357367.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000357367/ENST00000357367.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000357367/stop-retained.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000573035-bt2212/ENST00000573035-bt2212.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000573035-bt2212/ENST00000573035-bt2212.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000573035-bt2212/complex-event.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000318249.2/ENST00000318249.2.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000318249.2/ENST00000318249.2.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000318249.2/synonymous-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000545279/ENST00000545279.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000545279/ENST00000545279.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000545279/splice-region-insert.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000368801/ENST00000368801.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000368801/ENST00000368801.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000368801/compound-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000381157/ENST00000381157.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000381157/ENST00000381157.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000381157/haploid-diploid.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000285021/ENST00000285021.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000285021/ENST00000285021.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000285021/stop-gained-inframe-indel.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000400151/ENST00000400151.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000400151/ENST00000400151.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000400151/long-del.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000420670/ENST00000420670.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000420670/ENST00000420670.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000420670/start-stop-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000420670/ENST00000420670.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000420670/ENST00000420670.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000420670/segfault.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.21/test/csq/ENST00000580206 && /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.ins-snv.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g short.gff compound.ins-snv.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff single.ins-snv.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g short.gff single.ins-snv.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.del-snv.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g short.gff compound.del-snv.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g short.gff single.del-snv.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.del-ins.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g short.gff compound.del-ins.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g short.gff single.del-ins.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000256452/ENST00000256452.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000256452/ENST00000256452.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000256452/intron.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENSG00000173376/ENSG00000173376.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENSG00000173376/ENSG00000173376.gff /build/reproducible-path/bcftools-1.21/test/csq/ENSG00000173376/synon.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000519442/ENST00000519442.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000519442/ENST00000519442.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000519442/synon-splice-region-del.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000390520/ENST00000390520.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000390520/ENST00000390520.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000390520/deletion-overlap.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.21/test/csq/ENST00000000000 && /build/reproducible-path/bcftools-1.21/bcftools csq -p a -f ENST00000000000.fa -g ENST00000000000.gff upstream-stop.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%REF\t%ALT\t%SAMPLE\t%GT\t%TBCSQ\n]' | ../sort-csq -q .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000269081/ENST00000269081.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000269081/ENST00000269081.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000269081/stop-gained-not-inframe-insertion.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000543077/ENST00000543077.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000543077/ENST00000543077.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000543077/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000543077/ENST00000543077.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000543077/ENST00000543077.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000543077/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000624631/ENST00000624631.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000624631/ENST00000624631.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000624631/ambiguous.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000479739/ENST00000479739.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000479739/ENST00000479739.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000479739/short-cds-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000479739/ENST00000479739.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000479739/ENST00000479739.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000479739/short-cds-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000301246/ENST00000301246.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000301246/ENST00000301246.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000301246/15bp-insert.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000368801.2/ENST00000368801.2.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000368801.2/ENST00000368801.2.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000368801.2/start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.21/test/csq/ENSMUST00000121418 && /build/reproducible-path/bcftools-1.21/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25500' --phase m | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.21/test/csq/ENSMUST00000121418 && /build/reproducible-path/bcftools-1.21/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25496' --phase m | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.21/test/csq/ENSMUST00000121418 && /build/reproducible-path/bcftools-1.21/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25105' --phase m | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000593942/ENST00000593942.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000593942/ENST00000593942.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000593942/last-codon-deletion.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000520795/ENST00000520795.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000520795/ENST00000520795.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000520795/long-inside-del.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000520795/ENST00000520795.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000520795/ENST00000520795.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000520795/long-inside-del.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000227471/ENST00000227471.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000227471/ENST00000227471.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000227471/insert-splice-vs-frameshift.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_roh: /build/reproducible-path/bcftools-1.21/bcftools roh /build/reproducible-path/bcftools-1.21/test/roh.1.vcf.gz -Or -G30 --AF-dflt 0.4| grep -v ^# .. ok test_roh: /build/reproducible-path/bcftools-1.21/bcftools roh /build/reproducible-path/bcftools-1.21/test/roh.1.vcf.gz -Or -G30 --AF-file /build/reproducible-path/bcftools-1.21/test/roh.1.tab.gz| grep -v ^# .. ok test_roh: /build/reproducible-path/bcftools-1.21/bcftools roh /build/reproducible-path/bcftools-1.21/test/roh.1.vcf.gz -Or -G30 --AF-file /build/reproducible-path/bcftools-1.21/test/roh.1.tab.gz --ignore-homref| grep -v ^# .. ok test_roh: /build/reproducible-path/bcftools-1.21/bcftools roh /build/reproducible-path/bcftools-1.21/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245| grep -v ^# .. ok test_roh: /build/reproducible-path/bcftools-1.21/bcftools roh /build/reproducible-path/bcftools-1.21/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --ignore-homref| grep -v ^# .. ok test_roh: /build/reproducible-path/bcftools-1.21/bcftools roh /build/reproducible-path/bcftools-1.21/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --ignore-homref --include-noalt| grep -v ^# .. ok test_roh: /build/reproducible-path/bcftools-1.21/bcftools roh /build/reproducible-path/bcftools-1.21/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --include-noalt| grep -v ^# .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 --no-HWE-prob /tmp/wj8A4a3te7/gtcheck.1.vcf.gz -g /tmp/wj8A4a3te7/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 /tmp/wj8A4a3te7/gtcheck.1.vcf.gz -g /tmp/wj8A4a3te7/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -u GT,GT /tmp/wj8A4a3te7/gtcheck.1.vcf.gz -g /tmp/wj8A4a3te7/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -u GT,PL /tmp/wj8A4a3te7/gtcheck.1.vcf.gz -g /tmp/wj8A4a3te7/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -u PL,GT /tmp/wj8A4a3te7/gtcheck.1.vcf.gz -g /tmp/wj8A4a3te7/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -u PL,PL /tmp/wj8A4a3te7/gtcheck.1.vcf.gz -g /tmp/wj8A4a3te7/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -p s1,s1 /tmp/wj8A4a3te7/gtcheck.1.vcf.gz -g /tmp/wj8A4a3te7/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 /tmp/wj8A4a3te7/gtcheck.2.vcf.gz -g /tmp/wj8A4a3te7/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 /tmp/wj8A4a3te7/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -p B,A,C,A,C,B,D,A,D,B,D,C,E,A,E,B,E,C,E,D /tmp/wj8A4a3te7/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -P /build/reproducible-path/bcftools-1.21/test/gtcheck.3.pairs /tmp/wj8A4a3te7/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -u PL /tmp/wj8A4a3te7/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 --n-matches 4 /tmp/wj8A4a3te7/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO | sort .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -s qry:E,D,C /tmp/wj8A4a3te7/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -s qry:E,D,C -u PL /tmp/wj8A4a3te7/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -s qry:B -s gt:D /tmp/wj8A4a3te7/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -s qry:B -s gt:D -u PL /tmp/wj8A4a3te7/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -s qry:B -s gt:D,C /tmp/wj8A4a3te7/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -p B,C,B,D /tmp/wj8A4a3te7/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -u GT,GT -H /tmp/wj8A4a3te7/gtcheck.1.vcf.gz -g /tmp/wj8A4a3te7/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -u GT,PL -H /tmp/wj8A4a3te7/gtcheck.1.vcf.gz -g /tmp/wj8A4a3te7/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -u PL,GT -H /tmp/wj8A4a3te7/gtcheck.1.vcf.gz -g /tmp/wj8A4a3te7/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -u PL,PL -H /tmp/wj8A4a3te7/gtcheck.1.vcf.gz -g /tmp/wj8A4a3te7/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -P /build/reproducible-path/bcftools-1.21/test/gtcheck.4.pairs --distinctive-sites 3 /tmp/wj8A4a3te7/gtcheck.4.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -P /build/reproducible-path/bcftools-1.21/test/gtcheck.4.pairs --distinctive-sites 3,1 /tmp/wj8A4a3te7/gtcheck.4.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -u GT -e 30 /tmp/wj8A4a3te7/gtcheck.1.vcf.gz -g /tmp/wj8A4a3te7/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -u GT -e 30 -p s1,s1 /tmp/wj8A4a3te7/gtcheck.1.vcf.gz -g /tmp/wj8A4a3te7/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -u GT -e 300 /tmp/wj8A4a3te7/gtcheck.1.vcf.gz -g /tmp/wj8A4a3te7/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -u PL -e 30 /tmp/wj8A4a3te7/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck /tmp/wj8A4a3te7/gtcheck.ntop.vcf.gz -g /tmp/wj8A4a3te7/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck --n-matches 2 /tmp/wj8A4a3te7/gtcheck.ntop.vcf.gz -g /tmp/wj8A4a3te7/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck /tmp/wj8A4a3te7/gtcheck.5.vcf.gz -g /tmp/wj8A4a3te7/gtcheck.5.gts.vcf.gz | grep -v ^# | grep -v Time .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -p A,B,B,C /tmp/wj8A4a3te7/gtcheck.6.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -t 11:33 -p A,D,A,E,D,E -u GT -e 10 /tmp/wj8A4a3te7/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok Number of tests: total .. 1805 passed .. 1805 failed .. 0 make[2]: Leaving directory '/build/reproducible-path/bcftools-1.21' make[1]: Leaving directory '/build/reproducible-path/bcftools-1.21' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/bcftools/ make -j40 install DESTDIR=/build/reproducible-path/bcftools-1.21/debian/bcftools AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/bcftools-1.21' mkdir -p -m 755 /build/reproducible-path/bcftools-1.21/debian/bcftools/usr/bin /build/reproducible-path/bcftools-1.21/debian/bcftools/usr/share/man/man1 /build/reproducible-path/bcftools-1.21/debian/bcftools/usr/lib/x86_64-linux-gnu/bcftools install -p bcftools /build/reproducible-path/bcftools-1.21/debian/bcftools/usr/bin install -p misc/color-chrs.pl misc/gff2gff.py misc/guess-ploidy.py misc/plot-vcfstats misc/plot-roh.py misc/run-roh.pl misc/vcfutils.pl /build/reproducible-path/bcftools-1.21/debian/bcftools/usr/bin install -p -m 644 doc/bcftools.1 /build/reproducible-path/bcftools-1.21/debian/bcftools/usr/share/man/man1 install -p plugins/*.so /build/reproducible-path/bcftools-1.21/debian/bcftools/usr/lib/x86_64-linux-gnu/bcftools make[1]: Leaving directory '/build/reproducible-path/bcftools-1.21' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/bcftools-1.21' dh_install # Fix Perl interpreter PATH for pscript in `grep -Rl '#!/usr/bin/env \+perl' debian/*` ; do \ sed -i '1s?#!/usr/bin/env \+perl?#!/usr/bin/perl?' ${pscript} ; \ done make[1]: Leaving directory '/build/reproducible-path/bcftools-1.21' dh_installdocs dh_installchangelogs debian/rules override_dh_installman make[1]: Entering directory '/build/reproducible-path/bcftools-1.21' dh_installman --language=C make[1]: Leaving directory '/build/reproducible-path/bcftools-1.21' dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dpkg-gencontrol: warning: package bcftools: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package bcftools: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'bcftools-dbgsym' in '../bcftools-dbgsym_1.21-1_amd64.deb'. dpkg-deb: building package 'bcftools' in '../bcftools_1.21-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../bcftools_1.21-1_amd64.buildinfo dpkg-genchanges --build=binary -O../bcftools_1.21-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/712482 and its subdirectories I: Current time: Sat Jul 5 06:05:45 -12 2025 I: pbuilder-time-stamp: 1751738745 Sat Jul 5 18:05:45 UTC 2025 I: Signing ./b1/bcftools_1.21-1_amd64.buildinfo as bcftools_1.21-1_amd64.buildinfo.asc Sat Jul 5 18:05:45 UTC 2025 I: Signed ./b1/bcftools_1.21-1_amd64.buildinfo as ./b1/bcftools_1.21-1_amd64.buildinfo.asc Sat Jul 5 18:05:45 UTC 2025 - build #1 for bcftools/unstable/amd64 on ionos11-amd64 done. Starting cleanup. All cleanup done. Sat Jul 5 18:05:45 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-iZU2XO2z, removing. /srv/reproducible-results/rbuild-debian/r-b-build.k066tCUN: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Jul 5 18:05 b1 drwxr-xr-x 2 jenkins jenkins 4096 Jul 5 18:01 b2 -rw-r--r-- 1 jenkins jenkins 2267 Feb 13 21:22 bcftools_1.21-1.dsc -rw------- 1 jenkins jenkins 3371 Jul 5 18:01 rbuildlog.A9v1TAx /srv/reproducible-results/rbuild-debian/r-b-build.k066tCUN/b1: total 7084 -rw-r--r-- 1 jenkins jenkins 2229324 Jul 5 18:05 bcftools-dbgsym_1.21-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 7504 Jul 5 18:05 bcftools_1.21-1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2267 Jul 5 18:05 bcftools_1.21-1.dsc -rw-r--r-- 1 jenkins jenkins 7023 Jul 5 18:05 bcftools_1.21-1_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 7905 Jul 5 18:05 bcftools_1.21-1_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1571 Jul 5 18:05 bcftools_1.21-1_amd64.changes -rw-r--r-- 1 jenkins jenkins 784124 Jul 5 18:05 bcftools_1.21-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 1675 Jul 5 18:05 bcftools_1.21-1_source.changes -rw-r--r-- 1 jenkins jenkins 3665160 Jul 5 18:05 bcftools_1.21.orig.tar.gz -rw-r--r-- 1 jenkins jenkins 528459 Jul 5 18:05 build.log /srv/reproducible-results/rbuild-debian/r-b-build.k066tCUN/b2: total 0 Sat Jul 5 18:05:46 UTC 2025 I: Deleting $TMPDIR on ionos11-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sat Jul 5 06:01:17 -12 2025 I: pbuilder-time-stamp: 1751738477 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [bcftools_1.21-1.dsc] I: copying [./bcftools_1.21.orig.tar.gz] I: copying [./bcftools_1.21-1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./bcftools_1.21-1.dsc: no acceptable signature found dpkg-source: info: extracting bcftools in bcftools-1.21 dpkg-source: info: unpacking bcftools_1.21.orig.tar.gz dpkg-source: info: unpacking bcftools_1.21-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying skip_new_test_failing_on_32bit.patch dpkg-source: info: applying 2to3.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/712482/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='9646257e45ef4c9dafc0d245b5209d67' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='712482' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.k066tCUN/pbuilderrc_K5ta --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.k066tCUN/b1 --logfile b1/build.log bcftools_1.21-1.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos11-amd64 6.1.0-37-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.140-1 (2025-05-22) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 12 19:25 /bin -> usr/bin I: user script /srv/workspace/pbuilder/712482/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), zlib1g-dev, libbz2-dev, liblzma-dev, libhts-dev (>= 1.14), libgsl-dev, tabix, libio-pty-perl dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19849 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. pbuilder-satisfydepends-dummy depends on liblzma-dev; however: Package liblzma-dev is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev (>= 1.14); however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on libgsl-dev; however: Package libgsl-dev is not installed. pbuilder-satisfydepends-dummy depends on tabix; however: Package tabix is not installed. pbuilder-satisfydepends-dummy depends on libio-pty-perl; however: Package libio-pty-perl is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} comerr-dev{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} krb5-multidev{a} libarchive-zip-perl{a} libbrotli-dev{a} libbrotli1{a} libbz2-dev{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1t64{a} libevent-2.1-7t64{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgnutls30t64{a} libgsl-dev{a} libgsl28{a} libgslcblas0{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libidn2-0{a} libidn2-dev{a} libio-pty-perl{a} libk5crypto3{a} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} libldap-dev{a} libldap2{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp2-dev{a} libnghttp3-9{a} libnghttp3-dev{a} libngtcp2-16{a} libngtcp2-crypto-gnutls-dev{a} libngtcp2-crypto-gnutls8{a} libngtcp2-dev{a} libp11-kit-dev{a} libp11-kit0{a} libpipeline1{a} libpkgconf3{a} libpsl-dev{a} libpsl5t64{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libtasn1-6{a} libtasn1-6-dev{a} libtool{a} libuchardet0{a} libunbound8{a} libunistring5{a} libxml2{a} libzstd-dev{a} m4{a} man-db{a} nettle-dev{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} sensible-utils{a} tabix{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc ca-certificates curl krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules libtasn1-doc lynx publicsuffix wget 0 packages upgraded, 98 newly installed, 0 to remove and 0 not upgraded. Need to get 33.8 MB of archives. After unpacking 124 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.25 [25.0 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2 [243 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41-5 [94.6 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-8 [294 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-3+b1 [25.0 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 comerr-dev amd64 2.1-1.47.2-3+b1 [56.7 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-4 [539 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 24 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-1 [698 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2 [1680 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.2 [919 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get: 35 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 libgssrpc4t64 amd64 1.21.3-5 [60.0 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 libkadm5clnt-mit12 amd64 1.21.3-5 [42.5 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libkdb5-10t64 amd64 1.21.3-5 [42.6 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 libkadm5srv-mit12 amd64 1.21.3-5 [54.2 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 krb5-multidev amd64 1.21.3-5 [126 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 libbrotli-dev amd64 1.1.0-2+b7 [316 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.8-2 [109 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.4.8-2 [24.1 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libgnutls30t64 amd64 3.8.9-2 [1464 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 libldap2 amd64 2.6.10+dfsg-1 [194 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1.1 [76.0 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.8.0-1 [67.7 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.11.0-1 [131 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.11.0-1 [29.3 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.14.1-2 [384 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libunbound8 amd64 1.22.0-1+b1 [598 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 libgnutls-dane0t64 amd64 3.8.9-2 [455 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 libgnutls-openssl27t64 amd64 3.8.9-2 [455 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 libidn2-dev amd64 2.3.8-2 [103 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 libp11-kit-dev amd64 0.25.5-3 [208 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 libtasn1-6-dev amd64 4.20.0-2 [99.2 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-3 [329 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-3 [642 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 nettle-dev amd64 3.10.1-1 [1318 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 libgnutls28-dev amd64 3.8.9-2 [1401 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 libkrb5-dev amd64 1.21.3-5 [16.1 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 libldap-dev amd64 2.6.10+dfsg-1 [312 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 libnghttp2-dev amd64 1.64.0-1.1 [116 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 libnghttp3-dev amd64 1.8.0-1 [91.3 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.11.0-1 [34.0 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 libngtcp2-dev amd64 1.11.0-1 [179 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 libpsl-dev amd64 0.21.2-1.1+b1 [77.6 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-2+b5 [68.0 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 libssl-dev amd64 3.5.0-2 [2950 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 libssh2-1-dev amd64 1.11.1-1 [393 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.7+dfsg-1 [371 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls-dev amd64 8.14.1-2 [503 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.23-2 [47.3 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 libdeflate-dev amd64 1.23-2 [55.9 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 libgslcblas0 amd64 2.8+dfsg-5 [116 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 libgsl28 amd64 2.8+dfsg-5 [994 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 libgsl-dev amd64 2.8+dfsg-5 [1222 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.1-2 [95.8 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.21+ds-1 [463 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.8.1-1 [348 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 libhts-dev amd64 1.21+ds-1 [1733 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 libio-pty-perl amd64 1:1.20-1+b3 [34.3 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 tabix amd64 1.21+ds-1 [496 kB] Fetched 33.8 MB in 3s (12.8 MB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19849 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.25_all.deb ... Unpacking sensible-utils (0.0.25) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.46-5_amd64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-2_amd64.deb ... Unpacking gettext-base (0.23.1-2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-9_amd64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.41-5_amd64.deb ... Unpacking bsdextrautils (2.41-5) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.1-1_amd64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-8_amd64.deb ... Unpacking m4 (1.4.19-8) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.23.1-2_all.deb ... Unpacking autopoint (0.23.1-2) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../15-libcom-err2_1.47.2-3+b1_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.2-3+b1) ... Selecting previously unselected package comerr-dev:amd64. Preparing to unpack .../16-comerr-dev_2.1-1.47.2-3+b1_amd64.deb ... Unpacking comerr-dev:amd64 (2.1-1.47.2-3+b1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../17-libdebhelper-perl_13.24.2_all.deb ... Unpacking libdebhelper-perl (13.24.2) ... Selecting previously unselected package libtool. Preparing to unpack .../18-libtool_2.5.4-4_all.deb ... Unpacking libtool (2.5.4-4) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../19-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../20-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. 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Setting up autoconf (2.72-3.1) ... Setting up libnghttp3-9:amd64 (1.8.0-1) ... Setting up libnghttp3-dev:amd64 (1.8.0-1) ... Setting up liblzma-dev:amd64 (5.8.1-1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libffi8:amd64 (3.4.8-2) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.25) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up libtasn1-6:amd64 (4.20.0-2) ... Setting up libngtcp2-16:amd64 (1.11.0-1) ... Setting up libkrb5-3:amd64 (1.21.3-5) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up libgsl28:amd64 (2.8+dfsg-5) ... Setting up libtasn1-6-dev:amd64 (4.20.0-2) ... Setting up libdeflate-dev:amd64 (1.23-2) ... Setting up tabix (1.21+ds-1) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-1) ... Setting up libldap2:amd64 (2.6.10+dfsg-1) ... Setting up libbrotli-dev:amd64 (1.1.0-2+b7) ... Setting up libbz2-dev:amd64 (1.0.8-6) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up gettext (0.23.1-2) ... Setting up libgsl-dev (2.8+dfsg-5) ... Setting up libgmp-dev:amd64 (2:6.3.0+dfsg-3) ... Setting up nettle-dev:amd64 (3.10.1-1) ... Setting up libtool (2.5.4-4) ... Setting up libidn2-0:amd64 (2.3.8-2) ... Setting up libngtcp2-dev:amd64 (1.11.0-1) ... Setting up pkgconf:amd64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libldap-dev:amd64 (2.6.10+dfsg-1) ... Setting up libp11-kit0:amd64 (0.25.5-3) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-5) ... Setting up libssh2-1-dev:amd64 (1.11.1-1) ... Setting up libidn2-dev:amd64 (2.3.8-2) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-9) ... Setting up libp11-kit-dev:amd64 (0.25.5-3) ... Setting up libgnutls30t64:amd64 (3.8.9-2) ... Setting up libgnutls-openssl27t64:amd64 (3.8.9-2) ... Setting up libnghttp2-dev:amd64 (1.64.0-1.1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libpsl-dev:amd64 (0.21.2-1.1+b1) ... Setting up libgnutls-dane0t64:amd64 (3.8.9-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libgssrpc4t64:amd64 (1.21.3-5) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.11.0-1) ... Setting up libkadm5clnt-mit12:amd64 (1.21.3-5) ... Setting up libgnutls28-dev:amd64 (3.8.9-2) ... Setting up libkdb5-10t64:amd64 (1.21.3-5) ... Setting up libcurl3t64-gnutls:amd64 (8.14.1-2) ... Setting up debhelper (13.24.2) ... Setting up libngtcp2-crypto-gnutls-dev:amd64 (1.11.0-1) ... Setting up librtmp-dev:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libkadm5srv-mit12:amd64 (1.21.3-5) ... Setting up libhts3t64:amd64 (1.21+ds-1) ... Setting up krb5-multidev:amd64 (1.21.3-5) ... Setting up libkrb5-dev:amd64 (1.21.3-5) ... Setting up libcurl4-gnutls-dev:amd64 (8.14.1-2) ... Setting up libhts-dev:amd64 (1.21+ds-1) ... Processing triggers for libc-bin (2.41-9) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/bcftools-1.21/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../bcftools_1.21-1_source.changes dpkg-buildpackage: info: source package bcftools dpkg-buildpackage: info: source version 1.21-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean rm -f config.mk && touch config.mk dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/bcftools-1.21' dh_auto_clean make -j40 distclean make[2]: Entering directory '/build/reproducible-path/bcftools-1.21' rm -f test/*.o test/*.fa.fai test/*~ test/test-rbuf test/test-regidx rm -f plugins/*.so plugins/*.P rm -rf plugins/*.dSYM rm -f test/*.unsorted.hex test/*.unsorted.tsv rm -f gmon.out *.o *.a *~ bcftools version.h rm -rf *.dSYM test/*.dSYM rm -f config.cache config.h config.log config.mk config.status rm -rf autom4te.cache rm -f TAGS make[2]: Leaving directory '/build/reproducible-path/bcftools-1.21' rm -f test/mpileup/indel-AD.1.out.new test/view-t.1.out.new test/view-t.2.out.new make[1]: Leaving directory '/build/reproducible-path/bcftools-1.21' dh_clean debian/rules binary dh binary dh_update_autotools_config debian/rules override_dh_autoreconf make[1]: Entering directory '/build/reproducible-path/bcftools-1.21' rm -f config.mk && touch config.mk export MAKEFLAGS="-s"; dh_autoreconf configure.ac:94: warning: _AC_CONFIG_SUBDIRS: you should use literals ./lib/autoconf/status.m4:1096: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:94: the top level make[1]: Leaving directory '/build/reproducible-path/bcftools-1.21' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/bcftools-1.21' dh_auto_configure -- \ --with-htslib=system \ --enable-gsl \ --with-cblas=gslcblas \ --with-bcf-plugin-dir=/usr/lib/x86_64-linux-gnu/bcftools ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system --enable-gsl --with-cblas=gslcblas --with-bcf-plugin-dir=/usr/lib/x86_64-linux-gnu/bcftools checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking for -Wdate-time -D_FORTIFY_SOURCE=2 option for large files... none needed checking for htslib/sam.h... yes checking for hts_version in -lhts... yes checking shared library type... plain .so checking for library containing dlopen... none required checking if the compiler accepts -rdynamic... yes checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing regcomp... none required configure: creating ./config.status config.status: creating config.mk config.status: creating config.h make[1]: Leaving directory '/build/reproducible-path/bcftools-1.21' dh_auto_build make -j40 make[1]: Entering directory '/build/reproducible-path/bcftools-1.21' echo '#define BCFTOOLS_VERSION "1.21"' > version.h gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfindex.o vcfindex.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tabix.o tabix.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfstats.o vcfstats.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfisec.o vcfisec.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfmerge.o vcfmerge.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfquery.o vcfquery.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcffilter.o vcffilter.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o filter.o filter.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfsom.o vcfsom.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfnorm.o vcfnorm.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfgtcheck.o vcfgtcheck.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfview.o vcfview.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfannotate.o vcfannotate.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfroh.o vcfroh.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfconcat.o vcfconcat.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcall.o vcfcall.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mcall.o mcall.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcmp.o vcmp.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gvcf.o gvcf.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o reheader.o reheader.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o convert.o convert.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfconvert.o vcfconvert.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tsv2vcf.o tsv2vcf.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcnv.o vcfcnv.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfhead.o vcfhead.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o HMM.o HMM.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o consensus.o consensus.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ploidy.o ploidy.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bin.o bin.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hclust.o hclust.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o version.o version.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o regidx.o regidx.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o smpl_ilist.o smpl_ilist.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o csq.o csq.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfbuf.o vcfbuf.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mpileup.o mpileup.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_iaux.o bam2bcf_iaux.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_edlib.o bam2bcf_edlib.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o read_consensus.o read_consensus.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sample.o bam_sample.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfsort.o vcfsort.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cols.o cols.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o extsort.o extsort.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dist.o dist.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o abuf.o abuf.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ccall.o ccall.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o em.o em.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o prob1.o prob1.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kmin.o kmin.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o str_finder.o str_finder.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gff.o gff.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o edlib.o edlib.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DPLUGINPATH='"/usr/lib/x86_64-linux-gnu/bcftools"' -c -o vcfplugin.o vcfplugin.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-rbuf.o test/test-rbuf.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-regidx.o test/test-regidx.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/GTisec.so version.c plugins/GTisec.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/GTsubset.so version.c plugins/GTsubset.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/ad-bias.so convert.c version.c plugins/ad-bias.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/add-variantkey.so version.c plugins/add-variantkey.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/af-dist.so bin.c version.c plugins/af-dist.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/allele-length.so version.c plugins/allele-length.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/check-ploidy.so version.c plugins/check-ploidy.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/check-sparsity.so version.c plugins/check-sparsity.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/color-chrs.so HMM.c version.c plugins/color-chrs.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/contrast.so version.c plugins/contrast.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/counts.so version.c plugins/counts.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/dosage.so version.c plugins/dosage.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/fill-AN-AC.so version.c plugins/fill-AN-AC.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/fill-from-fasta.so filter.c version.c plugins/fill-from-fasta.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/fill-tags.so version.c plugins/fill-tags.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/fixploidy.so ploidy.c regidx.c version.c plugins/fixploidy.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/fixref.so version.c plugins/fixref.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/frameshifts.so version.c plugins/frameshifts.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/guess-ploidy.so version.c plugins/guess-ploidy.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/gvcfz.so version.c plugins/gvcfz.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/impute-info.so version.c plugins/impute-info.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/indel-stats.so version.c plugins/indel-stats.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/isecGT.so smpl_ilist.c version.c plugins/isecGT.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/mendelian2.so version.c plugins/mendelian2.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/missing2ref.so version.c plugins/missing2ref.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/parental-origin.so version.c plugins/parental-origin.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/prune.so version.c plugins/prune.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/remove-overlaps.so version.c plugins/remove-overlaps.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/scatter.so version.c plugins/scatter.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/setGT.so version.c plugins/setGT.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/smpl-stats.so version.c plugins/smpl-stats.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/split-vep.so version.c plugins/split-vep.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/split.so version.c plugins/split.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/tag2tag.so version.c plugins/tag2tag.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/trio-dnm2.so version.c plugins/trio-dnm2.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/trio-stats.so version.c plugins/trio-stats.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/trio-switch-rate.so version.c plugins/trio-switch-rate.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/variant-distance.so version.c plugins/variant-distance.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/variantkey-hex.so version.c plugins/variantkey-hex.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o main.o main.c gcc -Wl,-z,relro -Wl,-z,now -o test/test-rbuf test/test-rbuf.o -lz gcc -Wl,-z,relro -Wl,-z,now -o test/test-regidx test/test-regidx.o regidx.o -lhts -lpthread -lz gcc -rdynamic -Wl,-z,relro -Wl,-z,now -o bcftools main.o vcfindex.o tabix.o vcfstats.o vcfisec.o vcfmerge.o vcfquery.o vcffilter.o filter.o vcfsom.o vcfnorm.o vcfgtcheck.o vcfview.o vcfannotate.o vcfroh.o vcfconcat.o vcfcall.o mcall.o vcmp.o gvcf.o reheader.o convert.o vcfconvert.o tsv2vcf.o vcfcnv.o vcfhead.o HMM.o consensus.o ploidy.o bin.o hclust.o version.o regidx.o smpl_ilist.o csq.o vcfbuf.o mpileup.o bam2bcf.o bam2bcf_indel.o bam2bcf_iaux.o bam2bcf_edlib.o read_consensus.o bam_sample.o vcfsort.o cols.o extsort.o dist.o abuf.o ccall.o em.o prob1.o kmin.o str_finder.o gff.o edlib.o vcfplugin.o -lhts -lm -lz -lpthread make[1]: Leaving directory '/build/reproducible-path/bcftools-1.21' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/bcftools-1.21' make test-no-plugins VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/bcftools-1.21' ./test/test-rbuf Inserted 1-9 starting at offset 5: 5 6 7 8 9 0 1 2 3 1 2 3 4 5 6 7 8 9 4th is 4 Deleting 1-2: 7 8 9 0 1 2 3 3 4 5 6 7 8 9 Prepending 0-8: 8 9 0 1 2 3 4 5 6 7 8 7 6 5 4 3 2 1 0 3 Expanding: 8 9 10 11 12 13 14 15 16 17 8 7 6 5 4 3 2 1 0 3 ./test/test-regidx REF_PATH=: ./test/test.pl --exec bgzip= --exec tabix= --htsdir= ${TEST_OPTS:-} test_usage: bcftools .. ok test_usage_subcommand: bcftools index .. ok test_usage_subcommand: bcftools annotate .. ok test_usage_subcommand: bcftools concat .. ok test_usage_subcommand: bcftools convert .. ok test_usage_subcommand: bcftools head .. ok test_usage_subcommand: bcftools isec .. ok test_usage_subcommand: bcftools merge .. ok test_usage_subcommand: bcftools norm .. ok test_usage_subcommand: bcftools plugin .. ok test_usage_subcommand: bcftools query .. ok test_usage_subcommand: bcftools reheader .. ok test_usage_subcommand: bcftools sort .. ok test_usage_subcommand: bcftools view .. ok test_usage_subcommand: bcftools call .. ok test_usage_subcommand: bcftools consensus .. ok test_usage_subcommand: bcftools cnv .. ok test_usage_subcommand: bcftools csq .. ok test_usage_subcommand: bcftools filter .. ok test_usage_subcommand: bcftools gtcheck .. ok test_usage_subcommand: bcftools mpileup .. ok test_usage_subcommand: bcftools roh .. ok test_usage_subcommand: bcftools stats .. ok test_tabix: tabix /tmp/wj8A4a3te7/merge.a.vcf.gz 2:3199812-3199812 .. ok test_tabix: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/wj8A4a3te7/merge.a.bcf 2:3199812-3199812 .. ok test_tabix: tabix /tmp/wj8A4a3te7/merge.a.vcf.gz 1:3000151-3000151 .. ok test_tabix: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/wj8A4a3te7/merge.a.bcf 1:3000151-3000151 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/wj8A4a3te7/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/wj8A4a3te7/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/wj8A4a3te7/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/wj8A4a3te7/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/wj8A4a3te7/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/wj8A4a3te7/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/wj8A4a3te7/large_chrom_csi_limit.bcf chr20 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/wj8A4a3te7/large_chrom_csi_limit.bcf chr20 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/wj8A4a3te7/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/wj8A4a3te7/large_chrom_csi_limit.bcf chr20 .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -s /tmp/wj8A4a3te7/idx.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -s /tmp/wj8A4a3te7/idx.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -s /tmp/wj8A4a3te7/idx.bcf .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/wj8A4a3te7/idx.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/wj8A4a3te7/idx.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/wj8A4a3te7/idx.vcf.gz.csi .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/wj8A4a3te7/idx.bcf .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/wj8A4a3te7/idx.bcf.csi .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -s /tmp/wj8A4a3te7/empty.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -s /tmp/wj8A4a3te7/empty.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -s /tmp/wj8A4a3te7/empty.bcf .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/wj8A4a3te7/empty.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/wj8A4a3te7/empty.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/wj8A4a3te7/empty.vcf.gz.csi .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/wj8A4a3te7/empty.bcf .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/wj8A4a3te7/empty.bcf.csi .. ok test_vcf_check: /build/reproducible-path/bcftools-1.21/bcftools stats -s - /tmp/wj8A4a3te7/check.vcf.gz | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/check.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools stats -s - | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check_merge: /build/reproducible-path/bcftools-1.21/misc/plot-vcfstats -m /tmp/wj8A4a3te7/check.1.chk /tmp/wj8A4a3te7/check.2.chk /tmp/wj8A4a3te7/check.3.chk /tmp/wj8A4a3te7/check.4.chk | grep -v 'plot-vcfstats' | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_stats: /build/reproducible-path/bcftools-1.21/bcftools stats -s - /tmp/wj8A4a3te7/stats.a.vcf.gz /tmp/wj8A4a3te7/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/reproducible-path/bcftools-1.21/bcftools stats -s B /tmp/wj8A4a3te7/stats.a.vcf.gz /tmp/wj8A4a3te7/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/reproducible-path/bcftools-1.21/bcftools stats -s - /tmp/wj8A4a3te7/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/reproducible-path/bcftools-1.21/bcftools stats -s - -i 'type="snp"' /tmp/wj8A4a3te7/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/reproducible-path/bcftools-1.21/bcftools stats -s - /tmp/wj8A4a3te7/stats.vaf.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -n =2 /tmp/wj8A4a3te7/isec.a.vcf.gz /tmp/wj8A4a3te7/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -n =2 /tmp/wj8A4a3te7/isec.a.vcf.gz /tmp/wj8A4a3te7/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/wj8A4a3te7/isec.a.vcf.gz /tmp/wj8A4a3te7/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -n =2 -i"STRLEN(REF)==2" /tmp/wj8A4a3te7/isec.a.vcf.gz /tmp/wj8A4a3te7/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -n =2 -c both /tmp/wj8A4a3te7/isec.a.vcf.gz /tmp/wj8A4a3te7/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -n =2 -c both /tmp/wj8A4a3te7/isec.a.vcf.gz /tmp/wj8A4a3te7/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -n =2 -c any /tmp/wj8A4a3te7/isec.a.vcf.gz /tmp/wj8A4a3te7/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -n =2 -c any /tmp/wj8A4a3te7/isec.a.vcf.gz /tmp/wj8A4a3te7/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -C -c any /tmp/wj8A4a3te7/isec.a.vcf.gz /tmp/wj8A4a3te7/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -C -c any /tmp/wj8A4a3te7/isec.a.vcf.gz /tmp/wj8A4a3te7/isec.b.vcf.gz .. ok test_vcf_isec2: /build/reproducible-path/bcftools-1.21/bcftools isec --no-version -T /tmp/wj8A4a3te7/isec.tab.gz /tmp/wj8A4a3te7/isec.a.vcf.gz .. ok test_vcf_isec2: /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -T /tmp/wj8A4a3te7/isec.tab.gz /tmp/wj8A4a3te7/isec.a.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/wj8A4a3te7/isec-miss.1.1.vcf.gz /tmp/wj8A4a3te7/isec-miss.1.2.vcf.gz /tmp/wj8A4a3te7/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/wj8A4a3te7/isec-miss.1.1.vcf.gz /tmp/wj8A4a3te7/isec-miss.1.2.vcf.gz /tmp/wj8A4a3te7/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -R /build/reproducible-path/bcftools-1.21/test/isec-miss.1.regs.txt -n +1 /tmp/wj8A4a3te7/isec-miss.1.1.vcf.gz /tmp/wj8A4a3te7/isec-miss.1.2.vcf.gz /tmp/wj8A4a3te7/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -R /build/reproducible-path/bcftools-1.21/test/isec-miss.1.regs.txt -n +1 /tmp/wj8A4a3te7/isec-miss.1.1.vcf.gz /tmp/wj8A4a3te7/isec-miss.1.2.vcf.gz /tmp/wj8A4a3te7/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/wj8A4a3te7/isec-miss.2.1.vcf.gz /tmp/wj8A4a3te7/isec-miss.2.2.vcf.gz /tmp/wj8A4a3te7/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/wj8A4a3te7/isec-miss.2.1.vcf.gz /tmp/wj8A4a3te7/isec-miss.2.2.vcf.gz /tmp/wj8A4a3te7/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -R /build/reproducible-path/bcftools-1.21/test/isec-miss.1.regs.txt -n +1 /tmp/wj8A4a3te7/isec-miss.2.1.vcf.gz /tmp/wj8A4a3te7/isec-miss.2.2.vcf.gz /tmp/wj8A4a3te7/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -R /build/reproducible-path/bcftools-1.21/test/isec-miss.1.regs.txt -n +1 /tmp/wj8A4a3te7/isec-miss.2.1.vcf.gz /tmp/wj8A4a3te7/isec-miss.2.2.vcf.gz /tmp/wj8A4a3te7/isec-miss.2.3.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/wj8A4a3te7/merge.11.a.vcf.gz /tmp/wj8A4a3te7/merge.11.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/wj8A4a3te7/merge.11.a.vcf.gz /tmp/wj8A4a3te7/merge.11.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/wj8A4a3te7/merge.11.a.bcf /tmp/wj8A4a3te7/merge.11.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/wj8A4a3te7/merge.11.a.bcf /tmp/wj8A4a3te7/merge.11.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -i AF:join /tmp/wj8A4a3te7/merge.join.a.vcf.gz /tmp/wj8A4a3te7/merge.join.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -i AF:join /tmp/wj8A4a3te7/merge.join.a.vcf.gz /tmp/wj8A4a3te7/merge.join.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -i AF:join /tmp/wj8A4a3te7/merge.join.a.bcf /tmp/wj8A4a3te7/merge.join.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -i AF:join /tmp/wj8A4a3te7/merge.join.a.bcf /tmp/wj8A4a3te7/merge.join.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-single /tmp/wj8A4a3te7/merge.LPL.a.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-single /tmp/wj8A4a3te7/merge.LPL.a.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-single /tmp/wj8A4a3te7/merge.LPL.a.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-single /tmp/wj8A4a3te7/merge.LPL.a.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples /tmp/wj8A4a3te7/merge.LPL.a.vcf.gz /tmp/wj8A4a3te7/merge.LPL.b.vcf.gz /tmp/wj8A4a3te7/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/wj8A4a3te7/merge.LPL.a.vcf.gz /tmp/wj8A4a3te7/merge.LPL.b.vcf.gz /tmp/wj8A4a3te7/merge.LPL.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples /tmp/wj8A4a3te7/merge.LPL.a.bcf /tmp/wj8A4a3te7/merge.LPL.b.bcf /tmp/wj8A4a3te7/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/wj8A4a3te7/merge.LPL.a.bcf /tmp/wj8A4a3te7/merge.LPL.b.bcf /tmp/wj8A4a3te7/merge.LPL.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -L 1 /tmp/wj8A4a3te7/merge.LPL.a.vcf.gz /tmp/wj8A4a3te7/merge.LPL.b.vcf.gz /tmp/wj8A4a3te7/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 1 /tmp/wj8A4a3te7/merge.LPL.a.vcf.gz /tmp/wj8A4a3te7/merge.LPL.b.vcf.gz /tmp/wj8A4a3te7/merge.LPL.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -L 1 /tmp/wj8A4a3te7/merge.LPL.a.bcf /tmp/wj8A4a3te7/merge.LPL.b.bcf /tmp/wj8A4a3te7/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 1 /tmp/wj8A4a3te7/merge.LPL.a.bcf /tmp/wj8A4a3te7/merge.LPL.b.bcf /tmp/wj8A4a3te7/merge.LPL.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -L 2 /tmp/wj8A4a3te7/merge.LPL.a.vcf.gz /tmp/wj8A4a3te7/merge.LPL.b.vcf.gz /tmp/wj8A4a3te7/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 2 /tmp/wj8A4a3te7/merge.LPL.a.vcf.gz /tmp/wj8A4a3te7/merge.LPL.b.vcf.gz /tmp/wj8A4a3te7/merge.LPL.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -L 2 /tmp/wj8A4a3te7/merge.LPL.a.bcf /tmp/wj8A4a3te7/merge.LPL.b.bcf /tmp/wj8A4a3te7/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 2 /tmp/wj8A4a3te7/merge.LPL.a.bcf /tmp/wj8A4a3te7/merge.LPL.b.bcf /tmp/wj8A4a3te7/merge.LPL.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -L 3 /tmp/wj8A4a3te7/merge.LPL.a.vcf.gz /tmp/wj8A4a3te7/merge.LPL.b.vcf.gz /tmp/wj8A4a3te7/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 3 /tmp/wj8A4a3te7/merge.LPL.a.vcf.gz /tmp/wj8A4a3te7/merge.LPL.b.vcf.gz /tmp/wj8A4a3te7/merge.LPL.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -L 3 /tmp/wj8A4a3te7/merge.LPL.a.bcf /tmp/wj8A4a3te7/merge.LPL.b.bcf /tmp/wj8A4a3te7/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 3 /tmp/wj8A4a3te7/merge.LPL.a.bcf /tmp/wj8A4a3te7/merge.LPL.b.bcf /tmp/wj8A4a3te7/merge.LPL.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -L 4 /tmp/wj8A4a3te7/merge.LPL.a.vcf.gz /tmp/wj8A4a3te7/merge.LPL.b.vcf.gz /tmp/wj8A4a3te7/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 4 /tmp/wj8A4a3te7/merge.LPL.a.vcf.gz /tmp/wj8A4a3te7/merge.LPL.b.vcf.gz /tmp/wj8A4a3te7/merge.LPL.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -L 4 /tmp/wj8A4a3te7/merge.LPL.a.bcf /tmp/wj8A4a3te7/merge.LPL.b.bcf /tmp/wj8A4a3te7/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 4 /tmp/wj8A4a3te7/merge.LPL.a.bcf /tmp/wj8A4a3te7/merge.LPL.b.bcf /tmp/wj8A4a3te7/merge.LPL.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -L 5 /tmp/wj8A4a3te7/merge.LPL.a.vcf.gz /tmp/wj8A4a3te7/merge.LPL.b.vcf.gz /tmp/wj8A4a3te7/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 5 /tmp/wj8A4a3te7/merge.LPL.a.vcf.gz /tmp/wj8A4a3te7/merge.LPL.b.vcf.gz /tmp/wj8A4a3te7/merge.LPL.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -L 5 /tmp/wj8A4a3te7/merge.LPL.a.bcf /tmp/wj8A4a3te7/merge.LPL.b.bcf /tmp/wj8A4a3te7/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 5 /tmp/wj8A4a3te7/merge.LPL.a.bcf /tmp/wj8A4a3te7/merge.LPL.b.bcf /tmp/wj8A4a3te7/merge.LPL.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples /tmp/wj8A4a3te7/merge.a.vcf.gz /tmp/wj8A4a3te7/merge.b.vcf.gz /tmp/wj8A4a3te7/merge.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/wj8A4a3te7/merge.a.vcf.gz /tmp/wj8A4a3te7/merge.b.vcf.gz /tmp/wj8A4a3te7/merge.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples /tmp/wj8A4a3te7/merge.a.bcf /tmp/wj8A4a3te7/merge.b.bcf /tmp/wj8A4a3te7/merge.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/wj8A4a3te7/merge.a.bcf /tmp/wj8A4a3te7/merge.b.bcf /tmp/wj8A4a3te7/merge.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -Fx /tmp/wj8A4a3te7/merge.a.vcf.gz /tmp/wj8A4a3te7/merge.b.vcf.gz /tmp/wj8A4a3te7/merge.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -Fx /tmp/wj8A4a3te7/merge.a.vcf.gz /tmp/wj8A4a3te7/merge.b.vcf.gz /tmp/wj8A4a3te7/merge.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -Fx /tmp/wj8A4a3te7/merge.a.bcf /tmp/wj8A4a3te7/merge.b.bcf /tmp/wj8A4a3te7/merge.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -Fx /tmp/wj8A4a3te7/merge.a.bcf /tmp/wj8A4a3te7/merge.b.bcf /tmp/wj8A4a3te7/merge.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -0 /tmp/wj8A4a3te7/merge.a.vcf.gz /tmp/wj8A4a3te7/merge.b.vcf.gz /tmp/wj8A4a3te7/merge.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -0 /tmp/wj8A4a3te7/merge.a.vcf.gz /tmp/wj8A4a3te7/merge.b.vcf.gz /tmp/wj8A4a3te7/merge.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -0 /tmp/wj8A4a3te7/merge.a.bcf /tmp/wj8A4a3te7/merge.b.bcf /tmp/wj8A4a3te7/merge.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -0 /tmp/wj8A4a3te7/merge.a.bcf /tmp/wj8A4a3te7/merge.b.bcf /tmp/wj8A4a3te7/merge.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -m none /tmp/wj8A4a3te7/merge.2.a.vcf.gz /tmp/wj8A4a3te7/merge.2.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m none /tmp/wj8A4a3te7/merge.2.a.vcf.gz /tmp/wj8A4a3te7/merge.2.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -m none /tmp/wj8A4a3te7/merge.2.a.bcf /tmp/wj8A4a3te7/merge.2.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m none /tmp/wj8A4a3te7/merge.2.a.bcf /tmp/wj8A4a3te7/merge.2.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -m both /tmp/wj8A4a3te7/merge.2.a.vcf.gz /tmp/wj8A4a3te7/merge.2.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m both /tmp/wj8A4a3te7/merge.2.a.vcf.gz /tmp/wj8A4a3te7/merge.2.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -m both /tmp/wj8A4a3te7/merge.2.a.bcf /tmp/wj8A4a3te7/merge.2.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m both /tmp/wj8A4a3te7/merge.2.a.bcf /tmp/wj8A4a3te7/merge.2.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -m all /tmp/wj8A4a3te7/merge.2.a.vcf.gz /tmp/wj8A4a3te7/merge.2.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m all /tmp/wj8A4a3te7/merge.2.a.vcf.gz /tmp/wj8A4a3te7/merge.2.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -m all /tmp/wj8A4a3te7/merge.2.a.bcf /tmp/wj8A4a3te7/merge.2.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m all /tmp/wj8A4a3te7/merge.2.a.bcf /tmp/wj8A4a3te7/merge.2.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/wj8A4a3te7/merge.3.a.vcf.gz /tmp/wj8A4a3te7/merge.3.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/wj8A4a3te7/merge.3.a.vcf.gz /tmp/wj8A4a3te7/merge.3.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/wj8A4a3te7/merge.3.a.bcf /tmp/wj8A4a3te7/merge.3.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/wj8A4a3te7/merge.3.a.bcf /tmp/wj8A4a3te7/merge.3.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -m id /tmp/wj8A4a3te7/merge.4.a.vcf.gz /tmp/wj8A4a3te7/merge.4.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m id /tmp/wj8A4a3te7/merge.4.a.vcf.gz /tmp/wj8A4a3te7/merge.4.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -m id /tmp/wj8A4a3te7/merge.4.a.bcf /tmp/wj8A4a3te7/merge.4.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m id /tmp/wj8A4a3te7/merge.4.a.bcf /tmp/wj8A4a3te7/merge.4.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/wj8A4a3te7/gvcf.merge.1.vcf.gz /tmp/wj8A4a3te7/gvcf.merge.2.vcf.gz /tmp/wj8A4a3te7/gvcf.merge.3.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/wj8A4a3te7/gvcf.merge.1.vcf.gz /tmp/wj8A4a3te7/gvcf.merge.2.vcf.gz /tmp/wj8A4a3te7/gvcf.merge.3.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/wj8A4a3te7/gvcf.merge.1.bcf /tmp/wj8A4a3te7/gvcf.merge.2.bcf /tmp/wj8A4a3te7/gvcf.merge.3.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/wj8A4a3te7/gvcf.merge.1.bcf /tmp/wj8A4a3te7/gvcf.merge.2.bcf /tmp/wj8A4a3te7/gvcf.merge.3.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/wj8A4a3te7/merge.gvcf.2.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.2.b.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/wj8A4a3te7/merge.gvcf.2.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.2.b.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.2.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - -m both,* /tmp/wj8A4a3te7/merge.gvcf.2.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.2.b.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - -m both,* /tmp/wj8A4a3te7/merge.gvcf.2.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.2.b.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.2.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - -m both,** /tmp/wj8A4a3te7/merge.gvcf.2.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.2.b.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - -m both,** /tmp/wj8A4a3te7/merge.gvcf.2.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.2.b.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.2.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - -i SRC:join /tmp/wj8A4a3te7/merge.gvcf.3.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.3.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - -i SRC:join /tmp/wj8A4a3te7/merge.gvcf.3.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.3.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/wj8A4a3te7/merge.gvcf.4.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.4.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/wj8A4a3te7/merge.gvcf.4.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.4.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/wj8A4a3te7/merge.gvcf.4.a.bcf /tmp/wj8A4a3te7/merge.gvcf.4.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/wj8A4a3te7/merge.gvcf.4.a.bcf /tmp/wj8A4a3te7/merge.gvcf.4.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/wj8A4a3te7/merge.5.a.vcf.gz /tmp/wj8A4a3te7/merge.5.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/wj8A4a3te7/merge.5.a.vcf.gz /tmp/wj8A4a3te7/merge.5.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/wj8A4a3te7/merge.5.a.bcf /tmp/wj8A4a3te7/merge.5.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/wj8A4a3te7/merge.5.a.bcf /tmp/wj8A4a3te7/merge.5.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/wj8A4a3te7/merge.6.a.vcf.gz /tmp/wj8A4a3te7/merge.6.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/wj8A4a3te7/merge.6.a.vcf.gz /tmp/wj8A4a3te7/merge.6.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/wj8A4a3te7/merge.6.a.bcf /tmp/wj8A4a3te7/merge.6.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/wj8A4a3te7/merge.6.a.bcf /tmp/wj8A4a3te7/merge.6.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/wj8A4a3te7/merge.gvcf.7.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.7.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/wj8A4a3te7/merge.gvcf.7.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.7.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/wj8A4a3te7/merge.gvcf.7.a.bcf /tmp/wj8A4a3te7/merge.gvcf.7.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/wj8A4a3te7/merge.gvcf.7.a.bcf /tmp/wj8A4a3te7/merge.gvcf.7.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/wj8A4a3te7/merge.gvcf.8.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.8.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/wj8A4a3te7/merge.gvcf.8.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.8.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/wj8A4a3te7/merge.gvcf.8.a.bcf /tmp/wj8A4a3te7/merge.gvcf.8.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/wj8A4a3te7/merge.gvcf.8.a.bcf /tmp/wj8A4a3te7/merge.gvcf.8.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples /tmp/wj8A4a3te7/merge.7.a.vcf.gz /tmp/wj8A4a3te7/merge.7.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/wj8A4a3te7/merge.7.a.vcf.gz /tmp/wj8A4a3te7/merge.7.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples /tmp/wj8A4a3te7/merge.7.a.bcf /tmp/wj8A4a3te7/merge.7.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/wj8A4a3te7/merge.7.a.bcf /tmp/wj8A4a3te7/merge.7.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa /tmp/wj8A4a3te7/merge.gvcf.9a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9b.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9c.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9d.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa /tmp/wj8A4a3te7/merge.gvcf.9a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9b.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9c.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9d.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa /tmp/wj8A4a3te7/merge.gvcf.9a.bcf /tmp/wj8A4a3te7/merge.gvcf.9b.bcf /tmp/wj8A4a3te7/merge.gvcf.9c.bcf /tmp/wj8A4a3te7/merge.gvcf.9d.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa /tmp/wj8A4a3te7/merge.gvcf.9a.bcf /tmp/wj8A4a3te7/merge.gvcf.9b.bcf /tmp/wj8A4a3te7/merge.gvcf.9c.bcf /tmp/wj8A4a3te7/merge.gvcf.9d.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa -r 22:21-23 /tmp/wj8A4a3te7/merge.gvcf.9a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9b.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9c.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9d.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa -r 22:21-23 /tmp/wj8A4a3te7/merge.gvcf.9a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9b.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9c.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9d.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa -r 22:21-23 /tmp/wj8A4a3te7/merge.gvcf.9a.bcf /tmp/wj8A4a3te7/merge.gvcf.9b.bcf /tmp/wj8A4a3te7/merge.gvcf.9c.bcf /tmp/wj8A4a3te7/merge.gvcf.9d.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa -r 22:21-23 /tmp/wj8A4a3te7/merge.gvcf.9a.bcf /tmp/wj8A4a3te7/merge.gvcf.9b.bcf /tmp/wj8A4a3te7/merge.gvcf.9c.bcf /tmp/wj8A4a3te7/merge.gvcf.9d.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa /tmp/wj8A4a3te7/merge.gvcf.9a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9b.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9c.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9d.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9e.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa /tmp/wj8A4a3te7/merge.gvcf.9a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9b.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9c.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9d.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9e.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa /tmp/wj8A4a3te7/merge.gvcf.9a.bcf /tmp/wj8A4a3te7/merge.gvcf.9b.bcf /tmp/wj8A4a3te7/merge.gvcf.9c.bcf /tmp/wj8A4a3te7/merge.gvcf.9d.bcf /tmp/wj8A4a3te7/merge.gvcf.9e.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa /tmp/wj8A4a3te7/merge.gvcf.9a.bcf /tmp/wj8A4a3te7/merge.gvcf.9b.bcf /tmp/wj8A4a3te7/merge.gvcf.9c.bcf /tmp/wj8A4a3te7/merge.gvcf.9d.bcf /tmp/wj8A4a3te7/merge.gvcf.9e.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa -r 22:21-23 /tmp/wj8A4a3te7/merge.gvcf.9a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9b.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9c.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9d.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9e.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa -r 22:21-23 /tmp/wj8A4a3te7/merge.gvcf.9a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9b.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9c.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9d.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9e.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa -r 22:21-23 /tmp/wj8A4a3te7/merge.gvcf.9a.bcf /tmp/wj8A4a3te7/merge.gvcf.9b.bcf /tmp/wj8A4a3te7/merge.gvcf.9c.bcf /tmp/wj8A4a3te7/merge.gvcf.9d.bcf /tmp/wj8A4a3te7/merge.gvcf.9e.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa -r 22:21-23 /tmp/wj8A4a3te7/merge.gvcf.9a.bcf /tmp/wj8A4a3te7/merge.gvcf.9b.bcf /tmp/wj8A4a3te7/merge.gvcf.9c.bcf /tmp/wj8A4a3te7/merge.gvcf.9d.bcf /tmp/wj8A4a3te7/merge.gvcf.9e.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/wj8A4a3te7/merge.gvcf.10.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/wj8A4a3te7/merge.gvcf.10.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.10.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/wj8A4a3te7/merge.gvcf.10.a.bcf /tmp/wj8A4a3te7/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/wj8A4a3te7/merge.gvcf.10.a.bcf /tmp/wj8A4a3te7/merge.gvcf.10.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -m none /tmp/wj8A4a3te7/merge.gvcf.10.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m none /tmp/wj8A4a3te7/merge.gvcf.10.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.10.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -m none /tmp/wj8A4a3te7/merge.gvcf.10.a.bcf /tmp/wj8A4a3te7/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m none /tmp/wj8A4a3te7/merge.gvcf.10.a.bcf /tmp/wj8A4a3te7/merge.gvcf.10.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -g /build/reproducible-path/bcftools-1.21/test/merge.gvcf.10.fa /tmp/wj8A4a3te7/merge.gvcf.10.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -g /build/reproducible-path/bcftools-1.21/test/merge.gvcf.10.fa /tmp/wj8A4a3te7/merge.gvcf.10.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.10.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -g /build/reproducible-path/bcftools-1.21/test/merge.gvcf.10.fa /tmp/wj8A4a3te7/merge.gvcf.10.a.bcf /tmp/wj8A4a3te7/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -g /build/reproducible-path/bcftools-1.21/test/merge.gvcf.10.fa /tmp/wj8A4a3te7/merge.gvcf.10.a.bcf /tmp/wj8A4a3te7/merge.gvcf.10.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -g /build/reproducible-path/bcftools-1.21/test/merge.gvcf.10.fa -m none /tmp/wj8A4a3te7/merge.gvcf.10.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -g /build/reproducible-path/bcftools-1.21/test/merge.gvcf.10.fa -m none /tmp/wj8A4a3te7/merge.gvcf.10.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.10.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -g /build/reproducible-path/bcftools-1.21/test/merge.gvcf.10.fa -m none /tmp/wj8A4a3te7/merge.gvcf.10.a.bcf /tmp/wj8A4a3te7/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -g /build/reproducible-path/bcftools-1.21/test/merge.gvcf.10.fa -m none /tmp/wj8A4a3te7/merge.gvcf.10.a.bcf /tmp/wj8A4a3te7/merge.gvcf.10.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/wj8A4a3te7/merge.noidx.a.vcf.gz /tmp/wj8A4a3te7/merge.noidx.b.vcf.gz /tmp/wj8A4a3te7/merge.noidx.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/wj8A4a3te7/merge.noidx.a.vcf.gz /tmp/wj8A4a3te7/merge.noidx.b.vcf.gz /tmp/wj8A4a3te7/merge.noidx.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/wj8A4a3te7/merge.noidx.a.bcf /tmp/wj8A4a3te7/merge.noidx.b.bcf /tmp/wj8A4a3te7/merge.noidx.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/wj8A4a3te7/merge.noidx.a.bcf /tmp/wj8A4a3te7/merge.noidx.b.bcf /tmp/wj8A4a3te7/merge.noidx.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --no-index /build/reproducible-path/bcftools-1.21/test/merge.noidx.a.vcf /build/reproducible-path/bcftools-1.21/test/merge.noidx.b.vcf /build/reproducible-path/bcftools-1.21/test/merge.noidx.c.vcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --no-index /build/reproducible-path/bcftools-1.21/test/merge.noidx.a.vcf /build/reproducible-path/bcftools-1.21/test/merge.noidx.b.vcf /build/reproducible-path/bcftools-1.21/test/merge.noidx.c.vcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --no-index /tmp/wj8A4a3te7/merge.noidx.a.bcf /tmp/wj8A4a3te7/merge.noidx.b.bcf /tmp/wj8A4a3te7/merge.noidx.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --no-index /tmp/wj8A4a3te7/merge.noidx.a.bcf /tmp/wj8A4a3te7/merge.noidx.b.bcf /tmp/wj8A4a3te7/merge.noidx.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/wj8A4a3te7/merge.8.a.vcf.gz /tmp/wj8A4a3te7/merge.8.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/wj8A4a3te7/merge.8.a.vcf.gz /tmp/wj8A4a3te7/merge.8.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/wj8A4a3te7/merge.8.a.bcf /tmp/wj8A4a3te7/merge.8.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/wj8A4a3te7/merge.8.a.bcf /tmp/wj8A4a3te7/merge.8.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -i AN:sum,AC:sum /tmp/wj8A4a3te7/merge.8.a.vcf.gz /tmp/wj8A4a3te7/merge.8.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/wj8A4a3te7/merge.8.a.vcf.gz /tmp/wj8A4a3te7/merge.8.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -i AN:sum,AC:sum /tmp/wj8A4a3te7/merge.8.a.bcf /tmp/wj8A4a3te7/merge.8.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/wj8A4a3te7/merge.8.a.bcf /tmp/wj8A4a3te7/merge.8.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/wj8A4a3te7/merge.9.a.vcf.gz /tmp/wj8A4a3te7/merge.9.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/wj8A4a3te7/merge.9.a.vcf.gz /tmp/wj8A4a3te7/merge.9.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/wj8A4a3te7/merge.9.a.bcf /tmp/wj8A4a3te7/merge.9.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/wj8A4a3te7/merge.9.a.bcf /tmp/wj8A4a3te7/merge.9.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -i AN:sum,AC:sum /tmp/wj8A4a3te7/merge.9.a.vcf.gz /tmp/wj8A4a3te7/merge.9.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/wj8A4a3te7/merge.9.a.vcf.gz /tmp/wj8A4a3te7/merge.9.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -i AN:sum,AC:sum /tmp/wj8A4a3te7/merge.9.a.bcf /tmp/wj8A4a3te7/merge.9.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/wj8A4a3te7/merge.9.a.bcf /tmp/wj8A4a3te7/merge.9.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -m none /tmp/wj8A4a3te7/merge.10.a.vcf.gz /tmp/wj8A4a3te7/merge.10.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m none /tmp/wj8A4a3te7/merge.10.a.vcf.gz /tmp/wj8A4a3te7/merge.10.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -m none /tmp/wj8A4a3te7/merge.10.a.bcf /tmp/wj8A4a3te7/merge.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m none /tmp/wj8A4a3te7/merge.10.a.bcf /tmp/wj8A4a3te7/merge.10.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -m both /tmp/wj8A4a3te7/merge.10.a.vcf.gz /tmp/wj8A4a3te7/merge.10.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m both /tmp/wj8A4a3te7/merge.10.a.vcf.gz /tmp/wj8A4a3te7/merge.10.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -m both /tmp/wj8A4a3te7/merge.10.a.bcf /tmp/wj8A4a3te7/merge.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m both /tmp/wj8A4a3te7/merge.10.a.bcf /tmp/wj8A4a3te7/merge.10.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -m snp-ins-del /tmp/wj8A4a3te7/merge.10.a.vcf.gz /tmp/wj8A4a3te7/merge.10.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m snp-ins-del /tmp/wj8A4a3te7/merge.10.a.vcf.gz /tmp/wj8A4a3te7/merge.10.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -m snp-ins-del /tmp/wj8A4a3te7/merge.10.a.bcf /tmp/wj8A4a3te7/merge.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m snp-ins-del /tmp/wj8A4a3te7/merge.10.a.bcf /tmp/wj8A4a3te7/merge.10.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/wj8A4a3te7/merge.mrules.1.a.vcf.gz /tmp/wj8A4a3te7/merge.mrules.1.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/wj8A4a3te7/merge.mrules.1.a.vcf.gz /tmp/wj8A4a3te7/merge.mrules.1.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/wj8A4a3te7/merge.mrules.1.a.bcf /tmp/wj8A4a3te7/merge.mrules.1.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/wj8A4a3te7/merge.mrules.1.a.bcf /tmp/wj8A4a3te7/merge.mrules.1.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - -M AD:.,PL:. /tmp/wj8A4a3te7/merge.mrules.1.a.vcf.gz /tmp/wj8A4a3te7/merge.mrules.1.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - -M AD:.,PL:. /tmp/wj8A4a3te7/merge.mrules.1.a.vcf.gz /tmp/wj8A4a3te7/merge.mrules.1.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - -M AD:.,PL:. /tmp/wj8A4a3te7/merge.mrules.1.a.bcf /tmp/wj8A4a3te7/merge.mrules.1.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - -M AD:.,PL:. /tmp/wj8A4a3te7/merge.mrules.1.a.bcf /tmp/wj8A4a3te7/merge.mrules.1.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/wj8A4a3te7/merge.gvcf.5.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.5.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/wj8A4a3te7/merge.gvcf.5.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.5.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/wj8A4a3te7/merge.gvcf.5.a.bcf /tmp/wj8A4a3te7/merge.gvcf.5.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/wj8A4a3te7/merge.gvcf.5.a.bcf /tmp/wj8A4a3te7/merge.gvcf.5.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - --merge none /tmp/wj8A4a3te7/merge.gvcf.5.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.5.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - --merge none /tmp/wj8A4a3te7/merge.gvcf.5.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.5.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - --merge none /tmp/wj8A4a3te7/merge.gvcf.5.a.bcf /tmp/wj8A4a3te7/merge.gvcf.5.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - --merge none /tmp/wj8A4a3te7/merge.gvcf.5.a.bcf /tmp/wj8A4a3te7/merge.gvcf.5.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/wj8A4a3te7/merge.gvcf.11.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.11.b.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.11.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/wj8A4a3te7/merge.gvcf.11.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.11.b.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.11.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/wj8A4a3te7/merge.gvcf.11.a.bcf /tmp/wj8A4a3te7/merge.gvcf.11.b.bcf /tmp/wj8A4a3te7/merge.gvcf.11.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/wj8A4a3te7/merge.gvcf.11.a.bcf /tmp/wj8A4a3te7/merge.gvcf.11.b.bcf /tmp/wj8A4a3te7/merge.gvcf.11.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided,_conflicting_interpretations"' /tmp/wj8A4a3te7/query.string.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.string.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided,_conflicting_interpretations"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" || CLNREVSTAT="_conflicting_interpretations"' /tmp/wj8A4a3te7/query.string.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.string.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" || CLNREVSTAT="_conflicting_interpretations"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" && CLNREVSTAT="_conflicting_interpretations"' /tmp/wj8A4a3te7/query.string.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.string.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" && CLNREVSTAT="_conflicting_interpretations"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%INFO/STR\n' -i'INFO/STR=@/build/reproducible-path/bcftools-1.21/test/query.string.2.1.txt' /tmp/wj8A4a3te7/query.string.2.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.string.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%INFO/STR\n' -i'INFO/STR=@/build/reproducible-path/bcftools-1.21/test/query.string.2.1.txt' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS[\t%STR]\n' -i'FMT/STR=@/build/reproducible-path/bcftools-1.21/test/query.string.2.2.txt' /tmp/wj8A4a3te7/query.string.2.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.string.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS[\t%STR]\n' -i'FMT/STR=@/build/reproducible-path/bcftools-1.21/test/query.string.2.2.txt' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' /tmp/wj8A4a3te7/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f '%RSX\t%VKX\n' /tmp/wj8A4a3te7/query.variantkey.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.variantkey.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f '%RSX\t%VKX\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%XRI\n' -i'XRI[*]>1111' /tmp/wj8A4a3te7/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%XRI\n' -i'XRI[*]>1111' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' /tmp/wj8A4a3te7/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' /tmp/wj8A4a3te7/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' /tmp/wj8A4a3te7/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' /tmp/wj8A4a3te7/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' /tmp/wj8A4a3te7/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' /tmp/wj8A4a3te7/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' /tmp/wj8A4a3te7/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' /tmp/wj8A4a3te7/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' /tmp/wj8A4a3te7/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' /tmp/wj8A4a3te7/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' /tmp/wj8A4a3te7/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' /tmp/wj8A4a3te7/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' /tmp/wj8A4a3te7/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' /tmp/wj8A4a3te7/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' /tmp/wj8A4a3te7/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'I8=%I8 I16=%I16 I32=%I32 IF=%IF IA8=%IA8 IA16=%IA16 IA32=%IA32 IAF=%IAF IA8=%IA8{1} IA16=%IA16{1} IA32=%IA32{1} IAF=%IAF{1} [ %F8:%F16:%F32:%FF]\n' /tmp/wj8A4a3te7/view.vectors.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.vectors.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'I8=%I8 I16=%I16 I32=%I32 IF=%IF IA8=%IA8 IA16=%IA16 IA32=%IA32 IAF=%IAF IA8=%IA8{1} IA16=%IA16{1} IA32=%IA32{1} IAF=%IAF{1} [ %F8:%F16:%F32:%FF]\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' /tmp/wj8A4a3te7/query.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' /tmp/wj8A4a3te7/query.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' /tmp/wj8A4a3te7/query.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' /tmp/wj8A4a3te7/query.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' /tmp/wj8A4a3te7/query.2.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'IINT="."' -f'%POS %IINT\n' /tmp/wj8A4a3te7/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'IINT!="."' -f'%POS %IINT\n' /tmp/wj8A4a3te7/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -e'IINT!="."' -f'%POS %IINT\n' /tmp/wj8A4a3te7/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -e'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -e'IINT="."' -f'%POS %IINT\n' /tmp/wj8A4a3te7/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -e'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' /tmp/wj8A4a3te7/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' /tmp/wj8A4a3te7/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' /tmp/wj8A4a3te7/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' /tmp/wj8A4a3te7/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' /tmp/wj8A4a3te7/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' /tmp/wj8A4a3te7/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' /tmp/wj8A4a3te7/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' /tmp/wj8A4a3te7/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' /tmp/wj8A4a3te7/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER="A"' -f'%POS %FILTER\n' /tmp/wj8A4a3te7/filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/filter.11.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER="A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER!="A"' -f'%POS %FILTER\n' /tmp/wj8A4a3te7/filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/filter.11.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER!="A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER~"A"' -f'%POS %FILTER\n' /tmp/wj8A4a3te7/filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/filter.11.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER~"A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n' /tmp/wj8A4a3te7/filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/filter.11.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%LINE' /tmp/wj8A4a3te7/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%LINE' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' /tmp/wj8A4a3te7/query.filter-type.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter-type.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' /tmp/wj8A4a3te7/query.filter-type.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter-type.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' /tmp/wj8A4a3te7/query.filter-type.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter-type.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' /tmp/wj8A4a3te7/query.filter-type.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter-type.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'INFO/TYPE="xxx"' /tmp/wj8A4a3te7/query.filter-type.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter-type.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'INFO/TYPE="xxx"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -i'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001' /tmp/wj8A4a3te7/filter-missing-floats.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/filter-missing-floats.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -i'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -e'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001' /tmp/wj8A4a3te7/filter-missing-floats.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/filter-missing-floats.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -e'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' /tmp/wj8A4a3te7/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' /tmp/wj8A4a3te7/query.filter.2.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' /tmp/wj8A4a3te7/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' /tmp/wj8A4a3te7/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' /tmp/wj8A4a3te7/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' /tmp/wj8A4a3te7/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' /tmp/wj8A4a3te7/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' /tmp/wj8A4a3te7/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' /tmp/wj8A4a3te7/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' /tmp/wj8A4a3te7/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' /tmp/wj8A4a3te7/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' /tmp/wj8A4a3te7/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' /tmp/wj8A4a3te7/filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/filter.5.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' /tmp/wj8A4a3te7/filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/filter.5.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' /tmp/wj8A4a3te7/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' /tmp/wj8A4a3te7/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' /tmp/wj8A4a3te7/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' /tmp/wj8A4a3te7/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' /tmp/wj8A4a3te7/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 & FMT/GQ=589' /tmp/wj8A4a3te7/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 & FMT/GQ=589' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' /tmp/wj8A4a3te7/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' /tmp/wj8A4a3te7/query.filter.3.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.3.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"' /tmp/wj8A4a3te7/query.filter.3.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.3.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' /tmp/wj8A4a3te7/query.filter.3.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.3.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %AD\n]\n' -i'AD[:0]+AD[:1] > 12' /tmp/wj8A4a3te7/filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/filter.5.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %AD\n]\n' -i'AD[:0]+AD[:1] > 12' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' /tmp/wj8A4a3te7/query.filter.4.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.4.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i 'ID=@/build/reproducible-path/bcftools-1.21/test/query.56.out' /tmp/wj8A4a3te7/view.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i 'ID=@/build/reproducible-path/bcftools-1.21/test/query.56.out' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD)>0.01' /tmp/wj8A4a3te7/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.5.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD)>0.01' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD[:0],FMT/AD[:1])>0.01' /tmp/wj8A4a3te7/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.5.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD[:0],FMT/AD[:1])>0.01' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%AD\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01' /tmp/wj8A4a3te7/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.5.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%AD\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[GT]==10' /tmp/wj8A4a3te7/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.5.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[GT]==10' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'sSUM(FMT/AD[GT])==210' /tmp/wj8A4a3te7/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.5.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'sSUM(FMT/AD[GT])==210' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[0:GT]==30' /tmp/wj8A4a3te7/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.5.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[0:GT]==30' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TF[:GT]==1 && FMT/TF[:GT]==2' /tmp/wj8A4a3te7/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.gtidx.1.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TF[:GT]==1 && FMT/TF[:GT]==2' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TI[:GT]==1 && FMT/TF[:GT]==2' /tmp/wj8A4a3te7/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.gtidx.1.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TI[:GT]==1 && FMT/TF[:GT]==2' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TS[:GT]=="BB" && FMT/TS[:GT]=="CC"' /tmp/wj8A4a3te7/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.gtidx.1.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TS[:GT]=="BB" && FMT/TS[:GT]=="CC"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TC[:GT]=="B" && FMT/TC[:GT]=="C"' /tmp/wj8A4a3te7/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.gtidx.1.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TC[:GT]=="B" && FMT/TC[:GT]=="C"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%GT %TI\n]' -i'FMT/TI[:GT]=="."' /tmp/wj8A4a3te7/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.gtidx.1.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%GT %TI\n]' -i'FMT/TI[:GT]=="."' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS\n' -i'CHROM="4"' /tmp/wj8A4a3te7/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS\n' -i'CHROM="4"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%TAG1\n' -i'(TAG1>=-129 && TAG1<=-120) || (TAG1>=-32769 && TAG1<=-32760)' /tmp/wj8A4a3te7/query.negative.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.negative.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%TAG1\n' -i'(TAG1>=-129 && TAG1<=-120) || (TAG1>=-32769 && TAG1<=-32760)' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%TAGV1\n' -i'(TAGV1>=-129 && TAGV1<=-120) || (TAGV1>=-32769 && TAGV1<=-32760)' /tmp/wj8A4a3te7/query.negative.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.negative.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%TAGV1\n' -i'(TAGV1>=-129 && TAGV1<=-120) || (TAGV1>=-32769 && TAGV1<=-32760)' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%TAG2\n' -i'(TAG2>=-129 && TAG2<=-120) || (TAG2>=-32769 && TAG2<=-32760)' /tmp/wj8A4a3te7/query.negative.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.negative.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%TAG2\n' -i'(TAG2>=-129 && TAG2<=-120) || (TAG2>=-32769 && TAG2<=-32760)' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%TAGV2\n' -i'(TAGV2>=-129 && TAGV2<=-120) || (TAGV2>=-32769 && TAGV2<=-32760)' /tmp/wj8A4a3te7/query.negative.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.negative.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%TAGV2\n' -i'(TAGV2>=-129 && TAGV2<=-120) || (TAGV2>=-32769 && TAGV2<=-32760)' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GQ\n]' -i'N_PASS(GQ<20)==1' /tmp/wj8A4a3te7/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GQ\n]' -i'N_PASS(GQ<20)==1' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")==1' /tmp/wj8A4a3te7/query.filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.11.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")==1' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")!=1' /tmp/wj8A4a3te7/query.filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.11.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")!=1' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")==1' /tmp/wj8A4a3te7/query.filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.11.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")==1' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")!=1' /tmp/wj8A4a3te7/query.filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.11.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")!=1' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM\t%POS\t%INFO\t%FORMAT\n' -s D,C /tmp/wj8A4a3te7/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM\t%POS\t%INFO\t%FORMAT\n' -s D,C .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\n' -i'POS==16777217 || POS==33554432 || POS=118673904' /tmp/wj8A4a3te7/query.filter.6.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.6.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\n' -i'POS==16777217 || POS==33554432 || POS=118673904' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(II)==6' /tmp/wj8A4a3te7/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(II)==6' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(FORMAT/FI)==7' /tmp/wj8A4a3te7/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(FORMAT/FI)==7' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(II)==2' /tmp/wj8A4a3te7/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(II)==2' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(FORMAT/FI)==1.75' /tmp/wj8A4a3te7/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(FORMAT/FI)==1.75' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(II)==2' /tmp/wj8A4a3te7/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(II)==2' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(FORMAT/FI)==1.75' /tmp/wj8A4a3te7/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(FORMAT/FI)==1.75' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(II)==2' /tmp/wj8A4a3te7/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(II)==2' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(FORMAT/FI)==1.5' /tmp/wj8A4a3te7/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(FORMAT/FI)==1.5' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'%ILEN==1' /tmp/wj8A4a3te7/query.filter.8.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.8.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'%ILEN==1' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'ILEN==1' /tmp/wj8A4a3te7/query.filter.8.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.8.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'ILEN==1' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] < FMT/AD[:1]' /tmp/wj8A4a3te7/query.filter.9.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.9.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] < FMT/AD[:1]' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] > FMT/AD[:1]' /tmp/wj8A4a3te7/query.filter.9.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.9.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] > FMT/AD[:1]' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[ %AD\n]' -i'AD[:1] / sum(AD[*]) > 0.5' /tmp/wj8A4a3te7/query.filter.13.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.13.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[ %AD\n]' -i'AD[:1] / sum(AD[*]) > 0.5' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %NUM_TAG\n' -i'COUNT(INFO/NUM_TAG)=2' /tmp/wj8A4a3te7/query.filter.10.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.10.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %NUM_TAG\n' -i'COUNT(INFO/NUM_TAG)=2' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2' /tmp/wj8A4a3te7/query.filter.10.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.10.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM:%POS\t%N_PASS(GT="alt" & GQ>110)\t[\t%GT]\t[\t%GQ]\n' /tmp/wj8A4a3te7/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM:%POS\t%N_PASS(GT="alt" & GQ>110)\t[\t%GT]\t[\t%GQ]\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 1,3,0 /tmp/wj8A4a3te7/query.filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.12.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 1,3,0 .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 0,1,3 /tmp/wj8A4a3te7/query.filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.12.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 0,1,3 .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f "[%SAMPLE %GT\n]" -S /build/reproducible-path/bcftools-1.21/test/query.smpl.11.txt /tmp/wj8A4a3te7/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.smpl.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f "[%SAMPLE %GT\n]" -S /build/reproducible-path/bcftools-1.21/test/query.smpl.11.txt .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -l -S /build/reproducible-path/bcftools-1.21/test/query.smpl.11.txt /tmp/wj8A4a3te7/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.smpl.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -l -S /build/reproducible-path/bcftools-1.21/test/query.smpl.11.txt .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f "[%SAMPLE %GT\n]" -S ^/build/reproducible-path/bcftools-1.21/test/query.smpl.11.txt /tmp/wj8A4a3te7/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.smpl.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f "[%SAMPLE %GT\n]" -S ^/build/reproducible-path/bcftools-1.21/test/query.smpl.11.txt .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -l -S ^/build/reproducible-path/bcftools-1.21/test/query.smpl.11.txt /tmp/wj8A4a3te7/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.smpl.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -l -S ^/build/reproducible-path/bcftools-1.21/test/query.smpl.11.txt .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f "[%SAMPLE %GT\n]" -S /build/reproducible-path/bcftools-1.21/test/query.smpl.txt /tmp/wj8A4a3te7/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.smpl.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f "[%SAMPLE %GT\n]" -S /build/reproducible-path/bcftools-1.21/test/query.smpl.txt .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -l -S /build/reproducible-path/bcftools-1.21/test/query.smpl.txt /tmp/wj8A4a3te7/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.smpl.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -l -S /build/reproducible-path/bcftools-1.21/test/query.smpl.txt .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID~"s12"' /tmp/wj8A4a3te7/query.filter.id.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.id.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID~"s12"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID="rs123"' /tmp/wj8A4a3te7/query.filter.id.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.id.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID="rs123"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID="abc"' /tmp/wj8A4a3te7/query.filter.id.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.id.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID="abc"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID=@/build/reproducible-path/bcftools-1.21/test/query.filter.id.3.txt' /tmp/wj8A4a3te7/query.filter.id.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.id.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID=@/build/reproducible-path/bcftools-1.21/test/query.filter.id.3.txt' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID!="abc"' /tmp/wj8A4a3te7/query.filter.id.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.id.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID!="abc"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID!=@/build/reproducible-path/bcftools-1.21/test/query.filter.id.3.txt' /tmp/wj8A4a3te7/query.filter.id.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.id.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID!=@/build/reproducible-path/bcftools-1.21/test/query.filter.id.3.txt' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER="A"' -f'%FILTER\n' /tmp/wj8A4a3te7/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/filter.12.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER="A"' -f'%FILTER\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER~"A"' -f'%FILTER\n' /tmp/wj8A4a3te7/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/filter.12.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER~"A"' -f'%FILTER\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER="A;B"' -f'%FILTER\n' /tmp/wj8A4a3te7/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/filter.12.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER="A;B"' -f'%FILTER\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER!="A;B"' -f'%FILTER\n' /tmp/wj8A4a3te7/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/filter.12.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER!="A;B"' -f'%FILTER\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER~"A;B"' -f'%FILTER\n' /tmp/wj8A4a3te7/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/filter.12.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER~"A;B"' -f'%FILTER\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER!~"A;B"' -f'%FILTER\n' /tmp/wj8A4a3te7/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/filter.12.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER!~"A;B"' -f'%FILTER\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'DP%10==2' -f'[ %DP]\n' /tmp/wj8A4a3te7/filter.10.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/filter.10.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'DP%10==2' -f'[ %DP]\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'REF="N"' -f'%CHROM %POS %REF %ALT %QUAL\n' /tmp/wj8A4a3te7/filter.13.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/filter.13.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'REF="N"' -f'%CHROM %POS %REF %ALT %QUAL\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -H -f'[%CHROM %POS %SAMPLE %DP %GT\n]' /tmp/wj8A4a3te7/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.header.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -H -f'[%CHROM %POS %SAMPLE %DP %GT\n]' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -H -f'[%CHROM %POS %SAMPLE %DP %GT\t]\n' /tmp/wj8A4a3te7/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.header.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -H -f'[%CHROM %POS %SAMPLE %DP %GT\t]\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]\n' /tmp/wj8A4a3te7/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.header.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]' /tmp/wj8A4a3te7/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.header.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]\n' /tmp/wj8A4a3te7/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.header.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]' /tmp/wj8A4a3te7/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.header.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -HH -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]' /tmp/wj8A4a3te7/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.header.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -HH -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%SAMPLE %DP\n]' -i'DP=1 || DP=2' /tmp/wj8A4a3te7/query.filter-or.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter-or.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%SAMPLE %DP\n]' -i'DP=1 || DP=2' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%SAMPLE %DP\n]' -i'DP=1 | DP=2' /tmp/wj8A4a3te7/query.filter-or.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter-or.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%SAMPLE %DP\n]' -i'DP=1 | DP=2' .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/wj8A4a3te7/norm.sort.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/wj8A4a3te7/norm.sort.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - -S lex /tmp/wj8A4a3te7/norm.sort.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - -S lex /tmp/wj8A4a3te7/norm.sort.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +both /tmp/wj8A4a3te7/norm.join-missing-ploidy.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +both /tmp/wj8A4a3te7/norm.join-missing-ploidy.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - --multi-overlaps . /tmp/wj8A4a3te7/norm.split.5.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - --multi-overlaps . /tmp/wj8A4a3te7/norm.split.5.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version /tmp/wj8A4a3te7/norm.symbolic.3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.symbolic.3.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version /tmp/wj8A4a3te7/norm.symbolic.3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.symbolic.3.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -cx /tmp/wj8A4a3te7/norm.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -cx /tmp/wj8A4a3te7/norm.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- /tmp/wj8A4a3te7/norm.split.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- /tmp/wj8A4a3te7/norm.split.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- /tmp/wj8A4a3te7/norm.split.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- /tmp/wj8A4a3te7/norm.split.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- --force /tmp/wj8A4a3te7/norm.split.3.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- --force /tmp/wj8A4a3te7/norm.split.3.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- /tmp/wj8A4a3te7/norm.split.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- /tmp/wj8A4a3te7/norm.split.4.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- --keep-sum AD /tmp/wj8A4a3te7/norm.split.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- --keep-sum AD /tmp/wj8A4a3te7/norm.split.4.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- /tmp/wj8A4a3te7/norm.split.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- /tmp/wj8A4a3te7/norm.split.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m+ /tmp/wj8A4a3te7/norm.merge.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m+ /tmp/wj8A4a3te7/norm.merge.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m+ /tmp/wj8A4a3te7/norm.merge.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m+ /tmp/wj8A4a3te7/norm.merge.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m+ /tmp/wj8A4a3te7/norm.merge.3.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m+ /tmp/wj8A4a3te7/norm.merge.3.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m+ -s /tmp/wj8A4a3te7/norm.merge.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m+ -s /tmp/wj8A4a3te7/norm.merge.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -Nc s /tmp/wj8A4a3te7/norm.setref.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -Nc s /tmp/wj8A4a3te7/norm.setref.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version /tmp/wj8A4a3te7/norm.telomere.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version /tmp/wj8A4a3te7/norm.telomere.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d snps /tmp/wj8A4a3te7/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d snps /tmp/wj8A4a3te7/norm.rmdup.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d indels /tmp/wj8A4a3te7/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d indels /tmp/wj8A4a3te7/norm.rmdup.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d both /tmp/wj8A4a3te7/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d both /tmp/wj8A4a3te7/norm.rmdup.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d all /tmp/wj8A4a3te7/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d all /tmp/wj8A4a3te7/norm.rmdup.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d none /tmp/wj8A4a3te7/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d none /tmp/wj8A4a3te7/norm.rmdup.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d exact /tmp/wj8A4a3te7/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d exact /tmp/wj8A4a3te7/norm.rmdup.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d none /tmp/wj8A4a3te7/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d none /tmp/wj8A4a3te7/norm.rmdup.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d exact /tmp/wj8A4a3te7/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d exact /tmp/wj8A4a3te7/norm.rmdup.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d indels /tmp/wj8A4a3te7/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d indels /tmp/wj8A4a3te7/norm.rmdup.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d any /tmp/wj8A4a3te7/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d any /tmp/wj8A4a3te7/norm.rmdup.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d both /tmp/wj8A4a3te7/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d both /tmp/wj8A4a3te7/norm.rmdup.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d snps /tmp/wj8A4a3te7/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d snps /tmp/wj8A4a3te7/norm.rmdup.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d exact /tmp/wj8A4a3te7/norm.rmdup.3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.rmdup.3.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d exact /tmp/wj8A4a3te7/norm.rmdup.3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.rmdup.3.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d all /tmp/wj8A4a3te7/norm.rmdup.3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.rmdup.3.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d all /tmp/wj8A4a3te7/norm.rmdup.3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.rmdup.3.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -c s -a /tmp/wj8A4a3te7/norm.2.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.2.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -c s -a /tmp/wj8A4a3te7/norm.2.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.2.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -c s /tmp/wj8A4a3te7/norm.iupac.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.iupac.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -c s /tmp/wj8A4a3te7/norm.iupac.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.iupac.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -c s /tmp/wj8A4a3te7/norm.3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.3.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -c s /tmp/wj8A4a3te7/norm.3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.3.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -c s -i'alt="N"' /tmp/wj8A4a3te7/norm.3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.3.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -c s -i'alt="N"' /tmp/wj8A4a3te7/norm.3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.3.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -a --old-rec-tag OLD_REC /tmp/wj8A4a3te7/atomize.split.1.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any --force .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -a --old-rec-tag OLD_REC /tmp/wj8A4a3te7/atomize.split.1.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any --force -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any --old-rec-tag OLD_REC --force /tmp/wj8A4a3te7/atomize.split.1.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -a .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any --old-rec-tag OLD_REC --force /tmp/wj8A4a3te7/atomize.split.1.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -a -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any --old-rec-tag OLD_REC --force -a /tmp/wj8A4a3te7/atomize.split.1.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any --old-rec-tag OLD_REC --force -a /tmp/wj8A4a3te7/atomize.split.1.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/wj8A4a3te7/atomize.split.1.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/wj8A4a3te7/atomize.split.1.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/wj8A4a3te7/atomize.split.1.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/wj8A4a3te7/atomize.split.1.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/wj8A4a3te7/atomize.split.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/wj8A4a3te7/atomize.split.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/wj8A4a3te7/atomize.split.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/wj8A4a3te7/atomize.split.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . /tmp/wj8A4a3te7/atomize.split.3.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . /tmp/wj8A4a3te7/atomize.split.3.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/wj8A4a3te7/atomize.split.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/wj8A4a3te7/atomize.split.4.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC -i 'ILEN=0' /tmp/wj8A4a3te7/atomize.split.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC -i 'ILEN=0' /tmp/wj8A4a3te7/atomize.split.4.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --old-rec-tag OLD_REC --atom-overlaps . /tmp/wj8A4a3te7/atomize.split.5.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --old-rec-tag OLD_REC --atom-overlaps . /tmp/wj8A4a3te7/atomize.split.5.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/wj8A4a3te7/atomize.split.5.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/wj8A4a3te7/atomize.split.5.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +both /tmp/wj8A4a3te7/norm.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +both /tmp/wj8A4a3te7/norm.4.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +any /tmp/wj8A4a3te7/norm.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +any /tmp/wj8A4a3te7/norm.4.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - --multi-overlaps 0 /tmp/wj8A4a3te7/norm.5.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - --multi-overlaps 0 /tmp/wj8A4a3te7/norm.5.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - --multi-overlaps . /tmp/wj8A4a3te7/norm.5.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - --multi-overlaps . /tmp/wj8A4a3te7/norm.5.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any /tmp/wj8A4a3te7/norm.m-any.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any /tmp/wj8A4a3te7/norm.m-any.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any /tmp/wj8A4a3te7/norm.phased-split.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any /tmp/wj8A4a3te7/norm.phased-split.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +any /tmp/wj8A4a3te7/norm.phased-join.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +any /tmp/wj8A4a3te7/norm.phased-join.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI /tmp/wj8A4a3te7/norm.symbolic.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.symbolic.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI /tmp/wj8A4a3te7/norm.symbolic.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.symbolic.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI /tmp/wj8A4a3te7/norm.symbolic.2.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.symbolic.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI /tmp/wj8A4a3te7/norm.symbolic.2.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.symbolic.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI /tmp/wj8A4a3te7/norm.right-align.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.right-align.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI /tmp/wj8A4a3te7/norm.right-align.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.right-align.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI -g /build/reproducible-path/bcftools-1.21/test/norm.right-align.gff /tmp/wj8A4a3te7/norm.right-align.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.right-align.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI -g /build/reproducible-path/bcftools-1.21/test/norm.right-align.gff /tmp/wj8A4a3te7/norm.right-align.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.right-align.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI -a -m -any /tmp/wj8A4a3te7/norm.atom-split-norm.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.atom-split-norm.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI -a -m -any /tmp/wj8A4a3te7/norm.atom-split-norm.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.atom-split-norm.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any /tmp/wj8A4a3te7/norm.string-tags.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any /tmp/wj8A4a3te7/norm.string-tags.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/wj8A4a3te7/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +both .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/wj8A4a3te7/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +both -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/wj8A4a3te7/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +indels .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/wj8A4a3te7/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +indels -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/wj8A4a3te7/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +snps .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/wj8A4a3te7/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +snps -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/wj8A4a3te7/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +snps .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/wj8A4a3te7/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +snps -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/wj8A4a3te7/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +any .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/wj8A4a3te7/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +any -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - -i 'type="snp"' /tmp/wj8A4a3te7/norm.split.merge.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - -i 'type="snp"' /tmp/wj8A4a3te7/norm.split.merge.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +any /tmp/wj8A4a3te7/norm.merge.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +any /tmp/wj8A4a3te7/norm.merge.4.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +both /tmp/wj8A4a3te7/norm.merge.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +both /tmp/wj8A4a3te7/norm.merge.4.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -i 'INFO/TAG=@/build/reproducible-path/bcftools-1.21/test/filter.string.1.txt' /tmp/wj8A4a3te7/filter.string.1.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -i 'INFO/TAG=@/build/reproducible-path/bcftools-1.21/test/filter.string.1.txt' /tmp/wj8A4a3te7/filter.string.1.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -i 'FMT/TAG=@/build/reproducible-path/bcftools-1.21/test/filter.string.1.txt' /tmp/wj8A4a3te7/filter.string.1.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -i 'FMT/TAG=@/build/reproducible-path/bcftools-1.21/test/filter.string.1.txt' /tmp/wj8A4a3te7/filter.string.1.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -HA /tmp/wj8A4a3te7/merge.gvcf.2.a.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -HAA /tmp/wj8A4a3te7/merge.gvcf.2.a.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r 1 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r 1 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r 1:1-2 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r 1:1-2 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r 1:1,1:2 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r 1:1,1:2 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r 1:1-1 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r 1:1-1 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r {1:1} .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r {1:1} | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r {1:1}:1-2 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r {1:1}:1-2 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r {1:1}:1,{1:1}:2 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r {1:1}:1,{1:1}:2 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r {1:1}:1-1 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r {1:1}:1-1 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r {1:1-1} .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r {1:1-1} | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r {1:1-1}:1-2 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r {1:1-1}:1-2 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r {1:1-1}:1,{1:1-1}:2 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r {1:1-1}:1,{1:1-1}:2 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r {1:1-1}:1-1 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r {1:1-1}:1-1 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r {1:1-1}-2 .. ok, expected non-zero status test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r {1:1-1}-2 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok, expected non-zero status test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -aUc1 -C1 -s NA00002 -v snps /tmp/wj8A4a3te7/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/wj8A4a3te7/view.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -f PASS -Xks NA00003 /tmp/wj8A4a3te7/view.vcf.gz -r20,Y .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -f PASS -Xks NA00003 /tmp/wj8A4a3te7/view.vcf.gz -r20,Y | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -xs NA00003 /tmp/wj8A4a3te7/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -xs NA00003 /tmp/wj8A4a3te7/view.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/wj8A4a3te7/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/wj8A4a3te7/view.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -p /tmp/wj8A4a3te7/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -p /tmp/wj8A4a3te7/view.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -P /tmp/wj8A4a3te7/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -P /tmp/wj8A4a3te7/view.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -hm2 -M2 -q0.3 -Q0.7 /tmp/wj8A4a3te7/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/wj8A4a3te7/view.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -Hu /tmp/wj8A4a3te7/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -GVsnps /tmp/wj8A4a3te7/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -GVsnps /tmp/wj8A4a3te7/view.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -ne 'INDEL=1 || PV4[0]<0.006' /tmp/wj8A4a3te7/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/wj8A4a3te7/view.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -s ^NA00003 /tmp/wj8A4a3te7/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -s ^NA00003 /tmp/wj8A4a3te7/view.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/wj8A4a3te7/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.omitgenotypes.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -G /tmp/wj8A4a3te7/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -G /tmp/wj8A4a3te7/view.omitgenotypes.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -HG /tmp/wj8A4a3te7/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -a /tmp/wj8A4a3te7/many.alleles.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -a /tmp/wj8A4a3te7/many.alleles.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -asA /tmp/wj8A4a3te7/view.vectors.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -asA /tmp/wj8A4a3te7/view.vectors.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -asB /tmp/wj8A4a3te7/view.vectors.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -asB /tmp/wj8A4a3te7/view.vectors.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -asA /tmp/wj8A4a3te7/view.vectors.2.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -asA /tmp/wj8A4a3te7/view.vectors.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -i'FMT/FGS[*:0]="AAAAAA"' /tmp/wj8A4a3te7/view.filter.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -i'FMT/FGS[*:2]="C"' /tmp/wj8A4a3te7/view.filter.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -i'FMT/FGS[*:4]="EE"' /tmp/wj8A4a3te7/view.filter.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -i'FMT/FRS[*:1]="BB"' /tmp/wj8A4a3te7/view.filter.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -i'TXT0="text"' /tmp/wj8A4a3te7/view.filter.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -T /build/reproducible-path/bcftools-1.21/test/view.chrs.tab /tmp/wj8A4a3te7/view.chrs.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -T /build/reproducible-path/bcftools-1.21/test/view.chrs.tab /tmp/wj8A4a3te7/view.chrs.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -i 'POS>=3062917' /tmp/wj8A4a3te7/filter.2.vcf.gz 1:3062917-3157410 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -i 'POS>=3062917' /tmp/wj8A4a3te7/filter.2.vcf.gz 1:3062917-3157410 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -r 1:10,1:12,1:10 /tmp/wj8A4a3te7/idx.1.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -r 1:1172777-1172804,1:1172806-1172808 /tmp/wj8A4a3te7/idx.2.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -R /build/reproducible-path/bcftools-1.21/test/idx.2.bed /tmp/wj8A4a3te7/idx.2.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -R /build/reproducible-path/bcftools-1.21/test/idx.3.bed /tmp/wj8A4a3te7/idx.3.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -R /build/reproducible-path/bcftools-1.21/test/idx.4.bed /tmp/wj8A4a3te7/idx.4.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -Ht 2 /tmp/wj8A4a3te7/view-t.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -Ht 3 /tmp/wj8A4a3te7/view-t.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 0 /tmp/wj8A4a3te7/overlap.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 1 /tmp/wj8A4a3te7/overlap.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 2 /tmp/wj8A4a3te7/overlap.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 0 /tmp/wj8A4a3te7/overlap.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 1 /tmp/wj8A4a3te7/overlap.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 2 /tmp/wj8A4a3te7/overlap.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 0 /tmp/wj8A4a3te7/overlap.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 1 /tmp/wj8A4a3te7/overlap.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 2 /tmp/wj8A4a3te7/overlap.vcf.gz .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.21/bcftools view /build/reproducible-path/bcftools-1.21/test/view64bit.1.vcf -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.21/bcftools view /build/reproducible-path/bcftools-1.21/test/view64bit.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.21/bcftools view /build/reproducible-path/bcftools-1.21/test/view64bit.1.vcf -Ou | /build/reproducible-path/bcftools-1.21/bcftools view -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.21/bcftools view /build/reproducible-path/bcftools-1.21/test/view64bit.2.vcf -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.21/bcftools view /build/reproducible-path/bcftools-1.21/test/view64bit.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.21/bcftools view /build/reproducible-path/bcftools-1.21/test/view64bit.2.vcf -Ou | /build/reproducible-path/bcftools-1.21/bcftools view -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.21/bcftools view /build/reproducible-path/bcftools-1.21/test/view64bit.3.vcf -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.21/bcftools view /build/reproducible-path/bcftools-1.21/test/view64bit.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.21/bcftools view /build/reproducible-path/bcftools-1.21/test/view64bit.4.vcf -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.21/bcftools view /build/reproducible-path/bcftools-1.21/test/view64bit.4.vcf | /build/reproducible-path/bcftools-1.21/bcftools view -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.21/bcftools view /build/reproducible-path/bcftools-1.21/test/view64bit.4.vcf -Ou | /build/reproducible-path/bcftools-1.21/bcftools view -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.21/bcftools view /build/reproducible-path/bcftools-1.21/test/view64bit.5.vcf -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.21/bcftools view /build/reproducible-path/bcftools-1.21/test/view64bit.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools view -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.21/bcftools view /build/reproducible-path/bcftools-1.21/test/view64bit.5.vcf -Ou | /build/reproducible-path/bcftools-1.21/bcftools view -H .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -C5:nonmajor /tmp/wj8A4a3te7/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -c6:nonmajor /tmp/wj8A4a3te7/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -q0.3:major /tmp/wj8A4a3te7/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/wj8A4a3te7/view.filter.annovar.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -i 'Gene.refGene~"NOD"' /tmp/wj8A4a3te7/view.filter.annovar.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -i 'LJB2_MutationTaster=="0.291000"' /tmp/wj8A4a3te7/view.filter.annovar.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -a /tmp/wj8A4a3te7/view-a.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -T /build/reproducible-path/bcftools-1.21/test/view.sites.txt /tmp/wj8A4a3te7/view.sites.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -T /build/reproducible-path/bcftools-1.21/test/view.sites.txt /tmp/wj8A4a3te7/view.sites.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -T /build/reproducible-path/bcftools-1.21/test/view.sites.txt.gz /tmp/wj8A4a3te7/view.sites.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -T /build/reproducible-path/bcftools-1.21/test/view.sites.txt.gz /tmp/wj8A4a3te7/view.sites.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_head: /build/reproducible-path/bcftools-1.21/bcftools head /build/reproducible-path/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_head: /build/reproducible-path/bcftools-1.21/bcftools head -h 0 /build/reproducible-path/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_head: /build/reproducible-path/bcftools-1.21/bcftools head -h 1 /build/reproducible-path/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_head: /build/reproducible-path/bcftools-1.21/bcftools head -h 5 /build/reproducible-path/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_head: /build/reproducible-path/bcftools-1.21/bcftools head -h 22 /build/reproducible-path/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_head: /build/reproducible-path/bcftools-1.21/bcftools head -h 23 /build/reproducible-path/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_head: /build/reproducible-path/bcftools-1.21/bcftools head -n 0 /build/reproducible-path/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_head: /build/reproducible-path/bcftools-1.21/bcftools head -n 1 /build/reproducible-path/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_head: /build/reproducible-path/bcftools-1.21/bcftools head -n 5 /build/reproducible-path/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_head: /build/reproducible-path/bcftools-1.21/bcftools head -h 5 -n 5 < /build/reproducible-path/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_head2: /build/reproducible-path/bcftools-1.21/bcftools head -s0 /tmp/wj8A4a3te7/mpileup.2.vcf.gz .. ok test_vcf_head2: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -Ob /tmp/wj8A4a3te7/mpileup.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools head -s0 .. ok test_vcf_head2: /build/reproducible-path/bcftools-1.21/bcftools head -s1 /tmp/wj8A4a3te7/mpileup.2.vcf.gz .. ok test_vcf_head2: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -Ob /tmp/wj8A4a3te7/mpileup.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools head -s1 .. ok test_vcf_head2: /build/reproducible-path/bcftools-1.21/bcftools head -s2 -h2 /tmp/wj8A4a3te7/mpileup.2.vcf.gz .. ok test_vcf_head2: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -Ob /tmp/wj8A4a3te7/mpileup.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools head -s2 -h2 .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mv /build/reproducible-path/bcftools-1.21/test/mpileup.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mv /build/reproducible-path/bcftools-1.21/test/mpileup.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mg0 /build/reproducible-path/bcftools-1.21/test/mpileup.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mg0 /build/reproducible-path/bcftools-1.21/test/mpileup.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mv -S /build/reproducible-path/bcftools-1.21/test/mpileup.3.samples /build/reproducible-path/bcftools-1.21/test/mpileup.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mv -S /build/reproducible-path/bcftools-1.21/test/mpileup.3.samples /build/reproducible-path/bcftools-1.21/test/mpileup.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mv -S /build/reproducible-path/bcftools-1.21/test/mpileup.4.samples /build/reproducible-path/bcftools-1.21/test/mpileup.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mv -S /build/reproducible-path/bcftools-1.21/test/mpileup.4.samples /build/reproducible-path/bcftools-1.21/test/mpileup.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mv -S /build/reproducible-path/bcftools-1.21/test/mpileup.5.samples /build/reproducible-path/bcftools-1.21/test/mpileup.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mv -S /build/reproducible-path/bcftools-1.21/test/mpileup.5.samples /build/reproducible-path/bcftools-1.21/test/mpileup.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mv --ploidy-file /build/reproducible-path/bcftools-1.21/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.21/test/mpileup.samples /build/reproducible-path/bcftools-1.21/test/mpileup.X.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mv --ploidy-file /build/reproducible-path/bcftools-1.21/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.21/test/mpileup.samples /build/reproducible-path/bcftools-1.21/test/mpileup.X.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mv --ploidy-file /build/reproducible-path/bcftools-1.21/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.21/test/mpileup.ped /build/reproducible-path/bcftools-1.21/test/mpileup.X.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mv --ploidy-file /build/reproducible-path/bcftools-1.21/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.21/test/mpileup.ped /build/reproducible-path/bcftools-1.21/test/mpileup.X.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mv --ploidy-file /build/reproducible-path/bcftools-1.21/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.21/test/mpileup.2.samples /build/reproducible-path/bcftools-1.21/test/mpileup.X.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mv --ploidy-file /build/reproducible-path/bcftools-1.21/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.21/test/mpileup.2.samples /build/reproducible-path/bcftools-1.21/test/mpileup.X.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mv /build/reproducible-path/bcftools-1.21/test/mpileup.NA19213.NA19129.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mv /build/reproducible-path/bcftools-1.21/test/mpileup.NA19213.NA19129.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mv -G - --group-samples-tag AD /build/reproducible-path/bcftools-1.21/test/mpileup.NA19213.NA19129.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mv -G - --group-samples-tag AD /build/reproducible-path/bcftools-1.21/test/mpileup.NA19213.NA19129.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mv /build/reproducible-path/bcftools-1.21/test/mpileup.hwe.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mv /build/reproducible-path/bcftools-1.21/test/mpileup.hwe.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mv -G - --group-samples-tag AD /build/reproducible-path/bcftools-1.21/test/mpileup.hwe.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mv -G - --group-samples-tag AD /build/reproducible-path/bcftools-1.21/test/mpileup.hwe.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mv -G /build/reproducible-path/bcftools-1.21/test/mpileup.hwe.samples --group-samples-tag AD /build/reproducible-path/bcftools-1.21/test/mpileup.hwe.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mv -G /build/reproducible-path/bcftools-1.21/test/mpileup.hwe.samples --group-samples-tag AD /build/reproducible-path/bcftools-1.21/test/mpileup.hwe.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/wj8A4a3te7/mpileup.tab.gz /build/reproducible-path/bcftools-1.21/test/mpileup.vcf .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/wj8A4a3te7/mpileup.tab.gz /build/reproducible-path/bcftools-1.21/test/mpileup.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/wj8A4a3te7/mpileup.2.tab.gz /build/reproducible-path/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/wj8A4a3te7/mpileup.2.tab.gz /build/reproducible-path/bcftools-1.21/test/mpileup.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/wj8A4a3te7/mpileup.3.tab.gz -i /build/reproducible-path/bcftools-1.21/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/wj8A4a3te7/mpileup.3.tab.gz -i /build/reproducible-path/bcftools-1.21/test/mpileup.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/wj8A4a3te7/mpileup.4.tab.gz -i /build/reproducible-path/bcftools-1.21/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/wj8A4a3te7/mpileup.4.tab.gz -i /build/reproducible-path/bcftools-1.21/test/mpileup.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/wj8A4a3te7/mpileup.5.tab.gz -i /build/reproducible-path/bcftools-1.21/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/wj8A4a3te7/mpileup.5.tab.gz -i /build/reproducible-path/bcftools-1.21/test/mpileup.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/wj8A4a3te7/mpileup.6.tab.gz -i /build/reproducible-path/bcftools-1.21/test/mpileup.4.vcf .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/wj8A4a3te7/mpileup.6.tab.gz -i /build/reproducible-path/bcftools-1.21/test/mpileup.4.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/wj8A4a3te7/mpileup.7.tab.gz -i /build/reproducible-path/bcftools-1.21/test/mpileup.5.vcf .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/wj8A4a3te7/mpileup.7.tab.gz -i /build/reproducible-path/bcftools-1.21/test/mpileup.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/wj8A4a3te7/mpileup.cals.1.tab.gz /build/reproducible-path/bcftools-1.21/test/mpileup.cals.1.vcf .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/wj8A4a3te7/mpileup.cals.1.tab.gz /build/reproducible-path/bcftools-1.21/test/mpileup.cals.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/wj8A4a3te7/mpileup.cals.2.tab.gz /build/reproducible-path/bcftools-1.21/test/mpileup.cals.2.vcf .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/wj8A4a3te7/mpileup.cals.2.tab.gz /build/reproducible-path/bcftools-1.21/test/mpileup.cals.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -cv /build/reproducible-path/bcftools-1.21/test/mpileup.c.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -cv /build/reproducible-path/bcftools-1.21/test/mpileup.c.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -cv --ploidy-file /build/reproducible-path/bcftools-1.21/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.21/test/mpileup.samples /build/reproducible-path/bcftools-1.21/test/mpileup.c.X.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -cv --ploidy-file /build/reproducible-path/bcftools-1.21/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.21/test/mpileup.samples /build/reproducible-path/bcftools-1.21/test/mpileup.c.X.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -cv --ploidy-file /build/reproducible-path/bcftools-1.21/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.21/test/mpileup.ped /build/reproducible-path/bcftools-1.21/test/mpileup.c.X.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -cv --ploidy-file /build/reproducible-path/bcftools-1.21/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.21/test/mpileup.ped /build/reproducible-path/bcftools-1.21/test/mpileup.c.X.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -cv --ploidy-file /build/reproducible-path/bcftools-1.21/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.21/test/mpileup.2.samples /build/reproducible-path/bcftools-1.21/test/mpileup.c.X.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -cv --ploidy-file /build/reproducible-path/bcftools-1.21/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.21/test/mpileup.2.samples /build/reproducible-path/bcftools-1.21/test/mpileup.c.X.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mv /build/reproducible-path/bcftools-1.21/test/call-G.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mv /build/reproducible-path/bcftools-1.21/test/call-G.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mv -G - --group-samples-tag AD /build/reproducible-path/bcftools-1.21/test/call-G.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mv -G - --group-samples-tag AD /build/reproducible-path/bcftools-1.21/test/call-G.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mv -F AN_POP,AC_POP /build/reproducible-path/bcftools-1.21/test/call-G.2.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mv -F AN_POP,AC_POP /build/reproducible-path/bcftools-1.21/test/call-G.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -m /build/reproducible-path/bcftools-1.21/test/call.af-fixation.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -m /build/reproducible-path/bcftools-1.21/test/call.af-fixation.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -m -G /build/reproducible-path/bcftools-1.21/test/call.af-fixation.txt /build/reproducible-path/bcftools-1.21/test/call.af-fixation.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -m -G /build/reproducible-path/bcftools-1.21/test/call.af-fixation.txt /build/reproducible-path/bcftools-1.21/test/call.af-fixation.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -m -G /build/reproducible-path/bcftools-1.21/test/call.af-fixation.txt -a GP,GQ /build/reproducible-path/bcftools-1.21/test/call.af-fixation.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -m -G /build/reproducible-path/bcftools-1.21/test/call.af-fixation.txt -a GP,GQ /build/reproducible-path/bcftools-1.21/test/call.af-fixation.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S. -e'TXT0="text"' /build/reproducible-path/bcftools-1.21/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S. -e'TXT0="text"' /build/reproducible-path/bcftools-1.21/test/view.filter.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S. -e'FMT/FRS[*:1]="BB"' /build/reproducible-path/bcftools-1.21/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S. -e'FMT/FRS[*:1]="BB"' /build/reproducible-path/bcftools-1.21/test/view.filter.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S. -e'FMT/FGS[*:0]="AAAAAA"' /build/reproducible-path/bcftools-1.21/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S. -e'FMT/FGS[*:0]="AAAAAA"' /build/reproducible-path/bcftools-1.21/test/view.filter.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S. -e'FMT/FGS[*:1]="BBB"' /build/reproducible-path/bcftools-1.21/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S. -e'FMT/FGS[*:1]="BBB"' /build/reproducible-path/bcftools-1.21/test/view.filter.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S. -e'FMT/FGS[*:4]="EE"' /build/reproducible-path/bcftools-1.21/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S. -e'FMT/FGS[*:4]="EE"' /build/reproducible-path/bcftools-1.21/test/view.filter.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S. -e'FMT/STR="XX"' /build/reproducible-path/bcftools-1.21/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S. -e'FMT/STR="XX"' /build/reproducible-path/bcftools-1.21/test/view.filter.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S. -e'FMT/FILTER="aaa"' /build/reproducible-path/bcftools-1.21/test/view.filter.2.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S. -e'FMT/FILTER="aaa"' /build/reproducible-path/bcftools-1.21/test/view.filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -mx -g2 -G2 /build/reproducible-path/bcftools-1.21/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -mx -g2 -G2 /build/reproducible-path/bcftools-1.21/test/filter.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -e'INFO/DP=19' /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -e'INFO/DP=19' /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -e'INFO/DP=19' -s XX /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -e'INFO/DP=19' -s XX /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -e'INFO/DP=19' -s XX -m+ /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+ /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -e'INFO/DP=19' -s XX -mx /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -e'INFO/DP=19' -s XX -mx /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -e'INFO/DP=19' -s XX -m+x /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+x /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -e'FMT/GT="0/2"' /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -e'FMT/GT="0/2"' /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -e'FMT/GT="0/2"' -s XX /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -e'FMT/GT="0/2"' -s XX -m+ /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+ /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -e'FMT/GT="0/2"' -s XX -mx /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -mx /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -e'FMT/GT="0/2"' -s XX -m+x /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+x /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'FMT/GT="0/0" && AC[*]=2' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'FMT/GT="0/0" && AC[*]=2' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'AC[*]=2 && FMT/GT="0/0"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'AC[*]=2 && FMT/GT="0/0"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'ALT="."' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'ALT="."' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -i 'FORMAT/TEST3<25' /build/reproducible-path/bcftools-1.21/test/filter.4.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -i 'FORMAT/TEST3<25' /build/reproducible-path/bcftools-1.21/test/filter.4.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -i 'FORMAT/TEST4<25' /build/reproducible-path/bcftools-1.21/test/filter.4.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -i 'FORMAT/TEST4<25' /build/reproducible-path/bcftools-1.21/test/filter.4.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'GT="A"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'GT="A"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'GT="RR"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'GT="RR"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'GT="RA"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'GT="RA"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'GT="AR"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'GT="AR"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'GT="AA"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'GT="AA"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'GT="aA"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'GT="aA"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'GT="Aa"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'GT="Aa"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'GT="HOM"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'GT="HOM"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'GT="HET"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'GT="HET"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'GT="HAP"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'GT="HAP"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'AD[:1]=11' /build/reproducible-path/bcftools-1.21/test/filter.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'AD[:1]=11' /build/reproducible-path/bcftools-1.21/test/filter.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'AD[1:]=11' /build/reproducible-path/bcftools-1.21/test/filter.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'AD[1:]=11' /build/reproducible-path/bcftools-1.21/test/filter.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'FR[0:1]=11' /build/reproducible-path/bcftools-1.21/test/filter.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%FR]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'FR[0:1]=11' /build/reproducible-path/bcftools-1.21/test/filter.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%FR]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'AD[*]="."' /build/reproducible-path/bcftools-1.21/test/filter.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'AD[*]="."' /build/reproducible-path/bcftools-1.21/test/filter.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'AD[0:0]=="."' /build/reproducible-path/bcftools-1.21/test/filter.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'AD[0:0]=="."' /build/reproducible-path/bcftools-1.21/test/filter.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'AD[0:0]!="."' /build/reproducible-path/bcftools-1.21/test/filter.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'AD[0:0]!="."' /build/reproducible-path/bcftools-1.21/test/filter.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'QUAL=="."' /build/reproducible-path/bcftools-1.21/test/filter.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%QUAL\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'QUAL=="."' /build/reproducible-path/bcftools-1.21/test/filter.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%QUAL\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'N_PASS(DP>32)=1' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'N_PASS(DP>32)=1' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'F_PASS(DP>32)=0.5' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'F_PASS(DP>32)=0.5' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'F_MISSING>=1/5' /build/reproducible-path/bcftools-1.21/test/filter.6.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'F_MISSING>=1/5' /build/reproducible-path/bcftools-1.21/test/filter.6.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'F_MISSING>=0.2' /build/reproducible-path/bcftools-1.21/test/filter.6.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'F_MISSING>=0.2' /build/reproducible-path/bcftools-1.21/test/filter.6.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'F_PASS(GT=="mis")>=1/5' /build/reproducible-path/bcftools-1.21/test/filter.6.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'F_PASS(GT=="mis")>=1/5' /build/reproducible-path/bcftools-1.21/test/filter.6.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'F_PASS(GT=="mis")>=0.2' /build/reproducible-path/bcftools-1.21/test/filter.6.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'F_PASS(GT=="mis")>=0.2' /build/reproducible-path/bcftools-1.21/test/filter.6.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -mx -s + -g2:mnp,indel,other /build/reproducible-path/bcftools-1.21/test/filter.7.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -mx -s + -g2:mnp,indel,other /build/reproducible-path/bcftools-1.21/test/filter.7.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'FORMAT/AO==4' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'FORMAT/AO==4' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'MAX(FORMAT/AO[0:])==4' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'MAX(FORMAT/AO[0:])==4' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'MAX(FORMAT/AO)==4' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'MAX(FORMAT/AO)==4' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'MIN(FORMAT/AO[0:])==3' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO[0:])==3' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'MIN(FORMAT/AO)==2' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO)==2' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'MIN(FORMAT/AO[0:])==3' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO[0:])==3' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'AVG(FORMAT/AO[2:])==4' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'AVG(FORMAT/AO[2:])==4' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'MEDIAN(FORMAT/AO[2:])==4' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'MEDIAN(FORMAT/AO[2:])==4' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'STDEV(FORMAT/AO[0:])=0.5' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'STDEV(FORMAT/AO[0:])=0.5' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'SUM(FORMAT/AO[0:])=7' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'SUM(FORMAT/AO[0:])=7' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'SMPL_MAX(FORMAT/AO)==4' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'SMPL_MAX(FORMAT/AO)==4' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'sMIN(FORMAT/AO)==2' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'sMIN(FORMAT/AO)==2' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'ABS(sAVG(FORMAT/AO)-3.66666)<1e-5' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'ABS(sAVG(FORMAT/AO)-3.66666)<1e-5' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'sMEDIAN(FORMAT/AO)==4' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'sMEDIAN(FORMAT/AO)==4' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'ABS(sSTDEV(FORMAT/AO)-1.2472191)<1e-5' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'ABS(sSTDEV(FORMAT/AO)-1.2472191)<1e-5' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'sSUM(FORMAT/AO)==11' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'sSUM(FORMAT/AO)==11' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i 'QUAL/FMT/AD==55' /build/reproducible-path/bcftools-1.21/test/filter.9.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i 'QUAL/FMT/AD==55' /build/reproducible-path/bcftools-1.21/test/filter.9.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i 'QUAL/INFO/AD==10' /build/reproducible-path/bcftools-1.21/test/filter.9.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i 'QUAL/INFO/AD==10' /build/reproducible-path/bcftools-1.21/test/filter.9.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'ABS(SMPL_MAX(FORMAT/AO))=5' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'ABS(SMPL_MAX(FORMAT/AO))=5' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'PHRED(AO[1:])>-4' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'PHRED(AO[1:])>-4' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'ABS(AO[1:])==2' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'ABS(AO[1:])==2' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i 'sum(AD[*]) > FORMAT/DP' /build/reproducible-path/bcftools-1.21/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i 'sum(AD[*]) > FORMAT/DP' /build/reproducible-path/bcftools-1.21/test/filter.10.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i 'FORMAT/DP < sum(AD[*])' /build/reproducible-path/bcftools-1.21/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i 'FORMAT/DP < sum(AD[*])' /build/reproducible-path/bcftools-1.21/test/filter.10.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i 'sum(AD[*]) < FORMAT/DP' /build/reproducible-path/bcftools-1.21/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i 'sum(AD[*]) < FORMAT/DP' /build/reproducible-path/bcftools-1.21/test/filter.10.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i 'FORMAT/DP > sum(AD[*])' /build/reproducible-path/bcftools-1.21/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i 'FORMAT/DP > sum(AD[*])' /build/reproducible-path/bcftools-1.21/test/filter.10.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 0 /build/reproducible-path/bcftools-1.21/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 0 /build/reproducible-path/bcftools-1.21/test/filter.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 1 /build/reproducible-path/bcftools-1.21/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 1 /build/reproducible-path/bcftools-1.21/test/filter.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 2 /build/reproducible-path/bcftools-1.21/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 2 /build/reproducible-path/bcftools-1.21/test/filter.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter --soft-filter xxx --mask ^2:1005-1008 /build/reproducible-path/bcftools-1.21/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob --soft-filter xxx --mask ^2:1005-1008 /build/reproducible-path/bcftools-1.21/test/filter.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_sort: /build/reproducible-path/bcftools-1.21/bcftools sort -m 0 /build/reproducible-path/bcftools-1.21/test/sort.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /build/reproducible-path/bcftools-1.21/bcftools sort -Ob -m 0 /build/reproducible-path/bcftools-1.21/test/sort.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /build/reproducible-path/bcftools-1.21/bcftools sort -m 1000 /build/reproducible-path/bcftools-1.21/test/sort.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /build/reproducible-path/bcftools-1.21/bcftools sort -Ob -m 1000 /build/reproducible-path/bcftools-1.21/test/sort.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /build/reproducible-path/bcftools-1.21/test/regions.tab /tmp/wj8A4a3te7/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/regions.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /build/reproducible-path/bcftools-1.21/test/regions.tab .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /build/reproducible-path/bcftools-1.21/test/regions.tab /tmp/wj8A4a3te7/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/wj8A4a3te7/regions.tab.gz /tmp/wj8A4a3te7/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/regions.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/wj8A4a3te7/regions.tab.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/wj8A4a3te7/regions.tab.gz /tmp/wj8A4a3te7/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/wj8A4a3te7/regions.bed /tmp/wj8A4a3te7/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/regions.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/wj8A4a3te7/regions.bed .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/wj8A4a3te7/regions.bed /tmp/wj8A4a3te7/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/wj8A4a3te7/regions.bed.gz /tmp/wj8A4a3te7/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/regions.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/wj8A4a3te7/regions.bed.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/wj8A4a3te7/regions.bed.gz /tmp/wj8A4a3te7/regions.vcf.gz .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate.escape.1.tab.gz -c CHROM,POS,ISTR,FMT/FSTR /build/reproducible-path/bcftools-1.21/test/annotate.escape.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate.escape.1.tab.gz -c CHROM,POS,ISTR,FMT/FSTR /build/reproducible-path/bcftools-1.21/test/annotate.escape.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate.match.1.tab.gz -c CHROM,POS,-,-,SCORE,~X,-,- -i'STR={X}' /build/reproducible-path/bcftools-1.21/test/annotate.match.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate.match.1.tab.gz -c CHROM,POS,-,-,SCORE,~X,-,- -i'STR={X}' /build/reproducible-path/bcftools-1.21/test/annotate.match.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate.match.1.tab.gz -c CHROM,POS,REF,ALT,SCORE,-,~X,- -i'INT={X}' /build/reproducible-path/bcftools-1.21/test/annotate.match.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate.match.1.tab.gz -c CHROM,POS,REF,ALT,SCORE,-,~X,- -i'INT={X}' /build/reproducible-path/bcftools-1.21/test/annotate.match.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate.match.1.tab.gz -c CHROM,POS,REF,ALT,SCORE,-,-,~X -i'FLT={X}' /build/reproducible-path/bcftools-1.21/test/annotate.match.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate.match.1.tab.gz -c CHROM,POS,REF,ALT,SCORE,-,-,~X -i'FLT={X}' /build/reproducible-path/bcftools-1.21/test/annotate.match.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /build/reproducible-path/bcftools-1.21/test/annotate.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /build/reproducible-path/bcftools-1.21/test/annotate.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate2.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate.hdr -c CHROM,POS,-,T_STR /build/reproducible-path/bcftools-1.21/test/annotate.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate2.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate.hdr -c CHROM,POS,-,T_STR /build/reproducible-path/bcftools-1.21/test/annotate.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate2.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate.hdr -c CHROM,FROM,TO,T_STR /build/reproducible-path/bcftools-1.21/test/annotate.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate2.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate.hdr -c CHROM,FROM,TO,T_STR /build/reproducible-path/bcftools-1.21/test/annotate.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/wj8A4a3te7/annotate.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/wj8A4a3te7/annotate.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /build/reproducible-path/bcftools-1.21/test/annotate3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /build/reproducible-path/bcftools-1.21/test/annotate3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -x FORMAT /build/reproducible-path/bcftools-1.21/test/annotate3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -x FORMAT /build/reproducible-path/bcftools-1.21/test/annotate3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots4.vcf.gz -c +INFO /tmp/wj8A4a3te7/annotate4.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots4.vcf.gz -c +INFO /tmp/wj8A4a3te7/annotate4.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots4.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /build/reproducible-path/bcftools-1.21/test/annotate4.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots4.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /build/reproducible-path/bcftools-1.21/test/annotate4.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots10.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /build/reproducible-path/bcftools-1.21/test/annotate10.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots10.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /build/reproducible-path/bcftools-1.21/test/annotate10.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /build/reproducible-path/bcftools-1.21/test/annotate2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /build/reproducible-path/bcftools-1.21/test/annotate2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots11.vcf.gz -c FMT /tmp/wj8A4a3te7/annotate11.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots11.vcf.gz -c FMT /tmp/wj8A4a3te7/annotate11.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots2.vcf.gz -c FMT/newGT:=GT /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots2.vcf.gz -c FMT/newGT:=GT /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots12.vcf.gz -c FMT/GT:=newGT /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots12.vcf.gz -c FMT/GT:=newGT /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots13.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate13.hdr -c CHROM,BEG,END,ABC /build/reproducible-path/bcftools-1.21/test/annotate13.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots13.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate13.hdr -c CHROM,BEG,END,ABC /build/reproducible-path/bcftools-1.21/test/annotate13.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots13.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:append /build/reproducible-path/bcftools-1.21/test/annotate13.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots13.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:append /build/reproducible-path/bcftools-1.21/test/annotate13.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots13.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:unique /build/reproducible-path/bcftools-1.21/test/annotate13.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots13.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:unique /build/reproducible-path/bcftools-1.21/test/annotate13.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -x FILTER/XX,INFO/XX --force /build/reproducible-path/bcftools-1.21/test/annotate14.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -x FILTER/XX,INFO/XX --force /build/reproducible-path/bcftools-1.21/test/annotate14.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate15.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate15.hdr -s SAMPLE1 -c CHROM,FROM,TO,FMT/FOO,BAR /build/reproducible-path/bcftools-1.21/test/annotate15.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate15.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate15.hdr -s SAMPLE1 -c CHROM,FROM,TO,FMT/FOO,BAR /build/reproducible-path/bcftools-1.21/test/annotate15.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate15.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate15.hdr -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR /build/reproducible-path/bcftools-1.21/test/annotate15.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate15.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate15.hdr -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR /build/reproducible-path/bcftools-1.21/test/annotate15.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate15.tab.gz -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR -H '##FORMAT=' -H '##INFO=' /build/reproducible-path/bcftools-1.21/test/annotate15.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate15.tab.gz -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR -H '##FORMAT=' -H '##INFO=' /build/reproducible-path/bcftools-1.21/test/annotate15.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -x FILTER /build/reproducible-path/bcftools-1.21/test/annotate16.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -x FILTER /build/reproducible-path/bcftools-1.21/test/annotate16.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/reproducible-path/bcftools-1.21/test/annotate17.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/reproducible-path/bcftools-1.21/test/annotate17.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/reproducible-path/bcftools-1.21/test/annotate17.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/reproducible-path/bcftools-1.21/test/annotate17.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate17.3.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/reproducible-path/bcftools-1.21/test/annotate17.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate17.3.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/reproducible-path/bcftools-1.21/test/annotate17.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate18.1.tab.gz -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /build/reproducible-path/bcftools-1.21/test/annotate18.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate18.1.tab.gz -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /build/reproducible-path/bcftools-1.21/test/annotate18.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate18.2.tab.gz -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /build/reproducible-path/bcftools-1.21/test/annotate18.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate18.2.tab.gz -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /build/reproducible-path/bcftools-1.21/test/annotate18.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/wj8A4a3te7/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/wj8A4a3te7/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/wj8A4a3te7/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/wj8A4a3te7/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/wj8A4a3te7/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/wj8A4a3te7/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -c INFO/FILTER:=FILTER /build/reproducible-path/bcftools-1.21/test/annotate19.dst.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -c INFO/FILTER:=FILTER /build/reproducible-path/bcftools-1.21/test/annotate19.dst.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER /tmp/wj8A4a3te7/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER /tmp/wj8A4a3te7/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER /tmp/wj8A4a3te7/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER /tmp/wj8A4a3te7/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER,FILTER /tmp/wj8A4a3te7/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER,FILTER /tmp/wj8A4a3te7/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=./FILTER /tmp/wj8A4a3te7/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=./FILTER /tmp/wj8A4a3te7/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate20.src.vcf.gz -c FMT/GT /tmp/wj8A4a3te7/annotate20.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate20.src.vcf.gz -c FMT/GT /tmp/wj8A4a3te7/annotate20.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate20.src.vcf.gz -c +FMT/GT /tmp/wj8A4a3te7/annotate20.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate20.src.vcf.gz -c +FMT/GT /tmp/wj8A4a3te7/annotate20.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate20.src.vcf.gz -c -FMT/GT /tmp/wj8A4a3te7/annotate20.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate20.src.vcf.gz -c -FMT/GT /tmp/wj8A4a3te7/annotate20.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate.multi.tab.gz -c CHROM,POS,REF,ALT,ANN -l ANN:append /build/reproducible-path/bcftools-1.21/test/annotate.multi.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate.multi.tab.gz -c CHROM,POS,REF,ALT,ANN -l ANN:append /build/reproducible-path/bcftools-1.21/test/annotate.multi.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate.missing-append.tab.gz -c CHROM,POS,REF,ALT,STR,INT,FLT -l STR:append-missing,INT:append-missing,FLT:append-missing /build/reproducible-path/bcftools-1.21/test/annotate.missing-append.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate.missing-append.tab.gz -c CHROM,POS,REF,ALT,STR,INT,FLT -l STR:append-missing,INT:append-missing,FLT:append-missing /build/reproducible-path/bcftools-1.21/test/annotate.missing-append.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /build/reproducible-path/bcftools-1.21/test/annotate9.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /build/reproducible-path/bcftools-1.21/test/annotate9.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate --rename-annots /build/reproducible-path/bcftools-1.21/test/annotate21.txt /build/reproducible-path/bcftools-1.21/test/annotate21.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob --rename-annots /build/reproducible-path/bcftools-1.21/test/annotate21.txt /build/reproducible-path/bcftools-1.21/test/annotate21.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -c XX:=FORMAT/X-X,YY:=FORMAT/Y-Y,AA:=FORMAT/A-A,AA:=INFO/A-A,BB:=INFO/B-B,XX:=INFO/X-X,YY:=INFO/Y-Y,fltA:=FILTER/flt-A,fltB:=FILTER/flt-B,fltX:=FILTER/flt-X,fltY:=FILTER/flt-Y /build/reproducible-path/bcftools-1.21/test/annotate21.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -c XX:=FORMAT/X-X,YY:=FORMAT/Y-Y,AA:=FORMAT/A-A,AA:=INFO/A-A,BB:=INFO/B-B,XX:=INFO/X-X,YY:=INFO/Y-Y,fltA:=FILTER/flt-A,fltB:=FILTER/flt-B,fltX:=FILTER/flt-X,fltY:=FILTER/flt-Y /build/reproducible-path/bcftools-1.21/test/annotate21.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/wj8A4a3te7/annotate22.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/wj8A4a3te7/annotate22.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate23.tab.gz -c CHROM,POS,~ID,REF,ALT,INFO/END /build/reproducible-path/bcftools-1.21/test/annotate23.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate23.tab.gz -c CHROM,POS,~ID,REF,ALT,INFO/END /build/reproducible-path/bcftools-1.21/test/annotate23.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate24.src.vcf.gz -c XX /tmp/wj8A4a3te7/annotate24.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate24.src.vcf.gz -c XX /tmp/wj8A4a3te7/annotate24.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate25.tab.gz -c CHROM,POS,ID,REF,ALT,~INFO/END /build/reproducible-path/bcftools-1.21/test/annotate25.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate25.tab.gz -c CHROM,POS,ID,REF,ALT,~INFO/END /build/reproducible-path/bcftools-1.21/test/annotate25.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate26.tab.gz -c CHROM,POS,-POS /build/reproducible-path/bcftools-1.21/test/annotate26.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate26.tab.gz -c CHROM,POS,-POS /build/reproducible-path/bcftools-1.21/test/annotate26.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,TSTR,TFLT,TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,TSTR,TFLT,TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.TSTR,.TFLT,.TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.TSTR,.TFLT,.TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.+TSTR,.+TFLT,.+TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.+TSTR,.+TFLT,.+TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,+TSTR,+TFLT,+TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,+TSTR,+TFLT,+TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.=TSTR,.=TFLT,.=TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.=TSTR,.=TFLT,.=TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,=TSTR,=TFLT,=TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,=TSTR,=TFLT,=TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique /build/reproducible-path/bcftools-1.21/test/annotate.olap.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique /build/reproducible-path/bcftools-1.21/test/annotate.olap.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique --min-overlap 0.4:0.5 -m XXX /build/reproducible-path/bcftools-1.21/test/annotate.olap.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique --min-overlap 0.4:0.5 -m XXX /build/reproducible-path/bcftools-1.21/test/annotate.olap.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots.id.vcf.gz -c ALT /tmp/wj8A4a3te7/annotate.id.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots.id.vcf.gz -c ALT /tmp/wj8A4a3te7/annotate.id.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots.id.vcf.gz -c +ALT /tmp/wj8A4a3te7/annotate.id.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots.id.vcf.gz -c +ALT /tmp/wj8A4a3te7/annotate.id.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots.id.2.vcf.gz --pair-logic some -c +ID /tmp/wj8A4a3te7/annotate.id.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots.id.2.vcf.gz --pair-logic some -c +ID /tmp/wj8A4a3te7/annotate.id.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots.id.2.vcf.gz --pair-logic any -c +ID /tmp/wj8A4a3te7/annotate.id.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots.id.2.vcf.gz --pair-logic any -c +ID /tmp/wj8A4a3te7/annotate.id.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate27.tab.gz -c CHROM,POS,REF,ALT,EVIDENCE /build/reproducible-path/bcftools-1.21/test/annotate27.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate27.tab.gz -c CHROM,POS,REF,ALT,EVIDENCE /build/reproducible-path/bcftools-1.21/test/annotate27.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1,smpl2 /build/reproducible-path/bcftools-1.21/test/annotate28.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1,smpl2 /build/reproducible-path/bcftools-1.21/test/annotate28.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2,smpl1 /build/reproducible-path/bcftools-1.21/test/annotate28.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2,smpl1 /build/reproducible-path/bcftools-1.21/test/annotate28.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1 /build/reproducible-path/bcftools-1.21/test/annotate28.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1 /build/reproducible-path/bcftools-1.21/test/annotate28.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2 /build/reproducible-path/bcftools-1.21/test/annotate28.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2 /build/reproducible-path/bcftools-1.21/test/annotate28.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -m XXX /build/reproducible-path/bcftools-1.21/test/annotate.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -m XXX /build/reproducible-path/bcftools-1.21/test/annotate.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots34.tab.gz -c CHROM,FROM,TO,INFO/END -H '##INFO=' /build/reproducible-path/bcftools-1.21/test/annotate34.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots34.tab.gz -c CHROM,FROM,TO,INFO/END -H '##INFO=' /build/reproducible-path/bcftools-1.21/test/annotate34.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots-mark.bed.gz -c CHROM,FROM,TO -m TAG /build/reproducible-path/bcftools-1.21/test/annots-mark.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots-mark.bed.gz -c CHROM,FROM,TO -m TAG /build/reproducible-path/bcftools-1.21/test/annots-mark.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --no-version /tmp/wj8A4a3te7/concat.1.a.vcf.gz /tmp/wj8A4a3te7/concat.1.b.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob /tmp/wj8A4a3te7/concat.1.a.vcf.gz /tmp/wj8A4a3te7/concat.1.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --no-version /tmp/wj8A4a3te7/concat.1.a.bcf /tmp/wj8A4a3te7/concat.1.b.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob /tmp/wj8A4a3te7/concat.1.a.bcf /tmp/wj8A4a3te7/concat.1.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -a /tmp/wj8A4a3te7/concat.2.a.vcf.gz /tmp/wj8A4a3te7/concat.2.b.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -a /tmp/wj8A4a3te7/concat.2.a.vcf.gz /tmp/wj8A4a3te7/concat.2.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -a /tmp/wj8A4a3te7/concat.2.a.bcf /tmp/wj8A4a3te7/concat.2.b.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -a /tmp/wj8A4a3te7/concat.2.a.bcf /tmp/wj8A4a3te7/concat.2.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -aD /tmp/wj8A4a3te7/concat.2.a.vcf.gz /tmp/wj8A4a3te7/concat.2.b.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -aD /tmp/wj8A4a3te7/concat.2.a.vcf.gz /tmp/wj8A4a3te7/concat.2.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -aD /tmp/wj8A4a3te7/concat.2.a.bcf /tmp/wj8A4a3te7/concat.2.b.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -aD /tmp/wj8A4a3te7/concat.2.a.bcf /tmp/wj8A4a3te7/concat.2.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -l --ligate-warn /tmp/wj8A4a3te7/concat.3.a.vcf.gz /tmp/wj8A4a3te7/concat.3.b.vcf.gz /tmp/wj8A4a3te7/concat.3.0.vcf.gz /tmp/wj8A4a3te7/concat.3.c.vcf.gz /tmp/wj8A4a3te7/concat.3.d.vcf.gz /tmp/wj8A4a3te7/concat.3.e.vcf.gz /tmp/wj8A4a3te7/concat.3.f.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -l --ligate-warn /tmp/wj8A4a3te7/concat.3.a.vcf.gz /tmp/wj8A4a3te7/concat.3.b.vcf.gz /tmp/wj8A4a3te7/concat.3.0.vcf.gz /tmp/wj8A4a3te7/concat.3.c.vcf.gz /tmp/wj8A4a3te7/concat.3.d.vcf.gz /tmp/wj8A4a3te7/concat.3.e.vcf.gz /tmp/wj8A4a3te7/concat.3.f.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -l --ligate-warn /tmp/wj8A4a3te7/concat.3.a.bcf /tmp/wj8A4a3te7/concat.3.b.bcf /tmp/wj8A4a3te7/concat.3.0.bcf /tmp/wj8A4a3te7/concat.3.c.bcf /tmp/wj8A4a3te7/concat.3.d.bcf /tmp/wj8A4a3te7/concat.3.e.bcf /tmp/wj8A4a3te7/concat.3.f.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -l --ligate-warn /tmp/wj8A4a3te7/concat.3.a.bcf /tmp/wj8A4a3te7/concat.3.b.bcf /tmp/wj8A4a3te7/concat.3.0.bcf /tmp/wj8A4a3te7/concat.3.c.bcf /tmp/wj8A4a3te7/concat.3.d.bcf /tmp/wj8A4a3te7/concat.3.e.bcf /tmp/wj8A4a3te7/concat.3.f.bcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ Random seed for test_naive_concat: 2755974125 .. ok test_naive_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --naive-force /tmp/wj8A4a3te7/naive_concat.0.bcf /tmp/wj8A4a3te7/naive_concat.1.bcf /tmp/wj8A4a3te7/naive_concat.2.bcf /tmp/wj8A4a3te7/naive_concat.3.bcf /tmp/wj8A4a3te7/naive_concat.4.bcf /tmp/wj8A4a3te7/naive_concat.5.bcf /tmp/wj8A4a3te7/naive_concat.6.bcf /tmp/wj8A4a3te7/naive_concat.7.bcf /tmp/wj8A4a3te7/naive_concat.8.bcf /tmp/wj8A4a3te7/naive_concat.9.bcf | /build/reproducible-path/bcftools-1.21/bcftools view -H .. ok test_naive_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --naive /tmp/wj8A4a3te7/naive_concat.0.vcf.gz /tmp/wj8A4a3te7/naive_concat.1.vcf.gz /tmp/wj8A4a3te7/naive_concat.2.vcf.gz /tmp/wj8A4a3te7/naive_concat.3.vcf.gz /tmp/wj8A4a3te7/naive_concat.4.vcf.gz /tmp/wj8A4a3te7/naive_concat.5.vcf.gz /tmp/wj8A4a3te7/naive_concat.6.vcf.gz /tmp/wj8A4a3te7/naive_concat.7.vcf.gz /tmp/wj8A4a3te7/naive_concat.8.vcf.gz /tmp/wj8A4a3te7/naive_concat.9.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view -H .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -l /tmp/wj8A4a3te7/concat.4.a.vcf.gz /tmp/wj8A4a3te7/concat.4.b.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -l /tmp/wj8A4a3te7/concat.4.a.vcf.gz /tmp/wj8A4a3te7/concat.4.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -l /tmp/wj8A4a3te7/concat.4.a.bcf /tmp/wj8A4a3te7/concat.4.b.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -l /tmp/wj8A4a3te7/concat.4.a.bcf /tmp/wj8A4a3te7/concat.4.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -l --ligate-warn /tmp/wj8A4a3te7/concat.5.a.vcf.gz /tmp/wj8A4a3te7/concat.5.b.vcf.gz /tmp/wj8A4a3te7/concat.5.c.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -l --ligate-warn /tmp/wj8A4a3te7/concat.5.a.vcf.gz /tmp/wj8A4a3te7/concat.5.b.vcf.gz /tmp/wj8A4a3te7/concat.5.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -l --ligate-warn /tmp/wj8A4a3te7/concat.5.a.bcf /tmp/wj8A4a3te7/concat.5.b.bcf /tmp/wj8A4a3te7/concat.5.c.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -l --ligate-warn /tmp/wj8A4a3te7/concat.5.a.bcf /tmp/wj8A4a3te7/concat.5.b.bcf /tmp/wj8A4a3te7/concat.5.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -l --ligate-force /tmp/wj8A4a3te7/concat.5.a.bcf /tmp/wj8A4a3te7/concat.5.b.bcf /tmp/wj8A4a3te7/concat.5.c.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -l --ligate-force /tmp/wj8A4a3te7/concat.5.a.bcf /tmp/wj8A4a3te7/concat.5.b.bcf /tmp/wj8A4a3te7/concat.5.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -G -a -D /tmp/wj8A4a3te7/concat.5.a.vcf.gz /tmp/wj8A4a3te7/concat.5.b.vcf.gz /tmp/wj8A4a3te7/concat.5.c.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -G -a -D /tmp/wj8A4a3te7/concat.5.a.vcf.gz /tmp/wj8A4a3te7/concat.5.b.vcf.gz /tmp/wj8A4a3te7/concat.5.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -G -a -D /tmp/wj8A4a3te7/concat.5.a.bcf /tmp/wj8A4a3te7/concat.5.b.bcf /tmp/wj8A4a3te7/concat.5.c.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -G -a -D /tmp/wj8A4a3te7/concat.5.a.bcf /tmp/wj8A4a3te7/concat.5.b.bcf /tmp/wj8A4a3te7/concat.5.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.hdr /build/reproducible-path/bcftools-1.21/test/reheader.vcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /build/reproducible-path/bcftools-1.21/test/reheader.vcf | /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.hdr | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.hdr /tmp/wj8A4a3te7/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/wj8A4a3te7/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.hdr | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.hdr /tmp/wj8A4a3te7/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/wj8A4a3te7/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.hdr | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples /build/reproducible-path/bcftools-1.21/test/reheader.vcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /build/reproducible-path/bcftools-1.21/test/reheader.vcf | /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples /tmp/wj8A4a3te7/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/wj8A4a3te7/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples /tmp/wj8A4a3te7/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/wj8A4a3te7/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples2 /build/reproducible-path/bcftools-1.21/test/reheader.vcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /build/reproducible-path/bcftools-1.21/test/reheader.vcf | /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples2 | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples2 /tmp/wj8A4a3te7/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/wj8A4a3te7/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples2 | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples2 /tmp/wj8A4a3te7/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/wj8A4a3te7/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples2 | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples3 /build/reproducible-path/bcftools-1.21/test/reheader.vcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /build/reproducible-path/bcftools-1.21/test/reheader.vcf | /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples3 | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples3 /tmp/wj8A4a3te7/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/wj8A4a3te7/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples3 | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples3 /tmp/wj8A4a3te7/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/wj8A4a3te7/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples3 | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples4 /build/reproducible-path/bcftools-1.21/test/reheader.vcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /build/reproducible-path/bcftools-1.21/test/reheader.vcf | /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples4 | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples4 /tmp/wj8A4a3te7/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/wj8A4a3te7/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples4 | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples4 /tmp/wj8A4a3te7/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/wj8A4a3te7/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples4 | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.empty.hdr /build/reproducible-path/bcftools-1.21/test/empty.vcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /build/reproducible-path/bcftools-1.21/test/empty.vcf | /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.empty.hdr | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.empty.hdr /tmp/wj8A4a3te7/empty.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/wj8A4a3te7/empty.bcf | /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.empty.hdr | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.empty.hdr /tmp/wj8A4a3te7/empty.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/wj8A4a3te7/empty.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.empty.hdr | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -f /build/reproducible-path/bcftools-1.21/test/reheader.fai /build/reproducible-path/bcftools-1.21/test/reheader.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -f /build/reproducible-path/bcftools-1.21/test/reheader.fai /tmp/wj8A4a3te7/reheader.2.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -f /build/reproducible-path/bcftools-1.21/test/reheader.fai /tmp/wj8A4a3te7/reheader.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.2.hdr -f /build/reproducible-path/bcftools-1.21/test/reheader.fai /build/reproducible-path/bcftools-1.21/test/reheader.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.2.hdr -f /build/reproducible-path/bcftools-1.21/test/reheader.fai /tmp/wj8A4a3te7/reheader.2.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.2.hdr -f /build/reproducible-path/bcftools-1.21/test/reheader.fai /tmp/wj8A4a3te7/reheader.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -f /build/reproducible-path/bcftools-1.21/test/reheader.3.fai /build/reproducible-path/bcftools-1.21/test/reheader.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -f /build/reproducible-path/bcftools-1.21/test/reheader.3.fai /tmp/wj8A4a3te7/reheader.3.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -f /build/reproducible-path/bcftools-1.21/test/reheader.3.fai /tmp/wj8A4a3te7/reheader.3.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_rename_chrs: /build/reproducible-path/bcftools-1.21/bcftools annotate --rename-chrs /tmp/wj8A4a3te7/rename.map -Ov /tmp/wj8A4a3te7/annotate.bcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /build/reproducible-path/bcftools-1.21/bcftools annotate --rename-chrs /tmp/wj8A4a3te7/rename.map -Ob /tmp/wj8A4a3te7/annotate.bcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /build/reproducible-path/bcftools-1.21/bcftools annotate --rename-chrs /tmp/wj8A4a3te7/rename.map -Ov /build/reproducible-path/bcftools-1.21/test/annotate.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /build/reproducible-path/bcftools-1.21/bcftools annotate --rename-chrs /tmp/wj8A4a3te7/rename.map -Ob /build/reproducible-path/bcftools-1.21/test/annotate.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM\t%POS\n' .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. /tmp/wj8A4a3te7/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --vcf-ids /tmp/wj8A4a3te7/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --vcf-ids .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --vcf-ids --3N6 /tmp/wj8A4a3te7/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --vcf-ids --3N6 .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert -g .,- /tmp/wj8A4a3te7/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g .,- .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert --vcf-ids -G /build/reproducible-path/bcftools-1.21/test/convert.gs.gt.ids.gen,/build/reproducible-path/bcftools-1.21/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert --vcf-ids -G /build/reproducible-path/bcftools-1.21/test/convert.gs.gt.ids.gen,/build/reproducible-path/bcftools-1.21/test/convert.gs.gt.samples -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert -G /build/reproducible-path/bcftools-1.21/test/convert.gs.gt.ids.gen,/build/reproducible-path/bcftools-1.21/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert -G /build/reproducible-path/bcftools-1.21/test/convert.gs.gt.ids.gen,/build/reproducible-path/bcftools-1.21/test/convert.gs.gt.samples -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert --3N6 -G /build/reproducible-path/bcftools-1.21/test/convert.gs.gt.ids.3N6.gen,/build/reproducible-path/bcftools-1.21/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert --3N6 -G /build/reproducible-path/bcftools-1.21/test/convert.gs.gt.ids.3N6.gen,/build/reproducible-path/bcftools-1.21/test/convert.gs.gt.samples -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert --vcf-ids -G /build/reproducible-path/bcftools-1.21/test/convert.gs.gt.ids.gen.rev,/build/reproducible-path/bcftools-1.21/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert --vcf-ids -G /build/reproducible-path/bcftools-1.21/test/convert.gs.gt.ids.gen.rev,/build/reproducible-path/bcftools-1.21/test/convert.gs.gt.samples -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert -G /build/reproducible-path/bcftools-1.21/test/convert.gs.gt.ids.gen.rev,/build/reproducible-path/bcftools-1.21/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert -G /build/reproducible-path/bcftools-1.21/test/convert.gs.gt.ids.gen.rev,/build/reproducible-path/bcftools-1.21/test/convert.gs.gt.samples -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^## .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --tag PL /tmp/wj8A4a3te7/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --tag PL .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert -g .,- --tag PL /tmp/wj8A4a3te7/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g .,- --tag PL .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --vcf-ids /tmp/wj8A4a3te7/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/check.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --vcf-ids .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert -g .,- --vcf-ids /tmp/wj8A4a3te7/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/check.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g .,- --vcf-ids .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --3N6 /tmp/wj8A4a3te7/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/check.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --3N6 .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert -g .,- --3N6 /tmp/wj8A4a3te7/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/check.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g .,- --3N6 .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --3N6 --vcf-ids /tmp/wj8A4a3te7/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/check.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --3N6 --vcf-ids .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert -g .,- --3N6 --vcf-ids /tmp/wj8A4a3te7/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/check.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g .,- --3N6 --vcf-ids .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert -h -,.,. /tmp/wj8A4a3te7/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -h -,.,. .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert -h .,-,. /tmp/wj8A4a3te7/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -h .,-,. .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert -h .,-,. --vcf-ids /tmp/wj8A4a3te7/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -h .,-,. --vcf-ids .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert -h .,.,- /tmp/wj8A4a3te7/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -h .,.,- .. ok test_vcf_convert_hls2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert -H /build/reproducible-path/bcftools-1.21/test/convert.hls.gt.hap,/build/reproducible-path/bcftools-1.21/test/convert.hls.gt.legend,/build/reproducible-path/bcftools-1.21/test/convert.hls.gt.samples | grep -v ^## .. ok test_vcf_convert_hls2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert -H /build/reproducible-path/bcftools-1.21/test/convert.hls.gt.hap,/build/reproducible-path/bcftools-1.21/test/convert.hls.gt.legend,/build/reproducible-path/bcftools-1.21/test/convert.hls.gt.samples -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^## .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert --haplegendsample -,.,. /tmp/wj8A4a3te7/convert.hap-missing.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/convert.hap-missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert --haplegendsample -,.,. .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert --hapsample -,. /tmp/wj8A4a3te7/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert --hapsample -,. .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert --hapsample -,. --vcf-ids /tmp/wj8A4a3te7/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert --hapsample -,. --vcf-ids .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert --hapsample .,- /tmp/wj8A4a3te7/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert --hapsample .,- .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert --hapsample2vcf /build/reproducible-path/bcftools-1.21/test/convert.hs.gt.hap,/build/reproducible-path/bcftools-1.21/test/convert.hs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert --hapsample2vcf /build/reproducible-path/bcftools-1.21/test/convert.hs.gt.hap,/build/reproducible-path/bcftools-1.21/test/convert.hs.gt.samples -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert --vcf-ids --hapsample2vcf /build/reproducible-path/bcftools-1.21/test/convert.hs.gt.ids.hap,/build/reproducible-path/bcftools-1.21/test/convert.hs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert --vcf-ids --hapsample2vcf /build/reproducible-path/bcftools-1.21/test/convert.hs.gt.ids.hap,/build/reproducible-path/bcftools-1.21/test/convert.hs.gt.samples -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^## .. ok test_vcf_convert_gvcf: /build/reproducible-path/bcftools-1.21/bcftools convert --no-version --gvcf2vcf -i'FILTER="PASS"' -f /build/reproducible-path/bcftools-1.21/test/gvcf.fa /tmp/wj8A4a3te7/convert.gvcf.vcf.gz .. ok test_vcf_convert_gvcf: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/convert.gvcf.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert --gvcf2vcf -i'FILTER="PASS"' -f /build/reproducible-path/bcftools-1.21/test/gvcf.fa | grep -v ^##bcftools .. ok test_vcf_convert_tsv2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert --no-version -c ID,CHROM,POS,AA -s SAMPLE1 -f /build/reproducible-path/bcftools-1.21/test/23andme.fa --tsv2vcf /build/reproducible-path/bcftools-1.21/test/convert.23andme .. ok test_vcf_convert_tsv2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert -Ou -c ID,CHROM,POS,AA -s SAMPLE1 -f /build/reproducible-path/bcftools-1.21/test/23andme.fa --tsv2vcf /build/reproducible-path/bcftools-1.21/test/convert.23andme | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_convert_tsv2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert --no-version -c -,CHROM,POS,REF,ALT -f /build/reproducible-path/bcftools-1.21/test/23andme.fa --tsv2vcf /build/reproducible-path/bcftools-1.21/test/convert.tsv .. ok test_vcf_convert_tsv2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert -Ou -c -,CHROM,POS,REF,ALT -f /build/reproducible-path/bcftools-1.21/test/23andme.fa --tsv2vcf /build/reproducible-path/bcftools-1.21/test/convert.tsv | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.overlaps.1.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.overlaps.1.fa -s A .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.overlaps.1.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.overlaps.1.fa -s A .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.overlaps.1.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.overlaps.1.fa -s B .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.overlaps.1.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.overlaps.1.fa -s B .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.overlaps.1.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.overlaps.1.fa -s A -a N .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.overlaps.1.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.overlaps.1.fa -s A -a N .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.overlaps.1.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.overlaps.1.fa -s B -a N .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.overlaps.1.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.overlaps.1.fa -s B -a N .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.beyond.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.beyond.fa .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.beyond.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.beyond.fa .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -m /build/reproducible-path/bcftools-1.21/test/consensus.tab .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -m /build/reproducible-path/bcftools-1.21/test/consensus.tab .. ok test_vcf_consensus_chain: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -m /build/reproducible-path/bcftools-1.21/test/consensus.tab -c /tmp/wj8A4a3te7/consensus.1.chain.new >/dev/null; cat /tmp/wj8A4a3te7/consensus.1.chain.new .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -H 1 -m /build/reproducible-path/bcftools-1.21/test/consensus.tab .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -H 1 -m /build/reproducible-path/bcftools-1.21/test/consensus.tab .. ok test_vcf_consensus_chain: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -H 1 -m /build/reproducible-path/bcftools-1.21/test/consensus.tab -c /tmp/wj8A4a3te7/consensus.2.chain.new >/dev/null; cat /tmp/wj8A4a3te7/consensus.2.chain.new .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -I -s - -m /build/reproducible-path/bcftools-1.21/test/consensus.tab .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -I -s - -m /build/reproducible-path/bcftools-1.21/test/consensus.tab .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -I -m /build/reproducible-path/bcftools-1.21/test/consensus.tab --mask-with X -m /build/reproducible-path/bcftools-1.21/test/consensus.tab --mask-with lc .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -I -m /build/reproducible-path/bcftools-1.21/test/consensus.tab --mask-with X -m /build/reproducible-path/bcftools-1.21/test/consensus.tab --mask-with lc .. ok test_vcf_consensus_chain: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -I -m /build/reproducible-path/bcftools-1.21/test/consensus.tab -c /tmp/wj8A4a3te7/consensus.3.chain.new >/dev/null; cat /tmp/wj8A4a3te7/consensus.3.chain.new .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -H 1 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -H 1 .. ok test_vcf_consensus_chain: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -H 1 -c /tmp/wj8A4a3te7/consensus.4.chain.new >/dev/null; cat /tmp/wj8A4a3te7/consensus.4.chain.new .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus2.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -H 1 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus2.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -H 1 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus2.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -H 2 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus2.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -H 2 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/empty.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/empty.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -H 2 -M "?" .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus3.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -H 2 -M "?" .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -H 2 -M "?" -p xx_ .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus3.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -H 2 -M "?" -p xx_ .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus4.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus4.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus5.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus5.fa --haplotype LA .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus5.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus5.fa --haplotype LA .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus6.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus6.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus6.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus6.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus7.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 2 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus7.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 2 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus7.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 4 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus7.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 4 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus7.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 2pIu .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus7.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 2pIu .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus7.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 4pIu .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus7.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 4pIu .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus7.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 1 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus7.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 1 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus7.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 3 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus7.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 3 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus7.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 1pIu .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus7.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 1pIu .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus7.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 3pIu .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus7.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 3pIu .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus8.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus8.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus8.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -a . .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus8.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -a . .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus8.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -a . -i 'type="snp" || type="ref"' .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus8.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -a . -i 'type="snp" || type="ref"' .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus8.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -a . -i 'ALT!=""' .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus8.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -a . -i 'ALT!=""' .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus8.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -a . -e 'MinDP>15' .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus8.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -a . -e 'MinDP>15' .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus8.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -a . -e 'MinDP<15' .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus8.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -a . -e 'MinDP<15' .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.9.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.9.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.9.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.9.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.10.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.10.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.10.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.10.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.11.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.11.fa -s smpl .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.11.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.11.fa -s smpl .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.11.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.11.fa -s smpl -a N .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.11.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.11.fa -s smpl -a N .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.12.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.12.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.12.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.12.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.13.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.13.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.13.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.13.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.14.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.14.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.14.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.14.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.12.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.12.fa -s - --mark-del - --mark-ins uc --mark-snv uc .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.12.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.12.fa -s - --mark-del - --mark-ins uc --mark-snv uc .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.12.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.12.fa -s - --mark-del - --mark-ins + --mark-snv : .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.12.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.12.fa -s - --mark-del - --mark-ins + --mark-snv : .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.15.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.15.fa -H I --mark-ins lc --mark-snv lc .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.15.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.15.fa -H I --mark-ins lc --mark-snv lc .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.16.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -I .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.16.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -I .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.16.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -H I .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.16.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -H I .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.17.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -s - -M N -m /build/reproducible-path/bcftools-1.21/test/consensus.17.bed .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.17.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -s - -M N -m /build/reproducible-path/bcftools-1.21/test/consensus.17.bed .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.18.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.18.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.18.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.18.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.19.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.19.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.19.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.19.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.20.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.20.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.20.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.20.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.20.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.20.fa .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.20.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.20.fa .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.20.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.20.fa -M . -s b .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.20.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.20.fa -M . -s b .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.20.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.20.fa -M . -s a .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.20.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.20.fa -M . -s a .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.21.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.21.fa .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.21.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.21.fa .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.22.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 0 --mark-del . .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.22.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 0 --mark-del . .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.22.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 1 --mark-del . .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.22.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 1 --mark-del . .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.22.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 2 --mark-del . .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.22.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 2 --mark-del . .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.22.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 0 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.22.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 0 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.22.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 1 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.22.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 1 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.22.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 2 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.22.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 2 .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -r17:100-150 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -r17:100-150 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -r17:100-150 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -b /tmp/wj8A4a3te7/mpileup.bam.list --no-version | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -r17:100-150 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob -b /tmp/wj8A4a3te7/mpileup.bam.urllist | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -r17:100-150 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -r17:100-150 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -r17:100-150 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -b /tmp/wj8A4a3te7/mpileup.cram.list --no-version | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -r17:100-150 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob -b /tmp/wj8A4a3te7/mpileup.cram.urllist | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DV -r17:100-600 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DV -r17:100-600 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DV -r17:100-600 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DV -r17:100-600 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP,-AD -r17:100-600 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP,-AD -r17:100-600 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP,-AD -r17:100-600 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP,-AD -r17:100-600 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DV,-AD -r17:100-600 --gvcf 0,2,5 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DV,-AD -r17:100-600 --gvcf 0,2,5 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DV,-AD -r17:100-600 --gvcf 0,2,5 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DV,-AD -r17:100-600 --gvcf 0,2,5 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DV,-AD -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DV,-AD -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DV,-AD -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DV,-AD -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -s HG00101,HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -s HG00101,HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -s HG00101,HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -s HG00101,HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -S /build/reproducible-path/bcftools-1.21/test/mplp.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -S /build/reproducible-path/bcftools-1.21/test/mplp.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -S /build/reproducible-path/bcftools-1.21/test/mplp.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -S /build/reproducible-path/bcftools-1.21/test/mplp.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -s ^HG00101,HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -s ^HG00101,HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -s ^HG00101,HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -s ^HG00101,HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -S ^/build/reproducible-path/bcftools-1.21/test/mplp.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -S ^/build/reproducible-path/bcftools-1.21/test/mplp.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -S ^/build/reproducible-path/bcftools-1.21/test/mplp.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -S ^/build/reproducible-path/bcftools-1.21/test/mplp.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -S /build/reproducible-path/bcftools-1.21/test/mplp.9.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -S /build/reproducible-path/bcftools-1.21/test/mplp.9.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -S /build/reproducible-path/bcftools-1.21/test/mplp.9.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -S /build/reproducible-path/bcftools-1.21/test/mplp.9.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -S /build/reproducible-path/bcftools-1.21/test/mplp.9.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -S /build/reproducible-path/bcftools-1.21/test/mplp.9.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -G /build/reproducible-path/bcftools-1.21/test/mplp.10.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -G /build/reproducible-path/bcftools-1.21/test/mplp.10.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -G /build/reproducible-path/bcftools-1.21/test/mplp.10.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -G /build/reproducible-path/bcftools-1.21/test/mplp.10.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -G /build/reproducible-path/bcftools-1.21/test/mplp.10.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -G /build/reproducible-path/bcftools-1.21/test/mplp.10.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -s HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -s HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.sam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -s HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -s HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -s HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -s HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -s ^HG99999 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -s ^HG99999 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.sam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -s ^HG99999 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -s ^HG99999 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -s ^HG99999 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -s ^HG99999 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -G /build/reproducible-path/bcftools-1.21/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -G /build/reproducible-path/bcftools-1.21/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.sam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -G /build/reproducible-path/bcftools-1.21/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -G /build/reproducible-path/bcftools-1.21/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -G /build/reproducible-path/bcftools-1.21/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -G /build/reproducible-path/bcftools-1.21/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -G /build/reproducible-path/bcftools-1.21/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -G /build/reproducible-path/bcftools-1.21/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.sam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -G /build/reproducible-path/bcftools-1.21/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -G /build/reproducible-path/bcftools-1.21/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -G /build/reproducible-path/bcftools-1.21/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -G /build/reproducible-path/bcftools-1.21/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.fa /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.sam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.fa /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.fa /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD --indels-cns -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.fa /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD --indels-cns -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.sam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD --indels-cns -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.fa /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD --indels-cns -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD --indels-cns -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.fa /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD --indels-cns -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -r 11:75 -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.fa /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -r 11:75 -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -r 11:75 -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.fa /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -r 11:75 -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.fa /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.fa /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.fa /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.fa /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD,INFO/SCR,FMT/SCR -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD,INFO/SCR,FMT/SCR -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD,INFO/SCR,FMT/SCR -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD,INFO/SCR,FMT/SCR -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t 1:100 --skip-all-set PAIRED,PROPER_PAIR,MREVERSE -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t 1:100 --skip-all-set PAIRED,PROPER_PAIR,MREVERSE -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-filter.sam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t 1:100 --skip-any-set READ1 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t 1:100 --skip-any-set READ1 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-filter.sam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t 1:100 --skip-all-unset READ1 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t 1:100 --skip-all-unset READ1 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-filter.sam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t 1:100 --skip-any-unset READ1 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t 1:100 --skip-any-unset READ1 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-filter.sam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD,INFO/NMBZ -r chr19:69-99 -f /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.1.fa /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD,INFO/NMBZ -r chr19:69-99 -f /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.1.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.1.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD,INFO/NMBZ -r chr6:75 -f /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.2.fa /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD,INFO/NMBZ -r chr6:75 -f /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.2.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.2.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD,INFO/NMBZ -r chr16:75 -f /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.3.fa /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.3.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.3.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD,INFO/NMBZ -r chr16:75 -f /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.3.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.3.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.3.2.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_csq: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq.fa -g /build/reproducible-path/bcftools-1.21/test/csq.gff3 /build/reproducible-path/bcftools-1.21/test/csq.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq.fa -g /build/reproducible-path/bcftools-1.21/test/csq.chr.gff3 /build/reproducible-path/bcftools-1.21/test/csq.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq.fa -g /build/reproducible-path/bcftools-1.21/test/csq.2.gff /build/reproducible-path/bcftools-1.21/test/csq.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq.fa -g /build/reproducible-path/bcftools-1.21/test/csq.2.gff --ncsq 64 /build/reproducible-path/bcftools-1.21/test/csq.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq.nchr.fa -g /build/reproducible-path/bcftools-1.21/test/csq.nchr.gff /build/reproducible-path/bcftools-1.21/test/csq.nchr.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq.ychr.fa -g /build/reproducible-path/bcftools-1.21/test/csq.nchr.gff /build/reproducible-path/bcftools-1.21/test/csq.nchr.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq.nchr.fa -g /build/reproducible-path/bcftools-1.21/test/csq.ychr.gff /build/reproducible-path/bcftools-1.21/test/csq.nchr.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq.ychr.fa -g /build/reproducible-path/bcftools-1.21/test/csq.ychr.gff /build/reproducible-path/bcftools-1.21/test/csq.nchr.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq.ychr.fa -g /build/reproducible-path/bcftools-1.21/test/csq.ychr.gff /build/reproducible-path/bcftools-1.21/test/csq.ychr.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq.ychr.fa -g /build/reproducible-path/bcftools-1.21/test/csq.nchr.gff /build/reproducible-path/bcftools-1.21/test/csq.ychr.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq.nchr.fa -g /build/reproducible-path/bcftools-1.21/test/csq.ychr.gff /build/reproducible-path/bcftools-1.21/test/csq.ychr.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq.nchr.fa -g /build/reproducible-path/bcftools-1.21/test/csq.nchr.gff /build/reproducible-path/bcftools-1.21/test/csq.ychr.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.21/test/csq/ENST00000410009 && /build/reproducible-path/bcftools-1.21/bcftools csq -lb -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.21/test/csq/ENST00000410009 && /build/reproducible-path/bcftools-1.21/bcftools csq -B 5 -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000410009/ENST00000410009.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000410009/ENST00000410009.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000410009/frameshift.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.21/test/csq/ENST00000410009 && /build/reproducible-path/bcftools-1.21/bcftools csq -b -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000557788/ENST00000557788.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000557788/ENST00000557788.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000557788/long-overlap-del.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.21/test/csq/ENSMUST00000133836 && /build/reproducible-path/bcftools-1.21/bcftools csq -f ENSMUST00000133836.fa -g ENSMUST00000133836.gff filter-problem.vcf -i 'FILTER="PASS"' --phase m | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000420190/ENST00000420190.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000420190/ENST00000420190.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000420190/abort-in-csq-push.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000448695/ENST00000448695.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000448695/ENST00000448695.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000448695/syn-and-splice-reg.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000520868/ENST00000520868.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000520868/ENST00000520868.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000520868/long-deletion.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000373833/ENST00000373833.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000373833/ENST00000373833.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000373833/boundary-insertion.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000373833/ENST00000373833.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000373833/ENST00000373833.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000373833/boundary-insertion.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000518414/ENST00000518414.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000518414/ENST00000518414.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000518414/incorrect-inframe-del.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000571540/ENST00000571540.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000571540/ENST00000571540.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000571540/nmd.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000318249/ENST00000318249.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000318249/ENST00000318249.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000318249/start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000318249/ENST00000318249.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000318249/ENST00000318249.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000318249/start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000218032/ENST00000218032.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000218032/ENST00000218032.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000218032/start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000218032/ENST00000218032.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000218032/ENST00000218032.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000218032/start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000218032/ENST00000218032.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000218032/ENST00000218032.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000218032/start-lost-del.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000329454/ENST00000329454.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000329454/ENST00000329454.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000329454/boundary-deletion.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000329454/ENST00000329454.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000329454/ENST00000329454.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000329454/boundary-deletion.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0002/EDUMMY0002.fa -g /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0002/EDUMMY0002.gff /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0002/boundaries.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0001/EDUMMY0001.fa -g /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0001/EDUMMY0001.gff /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0001/starts-with-1.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0001/EDUMMY0001.fa -g /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0001/EDUMMY0001.gff /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0001/starts-with-1.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/frame2.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/frame2.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/frame1.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/frame1.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/frame3.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/frame3.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000382647/ENST00000382647.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000382647/ENST00000382647.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000382647/synon-splice-region-insert.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000303039/ENST00000303039.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000303039/ENST00000303039.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000303039/not-a-stop.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000303039/ENST00000303039.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000303039/ENST00000303039.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000303039/not-a-stop.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000409523/ENST00000409523.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000409523/ENST00000409523.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000409523/long-overlapping-del.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000573314/ENST00000573314.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000573314/ENST00000573314.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000573314/ENST00000573314.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000573314/ENST00000573314.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000230048/ENST00000230048.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000230048/ENST00000230048.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000230048/start-del.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/snps.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/snps.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/insert3.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/insert3.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0003/EDUMMY0003.fa -g /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0003/EDUMMY0003.gff /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0003/long-del.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000375992/ENST00000375992.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000375992/ENST00000375992.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000375992/incorrect-synon-del-not-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000263103-INS/ENST00000263103-INS.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000263103-INS/ENST00000263103-INS.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000263103-INS/insertions.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000413103/ENST00000413103.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000413103/ENST00000413103.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000413103/long-deletion.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000295641/ENST00000295641.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000295641/ENST00000295641.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000295641/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000295641/ENST00000295641.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000295641/ENST00000295641.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000295641/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000378322/ENST00000378322.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000378322/ENST00000378322.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000378322/end-overlap-tscript.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000378322/ENST00000378322.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000378322/ENST00000378322.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000378322/end-overlap-tscript.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000542803/ENST00000542803.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000542803/ENST00000542803.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000542803/splice-region.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000542803/ENST00000542803.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000542803/ENST00000542803.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000542803/splice-region.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000271583/ENST00000271583.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000271583/ENST00000271583.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000271583/splice-acceptor.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000294661/ENST00000294661.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000294661/ENST00000294661.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000294661/non-coding-boundary.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000294661/ENST00000294661.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000294661/ENST00000294661.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000294661/non-coding-boundary.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000360372/ENST00000360372.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000360372/ENST00000360372.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000360372/mnp.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.21/test/csq/ENST00000422159 && /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000422159.fa -g ENST00000422159.gff multiallelic.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%REF\t%ALT\t%GT\t%TBCSQ\n]' | ../sort-csq -q ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000422159.fa -g short.gff multiallelic.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%REF\t%ALT\t%GT\t%TBCSQ\n]' | ../sort-csq -q .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000518414-ENST00000521270/valgrind.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000528237/ENST00000528237.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000528237/ENST00000528237.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000528237/retained-stop-incomplete-cds.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.21/test/csq/ENST00000379416 && /build/reproducible-path/bcftools-1.21/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.del-snp.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-del.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-ins.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-snp.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff single.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000536784/ENST00000536784.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000536784/ENST00000536784.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000536784/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000536784/ENST00000536784.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000536784/ENST00000536784.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000536784/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000436063/ENST00000436063.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000436063/ENST00000436063.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000436063/insert-before-utr.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.21/test/csq/EMN908947 && /build/reproducible-path/bcftools-1.21/bcftools csq -f EMN908947.fa -g ribosomal-slippage.gff ribosomal-slippage.vcf --force | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.21/test/csq/EMN908947 && /build/reproducible-path/bcftools-1.21/bcftools csq -f EMN908947.fa -g simple.gff simple.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000357367/ENST00000357367.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000357367/ENST00000357367.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000357367/stop-retained.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000573035-bt2212/ENST00000573035-bt2212.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000573035-bt2212/ENST00000573035-bt2212.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000573035-bt2212/complex-event.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000318249.2/ENST00000318249.2.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000318249.2/ENST00000318249.2.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000318249.2/synonymous-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000545279/ENST00000545279.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000545279/ENST00000545279.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000545279/splice-region-insert.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000368801/ENST00000368801.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000368801/ENST00000368801.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000368801/compound-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000381157/ENST00000381157.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000381157/ENST00000381157.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000381157/haploid-diploid.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000285021/ENST00000285021.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000285021/ENST00000285021.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000285021/stop-gained-inframe-indel.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000400151/ENST00000400151.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000400151/ENST00000400151.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000400151/long-del.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000420670/ENST00000420670.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000420670/ENST00000420670.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000420670/start-stop-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000420670/ENST00000420670.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000420670/ENST00000420670.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000420670/segfault.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.21/test/csq/ENST00000580206 && /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.ins-snv.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g short.gff compound.ins-snv.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff single.ins-snv.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g short.gff single.ins-snv.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.del-snv.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g short.gff compound.del-snv.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g short.gff single.del-snv.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.del-ins.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g short.gff compound.del-ins.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g short.gff single.del-ins.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000256452/ENST00000256452.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000256452/ENST00000256452.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000256452/intron.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENSG00000173376/ENSG00000173376.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENSG00000173376/ENSG00000173376.gff /build/reproducible-path/bcftools-1.21/test/csq/ENSG00000173376/synon.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000519442/ENST00000519442.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000519442/ENST00000519442.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000519442/synon-splice-region-del.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000390520/ENST00000390520.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000390520/ENST00000390520.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000390520/deletion-overlap.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.21/test/csq/ENST00000000000 && /build/reproducible-path/bcftools-1.21/bcftools csq -p a -f ENST00000000000.fa -g ENST00000000000.gff upstream-stop.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%REF\t%ALT\t%SAMPLE\t%GT\t%TBCSQ\n]' | ../sort-csq -q .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000269081/ENST00000269081.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000269081/ENST00000269081.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000269081/stop-gained-not-inframe-insertion.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000543077/ENST00000543077.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000543077/ENST00000543077.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000543077/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000543077/ENST00000543077.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000543077/ENST00000543077.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000543077/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000624631/ENST00000624631.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000624631/ENST00000624631.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000624631/ambiguous.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000479739/ENST00000479739.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000479739/ENST00000479739.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000479739/short-cds-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000479739/ENST00000479739.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000479739/ENST00000479739.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000479739/short-cds-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000301246/ENST00000301246.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000301246/ENST00000301246.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000301246/15bp-insert.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000368801.2/ENST00000368801.2.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000368801.2/ENST00000368801.2.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000368801.2/start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.21/test/csq/ENSMUST00000121418 && /build/reproducible-path/bcftools-1.21/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25500' --phase m | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.21/test/csq/ENSMUST00000121418 && /build/reproducible-path/bcftools-1.21/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25496' --phase m | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.21/test/csq/ENSMUST00000121418 && /build/reproducible-path/bcftools-1.21/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25105' --phase m | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000593942/ENST00000593942.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000593942/ENST00000593942.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000593942/last-codon-deletion.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000520795/ENST00000520795.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000520795/ENST00000520795.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000520795/long-inside-del.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000520795/ENST00000520795.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000520795/ENST00000520795.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000520795/long-inside-del.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000227471/ENST00000227471.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000227471/ENST00000227471.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000227471/insert-splice-vs-frameshift.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_roh: /build/reproducible-path/bcftools-1.21/bcftools roh /build/reproducible-path/bcftools-1.21/test/roh.1.vcf.gz -Or -G30 --AF-dflt 0.4| grep -v ^# .. ok test_roh: /build/reproducible-path/bcftools-1.21/bcftools roh /build/reproducible-path/bcftools-1.21/test/roh.1.vcf.gz -Or -G30 --AF-file /build/reproducible-path/bcftools-1.21/test/roh.1.tab.gz| grep -v ^# .. ok test_roh: /build/reproducible-path/bcftools-1.21/bcftools roh /build/reproducible-path/bcftools-1.21/test/roh.1.vcf.gz -Or -G30 --AF-file /build/reproducible-path/bcftools-1.21/test/roh.1.tab.gz --ignore-homref| grep -v ^# .. ok test_roh: /build/reproducible-path/bcftools-1.21/bcftools roh /build/reproducible-path/bcftools-1.21/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245| grep -v ^# .. ok test_roh: /build/reproducible-path/bcftools-1.21/bcftools roh /build/reproducible-path/bcftools-1.21/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --ignore-homref| grep -v ^# .. ok test_roh: /build/reproducible-path/bcftools-1.21/bcftools roh /build/reproducible-path/bcftools-1.21/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --ignore-homref --include-noalt| grep -v ^# .. ok test_roh: /build/reproducible-path/bcftools-1.21/bcftools roh /build/reproducible-path/bcftools-1.21/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --include-noalt| grep -v ^# .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 --no-HWE-prob /tmp/wj8A4a3te7/gtcheck.1.vcf.gz -g /tmp/wj8A4a3te7/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 /tmp/wj8A4a3te7/gtcheck.1.vcf.gz -g /tmp/wj8A4a3te7/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -u GT,GT /tmp/wj8A4a3te7/gtcheck.1.vcf.gz -g /tmp/wj8A4a3te7/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -u GT,PL /tmp/wj8A4a3te7/gtcheck.1.vcf.gz -g /tmp/wj8A4a3te7/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -u PL,GT /tmp/wj8A4a3te7/gtcheck.1.vcf.gz -g /tmp/wj8A4a3te7/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -u PL,PL /tmp/wj8A4a3te7/gtcheck.1.vcf.gz -g /tmp/wj8A4a3te7/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -p s1,s1 /tmp/wj8A4a3te7/gtcheck.1.vcf.gz -g /tmp/wj8A4a3te7/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 /tmp/wj8A4a3te7/gtcheck.2.vcf.gz -g /tmp/wj8A4a3te7/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 /tmp/wj8A4a3te7/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -p B,A,C,A,C,B,D,A,D,B,D,C,E,A,E,B,E,C,E,D /tmp/wj8A4a3te7/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -P /build/reproducible-path/bcftools-1.21/test/gtcheck.3.pairs /tmp/wj8A4a3te7/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -u PL /tmp/wj8A4a3te7/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 --n-matches 4 /tmp/wj8A4a3te7/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO | sort .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -s qry:E,D,C /tmp/wj8A4a3te7/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -s qry:E,D,C -u PL /tmp/wj8A4a3te7/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -s qry:B -s gt:D /tmp/wj8A4a3te7/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -s qry:B -s gt:D -u PL /tmp/wj8A4a3te7/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -s qry:B -s gt:D,C /tmp/wj8A4a3te7/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -p B,C,B,D /tmp/wj8A4a3te7/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -u GT,GT -H /tmp/wj8A4a3te7/gtcheck.1.vcf.gz -g /tmp/wj8A4a3te7/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -u GT,PL -H /tmp/wj8A4a3te7/gtcheck.1.vcf.gz -g /tmp/wj8A4a3te7/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -u PL,GT -H /tmp/wj8A4a3te7/gtcheck.1.vcf.gz -g /tmp/wj8A4a3te7/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -u PL,PL -H /tmp/wj8A4a3te7/gtcheck.1.vcf.gz -g /tmp/wj8A4a3te7/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -P /build/reproducible-path/bcftools-1.21/test/gtcheck.4.pairs --distinctive-sites 3 /tmp/wj8A4a3te7/gtcheck.4.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -P /build/reproducible-path/bcftools-1.21/test/gtcheck.4.pairs --distinctive-sites 3,1 /tmp/wj8A4a3te7/gtcheck.4.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -u GT -e 30 /tmp/wj8A4a3te7/gtcheck.1.vcf.gz -g /tmp/wj8A4a3te7/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -u GT -e 30 -p s1,s1 /tmp/wj8A4a3te7/gtcheck.1.vcf.gz -g /tmp/wj8A4a3te7/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -u GT -e 300 /tmp/wj8A4a3te7/gtcheck.1.vcf.gz -g /tmp/wj8A4a3te7/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -u PL -e 30 /tmp/wj8A4a3te7/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck /tmp/wj8A4a3te7/gtcheck.ntop.vcf.gz -g /tmp/wj8A4a3te7/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck --n-matches 2 /tmp/wj8A4a3te7/gtcheck.ntop.vcf.gz -g /tmp/wj8A4a3te7/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck /tmp/wj8A4a3te7/gtcheck.5.vcf.gz -g /tmp/wj8A4a3te7/gtcheck.5.gts.vcf.gz | grep -v ^# | grep -v Time .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -p A,B,B,C /tmp/wj8A4a3te7/gtcheck.6.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -t 11:33 -p A,D,A,E,D,E -u GT -e 10 /tmp/wj8A4a3te7/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok Number of tests: total .. 1805 passed .. 1805 failed .. 0 make[2]: Leaving directory '/build/reproducible-path/bcftools-1.21' make[1]: Leaving directory '/build/reproducible-path/bcftools-1.21' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/bcftools/ make -j40 install DESTDIR=/build/reproducible-path/bcftools-1.21/debian/bcftools AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/bcftools-1.21' mkdir -p -m 755 /build/reproducible-path/bcftools-1.21/debian/bcftools/usr/bin /build/reproducible-path/bcftools-1.21/debian/bcftools/usr/share/man/man1 /build/reproducible-path/bcftools-1.21/debian/bcftools/usr/lib/x86_64-linux-gnu/bcftools install -p bcftools /build/reproducible-path/bcftools-1.21/debian/bcftools/usr/bin install -p misc/color-chrs.pl misc/gff2gff.py misc/guess-ploidy.py misc/plot-vcfstats misc/plot-roh.py misc/run-roh.pl misc/vcfutils.pl /build/reproducible-path/bcftools-1.21/debian/bcftools/usr/bin install -p -m 644 doc/bcftools.1 /build/reproducible-path/bcftools-1.21/debian/bcftools/usr/share/man/man1 install -p plugins/*.so /build/reproducible-path/bcftools-1.21/debian/bcftools/usr/lib/x86_64-linux-gnu/bcftools make[1]: Leaving directory '/build/reproducible-path/bcftools-1.21' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/bcftools-1.21' dh_install # Fix Perl interpreter PATH for pscript in `grep -Rl '#!/usr/bin/env \+perl' debian/*` ; do \ sed -i '1s?#!/usr/bin/env \+perl?#!/usr/bin/perl?' ${pscript} ; \ done make[1]: Leaving directory '/build/reproducible-path/bcftools-1.21' dh_installdocs dh_installchangelogs debian/rules override_dh_installman make[1]: Entering directory '/build/reproducible-path/bcftools-1.21' dh_installman --language=C make[1]: Leaving directory '/build/reproducible-path/bcftools-1.21' dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dpkg-gencontrol: warning: package bcftools: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package bcftools: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'bcftools-dbgsym' in '../bcftools-dbgsym_1.21-1_amd64.deb'. dpkg-deb: building package 'bcftools' in '../bcftools_1.21-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../bcftools_1.21-1_amd64.buildinfo dpkg-genchanges --build=binary -O../bcftools_1.21-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/712482 and its subdirectories I: Current time: Sat Jul 5 06:05:45 -12 2025 I: pbuilder-time-stamp: 1751738745 Sat Jul 5 18:05:46 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos5-amd64.debian.net. Sat Jul 5 18:05:46 UTC 2025 I: Preparing to do remote build '2' on ionos5-amd64.debian.net. Sat Jul 5 18:05:46 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos5-amd64.debian.net is marked as down. Sat Jul 5 18:05:46 UTC 2025 - checking via ssh if ionos5-amd64.debian.net is up. removed '/tmp/read-only-fs-test-H6A2vT' ==================================================================================== Sat Aug 8 00:28:47 UTC 2026 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos5-amd64, called using "2 bcftools unstable /srv/reproducible-results/rbuild-debian/r-b-build.k066tCUN 1.21-1" as arguments. Sat Aug 8 00:28:47 UTC 2026 - actually running "reproducible_build.sh" (md5sum 44ec6a3142940d5e9a7ab76543d96029) as "/tmp/jenkins-script-xixHwCfY" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Sat Aug 8 00:28:47 UTC 2026 I: Downloading source for unstable/bcftools=1.21-1 Reading package lists... NOTICE: 'bcftools' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/bcftools.git Please use: git clone https://salsa.debian.org/med-team/bcftools.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 3675 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main bcftools 1.21-1 (dsc) [2267 B] Get:2 http://deb.debian.org/debian unstable/main bcftools 1.21-1 (tar) [3665 kB] Get:3 http://deb.debian.org/debian unstable/main bcftools 1.21-1 (diff) [7504 B] Fetched 3675 kB in 0s (52.0 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'bcftools' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/bcftools.git Please use: git clone https://salsa.debian.org/med-team/bcftools.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 3675 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main bcftools 1.21-1 (dsc) [2267 B] Get:2 http://deb.debian.org/debian unstable/main bcftools 1.21-1 (tar) [3665 kB] Get:3 http://deb.debian.org/debian unstable/main bcftools 1.21-1 (diff) [7504 B] Fetched 3675 kB in 0s (52.0 MB/s) Download complete and in download only mode ============================================================================= Re-Building bcftools in unstable on amd64 on ionos5-amd64 now. Date: Sat Aug 8 00:28:47 UTC 2026 Date UTC: Sat Aug 8 00:28:47 UTC 2026 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.k066tCUN + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.k066tCUN/pbuilderrc_BuXt + case ${ARCH} in + case $ARCH in + locale=et_EE + language=et + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' bcftools = debian-installer -o bcftools = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' bcftools = u-boot ']' + case "${SRCPACKAGE}" in + PBUILDERTIMEOUT=24 + local PRESULT=0 + sudo timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.k066tCUN/pbuilderrc_BuXt --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.k066tCUN/b2 --logfile b2/build.log bcftools_1.21-1.dsc W: /root/.pbuilderrc does not exist I: Logging to b2/build.log I: pbuilder: network access will be disabled during build I: Current time: Sat Aug 8 14:28:47 +14 2026 I: pbuilder-time-stamp: 1786148927 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [bcftools_1.21-1.dsc] I: copying [./bcftools_1.21.orig.tar.gz] I: copying [./bcftools_1.21-1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./bcftools_1.21-1.dsc: no acceptable signature found dpkg-source: info: extracting bcftools in bcftools-1.21 dpkg-source: info: unpacking bcftools_1.21.orig.tar.gz dpkg-source: info: unpacking bcftools_1.21-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying skip_new_test_failing_on_32bit.patch dpkg-source: info: applying 2to3.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/95539/tmp/hooks/D01_modify_environment starting debug: Running on ionos5-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Aug 8 00:29 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/95539/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/95539/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.37(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=0183688a57524f368d404b632f7b90d4 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=95539 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.k066tCUN/pbuilderrc_BuXt --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.k066tCUN/b2 --logfile b2/build.log bcftools_1.21-1.dsc' SUDO_GID=110 SUDO_UID=105 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://213.165.73.152:3128 I: uname -a Linux i-capture-the-hostname 6.12.32+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.32-1~bpo12+1 (2025-06-21) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 12 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/95539/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), zlib1g-dev, libbz2-dev, liblzma-dev, libhts-dev (>= 1.14), libgsl-dev, tabix, libio-pty-perl dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19849 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. pbuilder-satisfydepends-dummy depends on liblzma-dev; however: Package liblzma-dev is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev (>= 1.14); however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on libgsl-dev; however: Package libgsl-dev is not installed. pbuilder-satisfydepends-dummy depends on tabix; however: Package tabix is not installed. pbuilder-satisfydepends-dummy depends on libio-pty-perl; however: Package libio-pty-perl is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} comerr-dev{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} krb5-multidev{a} libarchive-zip-perl{a} libbrotli-dev{a} libbrotli1{a} libbz2-dev{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1t64{a} libevent-2.1-7t64{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgnutls30t64{a} libgsl-dev{a} libgsl28{a} libgslcblas0{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libidn2-0{a} libidn2-dev{a} libio-pty-perl{a} libk5crypto3{a} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} libldap-dev{a} libldap2{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp2-dev{a} libnghttp3-9{a} libnghttp3-dev{a} libngtcp2-16{a} libngtcp2-crypto-gnutls-dev{a} libngtcp2-crypto-gnutls8{a} libngtcp2-dev{a} libp11-kit-dev{a} libp11-kit0{a} libpipeline1{a} libpkgconf3{a} libpsl-dev{a} libpsl5t64{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libtasn1-6{a} libtasn1-6-dev{a} libtool{a} libuchardet0{a} libunbound8{a} libunistring5{a} libxml2{a} libzstd-dev{a} m4{a} man-db{a} nettle-dev{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} sensible-utils{a} tabix{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc ca-certificates curl krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules libtasn1-doc lynx publicsuffix wget 0 packages upgraded, 98 newly installed, 0 to remove and 0 not upgraded. Need to get 33.8 MB of archives. After unpacking 124 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.25 [25.0 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2 [243 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41-5 [94.6 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-8 [294 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-3+b1 [25.0 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 comerr-dev amd64 2.1-1.47.2-3+b1 [56.7 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-4 [539 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 24 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-1 [698 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2 [1680 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.2 [919 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get: 35 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 libgssrpc4t64 amd64 1.21.3-5 [60.0 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 libkadm5clnt-mit12 amd64 1.21.3-5 [42.5 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libkdb5-10t64 amd64 1.21.3-5 [42.6 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 libkadm5srv-mit12 amd64 1.21.3-5 [54.2 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 krb5-multidev amd64 1.21.3-5 [126 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 libbrotli-dev amd64 1.1.0-2+b7 [316 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.8-2 [109 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.4.8-2 [24.1 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libgnutls30t64 amd64 3.8.9-2 [1464 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 libldap2 amd64 2.6.10+dfsg-1 [194 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1.1 [76.0 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.8.0-1 [67.7 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.11.0-1 [131 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.11.0-1 [29.3 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.14.1-2 [384 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libunbound8 amd64 1.22.0-1+b1 [598 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 libgnutls-dane0t64 amd64 3.8.9-2 [455 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 libgnutls-openssl27t64 amd64 3.8.9-2 [455 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 libidn2-dev amd64 2.3.8-2 [103 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 libp11-kit-dev amd64 0.25.5-3 [208 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 libtasn1-6-dev amd64 4.20.0-2 [99.2 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-3 [329 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-3 [642 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 nettle-dev amd64 3.10.1-1 [1318 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 libgnutls28-dev amd64 3.8.9-2 [1401 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 libkrb5-dev amd64 1.21.3-5 [16.1 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 libldap-dev amd64 2.6.10+dfsg-1 [312 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 libnghttp2-dev amd64 1.64.0-1.1 [116 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 libnghttp3-dev amd64 1.8.0-1 [91.3 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.11.0-1 [34.0 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 libngtcp2-dev amd64 1.11.0-1 [179 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 libpsl-dev amd64 0.21.2-1.1+b1 [77.6 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-2+b5 [68.0 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 libssl-dev amd64 3.5.0-2 [2950 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 libssh2-1-dev amd64 1.11.1-1 [393 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.7+dfsg-1 [371 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls-dev amd64 8.14.1-2 [503 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.23-2 [47.3 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 libdeflate-dev amd64 1.23-2 [55.9 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 libgslcblas0 amd64 2.8+dfsg-5 [116 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 libgsl28 amd64 2.8+dfsg-5 [994 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 libgsl-dev amd64 2.8+dfsg-5 [1222 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.1-2 [95.8 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.21+ds-1 [463 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.8.1-1 [348 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 libhts-dev amd64 1.21+ds-1 [1733 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 libio-pty-perl amd64 1:1.20-1+b3 [34.3 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 tabix amd64 1.21+ds-1 [496 kB] Fetched 33.8 MB in 1s (42.3 MB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19849 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.25_all.deb ... Unpacking sensible-utils (0.0.25) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.46-5_amd64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-2_amd64.deb ... Unpacking gettext-base (0.23.1-2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-9_amd64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.41-5_amd64.deb ... Unpacking bsdextrautils (2.41-5) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.1-1_amd64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-8_amd64.deb ... Unpacking m4 (1.4.19-8) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.23.1-2_all.deb ... Unpacking autopoint (0.23.1-2) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../15-libcom-err2_1.47.2-3+b1_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.2-3+b1) ... Selecting previously unselected package comerr-dev:amd64. Preparing to unpack .../16-comerr-dev_2.1-1.47.2-3+b1_amd64.deb ... Unpacking comerr-dev:amd64 (2.1-1.47.2-3+b1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../17-libdebhelper-perl_13.24.2_all.deb ... Unpacking libdebhelper-perl (13.24.2) ... Selecting previously unselected package libtool. Preparing to unpack .../18-libtool_2.5.4-4_all.deb ... Unpacking libtool (2.5.4-4) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../19-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../20-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../21-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../22-dh-strip-nondeterminism_1.14.1-2_all.deb ... Unpacking dh-strip-nondeterminism (1.14.1-2) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../23-libelf1t64_0.192-4_amd64.deb ... Unpacking libelf1t64:amd64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../24-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libunistring5:amd64. Preparing to unpack .../25-libunistring5_1.3-2_amd64.deb ... Unpacking libunistring5:amd64 (1.3-2) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../26-libxml2_2.12.7+dfsg+really2.9.14-1_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-1) ... Selecting previously unselected package gettext. Preparing to unpack .../27-gettext_0.23.1-2_amd64.deb ... Unpacking gettext (0.23.1-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../28-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../29-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../30-debhelper_13.24.2_all.deb ... Unpacking debhelper (13.24.2) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../31-libkrb5support0_1.21.3-5_amd64.deb ... Unpacking libkrb5support0:amd64 (1.21.3-5) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../32-libk5crypto3_1.21.3-5_amd64.deb ... Unpacking libk5crypto3:amd64 (1.21.3-5) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../33-libkeyutils1_1.6.3-6_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-6) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../34-libkrb5-3_1.21.3-5_amd64.deb ... Unpacking libkrb5-3:amd64 (1.21.3-5) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../35-libgssapi-krb5-2_1.21.3-5_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.21.3-5) ... Selecting previously unselected package libgssrpc4t64:amd64. Preparing to unpack .../36-libgssrpc4t64_1.21.3-5_amd64.deb ... Unpacking libgssrpc4t64:amd64 (1.21.3-5) ... Selecting previously unselected package libkadm5clnt-mit12:amd64. Preparing to unpack .../37-libkadm5clnt-mit12_1.21.3-5_amd64.deb ... Unpacking libkadm5clnt-mit12:amd64 (1.21.3-5) ... Selecting previously unselected package libkdb5-10t64:amd64. Preparing to unpack .../38-libkdb5-10t64_1.21.3-5_amd64.deb ... Unpacking libkdb5-10t64:amd64 (1.21.3-5) ... Selecting previously unselected package libkadm5srv-mit12:amd64. Preparing to unpack .../39-libkadm5srv-mit12_1.21.3-5_amd64.deb ... Unpacking libkadm5srv-mit12:amd64 (1.21.3-5) ... Selecting previously unselected package krb5-multidev:amd64. Preparing to unpack .../40-krb5-multidev_1.21.3-5_amd64.deb ... Unpacking krb5-multidev:amd64 (1.21.3-5) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../41-libbrotli1_1.1.0-2+b7_amd64.deb ... Unpacking libbrotli1:amd64 (1.1.0-2+b7) ... Selecting previously unselected package libbrotli-dev:amd64. Preparing to unpack .../42-libbrotli-dev_1.1.0-2+b7_amd64.deb ... Unpacking libbrotli-dev:amd64 (1.1.0-2+b7) ... Selecting previously unselected package libbz2-dev:amd64. Preparing to unpack .../43-libbz2-dev_1.0.8-6_amd64.deb ... Unpacking libbz2-dev:amd64 (1.0.8-6) ... Selecting previously unselected package libidn2-0:amd64. Preparing to unpack .../44-libidn2-0_2.3.8-2_amd64.deb ... Unpacking libidn2-0:amd64 (2.3.8-2) ... Selecting previously unselected package libffi8:amd64. Preparing to unpack .../45-libffi8_3.4.8-2_amd64.deb ... Unpacking libffi8:amd64 (3.4.8-2) ... Selecting previously unselected package libp11-kit0:amd64. Preparing to unpack .../46-libp11-kit0_0.25.5-3_amd64.deb ... Unpacking libp11-kit0:amd64 (0.25.5-3) ... Selecting previously unselected package libtasn1-6:amd64. Preparing to unpack .../47-libtasn1-6_4.20.0-2_amd64.deb ... Unpacking libtasn1-6:amd64 (4.20.0-2) ... Selecting previously unselected package libgnutls30t64:amd64. Preparing to unpack .../48-libgnutls30t64_3.8.9-2_amd64.deb ... Unpacking libgnutls30t64:amd64 (3.8.9-2) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../49-libsasl2-modules-db_2.1.28+dfsg1-9_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg1-9) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../50-libsasl2-2_2.1.28+dfsg1-9_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg1-9) ... Selecting previously unselected package libldap2:amd64. Preparing to unpack .../51-libldap2_2.6.10+dfsg-1_amd64.deb ... Unpacking libldap2:amd64 (2.6.10+dfsg-1) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../52-libnghttp2-14_1.64.0-1.1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.64.0-1.1) ... Selecting previously unselected package libnghttp3-9:amd64. Preparing to unpack .../53-libnghttp3-9_1.8.0-1_amd64.deb ... Unpacking libnghttp3-9:amd64 (1.8.0-1) ... Selecting previously unselected package libngtcp2-16:amd64. Preparing to unpack .../54-libngtcp2-16_1.11.0-1_amd64.deb ... Unpacking libngtcp2-16:amd64 (1.11.0-1) ... Selecting previously unselected package libngtcp2-crypto-gnutls8:amd64. Preparing to unpack .../55-libngtcp2-crypto-gnutls8_1.11.0-1_amd64.deb ... Unpacking libngtcp2-crypto-gnutls8:amd64 (1.11.0-1) ... Selecting previously unselected package libpsl5t64:amd64. Preparing to unpack .../56-libpsl5t64_0.21.2-1.1+b1_amd64.deb ... Unpacking libpsl5t64:amd64 (0.21.2-1.1+b1) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../57-librtmp1_2.4+20151223.gitfa8646d.1-2+b5_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Selecting previously unselected package libssh2-1t64:amd64. Preparing to unpack .../58-libssh2-1t64_1.11.1-1_amd64.deb ... Unpacking libssh2-1t64:amd64 (1.11.1-1) ... Selecting previously unselected package libcurl3t64-gnutls:amd64. Preparing to unpack .../59-libcurl3t64-gnutls_8.14.1-2_amd64.deb ... Unpacking libcurl3t64-gnutls:amd64 (8.14.1-2) ... Selecting previously unselected package libevent-2.1-7t64:amd64. Preparing to unpack .../60-libevent-2.1-7t64_2.1.12-stable-10+b1_amd64.deb ... Unpacking libevent-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Selecting previously unselected package libunbound8:amd64. Preparing to unpack .../61-libunbound8_1.22.0-1+b1_amd64.deb ... Unpacking libunbound8:amd64 (1.22.0-1+b1) ... Selecting previously unselected package libgnutls-dane0t64:amd64. Preparing to unpack .../62-libgnutls-dane0t64_3.8.9-2_amd64.deb ... Unpacking libgnutls-dane0t64:amd64 (3.8.9-2) ... Selecting previously unselected package libgnutls-openssl27t64:amd64. Preparing to unpack .../63-libgnutls-openssl27t64_3.8.9-2_amd64.deb ... Unpacking libgnutls-openssl27t64:amd64 (3.8.9-2) ... Selecting previously unselected package libidn2-dev:amd64. Preparing to unpack .../64-libidn2-dev_2.3.8-2_amd64.deb ... Unpacking libidn2-dev:amd64 (2.3.8-2) ... Selecting previously unselected package libp11-kit-dev:amd64. Preparing to unpack .../65-libp11-kit-dev_0.25.5-3_amd64.deb ... Unpacking libp11-kit-dev:amd64 (0.25.5-3) ... Selecting previously unselected package libtasn1-6-dev:amd64. Preparing to unpack .../66-libtasn1-6-dev_4.20.0-2_amd64.deb ... Unpacking libtasn1-6-dev:amd64 (4.20.0-2) ... Selecting previously unselected package libgmpxx4ldbl:amd64. Preparing to unpack .../67-libgmpxx4ldbl_2%3a6.3.0+dfsg-3_amd64.deb ... Unpacking libgmpxx4ldbl:amd64 (2:6.3.0+dfsg-3) ... Selecting previously unselected package libgmp-dev:amd64. Preparing to unpack .../68-libgmp-dev_2%3a6.3.0+dfsg-3_amd64.deb ... Unpacking libgmp-dev:amd64 (2:6.3.0+dfsg-3) ... Selecting previously unselected package nettle-dev:amd64. Preparing to unpack .../69-nettle-dev_3.10.1-1_amd64.deb ... Unpacking nettle-dev:amd64 (3.10.1-1) ... Selecting previously unselected package libgnutls28-dev:amd64. Preparing to unpack .../70-libgnutls28-dev_3.8.9-2_amd64.deb ... Unpacking libgnutls28-dev:amd64 (3.8.9-2) ... Selecting previously unselected package libkrb5-dev:amd64. Preparing to unpack .../71-libkrb5-dev_1.21.3-5_amd64.deb ... Unpacking libkrb5-dev:amd64 (1.21.3-5) ... 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Setting up autoconf (2.72-3.1) ... Setting up libnghttp3-9:amd64 (1.8.0-1) ... Setting up libnghttp3-dev:amd64 (1.8.0-1) ... Setting up liblzma-dev:amd64 (5.8.1-1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libffi8:amd64 (3.4.8-2) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.25) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up libtasn1-6:amd64 (4.20.0-2) ... Setting up libngtcp2-16:amd64 (1.11.0-1) ... Setting up libkrb5-3:amd64 (1.21.3-5) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up libgsl28:amd64 (2.8+dfsg-5) ... Setting up libtasn1-6-dev:amd64 (4.20.0-2) ... Setting up libdeflate-dev:amd64 (1.23-2) ... Setting up tabix (1.21+ds-1) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-1) ... Setting up libldap2:amd64 (2.6.10+dfsg-1) ... Setting up libbrotli-dev:amd64 (1.1.0-2+b7) ... Setting up libbz2-dev:amd64 (1.0.8-6) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up gettext (0.23.1-2) ... Setting up libgsl-dev (2.8+dfsg-5) ... Setting up libgmp-dev:amd64 (2:6.3.0+dfsg-3) ... Setting up nettle-dev:amd64 (3.10.1-1) ... Setting up libtool (2.5.4-4) ... Setting up libidn2-0:amd64 (2.3.8-2) ... Setting up libngtcp2-dev:amd64 (1.11.0-1) ... Setting up pkgconf:amd64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libldap-dev:amd64 (2.6.10+dfsg-1) ... Setting up libp11-kit0:amd64 (0.25.5-3) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-5) ... Setting up libssh2-1-dev:amd64 (1.11.1-1) ... Setting up libidn2-dev:amd64 (2.3.8-2) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-9) ... Setting up libp11-kit-dev:amd64 (0.25.5-3) ... Setting up libgnutls30t64:amd64 (3.8.9-2) ... Setting up libgnutls-openssl27t64:amd64 (3.8.9-2) ... Setting up libnghttp2-dev:amd64 (1.64.0-1.1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libpsl-dev:amd64 (0.21.2-1.1+b1) ... Setting up libgnutls-dane0t64:amd64 (3.8.9-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libgssrpc4t64:amd64 (1.21.3-5) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.11.0-1) ... Setting up libkadm5clnt-mit12:amd64 (1.21.3-5) ... Setting up libgnutls28-dev:amd64 (3.8.9-2) ... Setting up libkdb5-10t64:amd64 (1.21.3-5) ... Setting up libcurl3t64-gnutls:amd64 (8.14.1-2) ... Setting up debhelper (13.24.2) ... Setting up libngtcp2-crypto-gnutls-dev:amd64 (1.11.0-1) ... Setting up librtmp-dev:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libkadm5srv-mit12:amd64 (1.21.3-5) ... Setting up libhts3t64:amd64 (1.21+ds-1) ... Setting up krb5-multidev:amd64 (1.21.3-5) ... Setting up libkrb5-dev:amd64 (1.21.3-5) ... Setting up libcurl4-gnutls-dev:amd64 (8.14.1-2) ... Setting up libhts-dev:amd64 (1.21+ds-1) ... Processing triggers for libc-bin (2.41-9) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/95539/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/95539/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/bcftools-1.21/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../bcftools_1.21-1_source.changes dpkg-buildpackage: info: source package bcftools dpkg-buildpackage: info: source version 1.21-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean rm -f config.mk && touch config.mk dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/bcftools-1.21' dh_auto_clean make -j42 distclean make[2]: Entering directory '/build/reproducible-path/bcftools-1.21' rm -f test/*.o test/*.fa.fai test/*~ test/test-rbuf test/test-regidx rm -f plugins/*.so plugins/*.P rm -rf plugins/*.dSYM rm -f test/*.unsorted.hex test/*.unsorted.tsv rm -f gmon.out *.o *.a *~ bcftools version.h rm -rf *.dSYM test/*.dSYM rm -f config.cache config.h config.log config.mk config.status rm -rf autom4te.cache rm -f TAGS make[2]: Leaving directory '/build/reproducible-path/bcftools-1.21' rm -f test/mpileup/indel-AD.1.out.new test/view-t.1.out.new test/view-t.2.out.new make[1]: Leaving directory '/build/reproducible-path/bcftools-1.21' dh_clean debian/rules binary dh binary dh_update_autotools_config debian/rules override_dh_autoreconf make[1]: Entering directory '/build/reproducible-path/bcftools-1.21' rm -f config.mk && touch config.mk export MAKEFLAGS="-s"; dh_autoreconf configure.ac:94: warning: _AC_CONFIG_SUBDIRS: you should use literals ./lib/autoconf/status.m4:1096: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:94: the top level make[1]: Leaving directory '/build/reproducible-path/bcftools-1.21' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/bcftools-1.21' dh_auto_configure -- \ --with-htslib=system \ --enable-gsl \ --with-cblas=gslcblas \ --with-bcf-plugin-dir=/usr/lib/x86_64-linux-gnu/bcftools ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system --enable-gsl --with-cblas=gslcblas --with-bcf-plugin-dir=/usr/lib/x86_64-linux-gnu/bcftools checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking for -Wdate-time -D_FORTIFY_SOURCE=2 option for large files... none needed checking for htslib/sam.h... yes checking for hts_version in -lhts... yes checking shared library type... plain .so checking for library containing dlopen... none required checking if the compiler accepts -rdynamic... yes checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing regcomp... none required configure: creating ./config.status config.status: creating config.mk config.status: creating config.h make[1]: Leaving directory '/build/reproducible-path/bcftools-1.21' dh_auto_build make -j42 make[1]: Entering directory '/build/reproducible-path/bcftools-1.21' echo '#define BCFTOOLS_VERSION "1.21"' > version.h gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfindex.o vcfindex.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tabix.o tabix.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfstats.o vcfstats.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfisec.o vcfisec.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfmerge.o vcfmerge.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfquery.o vcfquery.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcffilter.o vcffilter.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o filter.o filter.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfsom.o vcfsom.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfnorm.o vcfnorm.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfgtcheck.o vcfgtcheck.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfview.o vcfview.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfannotate.o vcfannotate.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfroh.o vcfroh.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfconcat.o vcfconcat.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcall.o vcfcall.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mcall.o mcall.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcmp.o vcmp.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gvcf.o gvcf.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o reheader.o reheader.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o convert.o convert.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfconvert.o vcfconvert.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tsv2vcf.o tsv2vcf.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcnv.o vcfcnv.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfhead.o vcfhead.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o HMM.o HMM.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o consensus.o consensus.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ploidy.o ploidy.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bin.o bin.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hclust.o hclust.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o version.o version.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o regidx.o regidx.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o smpl_ilist.o smpl_ilist.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o csq.o csq.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfbuf.o vcfbuf.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mpileup.o mpileup.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_iaux.o bam2bcf_iaux.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_edlib.o bam2bcf_edlib.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o read_consensus.o read_consensus.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sample.o bam_sample.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfsort.o vcfsort.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cols.o cols.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o extsort.o extsort.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dist.o dist.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o abuf.o abuf.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ccall.o ccall.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o em.o em.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o prob1.o prob1.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kmin.o kmin.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o str_finder.o str_finder.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gff.o gff.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o edlib.o edlib.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DPLUGINPATH='"/usr/lib/x86_64-linux-gnu/bcftools"' -c -o vcfplugin.o vcfplugin.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-rbuf.o test/test-rbuf.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-regidx.o test/test-regidx.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/GTisec.so version.c plugins/GTisec.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/GTsubset.so version.c plugins/GTsubset.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/ad-bias.so convert.c version.c plugins/ad-bias.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/add-variantkey.so version.c plugins/add-variantkey.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/af-dist.so bin.c version.c plugins/af-dist.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/allele-length.so version.c plugins/allele-length.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/check-ploidy.so version.c plugins/check-ploidy.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/check-sparsity.so version.c plugins/check-sparsity.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/color-chrs.so HMM.c version.c plugins/color-chrs.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/contrast.so version.c plugins/contrast.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/counts.so version.c plugins/counts.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/dosage.so version.c plugins/dosage.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/fill-AN-AC.so version.c plugins/fill-AN-AC.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/fill-from-fasta.so filter.c version.c plugins/fill-from-fasta.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/fill-tags.so version.c plugins/fill-tags.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/fixploidy.so ploidy.c regidx.c version.c plugins/fixploidy.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/fixref.so version.c plugins/fixref.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/frameshifts.so version.c plugins/frameshifts.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/guess-ploidy.so version.c plugins/guess-ploidy.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/gvcfz.so version.c plugins/gvcfz.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/impute-info.so version.c plugins/impute-info.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/indel-stats.so version.c plugins/indel-stats.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/isecGT.so smpl_ilist.c version.c plugins/isecGT.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/mendelian2.so version.c plugins/mendelian2.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/missing2ref.so version.c plugins/missing2ref.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/parental-origin.so version.c plugins/parental-origin.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/prune.so version.c plugins/prune.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/remove-overlaps.so version.c plugins/remove-overlaps.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/scatter.so version.c plugins/scatter.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/setGT.so version.c plugins/setGT.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/smpl-stats.so version.c plugins/smpl-stats.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/split-vep.so version.c plugins/split-vep.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/split.so version.c plugins/split.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/tag2tag.so version.c plugins/tag2tag.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/trio-dnm2.so version.c plugins/trio-dnm2.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/trio-stats.so version.c plugins/trio-stats.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/trio-switch-rate.so version.c plugins/trio-switch-rate.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/variant-distance.so version.c plugins/variant-distance.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/variantkey-hex.so version.c plugins/variantkey-hex.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o main.o main.c gcc -Wl,-z,relro -Wl,-z,now -o test/test-rbuf test/test-rbuf.o -lz gcc -Wl,-z,relro -Wl,-z,now -o test/test-regidx test/test-regidx.o regidx.o -lhts -lpthread -lz gcc -rdynamic -Wl,-z,relro -Wl,-z,now -o bcftools main.o vcfindex.o tabix.o vcfstats.o vcfisec.o vcfmerge.o vcfquery.o vcffilter.o filter.o vcfsom.o vcfnorm.o vcfgtcheck.o vcfview.o vcfannotate.o vcfroh.o vcfconcat.o vcfcall.o mcall.o vcmp.o gvcf.o reheader.o convert.o vcfconvert.o tsv2vcf.o vcfcnv.o vcfhead.o HMM.o consensus.o ploidy.o bin.o hclust.o version.o regidx.o smpl_ilist.o csq.o vcfbuf.o mpileup.o bam2bcf.o bam2bcf_indel.o bam2bcf_iaux.o bam2bcf_edlib.o read_consensus.o bam_sample.o vcfsort.o cols.o extsort.o dist.o abuf.o ccall.o em.o prob1.o kmin.o str_finder.o gff.o edlib.o vcfplugin.o -lhts -lm -lz -lpthread make[1]: Leaving directory '/build/reproducible-path/bcftools-1.21' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/bcftools-1.21' make test-no-plugins VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/bcftools-1.21' ./test/test-rbuf Inserted 1-9 starting at offset 5: 5 6 7 8 9 0 1 2 3 1 2 3 4 5 6 7 8 9 4th is 4 Deleting 1-2: 7 8 9 0 1 2 3 3 4 5 6 7 8 9 Prepending 0-8: 8 9 0 1 2 3 4 5 6 7 8 7 6 5 4 3 2 1 0 3 Expanding: 8 9 10 11 12 13 14 15 16 17 8 7 6 5 4 3 2 1 0 3 ./test/test-regidx REF_PATH=: ./test/test.pl --exec bgzip= --exec tabix= --htsdir= ${TEST_OPTS:-} test_usage: bcftools .. ok test_usage_subcommand: bcftools index .. ok test_usage_subcommand: bcftools annotate .. ok test_usage_subcommand: bcftools concat .. ok test_usage_subcommand: bcftools convert .. ok test_usage_subcommand: bcftools head .. ok test_usage_subcommand: bcftools isec .. ok test_usage_subcommand: bcftools merge .. ok test_usage_subcommand: bcftools norm .. ok test_usage_subcommand: bcftools plugin .. ok test_usage_subcommand: bcftools query .. ok test_usage_subcommand: bcftools reheader .. ok test_usage_subcommand: bcftools sort .. ok test_usage_subcommand: bcftools view .. ok test_usage_subcommand: bcftools call .. ok test_usage_subcommand: bcftools consensus .. ok test_usage_subcommand: bcftools cnv .. ok test_usage_subcommand: bcftools csq .. ok test_usage_subcommand: bcftools filter .. ok test_usage_subcommand: bcftools gtcheck .. ok test_usage_subcommand: bcftools mpileup .. ok test_usage_subcommand: bcftools roh .. ok test_usage_subcommand: bcftools stats .. ok test_tabix: tabix /tmp/zPov9rP7t1/merge.a.vcf.gz 2:3199812-3199812 .. ok test_tabix: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/zPov9rP7t1/merge.a.bcf 2:3199812-3199812 .. ok test_tabix: tabix /tmp/zPov9rP7t1/merge.a.vcf.gz 1:3000151-3000151 .. ok test_tabix: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/zPov9rP7t1/merge.a.bcf 1:3000151-3000151 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/zPov9rP7t1/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/zPov9rP7t1/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/zPov9rP7t1/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/zPov9rP7t1/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/zPov9rP7t1/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/zPov9rP7t1/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/zPov9rP7t1/large_chrom_csi_limit.bcf chr20 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/zPov9rP7t1/large_chrom_csi_limit.bcf chr20 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/zPov9rP7t1/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/zPov9rP7t1/large_chrom_csi_limit.bcf chr20 .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -s /tmp/zPov9rP7t1/idx.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -s /tmp/zPov9rP7t1/idx.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -s /tmp/zPov9rP7t1/idx.bcf .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/zPov9rP7t1/idx.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/zPov9rP7t1/idx.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/zPov9rP7t1/idx.vcf.gz.csi .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/zPov9rP7t1/idx.bcf .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/zPov9rP7t1/idx.bcf.csi .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -s /tmp/zPov9rP7t1/empty.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -s /tmp/zPov9rP7t1/empty.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -s /tmp/zPov9rP7t1/empty.bcf .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/zPov9rP7t1/empty.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/zPov9rP7t1/empty.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/zPov9rP7t1/empty.vcf.gz.csi .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/zPov9rP7t1/empty.bcf .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/zPov9rP7t1/empty.bcf.csi .. ok test_vcf_check: /build/reproducible-path/bcftools-1.21/bcftools stats -s - /tmp/zPov9rP7t1/check.vcf.gz | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/check.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools stats -s - | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check_merge: /build/reproducible-path/bcftools-1.21/misc/plot-vcfstats -m /tmp/zPov9rP7t1/check.1.chk /tmp/zPov9rP7t1/check.2.chk /tmp/zPov9rP7t1/check.3.chk /tmp/zPov9rP7t1/check.4.chk | grep -v 'plot-vcfstats' | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_stats: /build/reproducible-path/bcftools-1.21/bcftools stats -s - /tmp/zPov9rP7t1/stats.a.vcf.gz /tmp/zPov9rP7t1/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/reproducible-path/bcftools-1.21/bcftools stats -s B /tmp/zPov9rP7t1/stats.a.vcf.gz /tmp/zPov9rP7t1/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/reproducible-path/bcftools-1.21/bcftools stats -s - /tmp/zPov9rP7t1/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/reproducible-path/bcftools-1.21/bcftools stats -s - -i 'type="snp"' /tmp/zPov9rP7t1/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/reproducible-path/bcftools-1.21/bcftools stats -s - /tmp/zPov9rP7t1/stats.vaf.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -n =2 /tmp/zPov9rP7t1/isec.a.vcf.gz /tmp/zPov9rP7t1/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -n =2 /tmp/zPov9rP7t1/isec.a.vcf.gz /tmp/zPov9rP7t1/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/zPov9rP7t1/isec.a.vcf.gz /tmp/zPov9rP7t1/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -n =2 -i"STRLEN(REF)==2" /tmp/zPov9rP7t1/isec.a.vcf.gz /tmp/zPov9rP7t1/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -n =2 -c both /tmp/zPov9rP7t1/isec.a.vcf.gz /tmp/zPov9rP7t1/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -n =2 -c both /tmp/zPov9rP7t1/isec.a.vcf.gz /tmp/zPov9rP7t1/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -n =2 -c any /tmp/zPov9rP7t1/isec.a.vcf.gz /tmp/zPov9rP7t1/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -n =2 -c any /tmp/zPov9rP7t1/isec.a.vcf.gz /tmp/zPov9rP7t1/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -C -c any /tmp/zPov9rP7t1/isec.a.vcf.gz /tmp/zPov9rP7t1/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -C -c any /tmp/zPov9rP7t1/isec.a.vcf.gz /tmp/zPov9rP7t1/isec.b.vcf.gz .. ok test_vcf_isec2: /build/reproducible-path/bcftools-1.21/bcftools isec --no-version -T /tmp/zPov9rP7t1/isec.tab.gz /tmp/zPov9rP7t1/isec.a.vcf.gz .. ok test_vcf_isec2: /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -T /tmp/zPov9rP7t1/isec.tab.gz /tmp/zPov9rP7t1/isec.a.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/zPov9rP7t1/isec-miss.1.1.vcf.gz /tmp/zPov9rP7t1/isec-miss.1.2.vcf.gz /tmp/zPov9rP7t1/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/zPov9rP7t1/isec-miss.1.1.vcf.gz /tmp/zPov9rP7t1/isec-miss.1.2.vcf.gz /tmp/zPov9rP7t1/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -R /build/reproducible-path/bcftools-1.21/test/isec-miss.1.regs.txt -n +1 /tmp/zPov9rP7t1/isec-miss.1.1.vcf.gz /tmp/zPov9rP7t1/isec-miss.1.2.vcf.gz /tmp/zPov9rP7t1/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -R /build/reproducible-path/bcftools-1.21/test/isec-miss.1.regs.txt -n +1 /tmp/zPov9rP7t1/isec-miss.1.1.vcf.gz /tmp/zPov9rP7t1/isec-miss.1.2.vcf.gz /tmp/zPov9rP7t1/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/zPov9rP7t1/isec-miss.2.1.vcf.gz /tmp/zPov9rP7t1/isec-miss.2.2.vcf.gz /tmp/zPov9rP7t1/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/zPov9rP7t1/isec-miss.2.1.vcf.gz /tmp/zPov9rP7t1/isec-miss.2.2.vcf.gz /tmp/zPov9rP7t1/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -R /build/reproducible-path/bcftools-1.21/test/isec-miss.1.regs.txt -n +1 /tmp/zPov9rP7t1/isec-miss.2.1.vcf.gz /tmp/zPov9rP7t1/isec-miss.2.2.vcf.gz /tmp/zPov9rP7t1/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -R /build/reproducible-path/bcftools-1.21/test/isec-miss.1.regs.txt -n +1 /tmp/zPov9rP7t1/isec-miss.2.1.vcf.gz /tmp/zPov9rP7t1/isec-miss.2.2.vcf.gz /tmp/zPov9rP7t1/isec-miss.2.3.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/zPov9rP7t1/merge.11.a.vcf.gz /tmp/zPov9rP7t1/merge.11.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/zPov9rP7t1/merge.11.a.vcf.gz /tmp/zPov9rP7t1/merge.11.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/zPov9rP7t1/merge.11.a.bcf /tmp/zPov9rP7t1/merge.11.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/zPov9rP7t1/merge.11.a.bcf /tmp/zPov9rP7t1/merge.11.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -i AF:join /tmp/zPov9rP7t1/merge.join.a.vcf.gz /tmp/zPov9rP7t1/merge.join.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -i AF:join /tmp/zPov9rP7t1/merge.join.a.vcf.gz /tmp/zPov9rP7t1/merge.join.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -i AF:join /tmp/zPov9rP7t1/merge.join.a.bcf /tmp/zPov9rP7t1/merge.join.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -i AF:join /tmp/zPov9rP7t1/merge.join.a.bcf /tmp/zPov9rP7t1/merge.join.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-single /tmp/zPov9rP7t1/merge.LPL.a.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-single /tmp/zPov9rP7t1/merge.LPL.a.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-single /tmp/zPov9rP7t1/merge.LPL.a.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-single /tmp/zPov9rP7t1/merge.LPL.a.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples /tmp/zPov9rP7t1/merge.LPL.a.vcf.gz /tmp/zPov9rP7t1/merge.LPL.b.vcf.gz /tmp/zPov9rP7t1/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/zPov9rP7t1/merge.LPL.a.vcf.gz /tmp/zPov9rP7t1/merge.LPL.b.vcf.gz /tmp/zPov9rP7t1/merge.LPL.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples /tmp/zPov9rP7t1/merge.LPL.a.bcf /tmp/zPov9rP7t1/merge.LPL.b.bcf /tmp/zPov9rP7t1/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/zPov9rP7t1/merge.LPL.a.bcf /tmp/zPov9rP7t1/merge.LPL.b.bcf /tmp/zPov9rP7t1/merge.LPL.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -L 1 /tmp/zPov9rP7t1/merge.LPL.a.vcf.gz /tmp/zPov9rP7t1/merge.LPL.b.vcf.gz /tmp/zPov9rP7t1/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 1 /tmp/zPov9rP7t1/merge.LPL.a.vcf.gz /tmp/zPov9rP7t1/merge.LPL.b.vcf.gz /tmp/zPov9rP7t1/merge.LPL.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -L 1 /tmp/zPov9rP7t1/merge.LPL.a.bcf /tmp/zPov9rP7t1/merge.LPL.b.bcf /tmp/zPov9rP7t1/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 1 /tmp/zPov9rP7t1/merge.LPL.a.bcf /tmp/zPov9rP7t1/merge.LPL.b.bcf /tmp/zPov9rP7t1/merge.LPL.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -L 2 /tmp/zPov9rP7t1/merge.LPL.a.vcf.gz /tmp/zPov9rP7t1/merge.LPL.b.vcf.gz /tmp/zPov9rP7t1/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 2 /tmp/zPov9rP7t1/merge.LPL.a.vcf.gz /tmp/zPov9rP7t1/merge.LPL.b.vcf.gz /tmp/zPov9rP7t1/merge.LPL.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -L 2 /tmp/zPov9rP7t1/merge.LPL.a.bcf /tmp/zPov9rP7t1/merge.LPL.b.bcf /tmp/zPov9rP7t1/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 2 /tmp/zPov9rP7t1/merge.LPL.a.bcf /tmp/zPov9rP7t1/merge.LPL.b.bcf /tmp/zPov9rP7t1/merge.LPL.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -L 3 /tmp/zPov9rP7t1/merge.LPL.a.vcf.gz /tmp/zPov9rP7t1/merge.LPL.b.vcf.gz /tmp/zPov9rP7t1/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 3 /tmp/zPov9rP7t1/merge.LPL.a.vcf.gz /tmp/zPov9rP7t1/merge.LPL.b.vcf.gz /tmp/zPov9rP7t1/merge.LPL.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -L 3 /tmp/zPov9rP7t1/merge.LPL.a.bcf /tmp/zPov9rP7t1/merge.LPL.b.bcf /tmp/zPov9rP7t1/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 3 /tmp/zPov9rP7t1/merge.LPL.a.bcf /tmp/zPov9rP7t1/merge.LPL.b.bcf /tmp/zPov9rP7t1/merge.LPL.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -L 4 /tmp/zPov9rP7t1/merge.LPL.a.vcf.gz /tmp/zPov9rP7t1/merge.LPL.b.vcf.gz /tmp/zPov9rP7t1/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 4 /tmp/zPov9rP7t1/merge.LPL.a.vcf.gz /tmp/zPov9rP7t1/merge.LPL.b.vcf.gz /tmp/zPov9rP7t1/merge.LPL.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -L 4 /tmp/zPov9rP7t1/merge.LPL.a.bcf /tmp/zPov9rP7t1/merge.LPL.b.bcf /tmp/zPov9rP7t1/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 4 /tmp/zPov9rP7t1/merge.LPL.a.bcf /tmp/zPov9rP7t1/merge.LPL.b.bcf /tmp/zPov9rP7t1/merge.LPL.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -L 5 /tmp/zPov9rP7t1/merge.LPL.a.vcf.gz /tmp/zPov9rP7t1/merge.LPL.b.vcf.gz /tmp/zPov9rP7t1/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 5 /tmp/zPov9rP7t1/merge.LPL.a.vcf.gz /tmp/zPov9rP7t1/merge.LPL.b.vcf.gz /tmp/zPov9rP7t1/merge.LPL.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -L 5 /tmp/zPov9rP7t1/merge.LPL.a.bcf /tmp/zPov9rP7t1/merge.LPL.b.bcf /tmp/zPov9rP7t1/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 5 /tmp/zPov9rP7t1/merge.LPL.a.bcf /tmp/zPov9rP7t1/merge.LPL.b.bcf /tmp/zPov9rP7t1/merge.LPL.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples /tmp/zPov9rP7t1/merge.a.vcf.gz /tmp/zPov9rP7t1/merge.b.vcf.gz /tmp/zPov9rP7t1/merge.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/zPov9rP7t1/merge.a.vcf.gz /tmp/zPov9rP7t1/merge.b.vcf.gz /tmp/zPov9rP7t1/merge.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples /tmp/zPov9rP7t1/merge.a.bcf /tmp/zPov9rP7t1/merge.b.bcf /tmp/zPov9rP7t1/merge.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/zPov9rP7t1/merge.a.bcf /tmp/zPov9rP7t1/merge.b.bcf /tmp/zPov9rP7t1/merge.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -Fx /tmp/zPov9rP7t1/merge.a.vcf.gz /tmp/zPov9rP7t1/merge.b.vcf.gz /tmp/zPov9rP7t1/merge.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -Fx /tmp/zPov9rP7t1/merge.a.vcf.gz /tmp/zPov9rP7t1/merge.b.vcf.gz /tmp/zPov9rP7t1/merge.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -Fx /tmp/zPov9rP7t1/merge.a.bcf /tmp/zPov9rP7t1/merge.b.bcf /tmp/zPov9rP7t1/merge.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -Fx /tmp/zPov9rP7t1/merge.a.bcf /tmp/zPov9rP7t1/merge.b.bcf /tmp/zPov9rP7t1/merge.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -0 /tmp/zPov9rP7t1/merge.a.vcf.gz /tmp/zPov9rP7t1/merge.b.vcf.gz /tmp/zPov9rP7t1/merge.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -0 /tmp/zPov9rP7t1/merge.a.vcf.gz /tmp/zPov9rP7t1/merge.b.vcf.gz /tmp/zPov9rP7t1/merge.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -0 /tmp/zPov9rP7t1/merge.a.bcf /tmp/zPov9rP7t1/merge.b.bcf /tmp/zPov9rP7t1/merge.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -0 /tmp/zPov9rP7t1/merge.a.bcf /tmp/zPov9rP7t1/merge.b.bcf /tmp/zPov9rP7t1/merge.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -m none /tmp/zPov9rP7t1/merge.2.a.vcf.gz /tmp/zPov9rP7t1/merge.2.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m none /tmp/zPov9rP7t1/merge.2.a.vcf.gz /tmp/zPov9rP7t1/merge.2.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -m none /tmp/zPov9rP7t1/merge.2.a.bcf /tmp/zPov9rP7t1/merge.2.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m none /tmp/zPov9rP7t1/merge.2.a.bcf /tmp/zPov9rP7t1/merge.2.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -m both /tmp/zPov9rP7t1/merge.2.a.vcf.gz /tmp/zPov9rP7t1/merge.2.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m both /tmp/zPov9rP7t1/merge.2.a.vcf.gz /tmp/zPov9rP7t1/merge.2.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -m both /tmp/zPov9rP7t1/merge.2.a.bcf /tmp/zPov9rP7t1/merge.2.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m both /tmp/zPov9rP7t1/merge.2.a.bcf /tmp/zPov9rP7t1/merge.2.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -m all /tmp/zPov9rP7t1/merge.2.a.vcf.gz /tmp/zPov9rP7t1/merge.2.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m all /tmp/zPov9rP7t1/merge.2.a.vcf.gz /tmp/zPov9rP7t1/merge.2.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -m all /tmp/zPov9rP7t1/merge.2.a.bcf /tmp/zPov9rP7t1/merge.2.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m all /tmp/zPov9rP7t1/merge.2.a.bcf /tmp/zPov9rP7t1/merge.2.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/zPov9rP7t1/merge.3.a.vcf.gz /tmp/zPov9rP7t1/merge.3.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/zPov9rP7t1/merge.3.a.vcf.gz /tmp/zPov9rP7t1/merge.3.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/zPov9rP7t1/merge.3.a.bcf /tmp/zPov9rP7t1/merge.3.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/zPov9rP7t1/merge.3.a.bcf /tmp/zPov9rP7t1/merge.3.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -m id /tmp/zPov9rP7t1/merge.4.a.vcf.gz /tmp/zPov9rP7t1/merge.4.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m id /tmp/zPov9rP7t1/merge.4.a.vcf.gz /tmp/zPov9rP7t1/merge.4.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -m id /tmp/zPov9rP7t1/merge.4.a.bcf /tmp/zPov9rP7t1/merge.4.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m id /tmp/zPov9rP7t1/merge.4.a.bcf /tmp/zPov9rP7t1/merge.4.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/zPov9rP7t1/gvcf.merge.1.vcf.gz /tmp/zPov9rP7t1/gvcf.merge.2.vcf.gz /tmp/zPov9rP7t1/gvcf.merge.3.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/zPov9rP7t1/gvcf.merge.1.vcf.gz /tmp/zPov9rP7t1/gvcf.merge.2.vcf.gz /tmp/zPov9rP7t1/gvcf.merge.3.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/zPov9rP7t1/gvcf.merge.1.bcf /tmp/zPov9rP7t1/gvcf.merge.2.bcf /tmp/zPov9rP7t1/gvcf.merge.3.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/zPov9rP7t1/gvcf.merge.1.bcf /tmp/zPov9rP7t1/gvcf.merge.2.bcf /tmp/zPov9rP7t1/gvcf.merge.3.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/zPov9rP7t1/merge.gvcf.2.a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.2.b.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/zPov9rP7t1/merge.gvcf.2.a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.2.b.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.2.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - -m both,* /tmp/zPov9rP7t1/merge.gvcf.2.a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.2.b.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - -m both,* /tmp/zPov9rP7t1/merge.gvcf.2.a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.2.b.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.2.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - -m both,** /tmp/zPov9rP7t1/merge.gvcf.2.a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.2.b.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - -m both,** /tmp/zPov9rP7t1/merge.gvcf.2.a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.2.b.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.2.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - -i SRC:join /tmp/zPov9rP7t1/merge.gvcf.3.a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.3.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - -i SRC:join /tmp/zPov9rP7t1/merge.gvcf.3.a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.3.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/zPov9rP7t1/merge.gvcf.4.a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.4.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/zPov9rP7t1/merge.gvcf.4.a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.4.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/zPov9rP7t1/merge.gvcf.4.a.bcf /tmp/zPov9rP7t1/merge.gvcf.4.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/zPov9rP7t1/merge.gvcf.4.a.bcf /tmp/zPov9rP7t1/merge.gvcf.4.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/zPov9rP7t1/merge.5.a.vcf.gz /tmp/zPov9rP7t1/merge.5.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/zPov9rP7t1/merge.5.a.vcf.gz /tmp/zPov9rP7t1/merge.5.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/zPov9rP7t1/merge.5.a.bcf /tmp/zPov9rP7t1/merge.5.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/zPov9rP7t1/merge.5.a.bcf /tmp/zPov9rP7t1/merge.5.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/zPov9rP7t1/merge.6.a.vcf.gz /tmp/zPov9rP7t1/merge.6.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/zPov9rP7t1/merge.6.a.vcf.gz /tmp/zPov9rP7t1/merge.6.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/zPov9rP7t1/merge.6.a.bcf /tmp/zPov9rP7t1/merge.6.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/zPov9rP7t1/merge.6.a.bcf /tmp/zPov9rP7t1/merge.6.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/zPov9rP7t1/merge.gvcf.7.a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.7.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/zPov9rP7t1/merge.gvcf.7.a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.7.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/zPov9rP7t1/merge.gvcf.7.a.bcf /tmp/zPov9rP7t1/merge.gvcf.7.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/zPov9rP7t1/merge.gvcf.7.a.bcf /tmp/zPov9rP7t1/merge.gvcf.7.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/zPov9rP7t1/merge.gvcf.8.a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.8.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/zPov9rP7t1/merge.gvcf.8.a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.8.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/zPov9rP7t1/merge.gvcf.8.a.bcf /tmp/zPov9rP7t1/merge.gvcf.8.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/zPov9rP7t1/merge.gvcf.8.a.bcf /tmp/zPov9rP7t1/merge.gvcf.8.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples /tmp/zPov9rP7t1/merge.7.a.vcf.gz /tmp/zPov9rP7t1/merge.7.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/zPov9rP7t1/merge.7.a.vcf.gz /tmp/zPov9rP7t1/merge.7.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples /tmp/zPov9rP7t1/merge.7.a.bcf /tmp/zPov9rP7t1/merge.7.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/zPov9rP7t1/merge.7.a.bcf /tmp/zPov9rP7t1/merge.7.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa /tmp/zPov9rP7t1/merge.gvcf.9a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.9b.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.9c.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.9d.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa /tmp/zPov9rP7t1/merge.gvcf.9a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.9b.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.9c.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.9d.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa /tmp/zPov9rP7t1/merge.gvcf.9a.bcf /tmp/zPov9rP7t1/merge.gvcf.9b.bcf /tmp/zPov9rP7t1/merge.gvcf.9c.bcf /tmp/zPov9rP7t1/merge.gvcf.9d.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa /tmp/zPov9rP7t1/merge.gvcf.9a.bcf /tmp/zPov9rP7t1/merge.gvcf.9b.bcf /tmp/zPov9rP7t1/merge.gvcf.9c.bcf /tmp/zPov9rP7t1/merge.gvcf.9d.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa -r 22:21-23 /tmp/zPov9rP7t1/merge.gvcf.9a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.9b.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.9c.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.9d.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa -r 22:21-23 /tmp/zPov9rP7t1/merge.gvcf.9a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.9b.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.9c.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.9d.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa -r 22:21-23 /tmp/zPov9rP7t1/merge.gvcf.9a.bcf /tmp/zPov9rP7t1/merge.gvcf.9b.bcf /tmp/zPov9rP7t1/merge.gvcf.9c.bcf /tmp/zPov9rP7t1/merge.gvcf.9d.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa -r 22:21-23 /tmp/zPov9rP7t1/merge.gvcf.9a.bcf /tmp/zPov9rP7t1/merge.gvcf.9b.bcf /tmp/zPov9rP7t1/merge.gvcf.9c.bcf /tmp/zPov9rP7t1/merge.gvcf.9d.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa /tmp/zPov9rP7t1/merge.gvcf.9a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.9b.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.9c.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.9d.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.9e.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa /tmp/zPov9rP7t1/merge.gvcf.9a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.9b.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.9c.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.9d.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.9e.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa /tmp/zPov9rP7t1/merge.gvcf.9a.bcf /tmp/zPov9rP7t1/merge.gvcf.9b.bcf /tmp/zPov9rP7t1/merge.gvcf.9c.bcf /tmp/zPov9rP7t1/merge.gvcf.9d.bcf /tmp/zPov9rP7t1/merge.gvcf.9e.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa /tmp/zPov9rP7t1/merge.gvcf.9a.bcf /tmp/zPov9rP7t1/merge.gvcf.9b.bcf /tmp/zPov9rP7t1/merge.gvcf.9c.bcf /tmp/zPov9rP7t1/merge.gvcf.9d.bcf /tmp/zPov9rP7t1/merge.gvcf.9e.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa -r 22:21-23 /tmp/zPov9rP7t1/merge.gvcf.9a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.9b.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.9c.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.9d.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.9e.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa -r 22:21-23 /tmp/zPov9rP7t1/merge.gvcf.9a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.9b.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.9c.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.9d.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.9e.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa -r 22:21-23 /tmp/zPov9rP7t1/merge.gvcf.9a.bcf /tmp/zPov9rP7t1/merge.gvcf.9b.bcf /tmp/zPov9rP7t1/merge.gvcf.9c.bcf /tmp/zPov9rP7t1/merge.gvcf.9d.bcf /tmp/zPov9rP7t1/merge.gvcf.9e.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa -r 22:21-23 /tmp/zPov9rP7t1/merge.gvcf.9a.bcf /tmp/zPov9rP7t1/merge.gvcf.9b.bcf /tmp/zPov9rP7t1/merge.gvcf.9c.bcf /tmp/zPov9rP7t1/merge.gvcf.9d.bcf /tmp/zPov9rP7t1/merge.gvcf.9e.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/zPov9rP7t1/merge.gvcf.10.a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/zPov9rP7t1/merge.gvcf.10.a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.10.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/zPov9rP7t1/merge.gvcf.10.a.bcf /tmp/zPov9rP7t1/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/zPov9rP7t1/merge.gvcf.10.a.bcf /tmp/zPov9rP7t1/merge.gvcf.10.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -m none /tmp/zPov9rP7t1/merge.gvcf.10.a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m none /tmp/zPov9rP7t1/merge.gvcf.10.a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.10.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -m none /tmp/zPov9rP7t1/merge.gvcf.10.a.bcf /tmp/zPov9rP7t1/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m none /tmp/zPov9rP7t1/merge.gvcf.10.a.bcf /tmp/zPov9rP7t1/merge.gvcf.10.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -g /build/reproducible-path/bcftools-1.21/test/merge.gvcf.10.fa /tmp/zPov9rP7t1/merge.gvcf.10.a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -g /build/reproducible-path/bcftools-1.21/test/merge.gvcf.10.fa /tmp/zPov9rP7t1/merge.gvcf.10.a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.10.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -g /build/reproducible-path/bcftools-1.21/test/merge.gvcf.10.fa /tmp/zPov9rP7t1/merge.gvcf.10.a.bcf /tmp/zPov9rP7t1/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -g /build/reproducible-path/bcftools-1.21/test/merge.gvcf.10.fa /tmp/zPov9rP7t1/merge.gvcf.10.a.bcf /tmp/zPov9rP7t1/merge.gvcf.10.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -g /build/reproducible-path/bcftools-1.21/test/merge.gvcf.10.fa -m none /tmp/zPov9rP7t1/merge.gvcf.10.a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -g /build/reproducible-path/bcftools-1.21/test/merge.gvcf.10.fa -m none /tmp/zPov9rP7t1/merge.gvcf.10.a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.10.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -g /build/reproducible-path/bcftools-1.21/test/merge.gvcf.10.fa -m none /tmp/zPov9rP7t1/merge.gvcf.10.a.bcf /tmp/zPov9rP7t1/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -g /build/reproducible-path/bcftools-1.21/test/merge.gvcf.10.fa -m none /tmp/zPov9rP7t1/merge.gvcf.10.a.bcf /tmp/zPov9rP7t1/merge.gvcf.10.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/zPov9rP7t1/merge.noidx.a.vcf.gz /tmp/zPov9rP7t1/merge.noidx.b.vcf.gz /tmp/zPov9rP7t1/merge.noidx.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/zPov9rP7t1/merge.noidx.a.vcf.gz /tmp/zPov9rP7t1/merge.noidx.b.vcf.gz /tmp/zPov9rP7t1/merge.noidx.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/zPov9rP7t1/merge.noidx.a.bcf /tmp/zPov9rP7t1/merge.noidx.b.bcf /tmp/zPov9rP7t1/merge.noidx.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/zPov9rP7t1/merge.noidx.a.bcf /tmp/zPov9rP7t1/merge.noidx.b.bcf /tmp/zPov9rP7t1/merge.noidx.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --no-index /build/reproducible-path/bcftools-1.21/test/merge.noidx.a.vcf /build/reproducible-path/bcftools-1.21/test/merge.noidx.b.vcf /build/reproducible-path/bcftools-1.21/test/merge.noidx.c.vcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --no-index /build/reproducible-path/bcftools-1.21/test/merge.noidx.a.vcf /build/reproducible-path/bcftools-1.21/test/merge.noidx.b.vcf /build/reproducible-path/bcftools-1.21/test/merge.noidx.c.vcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --no-index /tmp/zPov9rP7t1/merge.noidx.a.bcf /tmp/zPov9rP7t1/merge.noidx.b.bcf /tmp/zPov9rP7t1/merge.noidx.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --no-index /tmp/zPov9rP7t1/merge.noidx.a.bcf /tmp/zPov9rP7t1/merge.noidx.b.bcf /tmp/zPov9rP7t1/merge.noidx.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/zPov9rP7t1/merge.8.a.vcf.gz /tmp/zPov9rP7t1/merge.8.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/zPov9rP7t1/merge.8.a.vcf.gz /tmp/zPov9rP7t1/merge.8.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/zPov9rP7t1/merge.8.a.bcf /tmp/zPov9rP7t1/merge.8.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/zPov9rP7t1/merge.8.a.bcf /tmp/zPov9rP7t1/merge.8.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -i AN:sum,AC:sum /tmp/zPov9rP7t1/merge.8.a.vcf.gz /tmp/zPov9rP7t1/merge.8.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/zPov9rP7t1/merge.8.a.vcf.gz /tmp/zPov9rP7t1/merge.8.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -i AN:sum,AC:sum /tmp/zPov9rP7t1/merge.8.a.bcf /tmp/zPov9rP7t1/merge.8.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/zPov9rP7t1/merge.8.a.bcf /tmp/zPov9rP7t1/merge.8.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/zPov9rP7t1/merge.9.a.vcf.gz /tmp/zPov9rP7t1/merge.9.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/zPov9rP7t1/merge.9.a.vcf.gz /tmp/zPov9rP7t1/merge.9.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/zPov9rP7t1/merge.9.a.bcf /tmp/zPov9rP7t1/merge.9.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/zPov9rP7t1/merge.9.a.bcf /tmp/zPov9rP7t1/merge.9.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -i AN:sum,AC:sum /tmp/zPov9rP7t1/merge.9.a.vcf.gz /tmp/zPov9rP7t1/merge.9.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/zPov9rP7t1/merge.9.a.vcf.gz /tmp/zPov9rP7t1/merge.9.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -i AN:sum,AC:sum /tmp/zPov9rP7t1/merge.9.a.bcf /tmp/zPov9rP7t1/merge.9.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/zPov9rP7t1/merge.9.a.bcf /tmp/zPov9rP7t1/merge.9.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -m none /tmp/zPov9rP7t1/merge.10.a.vcf.gz /tmp/zPov9rP7t1/merge.10.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m none /tmp/zPov9rP7t1/merge.10.a.vcf.gz /tmp/zPov9rP7t1/merge.10.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -m none /tmp/zPov9rP7t1/merge.10.a.bcf /tmp/zPov9rP7t1/merge.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m none /tmp/zPov9rP7t1/merge.10.a.bcf /tmp/zPov9rP7t1/merge.10.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -m both /tmp/zPov9rP7t1/merge.10.a.vcf.gz /tmp/zPov9rP7t1/merge.10.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m both /tmp/zPov9rP7t1/merge.10.a.vcf.gz /tmp/zPov9rP7t1/merge.10.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -m both /tmp/zPov9rP7t1/merge.10.a.bcf /tmp/zPov9rP7t1/merge.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m both /tmp/zPov9rP7t1/merge.10.a.bcf /tmp/zPov9rP7t1/merge.10.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -m snp-ins-del /tmp/zPov9rP7t1/merge.10.a.vcf.gz /tmp/zPov9rP7t1/merge.10.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m snp-ins-del /tmp/zPov9rP7t1/merge.10.a.vcf.gz /tmp/zPov9rP7t1/merge.10.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -m snp-ins-del /tmp/zPov9rP7t1/merge.10.a.bcf /tmp/zPov9rP7t1/merge.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m snp-ins-del /tmp/zPov9rP7t1/merge.10.a.bcf /tmp/zPov9rP7t1/merge.10.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/zPov9rP7t1/merge.mrules.1.a.vcf.gz /tmp/zPov9rP7t1/merge.mrules.1.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/zPov9rP7t1/merge.mrules.1.a.vcf.gz /tmp/zPov9rP7t1/merge.mrules.1.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/zPov9rP7t1/merge.mrules.1.a.bcf /tmp/zPov9rP7t1/merge.mrules.1.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/zPov9rP7t1/merge.mrules.1.a.bcf /tmp/zPov9rP7t1/merge.mrules.1.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - -M AD:.,PL:. /tmp/zPov9rP7t1/merge.mrules.1.a.vcf.gz /tmp/zPov9rP7t1/merge.mrules.1.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - -M AD:.,PL:. /tmp/zPov9rP7t1/merge.mrules.1.a.vcf.gz /tmp/zPov9rP7t1/merge.mrules.1.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - -M AD:.,PL:. /tmp/zPov9rP7t1/merge.mrules.1.a.bcf /tmp/zPov9rP7t1/merge.mrules.1.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - -M AD:.,PL:. /tmp/zPov9rP7t1/merge.mrules.1.a.bcf /tmp/zPov9rP7t1/merge.mrules.1.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/zPov9rP7t1/merge.gvcf.5.a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.5.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/zPov9rP7t1/merge.gvcf.5.a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.5.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/zPov9rP7t1/merge.gvcf.5.a.bcf /tmp/zPov9rP7t1/merge.gvcf.5.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/zPov9rP7t1/merge.gvcf.5.a.bcf /tmp/zPov9rP7t1/merge.gvcf.5.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - --merge none /tmp/zPov9rP7t1/merge.gvcf.5.a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.5.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - --merge none /tmp/zPov9rP7t1/merge.gvcf.5.a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.5.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - --merge none /tmp/zPov9rP7t1/merge.gvcf.5.a.bcf /tmp/zPov9rP7t1/merge.gvcf.5.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - --merge none /tmp/zPov9rP7t1/merge.gvcf.5.a.bcf /tmp/zPov9rP7t1/merge.gvcf.5.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/zPov9rP7t1/merge.gvcf.11.a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.11.b.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.11.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/zPov9rP7t1/merge.gvcf.11.a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.11.b.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.11.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/zPov9rP7t1/merge.gvcf.11.a.bcf /tmp/zPov9rP7t1/merge.gvcf.11.b.bcf /tmp/zPov9rP7t1/merge.gvcf.11.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/zPov9rP7t1/merge.gvcf.11.a.bcf /tmp/zPov9rP7t1/merge.gvcf.11.b.bcf /tmp/zPov9rP7t1/merge.gvcf.11.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided,_conflicting_interpretations"' /tmp/zPov9rP7t1/query.string.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.string.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided,_conflicting_interpretations"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" || CLNREVSTAT="_conflicting_interpretations"' /tmp/zPov9rP7t1/query.string.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.string.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" || CLNREVSTAT="_conflicting_interpretations"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" && CLNREVSTAT="_conflicting_interpretations"' /tmp/zPov9rP7t1/query.string.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.string.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" && CLNREVSTAT="_conflicting_interpretations"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%INFO/STR\n' -i'INFO/STR=@/build/reproducible-path/bcftools-1.21/test/query.string.2.1.txt' /tmp/zPov9rP7t1/query.string.2.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.string.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%INFO/STR\n' -i'INFO/STR=@/build/reproducible-path/bcftools-1.21/test/query.string.2.1.txt' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS[\t%STR]\n' -i'FMT/STR=@/build/reproducible-path/bcftools-1.21/test/query.string.2.2.txt' /tmp/zPov9rP7t1/query.string.2.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.string.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS[\t%STR]\n' -i'FMT/STR=@/build/reproducible-path/bcftools-1.21/test/query.string.2.2.txt' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' /tmp/zPov9rP7t1/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f '%RSX\t%VKX\n' /tmp/zPov9rP7t1/query.variantkey.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.variantkey.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f '%RSX\t%VKX\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%XRI\n' -i'XRI[*]>1111' /tmp/zPov9rP7t1/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%XRI\n' -i'XRI[*]>1111' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' /tmp/zPov9rP7t1/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' /tmp/zPov9rP7t1/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' /tmp/zPov9rP7t1/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' /tmp/zPov9rP7t1/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' /tmp/zPov9rP7t1/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' /tmp/zPov9rP7t1/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' /tmp/zPov9rP7t1/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' /tmp/zPov9rP7t1/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' /tmp/zPov9rP7t1/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' /tmp/zPov9rP7t1/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' /tmp/zPov9rP7t1/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' /tmp/zPov9rP7t1/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' /tmp/zPov9rP7t1/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' /tmp/zPov9rP7t1/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' /tmp/zPov9rP7t1/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'I8=%I8 I16=%I16 I32=%I32 IF=%IF IA8=%IA8 IA16=%IA16 IA32=%IA32 IAF=%IAF IA8=%IA8{1} IA16=%IA16{1} IA32=%IA32{1} IAF=%IAF{1} [ %F8:%F16:%F32:%FF]\n' /tmp/zPov9rP7t1/view.vectors.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/view.vectors.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'I8=%I8 I16=%I16 I32=%I32 IF=%IF IA8=%IA8 IA16=%IA16 IA32=%IA32 IAF=%IAF IA8=%IA8{1} IA16=%IA16{1} IA32=%IA32{1} IAF=%IAF{1} [ %F8:%F16:%F32:%FF]\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' /tmp/zPov9rP7t1/query.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' /tmp/zPov9rP7t1/query.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' /tmp/zPov9rP7t1/query.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' /tmp/zPov9rP7t1/query.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' /tmp/zPov9rP7t1/query.2.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'IINT="."' -f'%POS %IINT\n' /tmp/zPov9rP7t1/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'IINT!="."' -f'%POS %IINT\n' /tmp/zPov9rP7t1/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -e'IINT!="."' -f'%POS %IINT\n' /tmp/zPov9rP7t1/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -e'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -e'IINT="."' -f'%POS %IINT\n' /tmp/zPov9rP7t1/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -e'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' /tmp/zPov9rP7t1/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' /tmp/zPov9rP7t1/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' /tmp/zPov9rP7t1/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' /tmp/zPov9rP7t1/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' /tmp/zPov9rP7t1/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' /tmp/zPov9rP7t1/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' /tmp/zPov9rP7t1/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' /tmp/zPov9rP7t1/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' /tmp/zPov9rP7t1/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER="A"' -f'%POS %FILTER\n' /tmp/zPov9rP7t1/filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/filter.11.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER="A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER!="A"' -f'%POS %FILTER\n' /tmp/zPov9rP7t1/filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/filter.11.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER!="A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER~"A"' -f'%POS %FILTER\n' /tmp/zPov9rP7t1/filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/filter.11.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER~"A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n' /tmp/zPov9rP7t1/filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/filter.11.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%LINE' /tmp/zPov9rP7t1/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%LINE' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' /tmp/zPov9rP7t1/query.filter-type.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter-type.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' /tmp/zPov9rP7t1/query.filter-type.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter-type.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' /tmp/zPov9rP7t1/query.filter-type.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter-type.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' /tmp/zPov9rP7t1/query.filter-type.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter-type.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'INFO/TYPE="xxx"' /tmp/zPov9rP7t1/query.filter-type.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter-type.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'INFO/TYPE="xxx"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -i'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001' /tmp/zPov9rP7t1/filter-missing-floats.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/filter-missing-floats.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -i'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -e'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001' /tmp/zPov9rP7t1/filter-missing-floats.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/filter-missing-floats.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -e'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' /tmp/zPov9rP7t1/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' /tmp/zPov9rP7t1/query.filter.2.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' /tmp/zPov9rP7t1/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' /tmp/zPov9rP7t1/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' /tmp/zPov9rP7t1/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' /tmp/zPov9rP7t1/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' /tmp/zPov9rP7t1/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' /tmp/zPov9rP7t1/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' /tmp/zPov9rP7t1/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' /tmp/zPov9rP7t1/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' /tmp/zPov9rP7t1/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' /tmp/zPov9rP7t1/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' /tmp/zPov9rP7t1/filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/filter.5.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' /tmp/zPov9rP7t1/filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/filter.5.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' /tmp/zPov9rP7t1/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' /tmp/zPov9rP7t1/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' /tmp/zPov9rP7t1/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' /tmp/zPov9rP7t1/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' /tmp/zPov9rP7t1/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 & FMT/GQ=589' /tmp/zPov9rP7t1/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 & FMT/GQ=589' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' /tmp/zPov9rP7t1/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' /tmp/zPov9rP7t1/query.filter.3.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.3.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"' /tmp/zPov9rP7t1/query.filter.3.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.3.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' /tmp/zPov9rP7t1/query.filter.3.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.3.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %AD\n]\n' -i'AD[:0]+AD[:1] > 12' /tmp/zPov9rP7t1/filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/filter.5.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %AD\n]\n' -i'AD[:0]+AD[:1] > 12' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' /tmp/zPov9rP7t1/query.filter.4.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.4.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i 'ID=@/build/reproducible-path/bcftools-1.21/test/query.56.out' /tmp/zPov9rP7t1/view.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/view.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i 'ID=@/build/reproducible-path/bcftools-1.21/test/query.56.out' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD)>0.01' /tmp/zPov9rP7t1/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.5.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD)>0.01' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD[:0],FMT/AD[:1])>0.01' /tmp/zPov9rP7t1/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.5.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD[:0],FMT/AD[:1])>0.01' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%AD\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01' /tmp/zPov9rP7t1/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.5.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%AD\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[GT]==10' /tmp/zPov9rP7t1/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.5.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[GT]==10' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'sSUM(FMT/AD[GT])==210' /tmp/zPov9rP7t1/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.5.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'sSUM(FMT/AD[GT])==210' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[0:GT]==30' /tmp/zPov9rP7t1/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.5.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[0:GT]==30' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TF[:GT]==1 && FMT/TF[:GT]==2' /tmp/zPov9rP7t1/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.gtidx.1.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TF[:GT]==1 && FMT/TF[:GT]==2' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TI[:GT]==1 && FMT/TF[:GT]==2' /tmp/zPov9rP7t1/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.gtidx.1.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TI[:GT]==1 && FMT/TF[:GT]==2' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TS[:GT]=="BB" && FMT/TS[:GT]=="CC"' /tmp/zPov9rP7t1/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.gtidx.1.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TS[:GT]=="BB" && FMT/TS[:GT]=="CC"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TC[:GT]=="B" && FMT/TC[:GT]=="C"' /tmp/zPov9rP7t1/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.gtidx.1.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TC[:GT]=="B" && FMT/TC[:GT]=="C"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%GT %TI\n]' -i'FMT/TI[:GT]=="."' /tmp/zPov9rP7t1/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.gtidx.1.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%GT %TI\n]' -i'FMT/TI[:GT]=="."' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS\n' -i'CHROM="4"' /tmp/zPov9rP7t1/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS\n' -i'CHROM="4"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%TAG1\n' -i'(TAG1>=-129 && TAG1<=-120) || (TAG1>=-32769 && TAG1<=-32760)' /tmp/zPov9rP7t1/query.negative.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.negative.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%TAG1\n' -i'(TAG1>=-129 && TAG1<=-120) || (TAG1>=-32769 && TAG1<=-32760)' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%TAGV1\n' -i'(TAGV1>=-129 && TAGV1<=-120) || (TAGV1>=-32769 && TAGV1<=-32760)' /tmp/zPov9rP7t1/query.negative.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.negative.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%TAGV1\n' -i'(TAGV1>=-129 && TAGV1<=-120) || (TAGV1>=-32769 && TAGV1<=-32760)' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%TAG2\n' -i'(TAG2>=-129 && TAG2<=-120) || (TAG2>=-32769 && TAG2<=-32760)' /tmp/zPov9rP7t1/query.negative.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.negative.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%TAG2\n' -i'(TAG2>=-129 && TAG2<=-120) || (TAG2>=-32769 && TAG2<=-32760)' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%TAGV2\n' -i'(TAGV2>=-129 && TAGV2<=-120) || (TAGV2>=-32769 && TAGV2<=-32760)' /tmp/zPov9rP7t1/query.negative.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.negative.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%TAGV2\n' -i'(TAGV2>=-129 && TAGV2<=-120) || (TAGV2>=-32769 && TAGV2<=-32760)' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GQ\n]' -i'N_PASS(GQ<20)==1' /tmp/zPov9rP7t1/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GQ\n]' -i'N_PASS(GQ<20)==1' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")==1' /tmp/zPov9rP7t1/query.filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.11.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")==1' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")!=1' /tmp/zPov9rP7t1/query.filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.11.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")!=1' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")==1' /tmp/zPov9rP7t1/query.filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.11.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")==1' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")!=1' /tmp/zPov9rP7t1/query.filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.11.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")!=1' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM\t%POS\t%INFO\t%FORMAT\n' -s D,C /tmp/zPov9rP7t1/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM\t%POS\t%INFO\t%FORMAT\n' -s D,C .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\n' -i'POS==16777217 || POS==33554432 || POS=118673904' /tmp/zPov9rP7t1/query.filter.6.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.6.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\n' -i'POS==16777217 || POS==33554432 || POS=118673904' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(II)==6' /tmp/zPov9rP7t1/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(II)==6' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(FORMAT/FI)==7' /tmp/zPov9rP7t1/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(FORMAT/FI)==7' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(II)==2' /tmp/zPov9rP7t1/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(II)==2' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(FORMAT/FI)==1.75' /tmp/zPov9rP7t1/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(FORMAT/FI)==1.75' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(II)==2' /tmp/zPov9rP7t1/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(II)==2' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(FORMAT/FI)==1.75' /tmp/zPov9rP7t1/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(FORMAT/FI)==1.75' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(II)==2' /tmp/zPov9rP7t1/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(II)==2' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(FORMAT/FI)==1.5' /tmp/zPov9rP7t1/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(FORMAT/FI)==1.5' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'%ILEN==1' /tmp/zPov9rP7t1/query.filter.8.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.8.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'%ILEN==1' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'ILEN==1' /tmp/zPov9rP7t1/query.filter.8.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.8.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'ILEN==1' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] < FMT/AD[:1]' /tmp/zPov9rP7t1/query.filter.9.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.9.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] < FMT/AD[:1]' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] > FMT/AD[:1]' /tmp/zPov9rP7t1/query.filter.9.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.9.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] > FMT/AD[:1]' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[ %AD\n]' -i'AD[:1] / sum(AD[*]) > 0.5' /tmp/zPov9rP7t1/query.filter.13.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.13.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[ %AD\n]' -i'AD[:1] / sum(AD[*]) > 0.5' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %NUM_TAG\n' -i'COUNT(INFO/NUM_TAG)=2' /tmp/zPov9rP7t1/query.filter.10.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.10.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %NUM_TAG\n' -i'COUNT(INFO/NUM_TAG)=2' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2' /tmp/zPov9rP7t1/query.filter.10.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.10.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM:%POS\t%N_PASS(GT="alt" & GQ>110)\t[\t%GT]\t[\t%GQ]\n' /tmp/zPov9rP7t1/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM:%POS\t%N_PASS(GT="alt" & GQ>110)\t[\t%GT]\t[\t%GQ]\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 1,3,0 /tmp/zPov9rP7t1/query.filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.12.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 1,3,0 .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 0,1,3 /tmp/zPov9rP7t1/query.filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.12.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 0,1,3 .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f "[%SAMPLE %GT\n]" -S /build/reproducible-path/bcftools-1.21/test/query.smpl.11.txt /tmp/zPov9rP7t1/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.smpl.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f "[%SAMPLE %GT\n]" -S /build/reproducible-path/bcftools-1.21/test/query.smpl.11.txt .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -l -S /build/reproducible-path/bcftools-1.21/test/query.smpl.11.txt /tmp/zPov9rP7t1/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.smpl.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -l -S /build/reproducible-path/bcftools-1.21/test/query.smpl.11.txt .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f "[%SAMPLE %GT\n]" -S ^/build/reproducible-path/bcftools-1.21/test/query.smpl.11.txt /tmp/zPov9rP7t1/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.smpl.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f "[%SAMPLE %GT\n]" -S ^/build/reproducible-path/bcftools-1.21/test/query.smpl.11.txt .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -l -S ^/build/reproducible-path/bcftools-1.21/test/query.smpl.11.txt /tmp/zPov9rP7t1/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.smpl.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -l -S ^/build/reproducible-path/bcftools-1.21/test/query.smpl.11.txt .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f "[%SAMPLE %GT\n]" -S /build/reproducible-path/bcftools-1.21/test/query.smpl.txt /tmp/zPov9rP7t1/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.smpl.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f "[%SAMPLE %GT\n]" -S /build/reproducible-path/bcftools-1.21/test/query.smpl.txt .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -l -S /build/reproducible-path/bcftools-1.21/test/query.smpl.txt /tmp/zPov9rP7t1/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.smpl.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -l -S /build/reproducible-path/bcftools-1.21/test/query.smpl.txt .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID~"s12"' /tmp/zPov9rP7t1/query.filter.id.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.id.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID~"s12"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID="rs123"' /tmp/zPov9rP7t1/query.filter.id.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.id.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID="rs123"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID="abc"' /tmp/zPov9rP7t1/query.filter.id.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.id.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID="abc"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID=@/build/reproducible-path/bcftools-1.21/test/query.filter.id.3.txt' /tmp/zPov9rP7t1/query.filter.id.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.id.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID=@/build/reproducible-path/bcftools-1.21/test/query.filter.id.3.txt' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID!="abc"' /tmp/zPov9rP7t1/query.filter.id.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.id.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID!="abc"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID!=@/build/reproducible-path/bcftools-1.21/test/query.filter.id.3.txt' /tmp/zPov9rP7t1/query.filter.id.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.id.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID!=@/build/reproducible-path/bcftools-1.21/test/query.filter.id.3.txt' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER="A"' -f'%FILTER\n' /tmp/zPov9rP7t1/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/filter.12.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER="A"' -f'%FILTER\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER~"A"' -f'%FILTER\n' /tmp/zPov9rP7t1/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/filter.12.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER~"A"' -f'%FILTER\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER="A;B"' -f'%FILTER\n' /tmp/zPov9rP7t1/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/filter.12.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER="A;B"' -f'%FILTER\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER!="A;B"' -f'%FILTER\n' /tmp/zPov9rP7t1/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/filter.12.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER!="A;B"' -f'%FILTER\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER~"A;B"' -f'%FILTER\n' /tmp/zPov9rP7t1/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/filter.12.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER~"A;B"' -f'%FILTER\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER!~"A;B"' -f'%FILTER\n' /tmp/zPov9rP7t1/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/filter.12.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER!~"A;B"' -f'%FILTER\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'DP%10==2' -f'[ %DP]\n' /tmp/zPov9rP7t1/filter.10.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/filter.10.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'DP%10==2' -f'[ %DP]\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'REF="N"' -f'%CHROM %POS %REF %ALT %QUAL\n' /tmp/zPov9rP7t1/filter.13.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/filter.13.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'REF="N"' -f'%CHROM %POS %REF %ALT %QUAL\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -H -f'[%CHROM %POS %SAMPLE %DP %GT\n]' /tmp/zPov9rP7t1/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.header.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -H -f'[%CHROM %POS %SAMPLE %DP %GT\n]' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -H -f'[%CHROM %POS %SAMPLE %DP %GT\t]\n' /tmp/zPov9rP7t1/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.header.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -H -f'[%CHROM %POS %SAMPLE %DP %GT\t]\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]\n' /tmp/zPov9rP7t1/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.header.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]' /tmp/zPov9rP7t1/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.header.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]\n' /tmp/zPov9rP7t1/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.header.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]' /tmp/zPov9rP7t1/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.header.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -HH -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]' /tmp/zPov9rP7t1/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.header.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -HH -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%SAMPLE %DP\n]' -i'DP=1 || DP=2' /tmp/zPov9rP7t1/query.filter-or.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter-or.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%SAMPLE %DP\n]' -i'DP=1 || DP=2' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%SAMPLE %DP\n]' -i'DP=1 | DP=2' /tmp/zPov9rP7t1/query.filter-or.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter-or.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%SAMPLE %DP\n]' -i'DP=1 | DP=2' .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/zPov9rP7t1/norm.sort.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/zPov9rP7t1/norm.sort.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - -S lex /tmp/zPov9rP7t1/norm.sort.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - -S lex /tmp/zPov9rP7t1/norm.sort.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +both /tmp/zPov9rP7t1/norm.join-missing-ploidy.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +both /tmp/zPov9rP7t1/norm.join-missing-ploidy.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - --multi-overlaps . /tmp/zPov9rP7t1/norm.split.5.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - --multi-overlaps . /tmp/zPov9rP7t1/norm.split.5.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version /tmp/zPov9rP7t1/norm.symbolic.3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.symbolic.3.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version /tmp/zPov9rP7t1/norm.symbolic.3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.symbolic.3.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -cx /tmp/zPov9rP7t1/norm.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -cx /tmp/zPov9rP7t1/norm.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- /tmp/zPov9rP7t1/norm.split.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- /tmp/zPov9rP7t1/norm.split.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- /tmp/zPov9rP7t1/norm.split.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- /tmp/zPov9rP7t1/norm.split.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- --force /tmp/zPov9rP7t1/norm.split.3.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- --force /tmp/zPov9rP7t1/norm.split.3.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- /tmp/zPov9rP7t1/norm.split.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- /tmp/zPov9rP7t1/norm.split.4.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- --keep-sum AD /tmp/zPov9rP7t1/norm.split.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- --keep-sum AD /tmp/zPov9rP7t1/norm.split.4.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- /tmp/zPov9rP7t1/norm.split.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- /tmp/zPov9rP7t1/norm.split.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m+ /tmp/zPov9rP7t1/norm.merge.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m+ /tmp/zPov9rP7t1/norm.merge.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m+ /tmp/zPov9rP7t1/norm.merge.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m+ /tmp/zPov9rP7t1/norm.merge.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m+ /tmp/zPov9rP7t1/norm.merge.3.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m+ /tmp/zPov9rP7t1/norm.merge.3.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m+ -s /tmp/zPov9rP7t1/norm.merge.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m+ -s /tmp/zPov9rP7t1/norm.merge.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -Nc s /tmp/zPov9rP7t1/norm.setref.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -Nc s /tmp/zPov9rP7t1/norm.setref.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version /tmp/zPov9rP7t1/norm.telomere.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version /tmp/zPov9rP7t1/norm.telomere.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d snps /tmp/zPov9rP7t1/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d snps /tmp/zPov9rP7t1/norm.rmdup.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d indels /tmp/zPov9rP7t1/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d indels /tmp/zPov9rP7t1/norm.rmdup.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d both /tmp/zPov9rP7t1/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d both /tmp/zPov9rP7t1/norm.rmdup.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d all /tmp/zPov9rP7t1/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d all /tmp/zPov9rP7t1/norm.rmdup.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d none /tmp/zPov9rP7t1/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d none /tmp/zPov9rP7t1/norm.rmdup.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d exact /tmp/zPov9rP7t1/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d exact /tmp/zPov9rP7t1/norm.rmdup.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d none /tmp/zPov9rP7t1/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d none /tmp/zPov9rP7t1/norm.rmdup.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d exact /tmp/zPov9rP7t1/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d exact /tmp/zPov9rP7t1/norm.rmdup.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d indels /tmp/zPov9rP7t1/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d indels /tmp/zPov9rP7t1/norm.rmdup.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d any /tmp/zPov9rP7t1/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d any /tmp/zPov9rP7t1/norm.rmdup.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d both /tmp/zPov9rP7t1/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d both /tmp/zPov9rP7t1/norm.rmdup.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d snps /tmp/zPov9rP7t1/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d snps /tmp/zPov9rP7t1/norm.rmdup.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d exact /tmp/zPov9rP7t1/norm.rmdup.3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.rmdup.3.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d exact /tmp/zPov9rP7t1/norm.rmdup.3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.rmdup.3.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d all /tmp/zPov9rP7t1/norm.rmdup.3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.rmdup.3.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d all /tmp/zPov9rP7t1/norm.rmdup.3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.rmdup.3.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -c s -a /tmp/zPov9rP7t1/norm.2.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.2.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -c s -a /tmp/zPov9rP7t1/norm.2.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.2.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -c s /tmp/zPov9rP7t1/norm.iupac.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.iupac.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -c s /tmp/zPov9rP7t1/norm.iupac.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.iupac.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -c s /tmp/zPov9rP7t1/norm.3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.3.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -c s /tmp/zPov9rP7t1/norm.3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.3.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -c s -i'alt="N"' /tmp/zPov9rP7t1/norm.3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.3.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -c s -i'alt="N"' /tmp/zPov9rP7t1/norm.3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.3.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -a --old-rec-tag OLD_REC /tmp/zPov9rP7t1/atomize.split.1.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any --force .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -a --old-rec-tag OLD_REC /tmp/zPov9rP7t1/atomize.split.1.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any --force -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any --old-rec-tag OLD_REC --force /tmp/zPov9rP7t1/atomize.split.1.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -a .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any --old-rec-tag OLD_REC --force /tmp/zPov9rP7t1/atomize.split.1.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -a -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any --old-rec-tag OLD_REC --force -a /tmp/zPov9rP7t1/atomize.split.1.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any --old-rec-tag OLD_REC --force -a /tmp/zPov9rP7t1/atomize.split.1.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/zPov9rP7t1/atomize.split.1.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/zPov9rP7t1/atomize.split.1.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/zPov9rP7t1/atomize.split.1.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/zPov9rP7t1/atomize.split.1.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/zPov9rP7t1/atomize.split.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/zPov9rP7t1/atomize.split.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/zPov9rP7t1/atomize.split.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/zPov9rP7t1/atomize.split.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . /tmp/zPov9rP7t1/atomize.split.3.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . /tmp/zPov9rP7t1/atomize.split.3.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/zPov9rP7t1/atomize.split.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/zPov9rP7t1/atomize.split.4.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC -i 'ILEN=0' /tmp/zPov9rP7t1/atomize.split.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC -i 'ILEN=0' /tmp/zPov9rP7t1/atomize.split.4.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --old-rec-tag OLD_REC --atom-overlaps . /tmp/zPov9rP7t1/atomize.split.5.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --old-rec-tag OLD_REC --atom-overlaps . /tmp/zPov9rP7t1/atomize.split.5.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/zPov9rP7t1/atomize.split.5.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/zPov9rP7t1/atomize.split.5.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +both /tmp/zPov9rP7t1/norm.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +both /tmp/zPov9rP7t1/norm.4.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +any /tmp/zPov9rP7t1/norm.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +any /tmp/zPov9rP7t1/norm.4.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - --multi-overlaps 0 /tmp/zPov9rP7t1/norm.5.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - --multi-overlaps 0 /tmp/zPov9rP7t1/norm.5.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - --multi-overlaps . /tmp/zPov9rP7t1/norm.5.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - --multi-overlaps . /tmp/zPov9rP7t1/norm.5.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any /tmp/zPov9rP7t1/norm.m-any.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any /tmp/zPov9rP7t1/norm.m-any.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any /tmp/zPov9rP7t1/norm.phased-split.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any /tmp/zPov9rP7t1/norm.phased-split.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +any /tmp/zPov9rP7t1/norm.phased-join.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +any /tmp/zPov9rP7t1/norm.phased-join.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI /tmp/zPov9rP7t1/norm.symbolic.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.symbolic.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI /tmp/zPov9rP7t1/norm.symbolic.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.symbolic.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI /tmp/zPov9rP7t1/norm.symbolic.2.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.symbolic.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI /tmp/zPov9rP7t1/norm.symbolic.2.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.symbolic.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI /tmp/zPov9rP7t1/norm.right-align.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.right-align.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI /tmp/zPov9rP7t1/norm.right-align.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.right-align.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI -g /build/reproducible-path/bcftools-1.21/test/norm.right-align.gff /tmp/zPov9rP7t1/norm.right-align.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.right-align.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI -g /build/reproducible-path/bcftools-1.21/test/norm.right-align.gff /tmp/zPov9rP7t1/norm.right-align.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.right-align.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI -a -m -any /tmp/zPov9rP7t1/norm.atom-split-norm.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.atom-split-norm.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI -a -m -any /tmp/zPov9rP7t1/norm.atom-split-norm.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.atom-split-norm.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any /tmp/zPov9rP7t1/norm.string-tags.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any /tmp/zPov9rP7t1/norm.string-tags.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/zPov9rP7t1/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +both .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/zPov9rP7t1/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +both -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/zPov9rP7t1/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +indels .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/zPov9rP7t1/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +indels -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/zPov9rP7t1/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +snps .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/zPov9rP7t1/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +snps -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/zPov9rP7t1/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +snps .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/zPov9rP7t1/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +snps -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/zPov9rP7t1/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +any .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/zPov9rP7t1/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +any -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - -i 'type="snp"' /tmp/zPov9rP7t1/norm.split.merge.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - -i 'type="snp"' /tmp/zPov9rP7t1/norm.split.merge.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +any /tmp/zPov9rP7t1/norm.merge.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +any /tmp/zPov9rP7t1/norm.merge.4.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +both /tmp/zPov9rP7t1/norm.merge.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +both /tmp/zPov9rP7t1/norm.merge.4.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -i 'INFO/TAG=@/build/reproducible-path/bcftools-1.21/test/filter.string.1.txt' /tmp/zPov9rP7t1/filter.string.1.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -i 'INFO/TAG=@/build/reproducible-path/bcftools-1.21/test/filter.string.1.txt' /tmp/zPov9rP7t1/filter.string.1.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -i 'FMT/TAG=@/build/reproducible-path/bcftools-1.21/test/filter.string.1.txt' /tmp/zPov9rP7t1/filter.string.1.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -i 'FMT/TAG=@/build/reproducible-path/bcftools-1.21/test/filter.string.1.txt' /tmp/zPov9rP7t1/filter.string.1.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -HA /tmp/zPov9rP7t1/merge.gvcf.2.a.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -HAA /tmp/zPov9rP7t1/merge.gvcf.2.a.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/zPov9rP7t1/weird-chr-names.vcf.gz -r 1 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/weird-chr-names.vcf.gz -r 1 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/zPov9rP7t1/weird-chr-names.vcf.gz -r 1:1-2 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/weird-chr-names.vcf.gz -r 1:1-2 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/zPov9rP7t1/weird-chr-names.vcf.gz -r 1:1,1:2 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/weird-chr-names.vcf.gz -r 1:1,1:2 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/zPov9rP7t1/weird-chr-names.vcf.gz -r 1:1-1 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/weird-chr-names.vcf.gz -r 1:1-1 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/zPov9rP7t1/weird-chr-names.vcf.gz -r {1:1} .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/weird-chr-names.vcf.gz -r {1:1} | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/zPov9rP7t1/weird-chr-names.vcf.gz -r {1:1}:1-2 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/weird-chr-names.vcf.gz -r {1:1}:1-2 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/zPov9rP7t1/weird-chr-names.vcf.gz -r {1:1}:1,{1:1}:2 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/weird-chr-names.vcf.gz -r {1:1}:1,{1:1}:2 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/zPov9rP7t1/weird-chr-names.vcf.gz -r {1:1}:1-1 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/weird-chr-names.vcf.gz -r {1:1}:1-1 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/zPov9rP7t1/weird-chr-names.vcf.gz -r {1:1-1} .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/weird-chr-names.vcf.gz -r {1:1-1} | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/zPov9rP7t1/weird-chr-names.vcf.gz -r {1:1-1}:1-2 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/weird-chr-names.vcf.gz -r {1:1-1}:1-2 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/zPov9rP7t1/weird-chr-names.vcf.gz -r {1:1-1}:1,{1:1-1}:2 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/weird-chr-names.vcf.gz -r {1:1-1}:1,{1:1-1}:2 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/zPov9rP7t1/weird-chr-names.vcf.gz -r {1:1-1}:1-1 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/weird-chr-names.vcf.gz -r {1:1-1}:1-1 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/zPov9rP7t1/weird-chr-names.vcf.gz -r {1:1-1}-2 .. ok, expected non-zero status test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/weird-chr-names.vcf.gz -r {1:1-1}-2 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok, expected non-zero status test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -aUc1 -C1 -s NA00002 -v snps /tmp/zPov9rP7t1/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/zPov9rP7t1/view.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -f PASS -Xks NA00003 /tmp/zPov9rP7t1/view.vcf.gz -r20,Y .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -f PASS -Xks NA00003 /tmp/zPov9rP7t1/view.vcf.gz -r20,Y | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -xs NA00003 /tmp/zPov9rP7t1/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -xs NA00003 /tmp/zPov9rP7t1/view.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/zPov9rP7t1/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/zPov9rP7t1/view.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -p /tmp/zPov9rP7t1/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -p /tmp/zPov9rP7t1/view.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -P /tmp/zPov9rP7t1/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -P /tmp/zPov9rP7t1/view.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -hm2 -M2 -q0.3 -Q0.7 /tmp/zPov9rP7t1/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/zPov9rP7t1/view.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -Hu /tmp/zPov9rP7t1/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -GVsnps /tmp/zPov9rP7t1/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -GVsnps /tmp/zPov9rP7t1/view.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -ne 'INDEL=1 || PV4[0]<0.006' /tmp/zPov9rP7t1/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/zPov9rP7t1/view.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -s ^NA00003 /tmp/zPov9rP7t1/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -s ^NA00003 /tmp/zPov9rP7t1/view.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/zPov9rP7t1/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/view.omitgenotypes.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -G /tmp/zPov9rP7t1/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -G /tmp/zPov9rP7t1/view.omitgenotypes.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -HG /tmp/zPov9rP7t1/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -a /tmp/zPov9rP7t1/many.alleles.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -a /tmp/zPov9rP7t1/many.alleles.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -asA /tmp/zPov9rP7t1/view.vectors.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -asA /tmp/zPov9rP7t1/view.vectors.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -asB /tmp/zPov9rP7t1/view.vectors.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -asB /tmp/zPov9rP7t1/view.vectors.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -asA /tmp/zPov9rP7t1/view.vectors.2.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -asA /tmp/zPov9rP7t1/view.vectors.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -i'FMT/FGS[*:0]="AAAAAA"' /tmp/zPov9rP7t1/view.filter.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -i'FMT/FGS[*:2]="C"' /tmp/zPov9rP7t1/view.filter.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -i'FMT/FGS[*:4]="EE"' /tmp/zPov9rP7t1/view.filter.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -i'FMT/FRS[*:1]="BB"' /tmp/zPov9rP7t1/view.filter.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -i'TXT0="text"' /tmp/zPov9rP7t1/view.filter.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -T /build/reproducible-path/bcftools-1.21/test/view.chrs.tab /tmp/zPov9rP7t1/view.chrs.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -T /build/reproducible-path/bcftools-1.21/test/view.chrs.tab /tmp/zPov9rP7t1/view.chrs.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -i 'POS>=3062917' /tmp/zPov9rP7t1/filter.2.vcf.gz 1:3062917-3157410 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -i 'POS>=3062917' /tmp/zPov9rP7t1/filter.2.vcf.gz 1:3062917-3157410 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -r 1:10,1:12,1:10 /tmp/zPov9rP7t1/idx.1.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -r 1:1172777-1172804,1:1172806-1172808 /tmp/zPov9rP7t1/idx.2.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -R /build/reproducible-path/bcftools-1.21/test/idx.2.bed /tmp/zPov9rP7t1/idx.2.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -R /build/reproducible-path/bcftools-1.21/test/idx.3.bed /tmp/zPov9rP7t1/idx.3.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -R /build/reproducible-path/bcftools-1.21/test/idx.4.bed /tmp/zPov9rP7t1/idx.4.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -Ht 2 /tmp/zPov9rP7t1/view-t.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -Ht 3 /tmp/zPov9rP7t1/view-t.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 0 /tmp/zPov9rP7t1/overlap.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 1 /tmp/zPov9rP7t1/overlap.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 2 /tmp/zPov9rP7t1/overlap.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 0 /tmp/zPov9rP7t1/overlap.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 1 /tmp/zPov9rP7t1/overlap.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 2 /tmp/zPov9rP7t1/overlap.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 0 /tmp/zPov9rP7t1/overlap.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 1 /tmp/zPov9rP7t1/overlap.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 2 /tmp/zPov9rP7t1/overlap.vcf.gz .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.21/bcftools view /build/reproducible-path/bcftools-1.21/test/view64bit.1.vcf -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.21/bcftools view /build/reproducible-path/bcftools-1.21/test/view64bit.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.21/bcftools view /build/reproducible-path/bcftools-1.21/test/view64bit.1.vcf -Ou | /build/reproducible-path/bcftools-1.21/bcftools view -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.21/bcftools view /build/reproducible-path/bcftools-1.21/test/view64bit.2.vcf -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.21/bcftools view /build/reproducible-path/bcftools-1.21/test/view64bit.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.21/bcftools view /build/reproducible-path/bcftools-1.21/test/view64bit.2.vcf -Ou | /build/reproducible-path/bcftools-1.21/bcftools view -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.21/bcftools view /build/reproducible-path/bcftools-1.21/test/view64bit.3.vcf -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.21/bcftools view /build/reproducible-path/bcftools-1.21/test/view64bit.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.21/bcftools view /build/reproducible-path/bcftools-1.21/test/view64bit.4.vcf -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.21/bcftools view /build/reproducible-path/bcftools-1.21/test/view64bit.4.vcf | /build/reproducible-path/bcftools-1.21/bcftools view -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.21/bcftools view /build/reproducible-path/bcftools-1.21/test/view64bit.4.vcf -Ou | /build/reproducible-path/bcftools-1.21/bcftools view -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.21/bcftools view /build/reproducible-path/bcftools-1.21/test/view64bit.5.vcf -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.21/bcftools view /build/reproducible-path/bcftools-1.21/test/view64bit.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools view -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.21/bcftools view /build/reproducible-path/bcftools-1.21/test/view64bit.5.vcf -Ou | /build/reproducible-path/bcftools-1.21/bcftools view -H .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -C5:nonmajor /tmp/zPov9rP7t1/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -c6:nonmajor /tmp/zPov9rP7t1/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -q0.3:major /tmp/zPov9rP7t1/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/zPov9rP7t1/view.filter.annovar.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -i 'Gene.refGene~"NOD"' /tmp/zPov9rP7t1/view.filter.annovar.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -i 'LJB2_MutationTaster=="0.291000"' /tmp/zPov9rP7t1/view.filter.annovar.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -a /tmp/zPov9rP7t1/view-a.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -T /build/reproducible-path/bcftools-1.21/test/view.sites.txt /tmp/zPov9rP7t1/view.sites.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -T /build/reproducible-path/bcftools-1.21/test/view.sites.txt /tmp/zPov9rP7t1/view.sites.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -T /build/reproducible-path/bcftools-1.21/test/view.sites.txt.gz /tmp/zPov9rP7t1/view.sites.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -T /build/reproducible-path/bcftools-1.21/test/view.sites.txt.gz /tmp/zPov9rP7t1/view.sites.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_head: /build/reproducible-path/bcftools-1.21/bcftools head /build/reproducible-path/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_head: /build/reproducible-path/bcftools-1.21/bcftools head -h 0 /build/reproducible-path/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_head: /build/reproducible-path/bcftools-1.21/bcftools head -h 1 /build/reproducible-path/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_head: /build/reproducible-path/bcftools-1.21/bcftools head -h 5 /build/reproducible-path/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_head: /build/reproducible-path/bcftools-1.21/bcftools head -h 22 /build/reproducible-path/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_head: /build/reproducible-path/bcftools-1.21/bcftools head -h 23 /build/reproducible-path/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_head: /build/reproducible-path/bcftools-1.21/bcftools head -n 0 /build/reproducible-path/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_head: /build/reproducible-path/bcftools-1.21/bcftools head -n 1 /build/reproducible-path/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_head: /build/reproducible-path/bcftools-1.21/bcftools head -n 5 /build/reproducible-path/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_head: /build/reproducible-path/bcftools-1.21/bcftools head -h 5 -n 5 < /build/reproducible-path/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_head2: /build/reproducible-path/bcftools-1.21/bcftools head -s0 /tmp/zPov9rP7t1/mpileup.2.vcf.gz .. ok test_vcf_head2: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -Ob /tmp/zPov9rP7t1/mpileup.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools head -s0 .. ok test_vcf_head2: /build/reproducible-path/bcftools-1.21/bcftools head -s1 /tmp/zPov9rP7t1/mpileup.2.vcf.gz .. ok test_vcf_head2: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -Ob /tmp/zPov9rP7t1/mpileup.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools head -s1 .. ok test_vcf_head2: /build/reproducible-path/bcftools-1.21/bcftools head -s2 -h2 /tmp/zPov9rP7t1/mpileup.2.vcf.gz .. ok test_vcf_head2: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -Ob /tmp/zPov9rP7t1/mpileup.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools head -s2 -h2 .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mv /build/reproducible-path/bcftools-1.21/test/mpileup.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mv /build/reproducible-path/bcftools-1.21/test/mpileup.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mg0 /build/reproducible-path/bcftools-1.21/test/mpileup.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mg0 /build/reproducible-path/bcftools-1.21/test/mpileup.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mv -S /build/reproducible-path/bcftools-1.21/test/mpileup.3.samples /build/reproducible-path/bcftools-1.21/test/mpileup.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mv -S /build/reproducible-path/bcftools-1.21/test/mpileup.3.samples /build/reproducible-path/bcftools-1.21/test/mpileup.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mv -S /build/reproducible-path/bcftools-1.21/test/mpileup.4.samples /build/reproducible-path/bcftools-1.21/test/mpileup.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mv -S /build/reproducible-path/bcftools-1.21/test/mpileup.4.samples /build/reproducible-path/bcftools-1.21/test/mpileup.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mv -S /build/reproducible-path/bcftools-1.21/test/mpileup.5.samples /build/reproducible-path/bcftools-1.21/test/mpileup.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mv -S /build/reproducible-path/bcftools-1.21/test/mpileup.5.samples /build/reproducible-path/bcftools-1.21/test/mpileup.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mv --ploidy-file /build/reproducible-path/bcftools-1.21/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.21/test/mpileup.samples /build/reproducible-path/bcftools-1.21/test/mpileup.X.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mv --ploidy-file /build/reproducible-path/bcftools-1.21/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.21/test/mpileup.samples /build/reproducible-path/bcftools-1.21/test/mpileup.X.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mv --ploidy-file /build/reproducible-path/bcftools-1.21/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.21/test/mpileup.ped /build/reproducible-path/bcftools-1.21/test/mpileup.X.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mv --ploidy-file /build/reproducible-path/bcftools-1.21/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.21/test/mpileup.ped /build/reproducible-path/bcftools-1.21/test/mpileup.X.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mv --ploidy-file /build/reproducible-path/bcftools-1.21/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.21/test/mpileup.2.samples /build/reproducible-path/bcftools-1.21/test/mpileup.X.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mv --ploidy-file /build/reproducible-path/bcftools-1.21/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.21/test/mpileup.2.samples /build/reproducible-path/bcftools-1.21/test/mpileup.X.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mv /build/reproducible-path/bcftools-1.21/test/mpileup.NA19213.NA19129.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mv /build/reproducible-path/bcftools-1.21/test/mpileup.NA19213.NA19129.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mv -G - --group-samples-tag AD /build/reproducible-path/bcftools-1.21/test/mpileup.NA19213.NA19129.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mv -G - --group-samples-tag AD /build/reproducible-path/bcftools-1.21/test/mpileup.NA19213.NA19129.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mv /build/reproducible-path/bcftools-1.21/test/mpileup.hwe.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mv /build/reproducible-path/bcftools-1.21/test/mpileup.hwe.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mv -G - --group-samples-tag AD /build/reproducible-path/bcftools-1.21/test/mpileup.hwe.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mv -G - --group-samples-tag AD /build/reproducible-path/bcftools-1.21/test/mpileup.hwe.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mv -G /build/reproducible-path/bcftools-1.21/test/mpileup.hwe.samples --group-samples-tag AD /build/reproducible-path/bcftools-1.21/test/mpileup.hwe.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mv -G /build/reproducible-path/bcftools-1.21/test/mpileup.hwe.samples --group-samples-tag AD /build/reproducible-path/bcftools-1.21/test/mpileup.hwe.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/zPov9rP7t1/mpileup.tab.gz /build/reproducible-path/bcftools-1.21/test/mpileup.vcf .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/zPov9rP7t1/mpileup.tab.gz /build/reproducible-path/bcftools-1.21/test/mpileup.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/zPov9rP7t1/mpileup.2.tab.gz /build/reproducible-path/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/zPov9rP7t1/mpileup.2.tab.gz /build/reproducible-path/bcftools-1.21/test/mpileup.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/zPov9rP7t1/mpileup.3.tab.gz -i /build/reproducible-path/bcftools-1.21/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/zPov9rP7t1/mpileup.3.tab.gz -i /build/reproducible-path/bcftools-1.21/test/mpileup.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/zPov9rP7t1/mpileup.4.tab.gz -i /build/reproducible-path/bcftools-1.21/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/zPov9rP7t1/mpileup.4.tab.gz -i /build/reproducible-path/bcftools-1.21/test/mpileup.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/zPov9rP7t1/mpileup.5.tab.gz -i /build/reproducible-path/bcftools-1.21/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/zPov9rP7t1/mpileup.5.tab.gz -i /build/reproducible-path/bcftools-1.21/test/mpileup.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/zPov9rP7t1/mpileup.6.tab.gz -i /build/reproducible-path/bcftools-1.21/test/mpileup.4.vcf .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/zPov9rP7t1/mpileup.6.tab.gz -i /build/reproducible-path/bcftools-1.21/test/mpileup.4.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/zPov9rP7t1/mpileup.7.tab.gz -i /build/reproducible-path/bcftools-1.21/test/mpileup.5.vcf .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/zPov9rP7t1/mpileup.7.tab.gz -i /build/reproducible-path/bcftools-1.21/test/mpileup.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/zPov9rP7t1/mpileup.cals.1.tab.gz /build/reproducible-path/bcftools-1.21/test/mpileup.cals.1.vcf .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/zPov9rP7t1/mpileup.cals.1.tab.gz /build/reproducible-path/bcftools-1.21/test/mpileup.cals.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/zPov9rP7t1/mpileup.cals.2.tab.gz /build/reproducible-path/bcftools-1.21/test/mpileup.cals.2.vcf .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/zPov9rP7t1/mpileup.cals.2.tab.gz /build/reproducible-path/bcftools-1.21/test/mpileup.cals.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -cv /build/reproducible-path/bcftools-1.21/test/mpileup.c.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -cv /build/reproducible-path/bcftools-1.21/test/mpileup.c.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -cv --ploidy-file /build/reproducible-path/bcftools-1.21/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.21/test/mpileup.samples /build/reproducible-path/bcftools-1.21/test/mpileup.c.X.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -cv --ploidy-file /build/reproducible-path/bcftools-1.21/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.21/test/mpileup.samples /build/reproducible-path/bcftools-1.21/test/mpileup.c.X.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -cv --ploidy-file /build/reproducible-path/bcftools-1.21/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.21/test/mpileup.ped /build/reproducible-path/bcftools-1.21/test/mpileup.c.X.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -cv --ploidy-file /build/reproducible-path/bcftools-1.21/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.21/test/mpileup.ped /build/reproducible-path/bcftools-1.21/test/mpileup.c.X.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -cv --ploidy-file /build/reproducible-path/bcftools-1.21/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.21/test/mpileup.2.samples /build/reproducible-path/bcftools-1.21/test/mpileup.c.X.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -cv --ploidy-file /build/reproducible-path/bcftools-1.21/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.21/test/mpileup.2.samples /build/reproducible-path/bcftools-1.21/test/mpileup.c.X.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mv /build/reproducible-path/bcftools-1.21/test/call-G.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mv /build/reproducible-path/bcftools-1.21/test/call-G.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mv -G - --group-samples-tag AD /build/reproducible-path/bcftools-1.21/test/call-G.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mv -G - --group-samples-tag AD /build/reproducible-path/bcftools-1.21/test/call-G.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mv -F AN_POP,AC_POP /build/reproducible-path/bcftools-1.21/test/call-G.2.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mv -F AN_POP,AC_POP /build/reproducible-path/bcftools-1.21/test/call-G.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -m /build/reproducible-path/bcftools-1.21/test/call.af-fixation.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -m /build/reproducible-path/bcftools-1.21/test/call.af-fixation.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -m -G /build/reproducible-path/bcftools-1.21/test/call.af-fixation.txt /build/reproducible-path/bcftools-1.21/test/call.af-fixation.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -m -G /build/reproducible-path/bcftools-1.21/test/call.af-fixation.txt /build/reproducible-path/bcftools-1.21/test/call.af-fixation.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -m -G /build/reproducible-path/bcftools-1.21/test/call.af-fixation.txt -a GP,GQ /build/reproducible-path/bcftools-1.21/test/call.af-fixation.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -m -G /build/reproducible-path/bcftools-1.21/test/call.af-fixation.txt -a GP,GQ /build/reproducible-path/bcftools-1.21/test/call.af-fixation.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S. -e'TXT0="text"' /build/reproducible-path/bcftools-1.21/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S. -e'TXT0="text"' /build/reproducible-path/bcftools-1.21/test/view.filter.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S. -e'FMT/FRS[*:1]="BB"' /build/reproducible-path/bcftools-1.21/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S. -e'FMT/FRS[*:1]="BB"' /build/reproducible-path/bcftools-1.21/test/view.filter.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S. -e'FMT/FGS[*:0]="AAAAAA"' /build/reproducible-path/bcftools-1.21/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S. -e'FMT/FGS[*:0]="AAAAAA"' /build/reproducible-path/bcftools-1.21/test/view.filter.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S. -e'FMT/FGS[*:1]="BBB"' /build/reproducible-path/bcftools-1.21/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S. -e'FMT/FGS[*:1]="BBB"' /build/reproducible-path/bcftools-1.21/test/view.filter.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S. -e'FMT/FGS[*:4]="EE"' /build/reproducible-path/bcftools-1.21/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S. -e'FMT/FGS[*:4]="EE"' /build/reproducible-path/bcftools-1.21/test/view.filter.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S. -e'FMT/STR="XX"' /build/reproducible-path/bcftools-1.21/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S. -e'FMT/STR="XX"' /build/reproducible-path/bcftools-1.21/test/view.filter.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S. -e'FMT/FILTER="aaa"' /build/reproducible-path/bcftools-1.21/test/view.filter.2.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S. -e'FMT/FILTER="aaa"' /build/reproducible-path/bcftools-1.21/test/view.filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -mx -g2 -G2 /build/reproducible-path/bcftools-1.21/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -mx -g2 -G2 /build/reproducible-path/bcftools-1.21/test/filter.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -e'INFO/DP=19' /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -e'INFO/DP=19' /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -e'INFO/DP=19' -s XX /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -e'INFO/DP=19' -s XX /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -e'INFO/DP=19' -s XX -m+ /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+ /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -e'INFO/DP=19' -s XX -mx /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -e'INFO/DP=19' -s XX -mx /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -e'INFO/DP=19' -s XX -m+x /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+x /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -e'FMT/GT="0/2"' /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -e'FMT/GT="0/2"' /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -e'FMT/GT="0/2"' -s XX /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -e'FMT/GT="0/2"' -s XX -m+ /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+ /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -e'FMT/GT="0/2"' -s XX -mx /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -mx /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -e'FMT/GT="0/2"' -s XX -m+x /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+x /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'FMT/GT="0/0" && AC[*]=2' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'FMT/GT="0/0" && AC[*]=2' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'AC[*]=2 && FMT/GT="0/0"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'AC[*]=2 && FMT/GT="0/0"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'ALT="."' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'ALT="."' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -i 'FORMAT/TEST3<25' /build/reproducible-path/bcftools-1.21/test/filter.4.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -i 'FORMAT/TEST3<25' /build/reproducible-path/bcftools-1.21/test/filter.4.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -i 'FORMAT/TEST4<25' /build/reproducible-path/bcftools-1.21/test/filter.4.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -i 'FORMAT/TEST4<25' /build/reproducible-path/bcftools-1.21/test/filter.4.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'GT="A"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'GT="A"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'GT="RR"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'GT="RR"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'GT="RA"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'GT="RA"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'GT="AR"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'GT="AR"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'GT="AA"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'GT="AA"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'GT="aA"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'GT="aA"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'GT="Aa"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'GT="Aa"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'GT="HOM"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'GT="HOM"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'GT="HET"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'GT="HET"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'GT="HAP"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'GT="HAP"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'AD[:1]=11' /build/reproducible-path/bcftools-1.21/test/filter.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'AD[:1]=11' /build/reproducible-path/bcftools-1.21/test/filter.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'AD[1:]=11' /build/reproducible-path/bcftools-1.21/test/filter.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'AD[1:]=11' /build/reproducible-path/bcftools-1.21/test/filter.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'FR[0:1]=11' /build/reproducible-path/bcftools-1.21/test/filter.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%FR]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'FR[0:1]=11' /build/reproducible-path/bcftools-1.21/test/filter.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%FR]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'AD[*]="."' /build/reproducible-path/bcftools-1.21/test/filter.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'AD[*]="."' /build/reproducible-path/bcftools-1.21/test/filter.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'AD[0:0]=="."' /build/reproducible-path/bcftools-1.21/test/filter.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'AD[0:0]=="."' /build/reproducible-path/bcftools-1.21/test/filter.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'AD[0:0]!="."' /build/reproducible-path/bcftools-1.21/test/filter.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'AD[0:0]!="."' /build/reproducible-path/bcftools-1.21/test/filter.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'QUAL=="."' /build/reproducible-path/bcftools-1.21/test/filter.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%QUAL\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'QUAL=="."' /build/reproducible-path/bcftools-1.21/test/filter.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%QUAL\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'N_PASS(DP>32)=1' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'N_PASS(DP>32)=1' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'F_PASS(DP>32)=0.5' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'F_PASS(DP>32)=0.5' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'F_MISSING>=1/5' /build/reproducible-path/bcftools-1.21/test/filter.6.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'F_MISSING>=1/5' /build/reproducible-path/bcftools-1.21/test/filter.6.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'F_MISSING>=0.2' /build/reproducible-path/bcftools-1.21/test/filter.6.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'F_MISSING>=0.2' /build/reproducible-path/bcftools-1.21/test/filter.6.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'F_PASS(GT=="mis")>=1/5' /build/reproducible-path/bcftools-1.21/test/filter.6.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'F_PASS(GT=="mis")>=1/5' /build/reproducible-path/bcftools-1.21/test/filter.6.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'F_PASS(GT=="mis")>=0.2' /build/reproducible-path/bcftools-1.21/test/filter.6.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'F_PASS(GT=="mis")>=0.2' /build/reproducible-path/bcftools-1.21/test/filter.6.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -mx -s + -g2:mnp,indel,other /build/reproducible-path/bcftools-1.21/test/filter.7.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -mx -s + -g2:mnp,indel,other /build/reproducible-path/bcftools-1.21/test/filter.7.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'FORMAT/AO==4' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'FORMAT/AO==4' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'MAX(FORMAT/AO[0:])==4' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'MAX(FORMAT/AO[0:])==4' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'MAX(FORMAT/AO)==4' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'MAX(FORMAT/AO)==4' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'MIN(FORMAT/AO[0:])==3' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO[0:])==3' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'MIN(FORMAT/AO)==2' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO)==2' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'MIN(FORMAT/AO[0:])==3' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO[0:])==3' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'AVG(FORMAT/AO[2:])==4' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'AVG(FORMAT/AO[2:])==4' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'MEDIAN(FORMAT/AO[2:])==4' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'MEDIAN(FORMAT/AO[2:])==4' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'STDEV(FORMAT/AO[0:])=0.5' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'STDEV(FORMAT/AO[0:])=0.5' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'SUM(FORMAT/AO[0:])=7' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'SUM(FORMAT/AO[0:])=7' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'SMPL_MAX(FORMAT/AO)==4' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'SMPL_MAX(FORMAT/AO)==4' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'sMIN(FORMAT/AO)==2' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'sMIN(FORMAT/AO)==2' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'ABS(sAVG(FORMAT/AO)-3.66666)<1e-5' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'ABS(sAVG(FORMAT/AO)-3.66666)<1e-5' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'sMEDIAN(FORMAT/AO)==4' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'sMEDIAN(FORMAT/AO)==4' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'ABS(sSTDEV(FORMAT/AO)-1.2472191)<1e-5' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'ABS(sSTDEV(FORMAT/AO)-1.2472191)<1e-5' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'sSUM(FORMAT/AO)==11' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'sSUM(FORMAT/AO)==11' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i 'QUAL/FMT/AD==55' /build/reproducible-path/bcftools-1.21/test/filter.9.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i 'QUAL/FMT/AD==55' /build/reproducible-path/bcftools-1.21/test/filter.9.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i 'QUAL/INFO/AD==10' /build/reproducible-path/bcftools-1.21/test/filter.9.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i 'QUAL/INFO/AD==10' /build/reproducible-path/bcftools-1.21/test/filter.9.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'ABS(SMPL_MAX(FORMAT/AO))=5' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'ABS(SMPL_MAX(FORMAT/AO))=5' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'PHRED(AO[1:])>-4' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'PHRED(AO[1:])>-4' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'ABS(AO[1:])==2' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'ABS(AO[1:])==2' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i 'sum(AD[*]) > FORMAT/DP' /build/reproducible-path/bcftools-1.21/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i 'sum(AD[*]) > FORMAT/DP' /build/reproducible-path/bcftools-1.21/test/filter.10.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i 'FORMAT/DP < sum(AD[*])' /build/reproducible-path/bcftools-1.21/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i 'FORMAT/DP < sum(AD[*])' /build/reproducible-path/bcftools-1.21/test/filter.10.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i 'sum(AD[*]) < FORMAT/DP' /build/reproducible-path/bcftools-1.21/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i 'sum(AD[*]) < FORMAT/DP' /build/reproducible-path/bcftools-1.21/test/filter.10.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i 'FORMAT/DP > sum(AD[*])' /build/reproducible-path/bcftools-1.21/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i 'FORMAT/DP > sum(AD[*])' /build/reproducible-path/bcftools-1.21/test/filter.10.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 0 /build/reproducible-path/bcftools-1.21/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 0 /build/reproducible-path/bcftools-1.21/test/filter.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 1 /build/reproducible-path/bcftools-1.21/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 1 /build/reproducible-path/bcftools-1.21/test/filter.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 2 /build/reproducible-path/bcftools-1.21/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 2 /build/reproducible-path/bcftools-1.21/test/filter.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter --soft-filter xxx --mask ^2:1005-1008 /build/reproducible-path/bcftools-1.21/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob --soft-filter xxx --mask ^2:1005-1008 /build/reproducible-path/bcftools-1.21/test/filter.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_sort: /build/reproducible-path/bcftools-1.21/bcftools sort -m 0 /build/reproducible-path/bcftools-1.21/test/sort.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /build/reproducible-path/bcftools-1.21/bcftools sort -Ob -m 0 /build/reproducible-path/bcftools-1.21/test/sort.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /build/reproducible-path/bcftools-1.21/bcftools sort -m 1000 /build/reproducible-path/bcftools-1.21/test/sort.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /build/reproducible-path/bcftools-1.21/bcftools sort -Ob -m 1000 /build/reproducible-path/bcftools-1.21/test/sort.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /build/reproducible-path/bcftools-1.21/test/regions.tab /tmp/zPov9rP7t1/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/regions.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /build/reproducible-path/bcftools-1.21/test/regions.tab .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /build/reproducible-path/bcftools-1.21/test/regions.tab /tmp/zPov9rP7t1/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/zPov9rP7t1/regions.tab.gz /tmp/zPov9rP7t1/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/regions.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/zPov9rP7t1/regions.tab.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/zPov9rP7t1/regions.tab.gz /tmp/zPov9rP7t1/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/zPov9rP7t1/regions.bed /tmp/zPov9rP7t1/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/regions.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/zPov9rP7t1/regions.bed .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/zPov9rP7t1/regions.bed /tmp/zPov9rP7t1/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/zPov9rP7t1/regions.bed.gz /tmp/zPov9rP7t1/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/regions.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/zPov9rP7t1/regions.bed.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/zPov9rP7t1/regions.bed.gz /tmp/zPov9rP7t1/regions.vcf.gz .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate.escape.1.tab.gz -c CHROM,POS,ISTR,FMT/FSTR /build/reproducible-path/bcftools-1.21/test/annotate.escape.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate.escape.1.tab.gz -c CHROM,POS,ISTR,FMT/FSTR /build/reproducible-path/bcftools-1.21/test/annotate.escape.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate.match.1.tab.gz -c CHROM,POS,-,-,SCORE,~X,-,- -i'STR={X}' /build/reproducible-path/bcftools-1.21/test/annotate.match.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate.match.1.tab.gz -c CHROM,POS,-,-,SCORE,~X,-,- -i'STR={X}' /build/reproducible-path/bcftools-1.21/test/annotate.match.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate.match.1.tab.gz -c CHROM,POS,REF,ALT,SCORE,-,~X,- -i'INT={X}' /build/reproducible-path/bcftools-1.21/test/annotate.match.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate.match.1.tab.gz -c CHROM,POS,REF,ALT,SCORE,-,~X,- -i'INT={X}' /build/reproducible-path/bcftools-1.21/test/annotate.match.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate.match.1.tab.gz -c CHROM,POS,REF,ALT,SCORE,-,-,~X -i'FLT={X}' /build/reproducible-path/bcftools-1.21/test/annotate.match.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate.match.1.tab.gz -c CHROM,POS,REF,ALT,SCORE,-,-,~X -i'FLT={X}' /build/reproducible-path/bcftools-1.21/test/annotate.match.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /build/reproducible-path/bcftools-1.21/test/annotate.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /build/reproducible-path/bcftools-1.21/test/annotate.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate2.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate.hdr -c CHROM,POS,-,T_STR /build/reproducible-path/bcftools-1.21/test/annotate.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate2.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate.hdr -c CHROM,POS,-,T_STR /build/reproducible-path/bcftools-1.21/test/annotate.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate2.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate.hdr -c CHROM,FROM,TO,T_STR /build/reproducible-path/bcftools-1.21/test/annotate.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate2.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate.hdr -c CHROM,FROM,TO,T_STR /build/reproducible-path/bcftools-1.21/test/annotate.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/zPov9rP7t1/annotate.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/zPov9rP7t1/annotate.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/zPov9rP7t1/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/zPov9rP7t1/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/zPov9rP7t1/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/zPov9rP7t1/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/zPov9rP7t1/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/zPov9rP7t1/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/zPov9rP7t1/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/zPov9rP7t1/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/zPov9rP7t1/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/zPov9rP7t1/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /build/reproducible-path/bcftools-1.21/test/annotate3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /build/reproducible-path/bcftools-1.21/test/annotate3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -x FORMAT /build/reproducible-path/bcftools-1.21/test/annotate3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -x FORMAT /build/reproducible-path/bcftools-1.21/test/annotate3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots4.vcf.gz -c +INFO /tmp/zPov9rP7t1/annotate4.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots4.vcf.gz -c +INFO /tmp/zPov9rP7t1/annotate4.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots4.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /build/reproducible-path/bcftools-1.21/test/annotate4.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots4.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /build/reproducible-path/bcftools-1.21/test/annotate4.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots10.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /build/reproducible-path/bcftools-1.21/test/annotate10.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots10.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /build/reproducible-path/bcftools-1.21/test/annotate10.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/zPov9rP7t1/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/zPov9rP7t1/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /build/reproducible-path/bcftools-1.21/test/annotate2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /build/reproducible-path/bcftools-1.21/test/annotate2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/zPov9rP7t1/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/zPov9rP7t1/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/zPov9rP7t1/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/zPov9rP7t1/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/zPov9rP7t1/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/zPov9rP7t1/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots11.vcf.gz -c FMT /tmp/zPov9rP7t1/annotate11.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots11.vcf.gz -c FMT /tmp/zPov9rP7t1/annotate11.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots2.vcf.gz -c FMT/newGT:=GT /tmp/zPov9rP7t1/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots2.vcf.gz -c FMT/newGT:=GT /tmp/zPov9rP7t1/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots12.vcf.gz -c FMT/GT:=newGT /tmp/zPov9rP7t1/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots12.vcf.gz -c FMT/GT:=newGT /tmp/zPov9rP7t1/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots13.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate13.hdr -c CHROM,BEG,END,ABC /build/reproducible-path/bcftools-1.21/test/annotate13.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots13.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate13.hdr -c CHROM,BEG,END,ABC /build/reproducible-path/bcftools-1.21/test/annotate13.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots13.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:append /build/reproducible-path/bcftools-1.21/test/annotate13.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots13.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:append /build/reproducible-path/bcftools-1.21/test/annotate13.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots13.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:unique /build/reproducible-path/bcftools-1.21/test/annotate13.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots13.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:unique /build/reproducible-path/bcftools-1.21/test/annotate13.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -x FILTER/XX,INFO/XX --force /build/reproducible-path/bcftools-1.21/test/annotate14.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -x FILTER/XX,INFO/XX --force /build/reproducible-path/bcftools-1.21/test/annotate14.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate15.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate15.hdr -s SAMPLE1 -c CHROM,FROM,TO,FMT/FOO,BAR /build/reproducible-path/bcftools-1.21/test/annotate15.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate15.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate15.hdr -s SAMPLE1 -c CHROM,FROM,TO,FMT/FOO,BAR /build/reproducible-path/bcftools-1.21/test/annotate15.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate15.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate15.hdr -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR /build/reproducible-path/bcftools-1.21/test/annotate15.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate15.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate15.hdr -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR /build/reproducible-path/bcftools-1.21/test/annotate15.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate15.tab.gz -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR -H '##FORMAT=' -H '##INFO=' /build/reproducible-path/bcftools-1.21/test/annotate15.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate15.tab.gz -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR -H '##FORMAT=' -H '##INFO=' /build/reproducible-path/bcftools-1.21/test/annotate15.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -x FILTER /build/reproducible-path/bcftools-1.21/test/annotate16.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -x FILTER /build/reproducible-path/bcftools-1.21/test/annotate16.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/reproducible-path/bcftools-1.21/test/annotate17.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/reproducible-path/bcftools-1.21/test/annotate17.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/reproducible-path/bcftools-1.21/test/annotate17.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/reproducible-path/bcftools-1.21/test/annotate17.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate17.3.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/reproducible-path/bcftools-1.21/test/annotate17.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate17.3.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/reproducible-path/bcftools-1.21/test/annotate17.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate18.1.tab.gz -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /build/reproducible-path/bcftools-1.21/test/annotate18.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate18.1.tab.gz -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /build/reproducible-path/bcftools-1.21/test/annotate18.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate18.2.tab.gz -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /build/reproducible-path/bcftools-1.21/test/annotate18.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate18.2.tab.gz -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /build/reproducible-path/bcftools-1.21/test/annotate18.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/zPov9rP7t1/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/zPov9rP7t1/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/zPov9rP7t1/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/zPov9rP7t1/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/zPov9rP7t1/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/zPov9rP7t1/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -c INFO/FILTER:=FILTER /build/reproducible-path/bcftools-1.21/test/annotate19.dst.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -c INFO/FILTER:=FILTER /build/reproducible-path/bcftools-1.21/test/annotate19.dst.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER /tmp/zPov9rP7t1/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER /tmp/zPov9rP7t1/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER /tmp/zPov9rP7t1/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER /tmp/zPov9rP7t1/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER,FILTER /tmp/zPov9rP7t1/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER,FILTER /tmp/zPov9rP7t1/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=./FILTER /tmp/zPov9rP7t1/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=./FILTER /tmp/zPov9rP7t1/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate20.src.vcf.gz -c FMT/GT /tmp/zPov9rP7t1/annotate20.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate20.src.vcf.gz -c FMT/GT /tmp/zPov9rP7t1/annotate20.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate20.src.vcf.gz -c +FMT/GT /tmp/zPov9rP7t1/annotate20.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate20.src.vcf.gz -c +FMT/GT /tmp/zPov9rP7t1/annotate20.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate20.src.vcf.gz -c -FMT/GT /tmp/zPov9rP7t1/annotate20.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate20.src.vcf.gz -c -FMT/GT /tmp/zPov9rP7t1/annotate20.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate.multi.tab.gz -c CHROM,POS,REF,ALT,ANN -l ANN:append /build/reproducible-path/bcftools-1.21/test/annotate.multi.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate.multi.tab.gz -c CHROM,POS,REF,ALT,ANN -l ANN:append /build/reproducible-path/bcftools-1.21/test/annotate.multi.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate.missing-append.tab.gz -c CHROM,POS,REF,ALT,STR,INT,FLT -l STR:append-missing,INT:append-missing,FLT:append-missing /build/reproducible-path/bcftools-1.21/test/annotate.missing-append.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate.missing-append.tab.gz -c CHROM,POS,REF,ALT,STR,INT,FLT -l STR:append-missing,INT:append-missing,FLT:append-missing /build/reproducible-path/bcftools-1.21/test/annotate.missing-append.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /build/reproducible-path/bcftools-1.21/test/annotate9.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /build/reproducible-path/bcftools-1.21/test/annotate9.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate --rename-annots /build/reproducible-path/bcftools-1.21/test/annotate21.txt /build/reproducible-path/bcftools-1.21/test/annotate21.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob --rename-annots /build/reproducible-path/bcftools-1.21/test/annotate21.txt /build/reproducible-path/bcftools-1.21/test/annotate21.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -c XX:=FORMAT/X-X,YY:=FORMAT/Y-Y,AA:=FORMAT/A-A,AA:=INFO/A-A,BB:=INFO/B-B,XX:=INFO/X-X,YY:=INFO/Y-Y,fltA:=FILTER/flt-A,fltB:=FILTER/flt-B,fltX:=FILTER/flt-X,fltY:=FILTER/flt-Y /build/reproducible-path/bcftools-1.21/test/annotate21.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -c XX:=FORMAT/X-X,YY:=FORMAT/Y-Y,AA:=FORMAT/A-A,AA:=INFO/A-A,BB:=INFO/B-B,XX:=INFO/X-X,YY:=INFO/Y-Y,fltA:=FILTER/flt-A,fltB:=FILTER/flt-B,fltX:=FILTER/flt-X,fltY:=FILTER/flt-Y /build/reproducible-path/bcftools-1.21/test/annotate21.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/zPov9rP7t1/annotate22.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/zPov9rP7t1/annotate22.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate23.tab.gz -c CHROM,POS,~ID,REF,ALT,INFO/END /build/reproducible-path/bcftools-1.21/test/annotate23.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate23.tab.gz -c CHROM,POS,~ID,REF,ALT,INFO/END /build/reproducible-path/bcftools-1.21/test/annotate23.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate24.src.vcf.gz -c XX /tmp/zPov9rP7t1/annotate24.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate24.src.vcf.gz -c XX /tmp/zPov9rP7t1/annotate24.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate25.tab.gz -c CHROM,POS,ID,REF,ALT,~INFO/END /build/reproducible-path/bcftools-1.21/test/annotate25.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate25.tab.gz -c CHROM,POS,ID,REF,ALT,~INFO/END /build/reproducible-path/bcftools-1.21/test/annotate25.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate26.tab.gz -c CHROM,POS,-POS /build/reproducible-path/bcftools-1.21/test/annotate26.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate26.tab.gz -c CHROM,POS,-POS /build/reproducible-path/bcftools-1.21/test/annotate26.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,TSTR,TFLT,TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,TSTR,TFLT,TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.TSTR,.TFLT,.TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.TSTR,.TFLT,.TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.+TSTR,.+TFLT,.+TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.+TSTR,.+TFLT,.+TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,+TSTR,+TFLT,+TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,+TSTR,+TFLT,+TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.=TSTR,.=TFLT,.=TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.=TSTR,.=TFLT,.=TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,=TSTR,=TFLT,=TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,=TSTR,=TFLT,=TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique /build/reproducible-path/bcftools-1.21/test/annotate.olap.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique /build/reproducible-path/bcftools-1.21/test/annotate.olap.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique --min-overlap 0.4:0.5 -m XXX /build/reproducible-path/bcftools-1.21/test/annotate.olap.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique --min-overlap 0.4:0.5 -m XXX /build/reproducible-path/bcftools-1.21/test/annotate.olap.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots.id.vcf.gz -c ALT /tmp/zPov9rP7t1/annotate.id.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots.id.vcf.gz -c ALT /tmp/zPov9rP7t1/annotate.id.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots.id.vcf.gz -c +ALT /tmp/zPov9rP7t1/annotate.id.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots.id.vcf.gz -c +ALT /tmp/zPov9rP7t1/annotate.id.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots.id.2.vcf.gz --pair-logic some -c +ID /tmp/zPov9rP7t1/annotate.id.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots.id.2.vcf.gz --pair-logic some -c +ID /tmp/zPov9rP7t1/annotate.id.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots.id.2.vcf.gz --pair-logic any -c +ID /tmp/zPov9rP7t1/annotate.id.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots.id.2.vcf.gz --pair-logic any -c +ID /tmp/zPov9rP7t1/annotate.id.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate27.tab.gz -c CHROM,POS,REF,ALT,EVIDENCE /build/reproducible-path/bcftools-1.21/test/annotate27.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate27.tab.gz -c CHROM,POS,REF,ALT,EVIDENCE /build/reproducible-path/bcftools-1.21/test/annotate27.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1,smpl2 /build/reproducible-path/bcftools-1.21/test/annotate28.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1,smpl2 /build/reproducible-path/bcftools-1.21/test/annotate28.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2,smpl1 /build/reproducible-path/bcftools-1.21/test/annotate28.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2,smpl1 /build/reproducible-path/bcftools-1.21/test/annotate28.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1 /build/reproducible-path/bcftools-1.21/test/annotate28.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1 /build/reproducible-path/bcftools-1.21/test/annotate28.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2 /build/reproducible-path/bcftools-1.21/test/annotate28.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2 /build/reproducible-path/bcftools-1.21/test/annotate28.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -m XXX /build/reproducible-path/bcftools-1.21/test/annotate.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -m XXX /build/reproducible-path/bcftools-1.21/test/annotate.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots34.tab.gz -c CHROM,FROM,TO,INFO/END -H '##INFO=' /build/reproducible-path/bcftools-1.21/test/annotate34.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots34.tab.gz -c CHROM,FROM,TO,INFO/END -H '##INFO=' /build/reproducible-path/bcftools-1.21/test/annotate34.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots-mark.bed.gz -c CHROM,FROM,TO -m TAG /build/reproducible-path/bcftools-1.21/test/annots-mark.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots-mark.bed.gz -c CHROM,FROM,TO -m TAG /build/reproducible-path/bcftools-1.21/test/annots-mark.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --no-version /tmp/zPov9rP7t1/concat.1.a.vcf.gz /tmp/zPov9rP7t1/concat.1.b.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob /tmp/zPov9rP7t1/concat.1.a.vcf.gz /tmp/zPov9rP7t1/concat.1.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --no-version /tmp/zPov9rP7t1/concat.1.a.bcf /tmp/zPov9rP7t1/concat.1.b.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob /tmp/zPov9rP7t1/concat.1.a.bcf /tmp/zPov9rP7t1/concat.1.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -a /tmp/zPov9rP7t1/concat.2.a.vcf.gz /tmp/zPov9rP7t1/concat.2.b.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -a /tmp/zPov9rP7t1/concat.2.a.vcf.gz /tmp/zPov9rP7t1/concat.2.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -a /tmp/zPov9rP7t1/concat.2.a.bcf /tmp/zPov9rP7t1/concat.2.b.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -a /tmp/zPov9rP7t1/concat.2.a.bcf /tmp/zPov9rP7t1/concat.2.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -aD /tmp/zPov9rP7t1/concat.2.a.vcf.gz /tmp/zPov9rP7t1/concat.2.b.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -aD /tmp/zPov9rP7t1/concat.2.a.vcf.gz /tmp/zPov9rP7t1/concat.2.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -aD /tmp/zPov9rP7t1/concat.2.a.bcf /tmp/zPov9rP7t1/concat.2.b.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -aD /tmp/zPov9rP7t1/concat.2.a.bcf /tmp/zPov9rP7t1/concat.2.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -l --ligate-warn /tmp/zPov9rP7t1/concat.3.a.vcf.gz /tmp/zPov9rP7t1/concat.3.b.vcf.gz /tmp/zPov9rP7t1/concat.3.0.vcf.gz /tmp/zPov9rP7t1/concat.3.c.vcf.gz /tmp/zPov9rP7t1/concat.3.d.vcf.gz /tmp/zPov9rP7t1/concat.3.e.vcf.gz /tmp/zPov9rP7t1/concat.3.f.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -l --ligate-warn /tmp/zPov9rP7t1/concat.3.a.vcf.gz /tmp/zPov9rP7t1/concat.3.b.vcf.gz /tmp/zPov9rP7t1/concat.3.0.vcf.gz /tmp/zPov9rP7t1/concat.3.c.vcf.gz /tmp/zPov9rP7t1/concat.3.d.vcf.gz /tmp/zPov9rP7t1/concat.3.e.vcf.gz /tmp/zPov9rP7t1/concat.3.f.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -l --ligate-warn /tmp/zPov9rP7t1/concat.3.a.bcf /tmp/zPov9rP7t1/concat.3.b.bcf /tmp/zPov9rP7t1/concat.3.0.bcf /tmp/zPov9rP7t1/concat.3.c.bcf /tmp/zPov9rP7t1/concat.3.d.bcf /tmp/zPov9rP7t1/concat.3.e.bcf /tmp/zPov9rP7t1/concat.3.f.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -l --ligate-warn /tmp/zPov9rP7t1/concat.3.a.bcf /tmp/zPov9rP7t1/concat.3.b.bcf /tmp/zPov9rP7t1/concat.3.0.bcf /tmp/zPov9rP7t1/concat.3.c.bcf /tmp/zPov9rP7t1/concat.3.d.bcf /tmp/zPov9rP7t1/concat.3.e.bcf /tmp/zPov9rP7t1/concat.3.f.bcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ Random seed for test_naive_concat: 1061134846 .. ok test_naive_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --naive-force /tmp/zPov9rP7t1/naive_concat.0.bcf /tmp/zPov9rP7t1/naive_concat.1.bcf /tmp/zPov9rP7t1/naive_concat.2.bcf /tmp/zPov9rP7t1/naive_concat.3.bcf /tmp/zPov9rP7t1/naive_concat.4.bcf /tmp/zPov9rP7t1/naive_concat.5.bcf /tmp/zPov9rP7t1/naive_concat.6.bcf /tmp/zPov9rP7t1/naive_concat.7.bcf /tmp/zPov9rP7t1/naive_concat.8.bcf /tmp/zPov9rP7t1/naive_concat.9.bcf | /build/reproducible-path/bcftools-1.21/bcftools view -H .. ok test_naive_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --naive /tmp/zPov9rP7t1/naive_concat.0.vcf.gz /tmp/zPov9rP7t1/naive_concat.1.vcf.gz /tmp/zPov9rP7t1/naive_concat.2.vcf.gz /tmp/zPov9rP7t1/naive_concat.3.vcf.gz /tmp/zPov9rP7t1/naive_concat.4.vcf.gz /tmp/zPov9rP7t1/naive_concat.5.vcf.gz /tmp/zPov9rP7t1/naive_concat.6.vcf.gz /tmp/zPov9rP7t1/naive_concat.7.vcf.gz /tmp/zPov9rP7t1/naive_concat.8.vcf.gz /tmp/zPov9rP7t1/naive_concat.9.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view -H .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -l /tmp/zPov9rP7t1/concat.4.a.vcf.gz /tmp/zPov9rP7t1/concat.4.b.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -l /tmp/zPov9rP7t1/concat.4.a.vcf.gz /tmp/zPov9rP7t1/concat.4.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -l /tmp/zPov9rP7t1/concat.4.a.bcf /tmp/zPov9rP7t1/concat.4.b.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -l /tmp/zPov9rP7t1/concat.4.a.bcf /tmp/zPov9rP7t1/concat.4.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -l --ligate-warn /tmp/zPov9rP7t1/concat.5.a.vcf.gz /tmp/zPov9rP7t1/concat.5.b.vcf.gz /tmp/zPov9rP7t1/concat.5.c.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -l --ligate-warn /tmp/zPov9rP7t1/concat.5.a.vcf.gz /tmp/zPov9rP7t1/concat.5.b.vcf.gz /tmp/zPov9rP7t1/concat.5.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -l --ligate-warn /tmp/zPov9rP7t1/concat.5.a.bcf /tmp/zPov9rP7t1/concat.5.b.bcf /tmp/zPov9rP7t1/concat.5.c.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -l --ligate-warn /tmp/zPov9rP7t1/concat.5.a.bcf /tmp/zPov9rP7t1/concat.5.b.bcf /tmp/zPov9rP7t1/concat.5.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -l --ligate-force /tmp/zPov9rP7t1/concat.5.a.bcf /tmp/zPov9rP7t1/concat.5.b.bcf /tmp/zPov9rP7t1/concat.5.c.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -l --ligate-force /tmp/zPov9rP7t1/concat.5.a.bcf /tmp/zPov9rP7t1/concat.5.b.bcf /tmp/zPov9rP7t1/concat.5.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -G -a -D /tmp/zPov9rP7t1/concat.5.a.vcf.gz /tmp/zPov9rP7t1/concat.5.b.vcf.gz /tmp/zPov9rP7t1/concat.5.c.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -G -a -D /tmp/zPov9rP7t1/concat.5.a.vcf.gz /tmp/zPov9rP7t1/concat.5.b.vcf.gz /tmp/zPov9rP7t1/concat.5.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -G -a -D /tmp/zPov9rP7t1/concat.5.a.bcf /tmp/zPov9rP7t1/concat.5.b.bcf /tmp/zPov9rP7t1/concat.5.c.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -G -a -D /tmp/zPov9rP7t1/concat.5.a.bcf /tmp/zPov9rP7t1/concat.5.b.bcf /tmp/zPov9rP7t1/concat.5.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.hdr /build/reproducible-path/bcftools-1.21/test/reheader.vcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /build/reproducible-path/bcftools-1.21/test/reheader.vcf | /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.hdr | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.hdr /tmp/zPov9rP7t1/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/zPov9rP7t1/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.hdr | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.hdr /tmp/zPov9rP7t1/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/zPov9rP7t1/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.hdr | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples /build/reproducible-path/bcftools-1.21/test/reheader.vcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /build/reproducible-path/bcftools-1.21/test/reheader.vcf | /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples /tmp/zPov9rP7t1/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/zPov9rP7t1/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples /tmp/zPov9rP7t1/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/zPov9rP7t1/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples2 /build/reproducible-path/bcftools-1.21/test/reheader.vcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /build/reproducible-path/bcftools-1.21/test/reheader.vcf | /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples2 | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples2 /tmp/zPov9rP7t1/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/zPov9rP7t1/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples2 | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples2 /tmp/zPov9rP7t1/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/zPov9rP7t1/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples2 | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples3 /build/reproducible-path/bcftools-1.21/test/reheader.vcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /build/reproducible-path/bcftools-1.21/test/reheader.vcf | /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples3 | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples3 /tmp/zPov9rP7t1/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/zPov9rP7t1/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples3 | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples3 /tmp/zPov9rP7t1/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/zPov9rP7t1/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples3 | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples4 /build/reproducible-path/bcftools-1.21/test/reheader.vcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /build/reproducible-path/bcftools-1.21/test/reheader.vcf | /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples4 | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples4 /tmp/zPov9rP7t1/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/zPov9rP7t1/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples4 | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples4 /tmp/zPov9rP7t1/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/zPov9rP7t1/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples4 | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.empty.hdr /build/reproducible-path/bcftools-1.21/test/empty.vcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /build/reproducible-path/bcftools-1.21/test/empty.vcf | /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.empty.hdr | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.empty.hdr /tmp/zPov9rP7t1/empty.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/zPov9rP7t1/empty.bcf | /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.empty.hdr | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.empty.hdr /tmp/zPov9rP7t1/empty.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/zPov9rP7t1/empty.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.empty.hdr | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -f /build/reproducible-path/bcftools-1.21/test/reheader.fai /build/reproducible-path/bcftools-1.21/test/reheader.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -f /build/reproducible-path/bcftools-1.21/test/reheader.fai /tmp/zPov9rP7t1/reheader.2.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -f /build/reproducible-path/bcftools-1.21/test/reheader.fai /tmp/zPov9rP7t1/reheader.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.2.hdr -f /build/reproducible-path/bcftools-1.21/test/reheader.fai /build/reproducible-path/bcftools-1.21/test/reheader.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.2.hdr -f /build/reproducible-path/bcftools-1.21/test/reheader.fai /tmp/zPov9rP7t1/reheader.2.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.2.hdr -f /build/reproducible-path/bcftools-1.21/test/reheader.fai /tmp/zPov9rP7t1/reheader.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -f /build/reproducible-path/bcftools-1.21/test/reheader.3.fai /build/reproducible-path/bcftools-1.21/test/reheader.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -f /build/reproducible-path/bcftools-1.21/test/reheader.3.fai /tmp/zPov9rP7t1/reheader.3.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -f /build/reproducible-path/bcftools-1.21/test/reheader.3.fai /tmp/zPov9rP7t1/reheader.3.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_rename_chrs: /build/reproducible-path/bcftools-1.21/bcftools annotate --rename-chrs /tmp/zPov9rP7t1/rename.map -Ov /tmp/zPov9rP7t1/annotate.bcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /build/reproducible-path/bcftools-1.21/bcftools annotate --rename-chrs /tmp/zPov9rP7t1/rename.map -Ob /tmp/zPov9rP7t1/annotate.bcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /build/reproducible-path/bcftools-1.21/bcftools annotate --rename-chrs /tmp/zPov9rP7t1/rename.map -Ov /build/reproducible-path/bcftools-1.21/test/annotate.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /build/reproducible-path/bcftools-1.21/bcftools annotate --rename-chrs /tmp/zPov9rP7t1/rename.map -Ob /build/reproducible-path/bcftools-1.21/test/annotate.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM\t%POS\n' .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. /tmp/zPov9rP7t1/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --vcf-ids /tmp/zPov9rP7t1/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --vcf-ids .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --vcf-ids --3N6 /tmp/zPov9rP7t1/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --vcf-ids --3N6 .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert -g .,- /tmp/zPov9rP7t1/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g .,- .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert --vcf-ids -G /build/reproducible-path/bcftools-1.21/test/convert.gs.gt.ids.gen,/build/reproducible-path/bcftools-1.21/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert --vcf-ids -G /build/reproducible-path/bcftools-1.21/test/convert.gs.gt.ids.gen,/build/reproducible-path/bcftools-1.21/test/convert.gs.gt.samples -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert -G /build/reproducible-path/bcftools-1.21/test/convert.gs.gt.ids.gen,/build/reproducible-path/bcftools-1.21/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert -G /build/reproducible-path/bcftools-1.21/test/convert.gs.gt.ids.gen,/build/reproducible-path/bcftools-1.21/test/convert.gs.gt.samples -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert --3N6 -G /build/reproducible-path/bcftools-1.21/test/convert.gs.gt.ids.3N6.gen,/build/reproducible-path/bcftools-1.21/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert --3N6 -G /build/reproducible-path/bcftools-1.21/test/convert.gs.gt.ids.3N6.gen,/build/reproducible-path/bcftools-1.21/test/convert.gs.gt.samples -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert --vcf-ids -G /build/reproducible-path/bcftools-1.21/test/convert.gs.gt.ids.gen.rev,/build/reproducible-path/bcftools-1.21/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert --vcf-ids -G /build/reproducible-path/bcftools-1.21/test/convert.gs.gt.ids.gen.rev,/build/reproducible-path/bcftools-1.21/test/convert.gs.gt.samples -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert -G /build/reproducible-path/bcftools-1.21/test/convert.gs.gt.ids.gen.rev,/build/reproducible-path/bcftools-1.21/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert -G /build/reproducible-path/bcftools-1.21/test/convert.gs.gt.ids.gen.rev,/build/reproducible-path/bcftools-1.21/test/convert.gs.gt.samples -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^## .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --tag PL /tmp/zPov9rP7t1/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --tag PL .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert -g .,- --tag PL /tmp/zPov9rP7t1/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g .,- --tag PL .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --vcf-ids /tmp/zPov9rP7t1/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/check.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --vcf-ids .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert -g .,- --vcf-ids /tmp/zPov9rP7t1/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/check.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g .,- --vcf-ids .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --3N6 /tmp/zPov9rP7t1/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/check.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --3N6 .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert -g .,- --3N6 /tmp/zPov9rP7t1/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/check.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g .,- --3N6 .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --3N6 --vcf-ids /tmp/zPov9rP7t1/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/check.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --3N6 --vcf-ids .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert -g .,- --3N6 --vcf-ids /tmp/zPov9rP7t1/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/check.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g .,- --3N6 --vcf-ids .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert -h -,.,. /tmp/zPov9rP7t1/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -h -,.,. .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert -h .,-,. /tmp/zPov9rP7t1/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -h .,-,. .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert -h .,-,. --vcf-ids /tmp/zPov9rP7t1/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -h .,-,. --vcf-ids .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert -h .,.,- /tmp/zPov9rP7t1/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -h .,.,- .. ok test_vcf_convert_hls2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert -H /build/reproducible-path/bcftools-1.21/test/convert.hls.gt.hap,/build/reproducible-path/bcftools-1.21/test/convert.hls.gt.legend,/build/reproducible-path/bcftools-1.21/test/convert.hls.gt.samples | grep -v ^## .. ok test_vcf_convert_hls2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert -H /build/reproducible-path/bcftools-1.21/test/convert.hls.gt.hap,/build/reproducible-path/bcftools-1.21/test/convert.hls.gt.legend,/build/reproducible-path/bcftools-1.21/test/convert.hls.gt.samples -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^## .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert --haplegendsample -,.,. /tmp/zPov9rP7t1/convert.hap-missing.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/convert.hap-missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert --haplegendsample -,.,. .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert --hapsample -,. /tmp/zPov9rP7t1/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert --hapsample -,. .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert --hapsample -,. --vcf-ids /tmp/zPov9rP7t1/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert --hapsample -,. --vcf-ids .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert --hapsample .,- /tmp/zPov9rP7t1/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert --hapsample .,- .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert --hapsample2vcf /build/reproducible-path/bcftools-1.21/test/convert.hs.gt.hap,/build/reproducible-path/bcftools-1.21/test/convert.hs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert --hapsample2vcf /build/reproducible-path/bcftools-1.21/test/convert.hs.gt.hap,/build/reproducible-path/bcftools-1.21/test/convert.hs.gt.samples -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert --vcf-ids --hapsample2vcf /build/reproducible-path/bcftools-1.21/test/convert.hs.gt.ids.hap,/build/reproducible-path/bcftools-1.21/test/convert.hs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert --vcf-ids --hapsample2vcf /build/reproducible-path/bcftools-1.21/test/convert.hs.gt.ids.hap,/build/reproducible-path/bcftools-1.21/test/convert.hs.gt.samples -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^## .. ok test_vcf_convert_gvcf: /build/reproducible-path/bcftools-1.21/bcftools convert --no-version --gvcf2vcf -i'FILTER="PASS"' -f /build/reproducible-path/bcftools-1.21/test/gvcf.fa /tmp/zPov9rP7t1/convert.gvcf.vcf.gz .. ok test_vcf_convert_gvcf: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/convert.gvcf.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert --gvcf2vcf -i'FILTER="PASS"' -f /build/reproducible-path/bcftools-1.21/test/gvcf.fa | grep -v ^##bcftools .. ok test_vcf_convert_tsv2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert --no-version -c ID,CHROM,POS,AA -s SAMPLE1 -f /build/reproducible-path/bcftools-1.21/test/23andme.fa --tsv2vcf /build/reproducible-path/bcftools-1.21/test/convert.23andme .. ok test_vcf_convert_tsv2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert -Ou -c ID,CHROM,POS,AA -s SAMPLE1 -f /build/reproducible-path/bcftools-1.21/test/23andme.fa --tsv2vcf /build/reproducible-path/bcftools-1.21/test/convert.23andme | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_convert_tsv2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert --no-version -c -,CHROM,POS,REF,ALT -f /build/reproducible-path/bcftools-1.21/test/23andme.fa --tsv2vcf /build/reproducible-path/bcftools-1.21/test/convert.tsv .. ok test_vcf_convert_tsv2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert -Ou -c -,CHROM,POS,REF,ALT -f /build/reproducible-path/bcftools-1.21/test/23andme.fa --tsv2vcf /build/reproducible-path/bcftools-1.21/test/convert.tsv | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.overlaps.1.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.overlaps.1.fa -s A .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.overlaps.1.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.overlaps.1.fa -s A .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.overlaps.1.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.overlaps.1.fa -s B .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.overlaps.1.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.overlaps.1.fa -s B .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.overlaps.1.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.overlaps.1.fa -s A -a N .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.overlaps.1.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.overlaps.1.fa -s A -a N .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.overlaps.1.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.overlaps.1.fa -s B -a N .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.overlaps.1.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.overlaps.1.fa -s B -a N .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.beyond.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.beyond.fa .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.beyond.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.beyond.fa .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -m /build/reproducible-path/bcftools-1.21/test/consensus.tab .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -m /build/reproducible-path/bcftools-1.21/test/consensus.tab .. ok test_vcf_consensus_chain: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -m /build/reproducible-path/bcftools-1.21/test/consensus.tab -c /tmp/zPov9rP7t1/consensus.1.chain.new >/dev/null; cat /tmp/zPov9rP7t1/consensus.1.chain.new .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -H 1 -m /build/reproducible-path/bcftools-1.21/test/consensus.tab .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -H 1 -m /build/reproducible-path/bcftools-1.21/test/consensus.tab .. ok test_vcf_consensus_chain: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -H 1 -m /build/reproducible-path/bcftools-1.21/test/consensus.tab -c /tmp/zPov9rP7t1/consensus.2.chain.new >/dev/null; cat /tmp/zPov9rP7t1/consensus.2.chain.new .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -I -s - -m /build/reproducible-path/bcftools-1.21/test/consensus.tab .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -I -s - -m /build/reproducible-path/bcftools-1.21/test/consensus.tab .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -I -m /build/reproducible-path/bcftools-1.21/test/consensus.tab --mask-with X -m /build/reproducible-path/bcftools-1.21/test/consensus.tab --mask-with lc .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -I -m /build/reproducible-path/bcftools-1.21/test/consensus.tab --mask-with X -m /build/reproducible-path/bcftools-1.21/test/consensus.tab --mask-with lc .. ok test_vcf_consensus_chain: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -I -m /build/reproducible-path/bcftools-1.21/test/consensus.tab -c /tmp/zPov9rP7t1/consensus.3.chain.new >/dev/null; cat /tmp/zPov9rP7t1/consensus.3.chain.new .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -H 1 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -H 1 .. ok test_vcf_consensus_chain: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -H 1 -c /tmp/zPov9rP7t1/consensus.4.chain.new >/dev/null; cat /tmp/zPov9rP7t1/consensus.4.chain.new .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus2.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -H 1 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus2.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -H 1 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus2.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -H 2 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus2.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -H 2 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/empty.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/empty.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -H 2 -M "?" .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus3.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -H 2 -M "?" .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -H 2 -M "?" -p xx_ .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus3.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -H 2 -M "?" -p xx_ .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus4.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus4.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus5.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus5.fa --haplotype LA .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus5.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus5.fa --haplotype LA .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus6.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus6.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus6.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus6.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus7.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 2 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus7.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 2 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus7.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 4 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus7.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 4 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus7.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 2pIu .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus7.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 2pIu .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus7.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 4pIu .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus7.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 4pIu .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus7.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 1 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus7.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 1 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus7.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 3 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus7.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 3 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus7.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 1pIu .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus7.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 1pIu .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus7.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 3pIu .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus7.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 3pIu .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus8.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus8.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus8.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -a . .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus8.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -a . .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus8.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -a . -i 'type="snp" || type="ref"' .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus8.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -a . -i 'type="snp" || type="ref"' .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus8.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -a . -i 'ALT!=""' .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus8.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -a . -i 'ALT!=""' .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus8.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -a . -e 'MinDP>15' .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus8.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -a . -e 'MinDP>15' .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus8.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -a . -e 'MinDP<15' .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus8.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -a . -e 'MinDP<15' .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.9.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.9.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.9.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.9.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.10.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.10.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.10.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.10.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.11.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.11.fa -s smpl .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.11.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.11.fa -s smpl .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.11.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.11.fa -s smpl -a N .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.11.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.11.fa -s smpl -a N .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.12.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.12.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.12.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.12.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.13.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.13.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.13.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.13.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.14.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.14.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.14.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.14.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.12.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.12.fa -s - --mark-del - --mark-ins uc --mark-snv uc .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.12.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.12.fa -s - --mark-del - --mark-ins uc --mark-snv uc .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.12.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.12.fa -s - --mark-del - --mark-ins + --mark-snv : .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.12.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.12.fa -s - --mark-del - --mark-ins + --mark-snv : .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.15.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.15.fa -H I --mark-ins lc --mark-snv lc .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.15.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.15.fa -H I --mark-ins lc --mark-snv lc .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.16.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -I .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.16.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -I .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.16.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -H I .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.16.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -H I .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.17.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -s - -M N -m /build/reproducible-path/bcftools-1.21/test/consensus.17.bed .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.17.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -s - -M N -m /build/reproducible-path/bcftools-1.21/test/consensus.17.bed .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.18.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.18.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.18.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.18.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.19.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.19.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.19.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.19.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.20.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.20.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.20.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.20.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.20.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.20.fa .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.20.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.20.fa .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.20.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.20.fa -M . -s b .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.20.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.20.fa -M . -s b .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.20.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.20.fa -M . -s a .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.20.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.20.fa -M . -s a .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.21.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.21.fa .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.21.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.21.fa .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.22.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 0 --mark-del . .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.22.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 0 --mark-del . .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.22.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 1 --mark-del . .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.22.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 1 --mark-del . .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.22.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 2 --mark-del . .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.22.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 2 --mark-del . .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.22.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 0 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.22.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 0 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.22.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 1 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.22.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 1 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.22.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 2 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.22.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 2 .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -r17:100-150 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -r17:100-150 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -r17:100-150 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -b /tmp/zPov9rP7t1/mpileup.bam.list --no-version | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -r17:100-150 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob -b /tmp/zPov9rP7t1/mpileup.bam.urllist | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -r17:100-150 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -r17:100-150 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -r17:100-150 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -b /tmp/zPov9rP7t1/mpileup.cram.list --no-version | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -r17:100-150 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob -b /tmp/zPov9rP7t1/mpileup.cram.urllist | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DV -r17:100-600 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DV -r17:100-600 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DV -r17:100-600 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DV -r17:100-600 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP,-AD -r17:100-600 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP,-AD -r17:100-600 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP,-AD -r17:100-600 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP,-AD -r17:100-600 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DV,-AD -r17:100-600 --gvcf 0,2,5 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DV,-AD -r17:100-600 --gvcf 0,2,5 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DV,-AD -r17:100-600 --gvcf 0,2,5 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DV,-AD -r17:100-600 --gvcf 0,2,5 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DV,-AD -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DV,-AD -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DV,-AD -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DV,-AD -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -s HG00101,HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -s HG00101,HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -s HG00101,HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -s HG00101,HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -S /build/reproducible-path/bcftools-1.21/test/mplp.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -S /build/reproducible-path/bcftools-1.21/test/mplp.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -S /build/reproducible-path/bcftools-1.21/test/mplp.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -S /build/reproducible-path/bcftools-1.21/test/mplp.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -s ^HG00101,HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -s ^HG00101,HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -s ^HG00101,HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -s ^HG00101,HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -S ^/build/reproducible-path/bcftools-1.21/test/mplp.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -S ^/build/reproducible-path/bcftools-1.21/test/mplp.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -S ^/build/reproducible-path/bcftools-1.21/test/mplp.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -S ^/build/reproducible-path/bcftools-1.21/test/mplp.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -S /build/reproducible-path/bcftools-1.21/test/mplp.9.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -S /build/reproducible-path/bcftools-1.21/test/mplp.9.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -S /build/reproducible-path/bcftools-1.21/test/mplp.9.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -S /build/reproducible-path/bcftools-1.21/test/mplp.9.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -S /build/reproducible-path/bcftools-1.21/test/mplp.9.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -S /build/reproducible-path/bcftools-1.21/test/mplp.9.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -G /build/reproducible-path/bcftools-1.21/test/mplp.10.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -G /build/reproducible-path/bcftools-1.21/test/mplp.10.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -G /build/reproducible-path/bcftools-1.21/test/mplp.10.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -G /build/reproducible-path/bcftools-1.21/test/mplp.10.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -G /build/reproducible-path/bcftools-1.21/test/mplp.10.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -G /build/reproducible-path/bcftools-1.21/test/mplp.10.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -s HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -s HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.sam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -s HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -s HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -s HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -s HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -s ^HG99999 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -s ^HG99999 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.sam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -s ^HG99999 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -s ^HG99999 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -s ^HG99999 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -s ^HG99999 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -G /build/reproducible-path/bcftools-1.21/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -G /build/reproducible-path/bcftools-1.21/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.sam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -G /build/reproducible-path/bcftools-1.21/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -G /build/reproducible-path/bcftools-1.21/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -G /build/reproducible-path/bcftools-1.21/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -G /build/reproducible-path/bcftools-1.21/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -G /build/reproducible-path/bcftools-1.21/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -G /build/reproducible-path/bcftools-1.21/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.sam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -G /build/reproducible-path/bcftools-1.21/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -G /build/reproducible-path/bcftools-1.21/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -G /build/reproducible-path/bcftools-1.21/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -G /build/reproducible-path/bcftools-1.21/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.fa /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.sam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.fa /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.fa /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD --indels-cns -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.fa /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD --indels-cns -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.sam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD --indels-cns -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.fa /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD --indels-cns -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD --indels-cns -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.fa /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD --indels-cns -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -r 11:75 -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.fa /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -r 11:75 -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -r 11:75 -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.fa /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -r 11:75 -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.fa /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.fa /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.fa /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.fa /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD,INFO/SCR,FMT/SCR -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD,INFO/SCR,FMT/SCR -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD,INFO/SCR,FMT/SCR -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD,INFO/SCR,FMT/SCR -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t 1:100 --skip-all-set PAIRED,PROPER_PAIR,MREVERSE -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t 1:100 --skip-all-set PAIRED,PROPER_PAIR,MREVERSE -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-filter.sam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t 1:100 --skip-any-set READ1 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t 1:100 --skip-any-set READ1 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-filter.sam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t 1:100 --skip-all-unset READ1 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t 1:100 --skip-all-unset READ1 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-filter.sam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t 1:100 --skip-any-unset READ1 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t 1:100 --skip-any-unset READ1 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-filter.sam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD,INFO/NMBZ -r chr19:69-99 -f /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.1.fa /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD,INFO/NMBZ -r chr19:69-99 -f /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.1.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.1.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD,INFO/NMBZ -r chr6:75 -f /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.2.fa /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD,INFO/NMBZ -r chr6:75 -f /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.2.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.2.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD,INFO/NMBZ -r chr16:75 -f /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.3.fa /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.3.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.3.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD,INFO/NMBZ -r chr16:75 -f /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.3.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.3.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.3.2.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_csq: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq.fa -g /build/reproducible-path/bcftools-1.21/test/csq.gff3 /build/reproducible-path/bcftools-1.21/test/csq.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq.fa -g /build/reproducible-path/bcftools-1.21/test/csq.chr.gff3 /build/reproducible-path/bcftools-1.21/test/csq.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq.fa -g /build/reproducible-path/bcftools-1.21/test/csq.2.gff /build/reproducible-path/bcftools-1.21/test/csq.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq.fa -g /build/reproducible-path/bcftools-1.21/test/csq.2.gff --ncsq 64 /build/reproducible-path/bcftools-1.21/test/csq.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq.nchr.fa -g /build/reproducible-path/bcftools-1.21/test/csq.nchr.gff /build/reproducible-path/bcftools-1.21/test/csq.nchr.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq.ychr.fa -g /build/reproducible-path/bcftools-1.21/test/csq.nchr.gff /build/reproducible-path/bcftools-1.21/test/csq.nchr.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq.nchr.fa -g /build/reproducible-path/bcftools-1.21/test/csq.ychr.gff /build/reproducible-path/bcftools-1.21/test/csq.nchr.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq.ychr.fa -g /build/reproducible-path/bcftools-1.21/test/csq.ychr.gff /build/reproducible-path/bcftools-1.21/test/csq.nchr.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq.ychr.fa -g /build/reproducible-path/bcftools-1.21/test/csq.ychr.gff /build/reproducible-path/bcftools-1.21/test/csq.ychr.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq.ychr.fa -g /build/reproducible-path/bcftools-1.21/test/csq.nchr.gff /build/reproducible-path/bcftools-1.21/test/csq.ychr.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq.nchr.fa -g /build/reproducible-path/bcftools-1.21/test/csq.ychr.gff /build/reproducible-path/bcftools-1.21/test/csq.ychr.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq.nchr.fa -g /build/reproducible-path/bcftools-1.21/test/csq.nchr.gff /build/reproducible-path/bcftools-1.21/test/csq.ychr.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000420670/ENST00000420670.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000420670/ENST00000420670.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000420670/start-stop-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000420670/ENST00000420670.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000420670/ENST00000420670.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000420670/segfault.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/frame2.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/frame2.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/frame3.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/frame3.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/frame1.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/frame1.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000375992/ENST00000375992.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000375992/ENST00000375992.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000375992/incorrect-synon-del-not-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000373833/ENST00000373833.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000373833/ENST00000373833.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000373833/boundary-insertion.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000373833/ENST00000373833.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000373833/ENST00000373833.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000373833/boundary-insertion.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000218032/ENST00000218032.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000218032/ENST00000218032.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000218032/start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000218032/ENST00000218032.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000218032/ENST00000218032.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000218032/start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000218032/ENST00000218032.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000218032/ENST00000218032.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000218032/start-lost-del.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0002/EDUMMY0002.fa -g /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0002/EDUMMY0002.gff /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0002/boundaries.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000420190/ENST00000420190.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000420190/ENST00000420190.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000420190/abort-in-csq-push.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000378322/ENST00000378322.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000378322/ENST00000378322.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000378322/end-overlap-tscript.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000378322/ENST00000378322.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000378322/ENST00000378322.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000378322/end-overlap-tscript.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000230048/ENST00000230048.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000230048/ENST00000230048.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000230048/start-del.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000400151/ENST00000400151.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000400151/ENST00000400151.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000400151/long-del.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000390520/ENST00000390520.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000390520/ENST00000390520.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000390520/deletion-overlap.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000542803/ENST00000542803.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000542803/ENST00000542803.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000542803/splice-region.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000542803/ENST00000542803.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000542803/ENST00000542803.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000542803/splice-region.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0003/EDUMMY0003.fa -g /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0003/EDUMMY0003.gff /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0003/long-del.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000545279/ENST00000545279.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000545279/ENST00000545279.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000545279/splice-region-insert.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.21/test/csq/ENSMUST00000121418 && /build/reproducible-path/bcftools-1.21/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25496' --phase m | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.21/test/csq/ENSMUST00000121418 && /build/reproducible-path/bcftools-1.21/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25500' --phase m | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.21/test/csq/ENSMUST00000121418 && /build/reproducible-path/bcftools-1.21/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25105' --phase m | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000520795/ENST00000520795.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000520795/ENST00000520795.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000520795/long-inside-del.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000520795/ENST00000520795.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000520795/ENST00000520795.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000520795/long-inside-del.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000528237/ENST00000528237.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000528237/ENST00000528237.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000528237/retained-stop-incomplete-cds.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000436063/ENST00000436063.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000436063/ENST00000436063.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000436063/insert-before-utr.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000573314/ENST00000573314.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000573314/ENST00000573314.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000573314/ENST00000573314.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000573314/ENST00000573314.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000285021/ENST00000285021.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000285021/ENST00000285021.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000285021/stop-gained-inframe-indel.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000382647/ENST00000382647.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000382647/ENST00000382647.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000382647/synon-splice-region-insert.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000571540/ENST00000571540.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000571540/ENST00000571540.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000571540/nmd.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000413103/ENST00000413103.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000413103/ENST00000413103.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000413103/long-deletion.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000536784/ENST00000536784.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000536784/ENST00000536784.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000536784/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000536784/ENST00000536784.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000536784/ENST00000536784.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000536784/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/snps.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/snps.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/insert3.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/insert3.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.21/test/csq/ENSMUST00000133836 && /build/reproducible-path/bcftools-1.21/bcftools csq -f ENSMUST00000133836.fa -g ENSMUST00000133836.gff filter-problem.vcf -i 'FILTER="PASS"' --phase m | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.21/test/csq/ENST00000000000 && /build/reproducible-path/bcftools-1.21/bcftools csq -p a -f ENST00000000000.fa -g ENST00000000000.gff upstream-stop.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%REF\t%ALT\t%SAMPLE\t%GT\t%TBCSQ\n]' | ../sort-csq -q .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.21/test/csq/ENST00000422159 && /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000422159.fa -g ENST00000422159.gff multiallelic.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%REF\t%ALT\t%GT\t%TBCSQ\n]' | ../sort-csq -q ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000422159.fa -g short.gff multiallelic.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%REF\t%ALT\t%GT\t%TBCSQ\n]' | ../sort-csq -q .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000479739/ENST00000479739.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000479739/ENST00000479739.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000479739/short-cds-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000479739/ENST00000479739.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000479739/ENST00000479739.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000479739/short-cds-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000557788/ENST00000557788.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000557788/ENST00000557788.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000557788/long-overlap-del.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.21/test/csq/ENST00000410009 && /build/reproducible-path/bcftools-1.21/bcftools csq -B 5 -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000410009/ENST00000410009.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000410009/ENST00000410009.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000410009/frameshift.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.21/test/csq/ENST00000410009 && /build/reproducible-path/bcftools-1.21/bcftools csq -lb -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.21/test/csq/ENST00000410009 && /build/reproducible-path/bcftools-1.21/bcftools csq -b -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000269081/ENST00000269081.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000269081/ENST00000269081.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000269081/stop-gained-not-inframe-insertion.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000573035-bt2212/ENST00000573035-bt2212.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000573035-bt2212/ENST00000573035-bt2212.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000573035-bt2212/complex-event.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000520868/ENST00000520868.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000520868/ENST00000520868.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000520868/long-deletion.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.21/test/csq/EMN908947 && /build/reproducible-path/bcftools-1.21/bcftools csq -f EMN908947.fa -g simple.gff simple.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.21/test/csq/EMN908947 && /build/reproducible-path/bcftools-1.21/bcftools csq -f EMN908947.fa -g ribosomal-slippage.gff ribosomal-slippage.vcf --force | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000409523/ENST00000409523.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000409523/ENST00000409523.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000409523/long-overlapping-del.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000368801.2/ENST00000368801.2.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000368801.2/ENST00000368801.2.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000368801.2/start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000357367/ENST00000357367.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000357367/ENST00000357367.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000357367/stop-retained.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000519442/ENST00000519442.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000519442/ENST00000519442.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000519442/synon-splice-region-del.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000256452/ENST00000256452.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000256452/ENST00000256452.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000256452/intron.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000518414-ENST00000521270/valgrind.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.21/test/csq/ENST00000580206 && /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.ins-snv.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g short.gff compound.ins-snv.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff single.ins-snv.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g short.gff single.ins-snv.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.del-snv.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g short.gff compound.del-snv.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g short.gff single.del-snv.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.del-ins.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g short.gff compound.del-ins.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g short.gff single.del-ins.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.21/test/csq/ENST00000379416 && /build/reproducible-path/bcftools-1.21/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.del-snp.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-del.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-ins.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-snp.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff single.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000263103-INS/ENST00000263103-INS.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000263103-INS/ENST00000263103-INS.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000263103-INS/insertions.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000381157/ENST00000381157.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000381157/ENST00000381157.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000381157/haploid-diploid.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000543077/ENST00000543077.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000543077/ENST00000543077.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000543077/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000543077/ENST00000543077.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000543077/ENST00000543077.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000543077/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENSG00000173376/ENSG00000173376.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENSG00000173376/ENSG00000173376.gff /build/reproducible-path/bcftools-1.21/test/csq/ENSG00000173376/synon.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000318249.2/ENST00000318249.2.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000318249.2/ENST00000318249.2.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000318249.2/synonymous-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000518414/ENST00000518414.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000518414/ENST00000518414.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000518414/incorrect-inframe-del.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000360372/ENST00000360372.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000360372/ENST00000360372.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000360372/mnp.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000593942/ENST00000593942.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000593942/ENST00000593942.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000593942/last-codon-deletion.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000448695/ENST00000448695.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000448695/ENST00000448695.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000448695/syn-and-splice-reg.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000227471/ENST00000227471.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000227471/ENST00000227471.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000227471/insert-splice-vs-frameshift.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000624631/ENST00000624631.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000624631/ENST00000624631.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000624631/ambiguous.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000295641/ENST00000295641.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000295641/ENST00000295641.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000295641/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000295641/ENST00000295641.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000295641/ENST00000295641.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000295641/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000294661/ENST00000294661.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000294661/ENST00000294661.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000294661/non-coding-boundary.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000294661/ENST00000294661.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000294661/ENST00000294661.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000294661/non-coding-boundary.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000303039/ENST00000303039.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000303039/ENST00000303039.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000303039/not-a-stop.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000303039/ENST00000303039.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000303039/ENST00000303039.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000303039/not-a-stop.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000318249/ENST00000318249.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000318249/ENST00000318249.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000318249/start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000318249/ENST00000318249.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000318249/ENST00000318249.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000318249/start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000368801/ENST00000368801.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000368801/ENST00000368801.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000368801/compound-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000329454/ENST00000329454.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000329454/ENST00000329454.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000329454/boundary-deletion.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000329454/ENST00000329454.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000329454/ENST00000329454.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000329454/boundary-deletion.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000271583/ENST00000271583.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000271583/ENST00000271583.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000271583/splice-acceptor.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000301246/ENST00000301246.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000301246/ENST00000301246.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000301246/15bp-insert.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0001/EDUMMY0001.fa -g /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0001/EDUMMY0001.gff /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0001/starts-with-1.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0001/EDUMMY0001.fa -g /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0001/EDUMMY0001.gff /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0001/starts-with-1.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_roh: /build/reproducible-path/bcftools-1.21/bcftools roh /build/reproducible-path/bcftools-1.21/test/roh.1.vcf.gz -Or -G30 --AF-dflt 0.4| grep -v ^# .. ok test_roh: /build/reproducible-path/bcftools-1.21/bcftools roh /build/reproducible-path/bcftools-1.21/test/roh.1.vcf.gz -Or -G30 --AF-file /build/reproducible-path/bcftools-1.21/test/roh.1.tab.gz| grep -v ^# .. ok test_roh: /build/reproducible-path/bcftools-1.21/bcftools roh /build/reproducible-path/bcftools-1.21/test/roh.1.vcf.gz -Or -G30 --AF-file /build/reproducible-path/bcftools-1.21/test/roh.1.tab.gz --ignore-homref| grep -v ^# .. ok test_roh: /build/reproducible-path/bcftools-1.21/bcftools roh /build/reproducible-path/bcftools-1.21/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245| grep -v ^# .. ok test_roh: /build/reproducible-path/bcftools-1.21/bcftools roh /build/reproducible-path/bcftools-1.21/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --ignore-homref| grep -v ^# .. ok test_roh: /build/reproducible-path/bcftools-1.21/bcftools roh /build/reproducible-path/bcftools-1.21/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --ignore-homref --include-noalt| grep -v ^# .. ok test_roh: /build/reproducible-path/bcftools-1.21/bcftools roh /build/reproducible-path/bcftools-1.21/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --include-noalt| grep -v ^# .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 --no-HWE-prob /tmp/zPov9rP7t1/gtcheck.1.vcf.gz -g /tmp/zPov9rP7t1/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 /tmp/zPov9rP7t1/gtcheck.1.vcf.gz -g /tmp/zPov9rP7t1/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -u GT,GT /tmp/zPov9rP7t1/gtcheck.1.vcf.gz -g /tmp/zPov9rP7t1/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -u GT,PL /tmp/zPov9rP7t1/gtcheck.1.vcf.gz -g /tmp/zPov9rP7t1/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -u PL,GT /tmp/zPov9rP7t1/gtcheck.1.vcf.gz -g /tmp/zPov9rP7t1/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -u PL,PL /tmp/zPov9rP7t1/gtcheck.1.vcf.gz -g /tmp/zPov9rP7t1/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -p s1,s1 /tmp/zPov9rP7t1/gtcheck.1.vcf.gz -g /tmp/zPov9rP7t1/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 /tmp/zPov9rP7t1/gtcheck.2.vcf.gz -g /tmp/zPov9rP7t1/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 /tmp/zPov9rP7t1/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -p B,A,C,A,C,B,D,A,D,B,D,C,E,A,E,B,E,C,E,D /tmp/zPov9rP7t1/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -P /build/reproducible-path/bcftools-1.21/test/gtcheck.3.pairs /tmp/zPov9rP7t1/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -u PL /tmp/zPov9rP7t1/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 --n-matches 4 /tmp/zPov9rP7t1/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO | sort .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -s qry:E,D,C /tmp/zPov9rP7t1/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -s qry:E,D,C -u PL /tmp/zPov9rP7t1/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -s qry:B -s gt:D /tmp/zPov9rP7t1/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -s qry:B -s gt:D -u PL /tmp/zPov9rP7t1/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -s qry:B -s gt:D,C /tmp/zPov9rP7t1/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -p B,C,B,D /tmp/zPov9rP7t1/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -u GT,GT -H /tmp/zPov9rP7t1/gtcheck.1.vcf.gz -g /tmp/zPov9rP7t1/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -u GT,PL -H /tmp/zPov9rP7t1/gtcheck.1.vcf.gz -g /tmp/zPov9rP7t1/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -u PL,GT -H /tmp/zPov9rP7t1/gtcheck.1.vcf.gz -g /tmp/zPov9rP7t1/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -u PL,PL -H /tmp/zPov9rP7t1/gtcheck.1.vcf.gz -g /tmp/zPov9rP7t1/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -P /build/reproducible-path/bcftools-1.21/test/gtcheck.4.pairs --distinctive-sites 3 /tmp/zPov9rP7t1/gtcheck.4.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -P /build/reproducible-path/bcftools-1.21/test/gtcheck.4.pairs --distinctive-sites 3,1 /tmp/zPov9rP7t1/gtcheck.4.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -u GT -e 30 /tmp/zPov9rP7t1/gtcheck.1.vcf.gz -g /tmp/zPov9rP7t1/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -u GT -e 30 -p s1,s1 /tmp/zPov9rP7t1/gtcheck.1.vcf.gz -g /tmp/zPov9rP7t1/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -u GT -e 300 /tmp/zPov9rP7t1/gtcheck.1.vcf.gz -g /tmp/zPov9rP7t1/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -u PL -e 30 /tmp/zPov9rP7t1/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck /tmp/zPov9rP7t1/gtcheck.ntop.vcf.gz -g /tmp/zPov9rP7t1/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck --n-matches 2 /tmp/zPov9rP7t1/gtcheck.ntop.vcf.gz -g /tmp/zPov9rP7t1/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck /tmp/zPov9rP7t1/gtcheck.5.vcf.gz -g /tmp/zPov9rP7t1/gtcheck.5.gts.vcf.gz | grep -v ^# | grep -v Time .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -p A,B,B,C /tmp/zPov9rP7t1/gtcheck.6.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -t 11:33 -p A,D,A,E,D,E -u GT -e 10 /tmp/zPov9rP7t1/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok Number of tests: total .. 1805 passed .. 1805 failed .. 0 make[2]: Leaving directory '/build/reproducible-path/bcftools-1.21' make[1]: Leaving directory '/build/reproducible-path/bcftools-1.21' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/bcftools/ make -j42 install DESTDIR=/build/reproducible-path/bcftools-1.21/debian/bcftools AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/bcftools-1.21' mkdir -p -m 755 /build/reproducible-path/bcftools-1.21/debian/bcftools/usr/bin /build/reproducible-path/bcftools-1.21/debian/bcftools/usr/share/man/man1 /build/reproducible-path/bcftools-1.21/debian/bcftools/usr/lib/x86_64-linux-gnu/bcftools install -p bcftools /build/reproducible-path/bcftools-1.21/debian/bcftools/usr/bin install -p misc/color-chrs.pl misc/gff2gff.py misc/guess-ploidy.py misc/plot-vcfstats misc/plot-roh.py misc/run-roh.pl misc/vcfutils.pl /build/reproducible-path/bcftools-1.21/debian/bcftools/usr/bin install -p -m 644 doc/bcftools.1 /build/reproducible-path/bcftools-1.21/debian/bcftools/usr/share/man/man1 install -p plugins/*.so /build/reproducible-path/bcftools-1.21/debian/bcftools/usr/lib/x86_64-linux-gnu/bcftools make[1]: Leaving directory '/build/reproducible-path/bcftools-1.21' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/bcftools-1.21' dh_install # Fix Perl interpreter PATH for pscript in `grep -Rl '#!/usr/bin/env \+perl' debian/*` ; do \ sed -i '1s?#!/usr/bin/env \+perl?#!/usr/bin/perl?' ${pscript} ; \ done make[1]: Leaving directory '/build/reproducible-path/bcftools-1.21' dh_installdocs dh_installchangelogs debian/rules override_dh_installman make[1]: Entering directory '/build/reproducible-path/bcftools-1.21' dh_installman --language=C make[1]: Leaving directory '/build/reproducible-path/bcftools-1.21' dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dpkg-gencontrol: warning: package bcftools: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package bcftools: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'bcftools' in '../bcftools_1.21-1_amd64.deb'. dpkg-deb: building package 'bcftools-dbgsym' in '../bcftools-dbgsym_1.21-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../bcftools_1.21-1_amd64.buildinfo dpkg-genchanges --build=binary -O../bcftools_1.21-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/95539/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/95539/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/95539 and its subdirectories I: Current time: Sat Aug 8 14:30:29 +14 2026 I: pbuilder-time-stamp: 1786149029 + false + set +x Sat Aug 8 00:30:29 UTC 2026 I: Signing ./b2/bcftools_1.21-1_amd64.buildinfo as bcftools_1.21-1_amd64.buildinfo.asc Sat Aug 8 00:30:29 UTC 2026 I: Signed ./b2/bcftools_1.21-1_amd64.buildinfo as ./b2/bcftools_1.21-1_amd64.buildinfo.asc Sat Aug 8 00:30:29 UTC 2026 - build #2 for bcftools/unstable/amd64 on ionos5-amd64 done. Starting cleanup. All cleanup done. Sat Aug 8 00:30:29 UTC 2026 - reproducible_build.sh stopped running as /tmp/jenkins-script-xixHwCfY, removing. /srv/reproducible-results/rbuild-debian/r-b-build.k066tCUN: total 536 drwxr-xr-x 2 jenkins jenkins 4096 Jul 5 18:05 b1 drwxr-xr-x 2 jenkins jenkins 4096 Jul 5 18:07 b2 -rw-r--r-- 1 jenkins jenkins 2267 Feb 13 21:22 bcftools_1.21-1.dsc -rw------- 1 jenkins jenkins 532117 Jul 5 18:05 rbuildlog.A9v1TAx /srv/reproducible-results/rbuild-debian/r-b-build.k066tCUN/b1: total 7100 -rw-r--r-- 1 jenkins jenkins 2229324 Jul 5 18:05 bcftools-dbgsym_1.21-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 7504 Jul 5 18:05 bcftools_1.21-1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2267 Jul 5 18:05 bcftools_1.21-1.dsc -rw-r--r-- 1 jenkins jenkins 7023 Jul 5 18:05 bcftools_1.21-1_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 7905 Jul 5 18:05 bcftools_1.21-1_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1571 Jul 5 18:05 bcftools_1.21-1_amd64.changes -rw-r--r-- 1 jenkins jenkins 784124 Jul 5 18:05 bcftools_1.21-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 1675 Jul 5 18:05 bcftools_1.21-1_source.changes -rw-r--r-- 1 jenkins jenkins 3665160 Jul 5 18:05 bcftools_1.21.orig.tar.gz -rw-r--r-- 1 jenkins jenkins 528459 Jul 5 18:05 build.log /srv/reproducible-results/rbuild-debian/r-b-build.k066tCUN/b2: total 7084 -rw-r--r-- 1 jenkins jenkins 2229324 Jul 5 18:07 bcftools-dbgsym_1.21-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 7504 Jul 5 18:07 bcftools_1.21-1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2267 Jul 5 18:07 bcftools_1.21-1.dsc -rw-r--r-- 1 jenkins jenkins 7034 Jul 5 18:07 bcftools_1.21-1_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 7916 Jul 5 18:07 bcftools_1.21-1_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1571 Jul 5 18:07 bcftools_1.21-1_amd64.changes -rw-r--r-- 1 jenkins jenkins 784124 Jul 5 18:07 bcftools_1.21-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 1675 Jul 5 18:07 bcftools_1.21-1_source.changes -rw-r--r-- 1 jenkins jenkins 3665160 Jul 5 18:07 bcftools_1.21.orig.tar.gz -rw-r--r-- 1 jenkins jenkins 530387 Jul 5 18:07 build.log Sat Jul 5 18:07:30 UTC 2025 I: Deleting $TMPDIR on ionos5-amd64.debian.net. Sat Jul 5 18:07:30 UTC 2025 I: bcftools_1.21-1_amd64.changes: Format: 1.8 Date: Thu, 13 Feb 2025 21:42:57 +0100 Source: bcftools Binary: bcftools bcftools-dbgsym Architecture: amd64 Version: 1.21-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: bcftools - genomic variant calling and manipulation of VCF/BCF files Changes: bcftools (1.21-1) unstable; urgency=medium . * New upstream version 1.21 * d/copyright: update copyright year. * skip_new_test_failing_on_32bit.patch: unfuzz. * tests-pluginpath.patch: delete: hunk inhibited upstream. * d/patches/*: normalise Last-Update timestamp. * d/rules: activate hardening. Checksums-Sha1: 9ec1690c0206d6cb0b4a310eb21cdb45420fe7ce 2229324 bcftools-dbgsym_1.21-1_amd64.deb 6b667f9ed4bd0e93bdd096e78899e43a4ab6a6f8 7023 bcftools_1.21-1_amd64.buildinfo 687680739d528c87b6b57378cdcef4774032faca 784124 bcftools_1.21-1_amd64.deb Checksums-Sha256: 64cfff7f511b48eb1d00177a9abe417191a1514f6957ded8848f3b3150d1befe 2229324 bcftools-dbgsym_1.21-1_amd64.deb 80ee4dfd68a14256acf2292b4dfe1e1dd93f5e65267085e832f74f055d5454e7 7023 bcftools_1.21-1_amd64.buildinfo ddb46db7df9be7c328281cbb13c7ccee9730c60b81a773f60c7056c87628cbe5 784124 bcftools_1.21-1_amd64.deb Files: f3bafde10985c0f25ab09eec407eb362 2229324 debug optional bcftools-dbgsym_1.21-1_amd64.deb 5cdc4863c1b86d2111498be0bda9f47a 7023 science optional bcftools_1.21-1_amd64.buildinfo 1ee550e6bd54e595be0b56e65a87acaf 784124 science optional bcftools_1.21-1_amd64.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/bcftools_1.21-1.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/bcftools_1.21-1.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/amd64/bcftools_1.21-1.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/amd64/bcftools_1.21-1.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/unstable/amd64/bcftools_1.21-1_amd64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/bcftools_1.21-1.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2025-07-05 18:05:46.243430963 +0000 +++ b2/build.log 2025-07-05 18:07:29.968124234 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Jul 5 06:01:17 -12 2025 -I: pbuilder-time-stamp: 1751738477 +I: Current time: Sat Aug 8 14:28:47 +14 2026 +I: pbuilder-time-stamp: 1786148927 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -25,52 +25,84 @@ dpkg-source: info: applying 2to3.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/712482/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/95539/tmp/hooks/D01_modify_environment starting +debug: Running on ionos5-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Aug 8 00:29 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/95539/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/95539/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='9646257e45ef4c9dafc0d245b5209d67' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='712482' - PS1='# ' - PS2='> ' + INVOCATION_ID=0183688a57524f368d404b632f7b90d4 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=95539 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.k066tCUN/pbuilderrc_K5ta --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.k066tCUN/b1 --logfile b1/build.log bcftools_1.21-1.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.k066tCUN/pbuilderrc_BuXt --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.k066tCUN/b2 --logfile b2/build.log bcftools_1.21-1.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos11-amd64 6.1.0-37-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.140-1 (2025-05-22) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.32+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.32-1~bpo12+1 (2025-06-21) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 12 19:25 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/712482/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 12 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/95539/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -218,7 +250,7 @@ Get: 96 http://deb.debian.org/debian unstable/main amd64 libhts-dev amd64 1.21+ds-1 [1733 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 libio-pty-perl amd64 1:1.20-1+b3 [34.3 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 tabix amd64 1.21+ds-1 [496 kB] -Fetched 33.8 MB in 3s (12.8 MB/s) +Fetched 33.8 MB in 1s (42.3 MB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19849 files and directories currently installed.) @@ -625,7 +657,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/bcftools-1.21/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../bcftools_1.21-1_source.changes +I: user script /srv/workspace/pbuilder/95539/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/95539/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/bcftools-1.21/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../bcftools_1.21-1_source.changes dpkg-buildpackage: info: source package bcftools dpkg-buildpackage: info: source version 1.21-1 dpkg-buildpackage: info: source distribution unstable @@ -638,7 +674,7 @@ debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/bcftools-1.21' dh_auto_clean - make -j40 distclean + make -j42 distclean make[2]: Entering directory '/build/reproducible-path/bcftools-1.21' rm -f test/*.o test/*.fa.fai test/*~ test/test-rbuf test/test-regidx rm -f plugins/*.so plugins/*.P @@ -698,7 +734,7 @@ config.status: creating config.h make[1]: Leaving directory '/build/reproducible-path/bcftools-1.21' dh_auto_build - make -j40 + make -j42 make[1]: Entering directory '/build/reproducible-path/bcftools-1.21' echo '#define BCFTOOLS_VERSION "1.21"' > version.h gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfindex.o vcfindex.c @@ -915,795 +951,795 @@ .. ok test_tabix: - tabix /tmp/wj8A4a3te7/merge.a.vcf.gz 2:3199812-3199812 + tabix /tmp/zPov9rP7t1/merge.a.vcf.gz 2:3199812-3199812 .. ok test_tabix: - /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/wj8A4a3te7/merge.a.bcf 2:3199812-3199812 + /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/zPov9rP7t1/merge.a.bcf 2:3199812-3199812 .. ok test_tabix: - tabix /tmp/wj8A4a3te7/merge.a.vcf.gz 1:3000151-3000151 + tabix /tmp/zPov9rP7t1/merge.a.vcf.gz 1:3000151-3000151 .. ok test_tabix: - /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/wj8A4a3te7/merge.a.bcf 1:3000151-3000151 + /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/zPov9rP7t1/merge.a.bcf 1:3000151-3000151 .. ok test_index: - /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/wj8A4a3te7/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 + /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/zPov9rP7t1/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: - /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/wj8A4a3te7/large_chrom_csi_limit.bcf chr20:1-2147483647 + /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/zPov9rP7t1/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: - /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/wj8A4a3te7/large_chrom_csi_limit.bcf chr20:1-2147483647 + /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/zPov9rP7t1/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: - /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/wj8A4a3te7/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 + /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/zPov9rP7t1/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: - /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/wj8A4a3te7/large_chrom_csi_limit.bcf chr20:1-2147483647 + /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/zPov9rP7t1/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: - /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/wj8A4a3te7/large_chrom_csi_limit.vcf.gz chr20 + /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/zPov9rP7t1/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: - /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/wj8A4a3te7/large_chrom_csi_limit.bcf chr20 + /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/zPov9rP7t1/large_chrom_csi_limit.bcf chr20 .. ok test_index: - /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/wj8A4a3te7/large_chrom_csi_limit.bcf chr20 + /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/zPov9rP7t1/large_chrom_csi_limit.bcf chr20 .. ok test_index: - /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/wj8A4a3te7/large_chrom_csi_limit.vcf.gz chr20 + /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/zPov9rP7t1/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: - /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/wj8A4a3te7/large_chrom_csi_limit.bcf chr20 + /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/zPov9rP7t1/large_chrom_csi_limit.bcf chr20 .. ok test_vcf_idxstats: - /build/reproducible-path/bcftools-1.21/bcftools index -s /tmp/wj8A4a3te7/idx.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools index -s /tmp/zPov9rP7t1/idx.vcf.gz .. ok test_vcf_idxstats: - /build/reproducible-path/bcftools-1.21/bcftools index -s /tmp/wj8A4a3te7/idx.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools index -s /tmp/zPov9rP7t1/idx.vcf.gz .. ok test_vcf_idxstats: - /build/reproducible-path/bcftools-1.21/bcftools index -s /tmp/wj8A4a3te7/idx.bcf + /build/reproducible-path/bcftools-1.21/bcftools index -s /tmp/zPov9rP7t1/idx.bcf .. ok test_vcf_idxstats: - /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/wj8A4a3te7/idx.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/zPov9rP7t1/idx.vcf.gz .. ok test_vcf_idxstats: - /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/wj8A4a3te7/idx.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/zPov9rP7t1/idx.vcf.gz .. ok test_vcf_idxstats: - /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/wj8A4a3te7/idx.vcf.gz.csi + /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/zPov9rP7t1/idx.vcf.gz.csi .. ok test_vcf_idxstats: - /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/wj8A4a3te7/idx.bcf + /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/zPov9rP7t1/idx.bcf .. ok test_vcf_idxstats: - /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/wj8A4a3te7/idx.bcf.csi + /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/zPov9rP7t1/idx.bcf.csi .. ok test_vcf_idxstats: - /build/reproducible-path/bcftools-1.21/bcftools index -s /tmp/wj8A4a3te7/empty.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools index -s /tmp/zPov9rP7t1/empty.vcf.gz .. ok test_vcf_idxstats: - /build/reproducible-path/bcftools-1.21/bcftools index -s /tmp/wj8A4a3te7/empty.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools index -s /tmp/zPov9rP7t1/empty.vcf.gz .. ok test_vcf_idxstats: - /build/reproducible-path/bcftools-1.21/bcftools index -s /tmp/wj8A4a3te7/empty.bcf + /build/reproducible-path/bcftools-1.21/bcftools index -s /tmp/zPov9rP7t1/empty.bcf .. ok test_vcf_idxstats: - /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/wj8A4a3te7/empty.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/zPov9rP7t1/empty.vcf.gz .. ok test_vcf_idxstats: - /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/wj8A4a3te7/empty.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/zPov9rP7t1/empty.vcf.gz .. ok test_vcf_idxstats: - /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/wj8A4a3te7/empty.vcf.gz.csi + /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/zPov9rP7t1/empty.vcf.gz.csi .. ok test_vcf_idxstats: - /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/wj8A4a3te7/empty.bcf + /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/zPov9rP7t1/empty.bcf .. ok test_vcf_idxstats: - /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/wj8A4a3te7/empty.bcf.csi + /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/zPov9rP7t1/empty.bcf.csi .. ok test_vcf_check: - /build/reproducible-path/bcftools-1.21/bcftools stats -s - /tmp/wj8A4a3te7/check.vcf.gz | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' + /build/reproducible-path/bcftools-1.21/bcftools stats -s - /tmp/zPov9rP7t1/check.vcf.gz | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/check.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools stats -s - | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/check.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools stats -s - | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check_merge: - /build/reproducible-path/bcftools-1.21/misc/plot-vcfstats -m /tmp/wj8A4a3te7/check.1.chk /tmp/wj8A4a3te7/check.2.chk /tmp/wj8A4a3te7/check.3.chk /tmp/wj8A4a3te7/check.4.chk | grep -v 'plot-vcfstats' | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' + /build/reproducible-path/bcftools-1.21/misc/plot-vcfstats -m /tmp/zPov9rP7t1/check.1.chk /tmp/zPov9rP7t1/check.2.chk /tmp/zPov9rP7t1/check.3.chk /tmp/zPov9rP7t1/check.4.chk | grep -v 'plot-vcfstats' | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_stats: - /build/reproducible-path/bcftools-1.21/bcftools stats -s - /tmp/wj8A4a3te7/stats.a.vcf.gz /tmp/wj8A4a3te7/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' + /build/reproducible-path/bcftools-1.21/bcftools stats -s - /tmp/zPov9rP7t1/stats.a.vcf.gz /tmp/zPov9rP7t1/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: - /build/reproducible-path/bcftools-1.21/bcftools stats -s B /tmp/wj8A4a3te7/stats.a.vcf.gz /tmp/wj8A4a3te7/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' + /build/reproducible-path/bcftools-1.21/bcftools stats -s B /tmp/zPov9rP7t1/stats.a.vcf.gz /tmp/zPov9rP7t1/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: - /build/reproducible-path/bcftools-1.21/bcftools stats -s - /tmp/wj8A4a3te7/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' + /build/reproducible-path/bcftools-1.21/bcftools stats -s - /tmp/zPov9rP7t1/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: - /build/reproducible-path/bcftools-1.21/bcftools stats -s - -i 'type="snp"' /tmp/wj8A4a3te7/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' + /build/reproducible-path/bcftools-1.21/bcftools stats -s - -i 'type="snp"' /tmp/zPov9rP7t1/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: - /build/reproducible-path/bcftools-1.21/bcftools stats -s - /tmp/wj8A4a3te7/stats.vaf.vcf.gz | grep -v '^#' | grep -v '^ID ' + /build/reproducible-path/bcftools-1.21/bcftools stats -s - /tmp/zPov9rP7t1/stats.vaf.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_isec: - /build/reproducible-path/bcftools-1.21/bcftools isec -n =2 /tmp/wj8A4a3te7/isec.a.vcf.gz /tmp/wj8A4a3te7/isec.b.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools isec -n =2 /tmp/zPov9rP7t1/isec.a.vcf.gz /tmp/zPov9rP7t1/isec.b.vcf.gz .. ok test_vcf_isec: - /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -n =2 /tmp/wj8A4a3te7/isec.a.vcf.gz /tmp/wj8A4a3te7/isec.b.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -n =2 /tmp/zPov9rP7t1/isec.a.vcf.gz /tmp/zPov9rP7t1/isec.b.vcf.gz .. ok test_vcf_isec: - /build/reproducible-path/bcftools-1.21/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/wj8A4a3te7/isec.a.vcf.gz /tmp/wj8A4a3te7/isec.b.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/zPov9rP7t1/isec.a.vcf.gz /tmp/zPov9rP7t1/isec.b.vcf.gz .. ok test_vcf_isec: - /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -n =2 -i"STRLEN(REF)==2" /tmp/wj8A4a3te7/isec.a.vcf.gz /tmp/wj8A4a3te7/isec.b.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -n =2 -i"STRLEN(REF)==2" /tmp/zPov9rP7t1/isec.a.vcf.gz /tmp/zPov9rP7t1/isec.b.vcf.gz .. ok test_vcf_isec: - /build/reproducible-path/bcftools-1.21/bcftools isec -n =2 -c both /tmp/wj8A4a3te7/isec.a.vcf.gz /tmp/wj8A4a3te7/isec.b.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools isec -n =2 -c both /tmp/zPov9rP7t1/isec.a.vcf.gz /tmp/zPov9rP7t1/isec.b.vcf.gz .. ok test_vcf_isec: - /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -n =2 -c both /tmp/wj8A4a3te7/isec.a.vcf.gz /tmp/wj8A4a3te7/isec.b.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -n =2 -c both /tmp/zPov9rP7t1/isec.a.vcf.gz /tmp/zPov9rP7t1/isec.b.vcf.gz .. ok test_vcf_isec: - /build/reproducible-path/bcftools-1.21/bcftools isec -n =2 -c any /tmp/wj8A4a3te7/isec.a.vcf.gz /tmp/wj8A4a3te7/isec.b.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools isec -n =2 -c any /tmp/zPov9rP7t1/isec.a.vcf.gz /tmp/zPov9rP7t1/isec.b.vcf.gz .. ok test_vcf_isec: - /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -n =2 -c any /tmp/wj8A4a3te7/isec.a.vcf.gz /tmp/wj8A4a3te7/isec.b.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -n =2 -c any /tmp/zPov9rP7t1/isec.a.vcf.gz /tmp/zPov9rP7t1/isec.b.vcf.gz .. ok test_vcf_isec: - /build/reproducible-path/bcftools-1.21/bcftools isec -C -c any /tmp/wj8A4a3te7/isec.a.vcf.gz /tmp/wj8A4a3te7/isec.b.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools isec -C -c any /tmp/zPov9rP7t1/isec.a.vcf.gz /tmp/zPov9rP7t1/isec.b.vcf.gz .. ok test_vcf_isec: - /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -C -c any /tmp/wj8A4a3te7/isec.a.vcf.gz /tmp/wj8A4a3te7/isec.b.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -C -c any /tmp/zPov9rP7t1/isec.a.vcf.gz /tmp/zPov9rP7t1/isec.b.vcf.gz .. ok test_vcf_isec2: - /build/reproducible-path/bcftools-1.21/bcftools isec --no-version -T /tmp/wj8A4a3te7/isec.tab.gz /tmp/wj8A4a3te7/isec.a.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools isec --no-version -T /tmp/zPov9rP7t1/isec.tab.gz /tmp/zPov9rP7t1/isec.a.vcf.gz .. ok test_vcf_isec2: - /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -T /tmp/wj8A4a3te7/isec.tab.gz /tmp/wj8A4a3te7/isec.a.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -T /tmp/zPov9rP7t1/isec.tab.gz /tmp/zPov9rP7t1/isec.a.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_isec: - /build/reproducible-path/bcftools-1.21/bcftools isec -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/wj8A4a3te7/isec-miss.1.1.vcf.gz /tmp/wj8A4a3te7/isec-miss.1.2.vcf.gz /tmp/wj8A4a3te7/isec-miss.1.3.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools isec -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/zPov9rP7t1/isec-miss.1.1.vcf.gz /tmp/zPov9rP7t1/isec-miss.1.2.vcf.gz /tmp/zPov9rP7t1/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: - /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/wj8A4a3te7/isec-miss.1.1.vcf.gz /tmp/wj8A4a3te7/isec-miss.1.2.vcf.gz /tmp/wj8A4a3te7/isec-miss.1.3.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/zPov9rP7t1/isec-miss.1.1.vcf.gz /tmp/zPov9rP7t1/isec-miss.1.2.vcf.gz /tmp/zPov9rP7t1/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: - /build/reproducible-path/bcftools-1.21/bcftools isec -R /build/reproducible-path/bcftools-1.21/test/isec-miss.1.regs.txt -n +1 /tmp/wj8A4a3te7/isec-miss.1.1.vcf.gz /tmp/wj8A4a3te7/isec-miss.1.2.vcf.gz /tmp/wj8A4a3te7/isec-miss.1.3.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools isec -R /build/reproducible-path/bcftools-1.21/test/isec-miss.1.regs.txt -n +1 /tmp/zPov9rP7t1/isec-miss.1.1.vcf.gz /tmp/zPov9rP7t1/isec-miss.1.2.vcf.gz /tmp/zPov9rP7t1/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: - /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -R /build/reproducible-path/bcftools-1.21/test/isec-miss.1.regs.txt -n +1 /tmp/wj8A4a3te7/isec-miss.1.1.vcf.gz /tmp/wj8A4a3te7/isec-miss.1.2.vcf.gz /tmp/wj8A4a3te7/isec-miss.1.3.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -R /build/reproducible-path/bcftools-1.21/test/isec-miss.1.regs.txt -n +1 /tmp/zPov9rP7t1/isec-miss.1.1.vcf.gz /tmp/zPov9rP7t1/isec-miss.1.2.vcf.gz /tmp/zPov9rP7t1/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: - /build/reproducible-path/bcftools-1.21/bcftools isec -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/wj8A4a3te7/isec-miss.2.1.vcf.gz /tmp/wj8A4a3te7/isec-miss.2.2.vcf.gz /tmp/wj8A4a3te7/isec-miss.2.3.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools isec -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/zPov9rP7t1/isec-miss.2.1.vcf.gz /tmp/zPov9rP7t1/isec-miss.2.2.vcf.gz /tmp/zPov9rP7t1/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: - /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/wj8A4a3te7/isec-miss.2.1.vcf.gz /tmp/wj8A4a3te7/isec-miss.2.2.vcf.gz /tmp/wj8A4a3te7/isec-miss.2.3.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/zPov9rP7t1/isec-miss.2.1.vcf.gz /tmp/zPov9rP7t1/isec-miss.2.2.vcf.gz /tmp/zPov9rP7t1/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: - /build/reproducible-path/bcftools-1.21/bcftools isec -R /build/reproducible-path/bcftools-1.21/test/isec-miss.1.regs.txt -n +1 /tmp/wj8A4a3te7/isec-miss.2.1.vcf.gz /tmp/wj8A4a3te7/isec-miss.2.2.vcf.gz /tmp/wj8A4a3te7/isec-miss.2.3.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools isec -R /build/reproducible-path/bcftools-1.21/test/isec-miss.1.regs.txt -n +1 /tmp/zPov9rP7t1/isec-miss.2.1.vcf.gz /tmp/zPov9rP7t1/isec-miss.2.2.vcf.gz /tmp/zPov9rP7t1/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: - /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -R /build/reproducible-path/bcftools-1.21/test/isec-miss.1.regs.txt -n +1 /tmp/wj8A4a3te7/isec-miss.2.1.vcf.gz /tmp/wj8A4a3te7/isec-miss.2.2.vcf.gz /tmp/wj8A4a3te7/isec-miss.2.3.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -R /build/reproducible-path/bcftools-1.21/test/isec-miss.1.regs.txt -n +1 /tmp/zPov9rP7t1/isec-miss.2.1.vcf.gz /tmp/zPov9rP7t1/isec-miss.2.2.vcf.gz /tmp/zPov9rP7t1/isec-miss.2.3.vcf.gz .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/wj8A4a3te7/merge.11.a.vcf.gz /tmp/wj8A4a3te7/merge.11.b.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/zPov9rP7t1/merge.11.a.vcf.gz /tmp/zPov9rP7t1/merge.11.b.vcf.gz .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/wj8A4a3te7/merge.11.a.vcf.gz /tmp/wj8A4a3te7/merge.11.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/zPov9rP7t1/merge.11.a.vcf.gz /tmp/zPov9rP7t1/merge.11.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/wj8A4a3te7/merge.11.a.bcf /tmp/wj8A4a3te7/merge.11.b.bcf + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/zPov9rP7t1/merge.11.a.bcf /tmp/zPov9rP7t1/merge.11.b.bcf .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/wj8A4a3te7/merge.11.a.bcf /tmp/wj8A4a3te7/merge.11.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/zPov9rP7t1/merge.11.a.bcf /tmp/zPov9rP7t1/merge.11.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -i AF:join /tmp/wj8A4a3te7/merge.join.a.vcf.gz /tmp/wj8A4a3te7/merge.join.b.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -i AF:join /tmp/zPov9rP7t1/merge.join.a.vcf.gz /tmp/zPov9rP7t1/merge.join.b.vcf.gz .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -i AF:join /tmp/wj8A4a3te7/merge.join.a.vcf.gz /tmp/wj8A4a3te7/merge.join.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -i AF:join /tmp/zPov9rP7t1/merge.join.a.vcf.gz /tmp/zPov9rP7t1/merge.join.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -i AF:join /tmp/wj8A4a3te7/merge.join.a.bcf /tmp/wj8A4a3te7/merge.join.b.bcf + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -i AF:join /tmp/zPov9rP7t1/merge.join.a.bcf /tmp/zPov9rP7t1/merge.join.b.bcf .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -i AF:join /tmp/wj8A4a3te7/merge.join.a.bcf /tmp/wj8A4a3te7/merge.join.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -i AF:join /tmp/zPov9rP7t1/merge.join.a.bcf /tmp/zPov9rP7t1/merge.join.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-single /tmp/wj8A4a3te7/merge.LPL.a.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-single /tmp/zPov9rP7t1/merge.LPL.a.vcf.gz .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-single /tmp/wj8A4a3te7/merge.LPL.a.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-single /tmp/zPov9rP7t1/merge.LPL.a.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-single /tmp/wj8A4a3te7/merge.LPL.a.bcf + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-single /tmp/zPov9rP7t1/merge.LPL.a.bcf .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-single /tmp/wj8A4a3te7/merge.LPL.a.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-single /tmp/zPov9rP7t1/merge.LPL.a.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples /tmp/wj8A4a3te7/merge.LPL.a.vcf.gz /tmp/wj8A4a3te7/merge.LPL.b.vcf.gz /tmp/wj8A4a3te7/merge.LPL.c.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples /tmp/zPov9rP7t1/merge.LPL.a.vcf.gz /tmp/zPov9rP7t1/merge.LPL.b.vcf.gz /tmp/zPov9rP7t1/merge.LPL.c.vcf.gz .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/wj8A4a3te7/merge.LPL.a.vcf.gz /tmp/wj8A4a3te7/merge.LPL.b.vcf.gz /tmp/wj8A4a3te7/merge.LPL.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/zPov9rP7t1/merge.LPL.a.vcf.gz /tmp/zPov9rP7t1/merge.LPL.b.vcf.gz /tmp/zPov9rP7t1/merge.LPL.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples /tmp/wj8A4a3te7/merge.LPL.a.bcf /tmp/wj8A4a3te7/merge.LPL.b.bcf /tmp/wj8A4a3te7/merge.LPL.c.bcf + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples /tmp/zPov9rP7t1/merge.LPL.a.bcf /tmp/zPov9rP7t1/merge.LPL.b.bcf /tmp/zPov9rP7t1/merge.LPL.c.bcf .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/wj8A4a3te7/merge.LPL.a.bcf /tmp/wj8A4a3te7/merge.LPL.b.bcf /tmp/wj8A4a3te7/merge.LPL.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/zPov9rP7t1/merge.LPL.a.bcf /tmp/zPov9rP7t1/merge.LPL.b.bcf /tmp/zPov9rP7t1/merge.LPL.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -L 1 /tmp/wj8A4a3te7/merge.LPL.a.vcf.gz /tmp/wj8A4a3te7/merge.LPL.b.vcf.gz /tmp/wj8A4a3te7/merge.LPL.c.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -L 1 /tmp/zPov9rP7t1/merge.LPL.a.vcf.gz /tmp/zPov9rP7t1/merge.LPL.b.vcf.gz /tmp/zPov9rP7t1/merge.LPL.c.vcf.gz .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 1 /tmp/wj8A4a3te7/merge.LPL.a.vcf.gz /tmp/wj8A4a3te7/merge.LPL.b.vcf.gz /tmp/wj8A4a3te7/merge.LPL.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 1 /tmp/zPov9rP7t1/merge.LPL.a.vcf.gz /tmp/zPov9rP7t1/merge.LPL.b.vcf.gz /tmp/zPov9rP7t1/merge.LPL.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -L 1 /tmp/wj8A4a3te7/merge.LPL.a.bcf /tmp/wj8A4a3te7/merge.LPL.b.bcf /tmp/wj8A4a3te7/merge.LPL.c.bcf + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -L 1 /tmp/zPov9rP7t1/merge.LPL.a.bcf /tmp/zPov9rP7t1/merge.LPL.b.bcf /tmp/zPov9rP7t1/merge.LPL.c.bcf .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 1 /tmp/wj8A4a3te7/merge.LPL.a.bcf /tmp/wj8A4a3te7/merge.LPL.b.bcf /tmp/wj8A4a3te7/merge.LPL.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 1 /tmp/zPov9rP7t1/merge.LPL.a.bcf /tmp/zPov9rP7t1/merge.LPL.b.bcf /tmp/zPov9rP7t1/merge.LPL.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -L 2 /tmp/wj8A4a3te7/merge.LPL.a.vcf.gz /tmp/wj8A4a3te7/merge.LPL.b.vcf.gz /tmp/wj8A4a3te7/merge.LPL.c.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -L 2 /tmp/zPov9rP7t1/merge.LPL.a.vcf.gz /tmp/zPov9rP7t1/merge.LPL.b.vcf.gz /tmp/zPov9rP7t1/merge.LPL.c.vcf.gz .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 2 /tmp/wj8A4a3te7/merge.LPL.a.vcf.gz /tmp/wj8A4a3te7/merge.LPL.b.vcf.gz /tmp/wj8A4a3te7/merge.LPL.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 2 /tmp/zPov9rP7t1/merge.LPL.a.vcf.gz /tmp/zPov9rP7t1/merge.LPL.b.vcf.gz /tmp/zPov9rP7t1/merge.LPL.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -L 2 /tmp/wj8A4a3te7/merge.LPL.a.bcf /tmp/wj8A4a3te7/merge.LPL.b.bcf /tmp/wj8A4a3te7/merge.LPL.c.bcf + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -L 2 /tmp/zPov9rP7t1/merge.LPL.a.bcf /tmp/zPov9rP7t1/merge.LPL.b.bcf /tmp/zPov9rP7t1/merge.LPL.c.bcf .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 2 /tmp/wj8A4a3te7/merge.LPL.a.bcf /tmp/wj8A4a3te7/merge.LPL.b.bcf /tmp/wj8A4a3te7/merge.LPL.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 2 /tmp/zPov9rP7t1/merge.LPL.a.bcf /tmp/zPov9rP7t1/merge.LPL.b.bcf /tmp/zPov9rP7t1/merge.LPL.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -L 3 /tmp/wj8A4a3te7/merge.LPL.a.vcf.gz /tmp/wj8A4a3te7/merge.LPL.b.vcf.gz /tmp/wj8A4a3te7/merge.LPL.c.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -L 3 /tmp/zPov9rP7t1/merge.LPL.a.vcf.gz /tmp/zPov9rP7t1/merge.LPL.b.vcf.gz /tmp/zPov9rP7t1/merge.LPL.c.vcf.gz .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 3 /tmp/wj8A4a3te7/merge.LPL.a.vcf.gz /tmp/wj8A4a3te7/merge.LPL.b.vcf.gz /tmp/wj8A4a3te7/merge.LPL.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 3 /tmp/zPov9rP7t1/merge.LPL.a.vcf.gz /tmp/zPov9rP7t1/merge.LPL.b.vcf.gz /tmp/zPov9rP7t1/merge.LPL.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -L 3 /tmp/wj8A4a3te7/merge.LPL.a.bcf /tmp/wj8A4a3te7/merge.LPL.b.bcf /tmp/wj8A4a3te7/merge.LPL.c.bcf + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -L 3 /tmp/zPov9rP7t1/merge.LPL.a.bcf /tmp/zPov9rP7t1/merge.LPL.b.bcf /tmp/zPov9rP7t1/merge.LPL.c.bcf .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 3 /tmp/wj8A4a3te7/merge.LPL.a.bcf /tmp/wj8A4a3te7/merge.LPL.b.bcf /tmp/wj8A4a3te7/merge.LPL.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 3 /tmp/zPov9rP7t1/merge.LPL.a.bcf /tmp/zPov9rP7t1/merge.LPL.b.bcf /tmp/zPov9rP7t1/merge.LPL.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -L 4 /tmp/wj8A4a3te7/merge.LPL.a.vcf.gz /tmp/wj8A4a3te7/merge.LPL.b.vcf.gz /tmp/wj8A4a3te7/merge.LPL.c.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -L 4 /tmp/zPov9rP7t1/merge.LPL.a.vcf.gz /tmp/zPov9rP7t1/merge.LPL.b.vcf.gz /tmp/zPov9rP7t1/merge.LPL.c.vcf.gz .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 4 /tmp/wj8A4a3te7/merge.LPL.a.vcf.gz /tmp/wj8A4a3te7/merge.LPL.b.vcf.gz /tmp/wj8A4a3te7/merge.LPL.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 4 /tmp/zPov9rP7t1/merge.LPL.a.vcf.gz /tmp/zPov9rP7t1/merge.LPL.b.vcf.gz /tmp/zPov9rP7t1/merge.LPL.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -L 4 /tmp/wj8A4a3te7/merge.LPL.a.bcf /tmp/wj8A4a3te7/merge.LPL.b.bcf /tmp/wj8A4a3te7/merge.LPL.c.bcf + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -L 4 /tmp/zPov9rP7t1/merge.LPL.a.bcf /tmp/zPov9rP7t1/merge.LPL.b.bcf /tmp/zPov9rP7t1/merge.LPL.c.bcf .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 4 /tmp/wj8A4a3te7/merge.LPL.a.bcf /tmp/wj8A4a3te7/merge.LPL.b.bcf /tmp/wj8A4a3te7/merge.LPL.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 4 /tmp/zPov9rP7t1/merge.LPL.a.bcf /tmp/zPov9rP7t1/merge.LPL.b.bcf /tmp/zPov9rP7t1/merge.LPL.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -L 5 /tmp/wj8A4a3te7/merge.LPL.a.vcf.gz /tmp/wj8A4a3te7/merge.LPL.b.vcf.gz /tmp/wj8A4a3te7/merge.LPL.c.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -L 5 /tmp/zPov9rP7t1/merge.LPL.a.vcf.gz /tmp/zPov9rP7t1/merge.LPL.b.vcf.gz /tmp/zPov9rP7t1/merge.LPL.c.vcf.gz .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 5 /tmp/wj8A4a3te7/merge.LPL.a.vcf.gz /tmp/wj8A4a3te7/merge.LPL.b.vcf.gz /tmp/wj8A4a3te7/merge.LPL.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 5 /tmp/zPov9rP7t1/merge.LPL.a.vcf.gz /tmp/zPov9rP7t1/merge.LPL.b.vcf.gz /tmp/zPov9rP7t1/merge.LPL.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -L 5 /tmp/wj8A4a3te7/merge.LPL.a.bcf /tmp/wj8A4a3te7/merge.LPL.b.bcf /tmp/wj8A4a3te7/merge.LPL.c.bcf + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -L 5 /tmp/zPov9rP7t1/merge.LPL.a.bcf /tmp/zPov9rP7t1/merge.LPL.b.bcf /tmp/zPov9rP7t1/merge.LPL.c.bcf .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 5 /tmp/wj8A4a3te7/merge.LPL.a.bcf /tmp/wj8A4a3te7/merge.LPL.b.bcf /tmp/wj8A4a3te7/merge.LPL.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 5 /tmp/zPov9rP7t1/merge.LPL.a.bcf /tmp/zPov9rP7t1/merge.LPL.b.bcf /tmp/zPov9rP7t1/merge.LPL.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples /tmp/wj8A4a3te7/merge.a.vcf.gz /tmp/wj8A4a3te7/merge.b.vcf.gz /tmp/wj8A4a3te7/merge.c.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples /tmp/zPov9rP7t1/merge.a.vcf.gz /tmp/zPov9rP7t1/merge.b.vcf.gz /tmp/zPov9rP7t1/merge.c.vcf.gz .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/wj8A4a3te7/merge.a.vcf.gz /tmp/wj8A4a3te7/merge.b.vcf.gz /tmp/wj8A4a3te7/merge.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/zPov9rP7t1/merge.a.vcf.gz /tmp/zPov9rP7t1/merge.b.vcf.gz /tmp/zPov9rP7t1/merge.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples /tmp/wj8A4a3te7/merge.a.bcf /tmp/wj8A4a3te7/merge.b.bcf /tmp/wj8A4a3te7/merge.c.bcf + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples /tmp/zPov9rP7t1/merge.a.bcf /tmp/zPov9rP7t1/merge.b.bcf /tmp/zPov9rP7t1/merge.c.bcf .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/wj8A4a3te7/merge.a.bcf /tmp/wj8A4a3te7/merge.b.bcf /tmp/wj8A4a3te7/merge.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/zPov9rP7t1/merge.a.bcf /tmp/zPov9rP7t1/merge.b.bcf /tmp/zPov9rP7t1/merge.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -Fx /tmp/wj8A4a3te7/merge.a.vcf.gz /tmp/wj8A4a3te7/merge.b.vcf.gz /tmp/wj8A4a3te7/merge.c.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -Fx /tmp/zPov9rP7t1/merge.a.vcf.gz /tmp/zPov9rP7t1/merge.b.vcf.gz /tmp/zPov9rP7t1/merge.c.vcf.gz .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -Fx /tmp/wj8A4a3te7/merge.a.vcf.gz /tmp/wj8A4a3te7/merge.b.vcf.gz /tmp/wj8A4a3te7/merge.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -Fx /tmp/zPov9rP7t1/merge.a.vcf.gz /tmp/zPov9rP7t1/merge.b.vcf.gz /tmp/zPov9rP7t1/merge.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -Fx /tmp/wj8A4a3te7/merge.a.bcf /tmp/wj8A4a3te7/merge.b.bcf /tmp/wj8A4a3te7/merge.c.bcf + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -Fx /tmp/zPov9rP7t1/merge.a.bcf /tmp/zPov9rP7t1/merge.b.bcf /tmp/zPov9rP7t1/merge.c.bcf .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -Fx /tmp/wj8A4a3te7/merge.a.bcf /tmp/wj8A4a3te7/merge.b.bcf /tmp/wj8A4a3te7/merge.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -Fx /tmp/zPov9rP7t1/merge.a.bcf /tmp/zPov9rP7t1/merge.b.bcf /tmp/zPov9rP7t1/merge.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -0 /tmp/wj8A4a3te7/merge.a.vcf.gz /tmp/wj8A4a3te7/merge.b.vcf.gz /tmp/wj8A4a3te7/merge.c.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -0 /tmp/zPov9rP7t1/merge.a.vcf.gz /tmp/zPov9rP7t1/merge.b.vcf.gz /tmp/zPov9rP7t1/merge.c.vcf.gz .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -0 /tmp/wj8A4a3te7/merge.a.vcf.gz /tmp/wj8A4a3te7/merge.b.vcf.gz /tmp/wj8A4a3te7/merge.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -0 /tmp/zPov9rP7t1/merge.a.vcf.gz /tmp/zPov9rP7t1/merge.b.vcf.gz /tmp/zPov9rP7t1/merge.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -0 /tmp/wj8A4a3te7/merge.a.bcf /tmp/wj8A4a3te7/merge.b.bcf /tmp/wj8A4a3te7/merge.c.bcf + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -0 /tmp/zPov9rP7t1/merge.a.bcf /tmp/zPov9rP7t1/merge.b.bcf /tmp/zPov9rP7t1/merge.c.bcf .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -0 /tmp/wj8A4a3te7/merge.a.bcf /tmp/wj8A4a3te7/merge.b.bcf /tmp/wj8A4a3te7/merge.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -0 /tmp/zPov9rP7t1/merge.a.bcf /tmp/zPov9rP7t1/merge.b.bcf /tmp/zPov9rP7t1/merge.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -m none /tmp/wj8A4a3te7/merge.2.a.vcf.gz /tmp/wj8A4a3te7/merge.2.b.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -m none /tmp/zPov9rP7t1/merge.2.a.vcf.gz /tmp/zPov9rP7t1/merge.2.b.vcf.gz .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m none /tmp/wj8A4a3te7/merge.2.a.vcf.gz /tmp/wj8A4a3te7/merge.2.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m none /tmp/zPov9rP7t1/merge.2.a.vcf.gz /tmp/zPov9rP7t1/merge.2.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -m none /tmp/wj8A4a3te7/merge.2.a.bcf /tmp/wj8A4a3te7/merge.2.b.bcf + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -m none /tmp/zPov9rP7t1/merge.2.a.bcf /tmp/zPov9rP7t1/merge.2.b.bcf .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m none /tmp/wj8A4a3te7/merge.2.a.bcf /tmp/wj8A4a3te7/merge.2.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m none /tmp/zPov9rP7t1/merge.2.a.bcf /tmp/zPov9rP7t1/merge.2.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -m both /tmp/wj8A4a3te7/merge.2.a.vcf.gz /tmp/wj8A4a3te7/merge.2.b.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -m both /tmp/zPov9rP7t1/merge.2.a.vcf.gz /tmp/zPov9rP7t1/merge.2.b.vcf.gz .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m both /tmp/wj8A4a3te7/merge.2.a.vcf.gz /tmp/wj8A4a3te7/merge.2.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m both /tmp/zPov9rP7t1/merge.2.a.vcf.gz /tmp/zPov9rP7t1/merge.2.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -m both /tmp/wj8A4a3te7/merge.2.a.bcf /tmp/wj8A4a3te7/merge.2.b.bcf + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -m both /tmp/zPov9rP7t1/merge.2.a.bcf /tmp/zPov9rP7t1/merge.2.b.bcf .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m both /tmp/wj8A4a3te7/merge.2.a.bcf /tmp/wj8A4a3te7/merge.2.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m both /tmp/zPov9rP7t1/merge.2.a.bcf /tmp/zPov9rP7t1/merge.2.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -m all /tmp/wj8A4a3te7/merge.2.a.vcf.gz /tmp/wj8A4a3te7/merge.2.b.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -m all /tmp/zPov9rP7t1/merge.2.a.vcf.gz /tmp/zPov9rP7t1/merge.2.b.vcf.gz .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m all /tmp/wj8A4a3te7/merge.2.a.vcf.gz /tmp/wj8A4a3te7/merge.2.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m all /tmp/zPov9rP7t1/merge.2.a.vcf.gz /tmp/zPov9rP7t1/merge.2.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -m all /tmp/wj8A4a3te7/merge.2.a.bcf /tmp/wj8A4a3te7/merge.2.b.bcf + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -m all /tmp/zPov9rP7t1/merge.2.a.bcf /tmp/zPov9rP7t1/merge.2.b.bcf .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m all /tmp/wj8A4a3te7/merge.2.a.bcf /tmp/wj8A4a3te7/merge.2.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m all /tmp/zPov9rP7t1/merge.2.a.bcf /tmp/zPov9rP7t1/merge.2.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/wj8A4a3te7/merge.3.a.vcf.gz /tmp/wj8A4a3te7/merge.3.b.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/zPov9rP7t1/merge.3.a.vcf.gz /tmp/zPov9rP7t1/merge.3.b.vcf.gz .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/wj8A4a3te7/merge.3.a.vcf.gz /tmp/wj8A4a3te7/merge.3.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/zPov9rP7t1/merge.3.a.vcf.gz /tmp/zPov9rP7t1/merge.3.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/wj8A4a3te7/merge.3.a.bcf /tmp/wj8A4a3te7/merge.3.b.bcf + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/zPov9rP7t1/merge.3.a.bcf /tmp/zPov9rP7t1/merge.3.b.bcf .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/wj8A4a3te7/merge.3.a.bcf /tmp/wj8A4a3te7/merge.3.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/zPov9rP7t1/merge.3.a.bcf /tmp/zPov9rP7t1/merge.3.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -m id /tmp/wj8A4a3te7/merge.4.a.vcf.gz /tmp/wj8A4a3te7/merge.4.b.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -m id /tmp/zPov9rP7t1/merge.4.a.vcf.gz /tmp/zPov9rP7t1/merge.4.b.vcf.gz .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m id /tmp/wj8A4a3te7/merge.4.a.vcf.gz /tmp/wj8A4a3te7/merge.4.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m id /tmp/zPov9rP7t1/merge.4.a.vcf.gz /tmp/zPov9rP7t1/merge.4.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -m id /tmp/wj8A4a3te7/merge.4.a.bcf /tmp/wj8A4a3te7/merge.4.b.bcf + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -m id /tmp/zPov9rP7t1/merge.4.a.bcf /tmp/zPov9rP7t1/merge.4.b.bcf .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m id /tmp/wj8A4a3te7/merge.4.a.bcf /tmp/wj8A4a3te7/merge.4.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m id /tmp/zPov9rP7t1/merge.4.a.bcf /tmp/zPov9rP7t1/merge.4.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/wj8A4a3te7/gvcf.merge.1.vcf.gz /tmp/wj8A4a3te7/gvcf.merge.2.vcf.gz /tmp/wj8A4a3te7/gvcf.merge.3.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/zPov9rP7t1/gvcf.merge.1.vcf.gz /tmp/zPov9rP7t1/gvcf.merge.2.vcf.gz /tmp/zPov9rP7t1/gvcf.merge.3.vcf.gz .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/wj8A4a3te7/gvcf.merge.1.vcf.gz /tmp/wj8A4a3te7/gvcf.merge.2.vcf.gz /tmp/wj8A4a3te7/gvcf.merge.3.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/zPov9rP7t1/gvcf.merge.1.vcf.gz /tmp/zPov9rP7t1/gvcf.merge.2.vcf.gz /tmp/zPov9rP7t1/gvcf.merge.3.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/wj8A4a3te7/gvcf.merge.1.bcf /tmp/wj8A4a3te7/gvcf.merge.2.bcf /tmp/wj8A4a3te7/gvcf.merge.3.bcf + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/zPov9rP7t1/gvcf.merge.1.bcf /tmp/zPov9rP7t1/gvcf.merge.2.bcf /tmp/zPov9rP7t1/gvcf.merge.3.bcf .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/wj8A4a3te7/gvcf.merge.1.bcf /tmp/wj8A4a3te7/gvcf.merge.2.bcf /tmp/wj8A4a3te7/gvcf.merge.3.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/zPov9rP7t1/gvcf.merge.1.bcf /tmp/zPov9rP7t1/gvcf.merge.2.bcf /tmp/zPov9rP7t1/gvcf.merge.3.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/wj8A4a3te7/merge.gvcf.2.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.2.b.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.2.c.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/zPov9rP7t1/merge.gvcf.2.a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.2.b.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/wj8A4a3te7/merge.gvcf.2.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.2.b.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.2.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/zPov9rP7t1/merge.gvcf.2.a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.2.b.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.2.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - -m both,* /tmp/wj8A4a3te7/merge.gvcf.2.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.2.b.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.2.c.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - -m both,* /tmp/zPov9rP7t1/merge.gvcf.2.a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.2.b.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - -m both,* /tmp/wj8A4a3te7/merge.gvcf.2.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.2.b.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.2.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - -m both,* /tmp/zPov9rP7t1/merge.gvcf.2.a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.2.b.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.2.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - -m both,** /tmp/wj8A4a3te7/merge.gvcf.2.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.2.b.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.2.c.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - -m both,** /tmp/zPov9rP7t1/merge.gvcf.2.a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.2.b.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - -m both,** /tmp/wj8A4a3te7/merge.gvcf.2.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.2.b.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.2.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - -m both,** /tmp/zPov9rP7t1/merge.gvcf.2.a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.2.b.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.2.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - -i SRC:join /tmp/wj8A4a3te7/merge.gvcf.3.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.3.b.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - -i SRC:join /tmp/zPov9rP7t1/merge.gvcf.3.a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.3.b.vcf.gz .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - -i SRC:join /tmp/wj8A4a3te7/merge.gvcf.3.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.3.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - -i SRC:join /tmp/zPov9rP7t1/merge.gvcf.3.a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.3.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/wj8A4a3te7/merge.gvcf.4.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.4.b.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/zPov9rP7t1/merge.gvcf.4.a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.4.b.vcf.gz .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/wj8A4a3te7/merge.gvcf.4.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.4.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/zPov9rP7t1/merge.gvcf.4.a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.4.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/wj8A4a3te7/merge.gvcf.4.a.bcf /tmp/wj8A4a3te7/merge.gvcf.4.b.bcf + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/zPov9rP7t1/merge.gvcf.4.a.bcf /tmp/zPov9rP7t1/merge.gvcf.4.b.bcf .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/wj8A4a3te7/merge.gvcf.4.a.bcf /tmp/wj8A4a3te7/merge.gvcf.4.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/zPov9rP7t1/merge.gvcf.4.a.bcf /tmp/zPov9rP7t1/merge.gvcf.4.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/wj8A4a3te7/merge.5.a.vcf.gz /tmp/wj8A4a3te7/merge.5.b.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/zPov9rP7t1/merge.5.a.vcf.gz /tmp/zPov9rP7t1/merge.5.b.vcf.gz .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/wj8A4a3te7/merge.5.a.vcf.gz /tmp/wj8A4a3te7/merge.5.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/zPov9rP7t1/merge.5.a.vcf.gz /tmp/zPov9rP7t1/merge.5.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/wj8A4a3te7/merge.5.a.bcf /tmp/wj8A4a3te7/merge.5.b.bcf + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/zPov9rP7t1/merge.5.a.bcf /tmp/zPov9rP7t1/merge.5.b.bcf .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/wj8A4a3te7/merge.5.a.bcf /tmp/wj8A4a3te7/merge.5.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/zPov9rP7t1/merge.5.a.bcf /tmp/zPov9rP7t1/merge.5.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/wj8A4a3te7/merge.6.a.vcf.gz /tmp/wj8A4a3te7/merge.6.b.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/zPov9rP7t1/merge.6.a.vcf.gz /tmp/zPov9rP7t1/merge.6.b.vcf.gz .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/wj8A4a3te7/merge.6.a.vcf.gz /tmp/wj8A4a3te7/merge.6.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/zPov9rP7t1/merge.6.a.vcf.gz /tmp/zPov9rP7t1/merge.6.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/wj8A4a3te7/merge.6.a.bcf /tmp/wj8A4a3te7/merge.6.b.bcf + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/zPov9rP7t1/merge.6.a.bcf /tmp/zPov9rP7t1/merge.6.b.bcf .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/wj8A4a3te7/merge.6.a.bcf /tmp/wj8A4a3te7/merge.6.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/zPov9rP7t1/merge.6.a.bcf /tmp/zPov9rP7t1/merge.6.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/wj8A4a3te7/merge.gvcf.7.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.7.b.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/zPov9rP7t1/merge.gvcf.7.a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.7.b.vcf.gz .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/wj8A4a3te7/merge.gvcf.7.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.7.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/zPov9rP7t1/merge.gvcf.7.a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.7.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/wj8A4a3te7/merge.gvcf.7.a.bcf /tmp/wj8A4a3te7/merge.gvcf.7.b.bcf + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/zPov9rP7t1/merge.gvcf.7.a.bcf /tmp/zPov9rP7t1/merge.gvcf.7.b.bcf .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/wj8A4a3te7/merge.gvcf.7.a.bcf /tmp/wj8A4a3te7/merge.gvcf.7.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/zPov9rP7t1/merge.gvcf.7.a.bcf /tmp/zPov9rP7t1/merge.gvcf.7.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/wj8A4a3te7/merge.gvcf.8.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.8.b.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/zPov9rP7t1/merge.gvcf.8.a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.8.b.vcf.gz .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/wj8A4a3te7/merge.gvcf.8.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.8.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/zPov9rP7t1/merge.gvcf.8.a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.8.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/wj8A4a3te7/merge.gvcf.8.a.bcf /tmp/wj8A4a3te7/merge.gvcf.8.b.bcf + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/zPov9rP7t1/merge.gvcf.8.a.bcf /tmp/zPov9rP7t1/merge.gvcf.8.b.bcf .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/wj8A4a3te7/merge.gvcf.8.a.bcf /tmp/wj8A4a3te7/merge.gvcf.8.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/zPov9rP7t1/merge.gvcf.8.a.bcf /tmp/zPov9rP7t1/merge.gvcf.8.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples /tmp/wj8A4a3te7/merge.7.a.vcf.gz /tmp/wj8A4a3te7/merge.7.b.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples /tmp/zPov9rP7t1/merge.7.a.vcf.gz /tmp/zPov9rP7t1/merge.7.b.vcf.gz .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/wj8A4a3te7/merge.7.a.vcf.gz /tmp/wj8A4a3te7/merge.7.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/zPov9rP7t1/merge.7.a.vcf.gz /tmp/zPov9rP7t1/merge.7.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples /tmp/wj8A4a3te7/merge.7.a.bcf /tmp/wj8A4a3te7/merge.7.b.bcf + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples /tmp/zPov9rP7t1/merge.7.a.bcf /tmp/zPov9rP7t1/merge.7.b.bcf .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/wj8A4a3te7/merge.7.a.bcf /tmp/wj8A4a3te7/merge.7.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/zPov9rP7t1/merge.7.a.bcf /tmp/zPov9rP7t1/merge.7.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa /tmp/wj8A4a3te7/merge.gvcf.9a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9b.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9c.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9d.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa /tmp/zPov9rP7t1/merge.gvcf.9a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.9b.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.9c.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.9d.vcf.gz .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa /tmp/wj8A4a3te7/merge.gvcf.9a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9b.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9c.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9d.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa /tmp/zPov9rP7t1/merge.gvcf.9a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.9b.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.9c.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.9d.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa /tmp/wj8A4a3te7/merge.gvcf.9a.bcf /tmp/wj8A4a3te7/merge.gvcf.9b.bcf /tmp/wj8A4a3te7/merge.gvcf.9c.bcf /tmp/wj8A4a3te7/merge.gvcf.9d.bcf + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa /tmp/zPov9rP7t1/merge.gvcf.9a.bcf /tmp/zPov9rP7t1/merge.gvcf.9b.bcf /tmp/zPov9rP7t1/merge.gvcf.9c.bcf /tmp/zPov9rP7t1/merge.gvcf.9d.bcf .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa /tmp/wj8A4a3te7/merge.gvcf.9a.bcf /tmp/wj8A4a3te7/merge.gvcf.9b.bcf /tmp/wj8A4a3te7/merge.gvcf.9c.bcf /tmp/wj8A4a3te7/merge.gvcf.9d.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa /tmp/zPov9rP7t1/merge.gvcf.9a.bcf /tmp/zPov9rP7t1/merge.gvcf.9b.bcf /tmp/zPov9rP7t1/merge.gvcf.9c.bcf /tmp/zPov9rP7t1/merge.gvcf.9d.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa -r 22:21-23 /tmp/wj8A4a3te7/merge.gvcf.9a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9b.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9c.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9d.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa -r 22:21-23 /tmp/zPov9rP7t1/merge.gvcf.9a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.9b.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.9c.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.9d.vcf.gz .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa -r 22:21-23 /tmp/wj8A4a3te7/merge.gvcf.9a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9b.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9c.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9d.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa -r 22:21-23 /tmp/zPov9rP7t1/merge.gvcf.9a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.9b.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.9c.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.9d.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa -r 22:21-23 /tmp/wj8A4a3te7/merge.gvcf.9a.bcf /tmp/wj8A4a3te7/merge.gvcf.9b.bcf /tmp/wj8A4a3te7/merge.gvcf.9c.bcf /tmp/wj8A4a3te7/merge.gvcf.9d.bcf + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa -r 22:21-23 /tmp/zPov9rP7t1/merge.gvcf.9a.bcf /tmp/zPov9rP7t1/merge.gvcf.9b.bcf /tmp/zPov9rP7t1/merge.gvcf.9c.bcf /tmp/zPov9rP7t1/merge.gvcf.9d.bcf .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa -r 22:21-23 /tmp/wj8A4a3te7/merge.gvcf.9a.bcf /tmp/wj8A4a3te7/merge.gvcf.9b.bcf /tmp/wj8A4a3te7/merge.gvcf.9c.bcf /tmp/wj8A4a3te7/merge.gvcf.9d.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa -r 22:21-23 /tmp/zPov9rP7t1/merge.gvcf.9a.bcf /tmp/zPov9rP7t1/merge.gvcf.9b.bcf /tmp/zPov9rP7t1/merge.gvcf.9c.bcf /tmp/zPov9rP7t1/merge.gvcf.9d.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa /tmp/wj8A4a3te7/merge.gvcf.9a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9b.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9c.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9d.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9e.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa /tmp/zPov9rP7t1/merge.gvcf.9a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.9b.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.9c.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.9d.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.9e.vcf.gz .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa /tmp/wj8A4a3te7/merge.gvcf.9a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9b.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9c.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9d.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9e.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa /tmp/zPov9rP7t1/merge.gvcf.9a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.9b.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.9c.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.9d.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.9e.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa /tmp/wj8A4a3te7/merge.gvcf.9a.bcf /tmp/wj8A4a3te7/merge.gvcf.9b.bcf /tmp/wj8A4a3te7/merge.gvcf.9c.bcf /tmp/wj8A4a3te7/merge.gvcf.9d.bcf /tmp/wj8A4a3te7/merge.gvcf.9e.bcf + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa /tmp/zPov9rP7t1/merge.gvcf.9a.bcf /tmp/zPov9rP7t1/merge.gvcf.9b.bcf /tmp/zPov9rP7t1/merge.gvcf.9c.bcf /tmp/zPov9rP7t1/merge.gvcf.9d.bcf /tmp/zPov9rP7t1/merge.gvcf.9e.bcf .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa /tmp/wj8A4a3te7/merge.gvcf.9a.bcf /tmp/wj8A4a3te7/merge.gvcf.9b.bcf /tmp/wj8A4a3te7/merge.gvcf.9c.bcf /tmp/wj8A4a3te7/merge.gvcf.9d.bcf /tmp/wj8A4a3te7/merge.gvcf.9e.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa /tmp/zPov9rP7t1/merge.gvcf.9a.bcf /tmp/zPov9rP7t1/merge.gvcf.9b.bcf /tmp/zPov9rP7t1/merge.gvcf.9c.bcf /tmp/zPov9rP7t1/merge.gvcf.9d.bcf /tmp/zPov9rP7t1/merge.gvcf.9e.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa -r 22:21-23 /tmp/wj8A4a3te7/merge.gvcf.9a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9b.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9c.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9d.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9e.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa -r 22:21-23 /tmp/zPov9rP7t1/merge.gvcf.9a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.9b.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.9c.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.9d.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.9e.vcf.gz .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa -r 22:21-23 /tmp/wj8A4a3te7/merge.gvcf.9a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9b.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9c.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9d.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.9e.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa -r 22:21-23 /tmp/zPov9rP7t1/merge.gvcf.9a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.9b.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.9c.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.9d.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.9e.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa -r 22:21-23 /tmp/wj8A4a3te7/merge.gvcf.9a.bcf /tmp/wj8A4a3te7/merge.gvcf.9b.bcf /tmp/wj8A4a3te7/merge.gvcf.9c.bcf /tmp/wj8A4a3te7/merge.gvcf.9d.bcf /tmp/wj8A4a3te7/merge.gvcf.9e.bcf + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa -r 22:21-23 /tmp/zPov9rP7t1/merge.gvcf.9a.bcf /tmp/zPov9rP7t1/merge.gvcf.9b.bcf /tmp/zPov9rP7t1/merge.gvcf.9c.bcf /tmp/zPov9rP7t1/merge.gvcf.9d.bcf /tmp/zPov9rP7t1/merge.gvcf.9e.bcf .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa -r 22:21-23 /tmp/wj8A4a3te7/merge.gvcf.9a.bcf /tmp/wj8A4a3te7/merge.gvcf.9b.bcf /tmp/wj8A4a3te7/merge.gvcf.9c.bcf /tmp/wj8A4a3te7/merge.gvcf.9d.bcf /tmp/wj8A4a3te7/merge.gvcf.9e.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa -r 22:21-23 /tmp/zPov9rP7t1/merge.gvcf.9a.bcf /tmp/zPov9rP7t1/merge.gvcf.9b.bcf /tmp/zPov9rP7t1/merge.gvcf.9c.bcf /tmp/zPov9rP7t1/merge.gvcf.9d.bcf /tmp/zPov9rP7t1/merge.gvcf.9e.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/wj8A4a3te7/merge.gvcf.10.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.10.b.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/zPov9rP7t1/merge.gvcf.10.a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/wj8A4a3te7/merge.gvcf.10.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.10.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/zPov9rP7t1/merge.gvcf.10.a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.10.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/wj8A4a3te7/merge.gvcf.10.a.bcf /tmp/wj8A4a3te7/merge.gvcf.10.b.bcf + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/zPov9rP7t1/merge.gvcf.10.a.bcf /tmp/zPov9rP7t1/merge.gvcf.10.b.bcf .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/wj8A4a3te7/merge.gvcf.10.a.bcf /tmp/wj8A4a3te7/merge.gvcf.10.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/zPov9rP7t1/merge.gvcf.10.a.bcf /tmp/zPov9rP7t1/merge.gvcf.10.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -m none /tmp/wj8A4a3te7/merge.gvcf.10.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.10.b.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -m none /tmp/zPov9rP7t1/merge.gvcf.10.a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m none /tmp/wj8A4a3te7/merge.gvcf.10.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.10.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m none /tmp/zPov9rP7t1/merge.gvcf.10.a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.10.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -m none /tmp/wj8A4a3te7/merge.gvcf.10.a.bcf /tmp/wj8A4a3te7/merge.gvcf.10.b.bcf + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -m none /tmp/zPov9rP7t1/merge.gvcf.10.a.bcf /tmp/zPov9rP7t1/merge.gvcf.10.b.bcf .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m none /tmp/wj8A4a3te7/merge.gvcf.10.a.bcf /tmp/wj8A4a3te7/merge.gvcf.10.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m none /tmp/zPov9rP7t1/merge.gvcf.10.a.bcf /tmp/zPov9rP7t1/merge.gvcf.10.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -g /build/reproducible-path/bcftools-1.21/test/merge.gvcf.10.fa /tmp/wj8A4a3te7/merge.gvcf.10.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.10.b.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -g /build/reproducible-path/bcftools-1.21/test/merge.gvcf.10.fa /tmp/zPov9rP7t1/merge.gvcf.10.a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -g /build/reproducible-path/bcftools-1.21/test/merge.gvcf.10.fa /tmp/wj8A4a3te7/merge.gvcf.10.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.10.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -g /build/reproducible-path/bcftools-1.21/test/merge.gvcf.10.fa /tmp/zPov9rP7t1/merge.gvcf.10.a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.10.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -g /build/reproducible-path/bcftools-1.21/test/merge.gvcf.10.fa /tmp/wj8A4a3te7/merge.gvcf.10.a.bcf /tmp/wj8A4a3te7/merge.gvcf.10.b.bcf + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -g /build/reproducible-path/bcftools-1.21/test/merge.gvcf.10.fa /tmp/zPov9rP7t1/merge.gvcf.10.a.bcf /tmp/zPov9rP7t1/merge.gvcf.10.b.bcf .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -g /build/reproducible-path/bcftools-1.21/test/merge.gvcf.10.fa /tmp/wj8A4a3te7/merge.gvcf.10.a.bcf /tmp/wj8A4a3te7/merge.gvcf.10.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -g /build/reproducible-path/bcftools-1.21/test/merge.gvcf.10.fa /tmp/zPov9rP7t1/merge.gvcf.10.a.bcf /tmp/zPov9rP7t1/merge.gvcf.10.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -g /build/reproducible-path/bcftools-1.21/test/merge.gvcf.10.fa -m none /tmp/wj8A4a3te7/merge.gvcf.10.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.10.b.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -g /build/reproducible-path/bcftools-1.21/test/merge.gvcf.10.fa -m none /tmp/zPov9rP7t1/merge.gvcf.10.a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -g /build/reproducible-path/bcftools-1.21/test/merge.gvcf.10.fa -m none /tmp/wj8A4a3te7/merge.gvcf.10.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.10.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -g /build/reproducible-path/bcftools-1.21/test/merge.gvcf.10.fa -m none /tmp/zPov9rP7t1/merge.gvcf.10.a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.10.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -g /build/reproducible-path/bcftools-1.21/test/merge.gvcf.10.fa -m none /tmp/wj8A4a3te7/merge.gvcf.10.a.bcf /tmp/wj8A4a3te7/merge.gvcf.10.b.bcf + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -g /build/reproducible-path/bcftools-1.21/test/merge.gvcf.10.fa -m none /tmp/zPov9rP7t1/merge.gvcf.10.a.bcf /tmp/zPov9rP7t1/merge.gvcf.10.b.bcf .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -g /build/reproducible-path/bcftools-1.21/test/merge.gvcf.10.fa -m none /tmp/wj8A4a3te7/merge.gvcf.10.a.bcf /tmp/wj8A4a3te7/merge.gvcf.10.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -g /build/reproducible-path/bcftools-1.21/test/merge.gvcf.10.fa -m none /tmp/zPov9rP7t1/merge.gvcf.10.a.bcf /tmp/zPov9rP7t1/merge.gvcf.10.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/wj8A4a3te7/merge.noidx.a.vcf.gz /tmp/wj8A4a3te7/merge.noidx.b.vcf.gz /tmp/wj8A4a3te7/merge.noidx.c.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/zPov9rP7t1/merge.noidx.a.vcf.gz /tmp/zPov9rP7t1/merge.noidx.b.vcf.gz /tmp/zPov9rP7t1/merge.noidx.c.vcf.gz .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/wj8A4a3te7/merge.noidx.a.vcf.gz /tmp/wj8A4a3te7/merge.noidx.b.vcf.gz /tmp/wj8A4a3te7/merge.noidx.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/zPov9rP7t1/merge.noidx.a.vcf.gz /tmp/zPov9rP7t1/merge.noidx.b.vcf.gz /tmp/zPov9rP7t1/merge.noidx.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/wj8A4a3te7/merge.noidx.a.bcf /tmp/wj8A4a3te7/merge.noidx.b.bcf /tmp/wj8A4a3te7/merge.noidx.c.bcf + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/zPov9rP7t1/merge.noidx.a.bcf /tmp/zPov9rP7t1/merge.noidx.b.bcf /tmp/zPov9rP7t1/merge.noidx.c.bcf .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/wj8A4a3te7/merge.noidx.a.bcf /tmp/wj8A4a3te7/merge.noidx.b.bcf /tmp/wj8A4a3te7/merge.noidx.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/zPov9rP7t1/merge.noidx.a.bcf /tmp/zPov9rP7t1/merge.noidx.b.bcf /tmp/zPov9rP7t1/merge.noidx.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: @@ -1715,2327 +1751,2327 @@ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --no-index /tmp/wj8A4a3te7/merge.noidx.a.bcf /tmp/wj8A4a3te7/merge.noidx.b.bcf /tmp/wj8A4a3te7/merge.noidx.c.bcf + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --no-index /tmp/zPov9rP7t1/merge.noidx.a.bcf /tmp/zPov9rP7t1/merge.noidx.b.bcf /tmp/zPov9rP7t1/merge.noidx.c.bcf .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --no-index /tmp/wj8A4a3te7/merge.noidx.a.bcf /tmp/wj8A4a3te7/merge.noidx.b.bcf /tmp/wj8A4a3te7/merge.noidx.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --no-index /tmp/zPov9rP7t1/merge.noidx.a.bcf /tmp/zPov9rP7t1/merge.noidx.b.bcf /tmp/zPov9rP7t1/merge.noidx.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/wj8A4a3te7/merge.8.a.vcf.gz /tmp/wj8A4a3te7/merge.8.b.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/zPov9rP7t1/merge.8.a.vcf.gz /tmp/zPov9rP7t1/merge.8.b.vcf.gz .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/wj8A4a3te7/merge.8.a.vcf.gz /tmp/wj8A4a3te7/merge.8.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/zPov9rP7t1/merge.8.a.vcf.gz /tmp/zPov9rP7t1/merge.8.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/wj8A4a3te7/merge.8.a.bcf /tmp/wj8A4a3te7/merge.8.b.bcf + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/zPov9rP7t1/merge.8.a.bcf /tmp/zPov9rP7t1/merge.8.b.bcf .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/wj8A4a3te7/merge.8.a.bcf /tmp/wj8A4a3te7/merge.8.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/zPov9rP7t1/merge.8.a.bcf /tmp/zPov9rP7t1/merge.8.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -i AN:sum,AC:sum /tmp/wj8A4a3te7/merge.8.a.vcf.gz /tmp/wj8A4a3te7/merge.8.b.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -i AN:sum,AC:sum /tmp/zPov9rP7t1/merge.8.a.vcf.gz /tmp/zPov9rP7t1/merge.8.b.vcf.gz .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/wj8A4a3te7/merge.8.a.vcf.gz /tmp/wj8A4a3te7/merge.8.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/zPov9rP7t1/merge.8.a.vcf.gz /tmp/zPov9rP7t1/merge.8.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -i AN:sum,AC:sum /tmp/wj8A4a3te7/merge.8.a.bcf /tmp/wj8A4a3te7/merge.8.b.bcf + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -i AN:sum,AC:sum /tmp/zPov9rP7t1/merge.8.a.bcf /tmp/zPov9rP7t1/merge.8.b.bcf .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/wj8A4a3te7/merge.8.a.bcf /tmp/wj8A4a3te7/merge.8.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/zPov9rP7t1/merge.8.a.bcf /tmp/zPov9rP7t1/merge.8.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/wj8A4a3te7/merge.9.a.vcf.gz /tmp/wj8A4a3te7/merge.9.b.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/zPov9rP7t1/merge.9.a.vcf.gz /tmp/zPov9rP7t1/merge.9.b.vcf.gz .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/wj8A4a3te7/merge.9.a.vcf.gz /tmp/wj8A4a3te7/merge.9.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/zPov9rP7t1/merge.9.a.vcf.gz /tmp/zPov9rP7t1/merge.9.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/wj8A4a3te7/merge.9.a.bcf /tmp/wj8A4a3te7/merge.9.b.bcf + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/zPov9rP7t1/merge.9.a.bcf /tmp/zPov9rP7t1/merge.9.b.bcf .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/wj8A4a3te7/merge.9.a.bcf /tmp/wj8A4a3te7/merge.9.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/zPov9rP7t1/merge.9.a.bcf /tmp/zPov9rP7t1/merge.9.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -i AN:sum,AC:sum /tmp/wj8A4a3te7/merge.9.a.vcf.gz /tmp/wj8A4a3te7/merge.9.b.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -i AN:sum,AC:sum /tmp/zPov9rP7t1/merge.9.a.vcf.gz /tmp/zPov9rP7t1/merge.9.b.vcf.gz .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/wj8A4a3te7/merge.9.a.vcf.gz /tmp/wj8A4a3te7/merge.9.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/zPov9rP7t1/merge.9.a.vcf.gz /tmp/zPov9rP7t1/merge.9.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -i AN:sum,AC:sum /tmp/wj8A4a3te7/merge.9.a.bcf /tmp/wj8A4a3te7/merge.9.b.bcf + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -i AN:sum,AC:sum /tmp/zPov9rP7t1/merge.9.a.bcf /tmp/zPov9rP7t1/merge.9.b.bcf .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/wj8A4a3te7/merge.9.a.bcf /tmp/wj8A4a3te7/merge.9.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/zPov9rP7t1/merge.9.a.bcf /tmp/zPov9rP7t1/merge.9.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -m none /tmp/wj8A4a3te7/merge.10.a.vcf.gz /tmp/wj8A4a3te7/merge.10.b.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -m none /tmp/zPov9rP7t1/merge.10.a.vcf.gz /tmp/zPov9rP7t1/merge.10.b.vcf.gz .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m none /tmp/wj8A4a3te7/merge.10.a.vcf.gz /tmp/wj8A4a3te7/merge.10.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m none /tmp/zPov9rP7t1/merge.10.a.vcf.gz /tmp/zPov9rP7t1/merge.10.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -m none /tmp/wj8A4a3te7/merge.10.a.bcf /tmp/wj8A4a3te7/merge.10.b.bcf + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -m none /tmp/zPov9rP7t1/merge.10.a.bcf /tmp/zPov9rP7t1/merge.10.b.bcf .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m none /tmp/wj8A4a3te7/merge.10.a.bcf /tmp/wj8A4a3te7/merge.10.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m none /tmp/zPov9rP7t1/merge.10.a.bcf /tmp/zPov9rP7t1/merge.10.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -m both /tmp/wj8A4a3te7/merge.10.a.vcf.gz /tmp/wj8A4a3te7/merge.10.b.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -m both /tmp/zPov9rP7t1/merge.10.a.vcf.gz /tmp/zPov9rP7t1/merge.10.b.vcf.gz .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m both /tmp/wj8A4a3te7/merge.10.a.vcf.gz /tmp/wj8A4a3te7/merge.10.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m both /tmp/zPov9rP7t1/merge.10.a.vcf.gz /tmp/zPov9rP7t1/merge.10.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -m both /tmp/wj8A4a3te7/merge.10.a.bcf /tmp/wj8A4a3te7/merge.10.b.bcf + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -m both /tmp/zPov9rP7t1/merge.10.a.bcf /tmp/zPov9rP7t1/merge.10.b.bcf .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m both /tmp/wj8A4a3te7/merge.10.a.bcf /tmp/wj8A4a3te7/merge.10.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m both /tmp/zPov9rP7t1/merge.10.a.bcf /tmp/zPov9rP7t1/merge.10.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -m snp-ins-del /tmp/wj8A4a3te7/merge.10.a.vcf.gz /tmp/wj8A4a3te7/merge.10.b.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -m snp-ins-del /tmp/zPov9rP7t1/merge.10.a.vcf.gz /tmp/zPov9rP7t1/merge.10.b.vcf.gz .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m snp-ins-del /tmp/wj8A4a3te7/merge.10.a.vcf.gz /tmp/wj8A4a3te7/merge.10.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m snp-ins-del /tmp/zPov9rP7t1/merge.10.a.vcf.gz /tmp/zPov9rP7t1/merge.10.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -m snp-ins-del /tmp/wj8A4a3te7/merge.10.a.bcf /tmp/wj8A4a3te7/merge.10.b.bcf + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -m snp-ins-del /tmp/zPov9rP7t1/merge.10.a.bcf /tmp/zPov9rP7t1/merge.10.b.bcf .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m snp-ins-del /tmp/wj8A4a3te7/merge.10.a.bcf /tmp/wj8A4a3te7/merge.10.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m snp-ins-del /tmp/zPov9rP7t1/merge.10.a.bcf /tmp/zPov9rP7t1/merge.10.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/wj8A4a3te7/merge.mrules.1.a.vcf.gz /tmp/wj8A4a3te7/merge.mrules.1.b.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/zPov9rP7t1/merge.mrules.1.a.vcf.gz /tmp/zPov9rP7t1/merge.mrules.1.b.vcf.gz .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/wj8A4a3te7/merge.mrules.1.a.vcf.gz /tmp/wj8A4a3te7/merge.mrules.1.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/zPov9rP7t1/merge.mrules.1.a.vcf.gz /tmp/zPov9rP7t1/merge.mrules.1.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/wj8A4a3te7/merge.mrules.1.a.bcf /tmp/wj8A4a3te7/merge.mrules.1.b.bcf + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/zPov9rP7t1/merge.mrules.1.a.bcf /tmp/zPov9rP7t1/merge.mrules.1.b.bcf .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/wj8A4a3te7/merge.mrules.1.a.bcf /tmp/wj8A4a3te7/merge.mrules.1.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/zPov9rP7t1/merge.mrules.1.a.bcf /tmp/zPov9rP7t1/merge.mrules.1.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - -M AD:.,PL:. /tmp/wj8A4a3te7/merge.mrules.1.a.vcf.gz /tmp/wj8A4a3te7/merge.mrules.1.b.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - -M AD:.,PL:. /tmp/zPov9rP7t1/merge.mrules.1.a.vcf.gz /tmp/zPov9rP7t1/merge.mrules.1.b.vcf.gz .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - -M AD:.,PL:. /tmp/wj8A4a3te7/merge.mrules.1.a.vcf.gz /tmp/wj8A4a3te7/merge.mrules.1.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - -M AD:.,PL:. /tmp/zPov9rP7t1/merge.mrules.1.a.vcf.gz /tmp/zPov9rP7t1/merge.mrules.1.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - -M AD:.,PL:. /tmp/wj8A4a3te7/merge.mrules.1.a.bcf /tmp/wj8A4a3te7/merge.mrules.1.b.bcf + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - -M AD:.,PL:. /tmp/zPov9rP7t1/merge.mrules.1.a.bcf /tmp/zPov9rP7t1/merge.mrules.1.b.bcf .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - -M AD:.,PL:. /tmp/wj8A4a3te7/merge.mrules.1.a.bcf /tmp/wj8A4a3te7/merge.mrules.1.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - -M AD:.,PL:. /tmp/zPov9rP7t1/merge.mrules.1.a.bcf /tmp/zPov9rP7t1/merge.mrules.1.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/wj8A4a3te7/merge.gvcf.5.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.5.b.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/zPov9rP7t1/merge.gvcf.5.a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.5.b.vcf.gz .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/wj8A4a3te7/merge.gvcf.5.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.5.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/zPov9rP7t1/merge.gvcf.5.a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.5.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/wj8A4a3te7/merge.gvcf.5.a.bcf /tmp/wj8A4a3te7/merge.gvcf.5.b.bcf + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/zPov9rP7t1/merge.gvcf.5.a.bcf /tmp/zPov9rP7t1/merge.gvcf.5.b.bcf .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/wj8A4a3te7/merge.gvcf.5.a.bcf /tmp/wj8A4a3te7/merge.gvcf.5.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/zPov9rP7t1/merge.gvcf.5.a.bcf /tmp/zPov9rP7t1/merge.gvcf.5.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - --merge none /tmp/wj8A4a3te7/merge.gvcf.5.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.5.b.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - --merge none /tmp/zPov9rP7t1/merge.gvcf.5.a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.5.b.vcf.gz .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - --merge none /tmp/wj8A4a3te7/merge.gvcf.5.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.5.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - --merge none /tmp/zPov9rP7t1/merge.gvcf.5.a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.5.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - --merge none /tmp/wj8A4a3te7/merge.gvcf.5.a.bcf /tmp/wj8A4a3te7/merge.gvcf.5.b.bcf + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - --merge none /tmp/zPov9rP7t1/merge.gvcf.5.a.bcf /tmp/zPov9rP7t1/merge.gvcf.5.b.bcf .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - --merge none /tmp/wj8A4a3te7/merge.gvcf.5.a.bcf /tmp/wj8A4a3te7/merge.gvcf.5.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - --merge none /tmp/zPov9rP7t1/merge.gvcf.5.a.bcf /tmp/zPov9rP7t1/merge.gvcf.5.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/wj8A4a3te7/merge.gvcf.11.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.11.b.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.11.c.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/zPov9rP7t1/merge.gvcf.11.a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.11.b.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.11.c.vcf.gz .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/wj8A4a3te7/merge.gvcf.11.a.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.11.b.vcf.gz /tmp/wj8A4a3te7/merge.gvcf.11.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/zPov9rP7t1/merge.gvcf.11.a.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.11.b.vcf.gz /tmp/zPov9rP7t1/merge.gvcf.11.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/wj8A4a3te7/merge.gvcf.11.a.bcf /tmp/wj8A4a3te7/merge.gvcf.11.b.bcf /tmp/wj8A4a3te7/merge.gvcf.11.c.bcf + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/zPov9rP7t1/merge.gvcf.11.a.bcf /tmp/zPov9rP7t1/merge.gvcf.11.b.bcf /tmp/zPov9rP7t1/merge.gvcf.11.c.bcf .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/wj8A4a3te7/merge.gvcf.11.a.bcf /tmp/wj8A4a3te7/merge.gvcf.11.b.bcf /tmp/wj8A4a3te7/merge.gvcf.11.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/zPov9rP7t1/merge.gvcf.11.a.bcf /tmp/zPov9rP7t1/merge.gvcf.11.b.bcf /tmp/zPov9rP7t1/merge.gvcf.11.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided,_conflicting_interpretations"' /tmp/wj8A4a3te7/query.string.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided,_conflicting_interpretations"' /tmp/zPov9rP7t1/query.string.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.string.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided,_conflicting_interpretations"' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.string.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided,_conflicting_interpretations"' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" || CLNREVSTAT="_conflicting_interpretations"' /tmp/wj8A4a3te7/query.string.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" || CLNREVSTAT="_conflicting_interpretations"' /tmp/zPov9rP7t1/query.string.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.string.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" || CLNREVSTAT="_conflicting_interpretations"' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.string.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" || CLNREVSTAT="_conflicting_interpretations"' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" && CLNREVSTAT="_conflicting_interpretations"' /tmp/wj8A4a3te7/query.string.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" && CLNREVSTAT="_conflicting_interpretations"' /tmp/zPov9rP7t1/query.string.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.string.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" && CLNREVSTAT="_conflicting_interpretations"' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.string.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" && CLNREVSTAT="_conflicting_interpretations"' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%INFO/STR\n' -i'INFO/STR=@/build/reproducible-path/bcftools-1.21/test/query.string.2.1.txt' /tmp/wj8A4a3te7/query.string.2.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%INFO/STR\n' -i'INFO/STR=@/build/reproducible-path/bcftools-1.21/test/query.string.2.1.txt' /tmp/zPov9rP7t1/query.string.2.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.string.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%INFO/STR\n' -i'INFO/STR=@/build/reproducible-path/bcftools-1.21/test/query.string.2.1.txt' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.string.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%INFO/STR\n' -i'INFO/STR=@/build/reproducible-path/bcftools-1.21/test/query.string.2.1.txt' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS[\t%STR]\n' -i'FMT/STR=@/build/reproducible-path/bcftools-1.21/test/query.string.2.2.txt' /tmp/wj8A4a3te7/query.string.2.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS[\t%STR]\n' -i'FMT/STR=@/build/reproducible-path/bcftools-1.21/test/query.string.2.2.txt' /tmp/zPov9rP7t1/query.string.2.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.string.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS[\t%STR]\n' -i'FMT/STR=@/build/reproducible-path/bcftools-1.21/test/query.string.2.2.txt' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.string.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS[\t%STR]\n' -i'FMT/STR=@/build/reproducible-path/bcftools-1.21/test/query.string.2.2.txt' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' /tmp/wj8A4a3te7/query.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' /tmp/zPov9rP7t1/query.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f '%RSX\t%VKX\n' /tmp/wj8A4a3te7/query.variantkey.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f '%RSX\t%VKX\n' /tmp/zPov9rP7t1/query.variantkey.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.variantkey.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f '%RSX\t%VKX\n' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.variantkey.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f '%RSX\t%VKX\n' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'%XRI\n' -i'XRI[*]>1111' /tmp/wj8A4a3te7/view.filter.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'%XRI\n' -i'XRI[*]>1111' /tmp/zPov9rP7t1/view.filter.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%XRI\n' -i'XRI[*]>1111' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%XRI\n' -i'XRI[*]>1111' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' /tmp/wj8A4a3te7/view.filter.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' /tmp/zPov9rP7t1/view.filter.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' /tmp/wj8A4a3te7/view.filter.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' /tmp/zPov9rP7t1/view.filter.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' /tmp/wj8A4a3te7/view.filter.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' /tmp/zPov9rP7t1/view.filter.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' /tmp/wj8A4a3te7/view.filter.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' /tmp/zPov9rP7t1/view.filter.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' /tmp/wj8A4a3te7/view.filter.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' /tmp/zPov9rP7t1/view.filter.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' /tmp/wj8A4a3te7/view.filter.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' /tmp/zPov9rP7t1/view.filter.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' /tmp/wj8A4a3te7/query.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' /tmp/zPov9rP7t1/query.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' /tmp/wj8A4a3te7/query.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' /tmp/zPov9rP7t1/query.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' /tmp/wj8A4a3te7/query.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' /tmp/zPov9rP7t1/query.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' /tmp/wj8A4a3te7/query.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' /tmp/zPov9rP7t1/query.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' /tmp/wj8A4a3te7/view.filter.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' /tmp/zPov9rP7t1/view.filter.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' /tmp/wj8A4a3te7/query.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' /tmp/zPov9rP7t1/query.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' /tmp/wj8A4a3te7/query.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' /tmp/zPov9rP7t1/query.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' /tmp/wj8A4a3te7/query.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' /tmp/zPov9rP7t1/query.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' /tmp/wj8A4a3te7/query.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' /tmp/zPov9rP7t1/query.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'I8=%I8 I16=%I16 I32=%I32 IF=%IF IA8=%IA8 IA16=%IA16 IA32=%IA32 IAF=%IAF IA8=%IA8{1} IA16=%IA16{1} IA32=%IA32{1} IAF=%IAF{1} [ %F8:%F16:%F32:%FF]\n' /tmp/wj8A4a3te7/view.vectors.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'I8=%I8 I16=%I16 I32=%I32 IF=%IF IA8=%IA8 IA16=%IA16 IA32=%IA32 IAF=%IAF IA8=%IA8{1} IA16=%IA16{1} IA32=%IA32{1} IAF=%IAF{1} [ %F8:%F16:%F32:%FF]\n' /tmp/zPov9rP7t1/view.vectors.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.vectors.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'I8=%I8 I16=%I16 I32=%I32 IF=%IF IA8=%IA8 IA16=%IA16 IA32=%IA32 IAF=%IAF IA8=%IA8{1} IA16=%IA16{1} IA32=%IA32{1} IAF=%IAF{1} [ %F8:%F16:%F32:%FF]\n' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/view.vectors.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'I8=%I8 I16=%I16 I32=%I32 IF=%IF IA8=%IA8 IA16=%IA16 IA32=%IA32 IAF=%IAF IA8=%IA8{1} IA16=%IA16{1} IA32=%IA32{1} IAF=%IAF{1} [ %F8:%F16:%F32:%FF]\n' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' /tmp/wj8A4a3te7/query.filter.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' /tmp/zPov9rP7t1/query.filter.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' /tmp/wj8A4a3te7/query.filter.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' /tmp/zPov9rP7t1/query.filter.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' /tmp/wj8A4a3te7/query.filter.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' /tmp/zPov9rP7t1/query.filter.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' /tmp/wj8A4a3te7/query.filter.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' /tmp/zPov9rP7t1/query.filter.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' /tmp/wj8A4a3te7/query.2.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' /tmp/zPov9rP7t1/query.2.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -i'IINT="."' -f'%POS %IINT\n' /tmp/wj8A4a3te7/missing.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -i'IINT="."' -f'%POS %IINT\n' /tmp/zPov9rP7t1/missing.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'IINT="."' -f'%POS %IINT\n' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -i'IINT!="."' -f'%POS %IINT\n' /tmp/wj8A4a3te7/missing.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -i'IINT!="."' -f'%POS %IINT\n' /tmp/zPov9rP7t1/missing.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'IINT!="."' -f'%POS %IINT\n' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -e'IINT!="."' -f'%POS %IINT\n' /tmp/wj8A4a3te7/missing.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -e'IINT!="."' -f'%POS %IINT\n' /tmp/zPov9rP7t1/missing.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -e'IINT!="."' -f'%POS %IINT\n' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -e'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -e'IINT="."' -f'%POS %IINT\n' /tmp/wj8A4a3te7/missing.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -e'IINT="."' -f'%POS %IINT\n' /tmp/zPov9rP7t1/missing.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -e'IINT="."' -f'%POS %IINT\n' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -e'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' /tmp/wj8A4a3te7/missing.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' /tmp/zPov9rP7t1/missing.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' /tmp/wj8A4a3te7/missing.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' /tmp/zPov9rP7t1/missing.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' /tmp/wj8A4a3te7/missing.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' /tmp/zPov9rP7t1/missing.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' /tmp/wj8A4a3te7/missing.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' /tmp/zPov9rP7t1/missing.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' /tmp/wj8A4a3te7/missing.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' /tmp/zPov9rP7t1/missing.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' /tmp/wj8A4a3te7/missing.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' /tmp/zPov9rP7t1/missing.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' /tmp/wj8A4a3te7/missing.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' /tmp/zPov9rP7t1/missing.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' /tmp/wj8A4a3te7/missing.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' /tmp/zPov9rP7t1/missing.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' /tmp/wj8A4a3te7/missing.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' /tmp/zPov9rP7t1/missing.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER="A"' -f'%POS %FILTER\n' /tmp/wj8A4a3te7/filter.11.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER="A"' -f'%POS %FILTER\n' /tmp/zPov9rP7t1/filter.11.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/filter.11.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER="A"' -f'%POS %FILTER\n' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/filter.11.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER="A"' -f'%POS %FILTER\n' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER!="A"' -f'%POS %FILTER\n' /tmp/wj8A4a3te7/filter.11.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER!="A"' -f'%POS %FILTER\n' /tmp/zPov9rP7t1/filter.11.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/filter.11.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER!="A"' -f'%POS %FILTER\n' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/filter.11.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER!="A"' -f'%POS %FILTER\n' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER~"A"' -f'%POS %FILTER\n' /tmp/wj8A4a3te7/filter.11.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER~"A"' -f'%POS %FILTER\n' /tmp/zPov9rP7t1/filter.11.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/filter.11.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER~"A"' -f'%POS %FILTER\n' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/filter.11.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER~"A"' -f'%POS %FILTER\n' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n' /tmp/wj8A4a3te7/filter.11.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n' /tmp/zPov9rP7t1/filter.11.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/filter.11.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/filter.11.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'%LINE' /tmp/wj8A4a3te7/query.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'%LINE' /tmp/zPov9rP7t1/query.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%LINE' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%LINE' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' /tmp/wj8A4a3te7/query.filter-type.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' /tmp/zPov9rP7t1/query.filter-type.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter-type.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter-type.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' /tmp/wj8A4a3te7/query.filter-type.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' /tmp/zPov9rP7t1/query.filter-type.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter-type.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter-type.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' /tmp/wj8A4a3te7/query.filter-type.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' /tmp/zPov9rP7t1/query.filter-type.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter-type.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter-type.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' /tmp/wj8A4a3te7/query.filter-type.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' /tmp/zPov9rP7t1/query.filter-type.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter-type.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter-type.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'INFO/TYPE="xxx"' /tmp/wj8A4a3te7/query.filter-type.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'INFO/TYPE="xxx"' /tmp/zPov9rP7t1/query.filter-type.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter-type.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'INFO/TYPE="xxx"' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter-type.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'INFO/TYPE="xxx"' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -i'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001' /tmp/wj8A4a3te7/filter-missing-floats.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -i'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001' /tmp/zPov9rP7t1/filter-missing-floats.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/filter-missing-floats.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -i'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/filter-missing-floats.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -i'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -e'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001' /tmp/wj8A4a3te7/filter-missing-floats.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -e'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001' /tmp/zPov9rP7t1/filter-missing-floats.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/filter-missing-floats.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -e'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/filter-missing-floats.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -e'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' /tmp/wj8A4a3te7/missing.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' /tmp/zPov9rP7t1/missing.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' /tmp/wj8A4a3te7/query.filter.2.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' /tmp/zPov9rP7t1/query.filter.2.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' /tmp/wj8A4a3te7/view.filter.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' /tmp/zPov9rP7t1/view.filter.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' /tmp/wj8A4a3te7/view.filter.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' /tmp/zPov9rP7t1/view.filter.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' /tmp/wj8A4a3te7/view.filter.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' /tmp/zPov9rP7t1/view.filter.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' /tmp/wj8A4a3te7/view.filter.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' /tmp/zPov9rP7t1/view.filter.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' /tmp/wj8A4a3te7/view.filter.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' /tmp/zPov9rP7t1/view.filter.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' /tmp/wj8A4a3te7/view.filter.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' /tmp/zPov9rP7t1/view.filter.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' /tmp/wj8A4a3te7/view.filter.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' /tmp/zPov9rP7t1/view.filter.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' /tmp/wj8A4a3te7/view.filter.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' /tmp/zPov9rP7t1/view.filter.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' /tmp/wj8A4a3te7/view.filter.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' /tmp/zPov9rP7t1/view.filter.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' /tmp/wj8A4a3te7/view.filter.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' /tmp/zPov9rP7t1/view.filter.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' /tmp/wj8A4a3te7/filter.5.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' /tmp/zPov9rP7t1/filter.5.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/filter.5.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/filter.5.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' /tmp/wj8A4a3te7/filter.5.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' /tmp/zPov9rP7t1/filter.5.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/filter.5.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/filter.5.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' /tmp/wj8A4a3te7/view.filter.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' /tmp/zPov9rP7t1/view.filter.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' /tmp/wj8A4a3te7/view.filter.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' /tmp/zPov9rP7t1/view.filter.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' /tmp/wj8A4a3te7/view.filter.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' /tmp/zPov9rP7t1/view.filter.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' /tmp/wj8A4a3te7/view.filter.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' /tmp/zPov9rP7t1/view.filter.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' /tmp/wj8A4a3te7/view.filter.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' /tmp/zPov9rP7t1/view.filter.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 & FMT/GQ=589' /tmp/wj8A4a3te7/view.filter.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 & FMT/GQ=589' /tmp/zPov9rP7t1/view.filter.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 & FMT/GQ=589' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 & FMT/GQ=589' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' /tmp/wj8A4a3te7/view.filter.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' /tmp/zPov9rP7t1/view.filter.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' /tmp/wj8A4a3te7/query.filter.3.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' /tmp/zPov9rP7t1/query.filter.3.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.3.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.3.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"' /tmp/wj8A4a3te7/query.filter.3.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"' /tmp/zPov9rP7t1/query.filter.3.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.3.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.3.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' /tmp/wj8A4a3te7/query.filter.3.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' /tmp/zPov9rP7t1/query.filter.3.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.3.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.3.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %AD\n]\n' -i'AD[:0]+AD[:1] > 12' /tmp/wj8A4a3te7/filter.5.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %AD\n]\n' -i'AD[:0]+AD[:1] > 12' /tmp/zPov9rP7t1/filter.5.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/filter.5.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %AD\n]\n' -i'AD[:0]+AD[:1] > 12' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/filter.5.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %AD\n]\n' -i'AD[:0]+AD[:1] > 12' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' /tmp/wj8A4a3te7/query.filter.4.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' /tmp/zPov9rP7t1/query.filter.4.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.4.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.4.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i 'ID=@/build/reproducible-path/bcftools-1.21/test/query.56.out' /tmp/wj8A4a3te7/view.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i 'ID=@/build/reproducible-path/bcftools-1.21/test/query.56.out' /tmp/zPov9rP7t1/view.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i 'ID=@/build/reproducible-path/bcftools-1.21/test/query.56.out' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/view.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i 'ID=@/build/reproducible-path/bcftools-1.21/test/query.56.out' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD)>0.01' /tmp/wj8A4a3te7/query.filter.5.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD)>0.01' /tmp/zPov9rP7t1/query.filter.5.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.5.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD)>0.01' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.5.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD)>0.01' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD[:0],FMT/AD[:1])>0.01' /tmp/wj8A4a3te7/query.filter.5.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD[:0],FMT/AD[:1])>0.01' /tmp/zPov9rP7t1/query.filter.5.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.5.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD[:0],FMT/AD[:1])>0.01' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.5.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD[:0],FMT/AD[:1])>0.01' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%AD\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01' /tmp/wj8A4a3te7/query.filter.5.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%AD\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01' /tmp/zPov9rP7t1/query.filter.5.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.5.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%AD\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.5.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%AD\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[GT]==10' /tmp/wj8A4a3te7/query.filter.5.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[GT]==10' /tmp/zPov9rP7t1/query.filter.5.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.5.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[GT]==10' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.5.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[GT]==10' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'sSUM(FMT/AD[GT])==210' /tmp/wj8A4a3te7/query.filter.5.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'sSUM(FMT/AD[GT])==210' /tmp/zPov9rP7t1/query.filter.5.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.5.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'sSUM(FMT/AD[GT])==210' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.5.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'sSUM(FMT/AD[GT])==210' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[0:GT]==30' /tmp/wj8A4a3te7/query.filter.5.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[0:GT]==30' /tmp/zPov9rP7t1/query.filter.5.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.5.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[0:GT]==30' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.5.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[0:GT]==30' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TF[:GT]==1 && FMT/TF[:GT]==2' /tmp/wj8A4a3te7/query.gtidx.1.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TF[:GT]==1 && FMT/TF[:GT]==2' /tmp/zPov9rP7t1/query.gtidx.1.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.gtidx.1.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TF[:GT]==1 && FMT/TF[:GT]==2' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.gtidx.1.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TF[:GT]==1 && FMT/TF[:GT]==2' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TI[:GT]==1 && FMT/TF[:GT]==2' /tmp/wj8A4a3te7/query.gtidx.1.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TI[:GT]==1 && FMT/TF[:GT]==2' /tmp/zPov9rP7t1/query.gtidx.1.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.gtidx.1.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TI[:GT]==1 && FMT/TF[:GT]==2' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.gtidx.1.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TI[:GT]==1 && FMT/TF[:GT]==2' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TS[:GT]=="BB" && FMT/TS[:GT]=="CC"' /tmp/wj8A4a3te7/query.gtidx.1.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TS[:GT]=="BB" && FMT/TS[:GT]=="CC"' /tmp/zPov9rP7t1/query.gtidx.1.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.gtidx.1.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TS[:GT]=="BB" && FMT/TS[:GT]=="CC"' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.gtidx.1.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TS[:GT]=="BB" && FMT/TS[:GT]=="CC"' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TC[:GT]=="B" && FMT/TC[:GT]=="C"' /tmp/wj8A4a3te7/query.gtidx.1.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TC[:GT]=="B" && FMT/TC[:GT]=="C"' /tmp/zPov9rP7t1/query.gtidx.1.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.gtidx.1.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TC[:GT]=="B" && FMT/TC[:GT]=="C"' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.gtidx.1.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TC[:GT]=="B" && FMT/TC[:GT]=="C"' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'[%GT %TI\n]' -i'FMT/TI[:GT]=="."' /tmp/wj8A4a3te7/query.gtidx.1.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'[%GT %TI\n]' -i'FMT/TI[:GT]=="."' /tmp/zPov9rP7t1/query.gtidx.1.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.gtidx.1.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%GT %TI\n]' -i'FMT/TI[:GT]=="."' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.gtidx.1.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%GT %TI\n]' -i'FMT/TI[:GT]=="."' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS\n' -i'CHROM="4"' /tmp/wj8A4a3te7/query.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS\n' -i'CHROM="4"' /tmp/zPov9rP7t1/query.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS\n' -i'CHROM="4"' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS\n' -i'CHROM="4"' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%TAG1\n' -i'(TAG1>=-129 && TAG1<=-120) || (TAG1>=-32769 && TAG1<=-32760)' /tmp/wj8A4a3te7/query.negative.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%TAG1\n' -i'(TAG1>=-129 && TAG1<=-120) || (TAG1>=-32769 && TAG1<=-32760)' /tmp/zPov9rP7t1/query.negative.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.negative.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%TAG1\n' -i'(TAG1>=-129 && TAG1<=-120) || (TAG1>=-32769 && TAG1<=-32760)' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.negative.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%TAG1\n' -i'(TAG1>=-129 && TAG1<=-120) || (TAG1>=-32769 && TAG1<=-32760)' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%TAGV1\n' -i'(TAGV1>=-129 && TAGV1<=-120) || (TAGV1>=-32769 && TAGV1<=-32760)' /tmp/wj8A4a3te7/query.negative.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%TAGV1\n' -i'(TAGV1>=-129 && TAGV1<=-120) || (TAGV1>=-32769 && TAGV1<=-32760)' /tmp/zPov9rP7t1/query.negative.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.negative.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%TAGV1\n' -i'(TAGV1>=-129 && TAGV1<=-120) || (TAGV1>=-32769 && TAGV1<=-32760)' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.negative.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%TAGV1\n' -i'(TAGV1>=-129 && TAGV1<=-120) || (TAGV1>=-32769 && TAGV1<=-32760)' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%TAG2\n' -i'(TAG2>=-129 && TAG2<=-120) || (TAG2>=-32769 && TAG2<=-32760)' /tmp/wj8A4a3te7/query.negative.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%TAG2\n' -i'(TAG2>=-129 && TAG2<=-120) || (TAG2>=-32769 && TAG2<=-32760)' /tmp/zPov9rP7t1/query.negative.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.negative.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%TAG2\n' -i'(TAG2>=-129 && TAG2<=-120) || (TAG2>=-32769 && TAG2<=-32760)' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.negative.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%TAG2\n' -i'(TAG2>=-129 && TAG2<=-120) || (TAG2>=-32769 && TAG2<=-32760)' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%TAGV2\n' -i'(TAGV2>=-129 && TAGV2<=-120) || (TAGV2>=-32769 && TAGV2<=-32760)' /tmp/wj8A4a3te7/query.negative.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%TAGV2\n' -i'(TAGV2>=-129 && TAGV2<=-120) || (TAGV2>=-32769 && TAGV2<=-32760)' /tmp/zPov9rP7t1/query.negative.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.negative.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%TAGV2\n' -i'(TAGV2>=-129 && TAGV2<=-120) || (TAGV2>=-32769 && TAGV2<=-32760)' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.negative.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%TAGV2\n' -i'(TAGV2>=-129 && TAGV2<=-120) || (TAGV2>=-32769 && TAGV2<=-32760)' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GQ\n]' -i'N_PASS(GQ<20)==1' /tmp/wj8A4a3te7/query.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GQ\n]' -i'N_PASS(GQ<20)==1' /tmp/zPov9rP7t1/query.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GQ\n]' -i'N_PASS(GQ<20)==1' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GQ\n]' -i'N_PASS(GQ<20)==1' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")==1' /tmp/wj8A4a3te7/query.filter.11.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")==1' /tmp/zPov9rP7t1/query.filter.11.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.11.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")==1' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.11.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")==1' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")!=1' /tmp/wj8A4a3te7/query.filter.11.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")!=1' /tmp/zPov9rP7t1/query.filter.11.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.11.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")!=1' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.11.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")!=1' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")==1' /tmp/wj8A4a3te7/query.filter.11.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")==1' /tmp/zPov9rP7t1/query.filter.11.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.11.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")==1' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.11.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")==1' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")!=1' /tmp/wj8A4a3te7/query.filter.11.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")!=1' /tmp/zPov9rP7t1/query.filter.11.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.11.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")!=1' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.11.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")!=1' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM\t%POS\t%INFO\t%FORMAT\n' -s D,C /tmp/wj8A4a3te7/query.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM\t%POS\t%INFO\t%FORMAT\n' -s D,C /tmp/zPov9rP7t1/query.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM\t%POS\t%INFO\t%FORMAT\n' -s D,C + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM\t%POS\t%INFO\t%FORMAT\n' -s D,C .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\n' -i'POS==16777217 || POS==33554432 || POS=118673904' /tmp/wj8A4a3te7/query.filter.6.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\n' -i'POS==16777217 || POS==33554432 || POS=118673904' /tmp/zPov9rP7t1/query.filter.6.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.6.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\n' -i'POS==16777217 || POS==33554432 || POS=118673904' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.6.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\n' -i'POS==16777217 || POS==33554432 || POS=118673904' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(II)==6' /tmp/wj8A4a3te7/query.filter.7.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(II)==6' /tmp/zPov9rP7t1/query.filter.7.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(II)==6' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(II)==6' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(FORMAT/FI)==7' /tmp/wj8A4a3te7/query.filter.7.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(FORMAT/FI)==7' /tmp/zPov9rP7t1/query.filter.7.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(FORMAT/FI)==7' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(FORMAT/FI)==7' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(II)==2' /tmp/wj8A4a3te7/query.filter.7.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(II)==2' /tmp/zPov9rP7t1/query.filter.7.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(II)==2' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(II)==2' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(FORMAT/FI)==1.75' /tmp/wj8A4a3te7/query.filter.7.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(FORMAT/FI)==1.75' /tmp/zPov9rP7t1/query.filter.7.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(FORMAT/FI)==1.75' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(FORMAT/FI)==1.75' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(II)==2' /tmp/wj8A4a3te7/query.filter.7.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(II)==2' /tmp/zPov9rP7t1/query.filter.7.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(II)==2' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(II)==2' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(FORMAT/FI)==1.75' /tmp/wj8A4a3te7/query.filter.7.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(FORMAT/FI)==1.75' /tmp/zPov9rP7t1/query.filter.7.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(FORMAT/FI)==1.75' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(FORMAT/FI)==1.75' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(II)==2' /tmp/wj8A4a3te7/query.filter.7.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(II)==2' /tmp/zPov9rP7t1/query.filter.7.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(II)==2' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(II)==2' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(FORMAT/FI)==1.5' /tmp/wj8A4a3te7/query.filter.7.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(FORMAT/FI)==1.5' /tmp/zPov9rP7t1/query.filter.7.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(FORMAT/FI)==1.5' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(FORMAT/FI)==1.5' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'%ILEN==1' /tmp/wj8A4a3te7/query.filter.8.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'%ILEN==1' /tmp/zPov9rP7t1/query.filter.8.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.8.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'%ILEN==1' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.8.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'%ILEN==1' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'ILEN==1' /tmp/wj8A4a3te7/query.filter.8.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'ILEN==1' /tmp/zPov9rP7t1/query.filter.8.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.8.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'ILEN==1' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.8.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'ILEN==1' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] < FMT/AD[:1]' /tmp/wj8A4a3te7/query.filter.9.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] < FMT/AD[:1]' /tmp/zPov9rP7t1/query.filter.9.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.9.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] < FMT/AD[:1]' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.9.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] < FMT/AD[:1]' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] > FMT/AD[:1]' /tmp/wj8A4a3te7/query.filter.9.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] > FMT/AD[:1]' /tmp/zPov9rP7t1/query.filter.9.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.9.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] > FMT/AD[:1]' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.9.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] > FMT/AD[:1]' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'[ %AD\n]' -i'AD[:1] / sum(AD[*]) > 0.5' /tmp/wj8A4a3te7/query.filter.13.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'[ %AD\n]' -i'AD[:1] / sum(AD[*]) > 0.5' /tmp/zPov9rP7t1/query.filter.13.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.13.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[ %AD\n]' -i'AD[:1] / sum(AD[*]) > 0.5' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.13.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[ %AD\n]' -i'AD[:1] / sum(AD[*]) > 0.5' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %NUM_TAG\n' -i'COUNT(INFO/NUM_TAG)=2' /tmp/wj8A4a3te7/query.filter.10.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %NUM_TAG\n' -i'COUNT(INFO/NUM_TAG)=2' /tmp/zPov9rP7t1/query.filter.10.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.10.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %NUM_TAG\n' -i'COUNT(INFO/NUM_TAG)=2' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.10.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %NUM_TAG\n' -i'COUNT(INFO/NUM_TAG)=2' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2' /tmp/wj8A4a3te7/query.filter.10.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2' /tmp/zPov9rP7t1/query.filter.10.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.10.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.10.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM:%POS\t%N_PASS(GT="alt" & GQ>110)\t[\t%GT]\t[\t%GQ]\n' /tmp/wj8A4a3te7/query.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM:%POS\t%N_PASS(GT="alt" & GQ>110)\t[\t%GT]\t[\t%GQ]\n' /tmp/zPov9rP7t1/query.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM:%POS\t%N_PASS(GT="alt" & GQ>110)\t[\t%GT]\t[\t%GQ]\n' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM:%POS\t%N_PASS(GT="alt" & GQ>110)\t[\t%GT]\t[\t%GQ]\n' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 1,3,0 /tmp/wj8A4a3te7/query.filter.12.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 1,3,0 /tmp/zPov9rP7t1/query.filter.12.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.12.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 1,3,0 + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.12.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 1,3,0 .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 0,1,3 /tmp/wj8A4a3te7/query.filter.12.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 0,1,3 /tmp/zPov9rP7t1/query.filter.12.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.12.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 0,1,3 + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.12.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 0,1,3 .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f "[%SAMPLE %GT\n]" -S /build/reproducible-path/bcftools-1.21/test/query.smpl.11.txt /tmp/wj8A4a3te7/query.smpl.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f "[%SAMPLE %GT\n]" -S /build/reproducible-path/bcftools-1.21/test/query.smpl.11.txt /tmp/zPov9rP7t1/query.smpl.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.smpl.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f "[%SAMPLE %GT\n]" -S /build/reproducible-path/bcftools-1.21/test/query.smpl.11.txt + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.smpl.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f "[%SAMPLE %GT\n]" -S /build/reproducible-path/bcftools-1.21/test/query.smpl.11.txt .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -l -S /build/reproducible-path/bcftools-1.21/test/query.smpl.11.txt /tmp/wj8A4a3te7/query.smpl.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -l -S /build/reproducible-path/bcftools-1.21/test/query.smpl.11.txt /tmp/zPov9rP7t1/query.smpl.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.smpl.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -l -S /build/reproducible-path/bcftools-1.21/test/query.smpl.11.txt + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.smpl.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -l -S /build/reproducible-path/bcftools-1.21/test/query.smpl.11.txt .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f "[%SAMPLE %GT\n]" -S ^/build/reproducible-path/bcftools-1.21/test/query.smpl.11.txt /tmp/wj8A4a3te7/query.smpl.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f "[%SAMPLE %GT\n]" -S ^/build/reproducible-path/bcftools-1.21/test/query.smpl.11.txt /tmp/zPov9rP7t1/query.smpl.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.smpl.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f "[%SAMPLE %GT\n]" -S ^/build/reproducible-path/bcftools-1.21/test/query.smpl.11.txt + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.smpl.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f "[%SAMPLE %GT\n]" -S ^/build/reproducible-path/bcftools-1.21/test/query.smpl.11.txt .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -l -S ^/build/reproducible-path/bcftools-1.21/test/query.smpl.11.txt /tmp/wj8A4a3te7/query.smpl.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -l -S ^/build/reproducible-path/bcftools-1.21/test/query.smpl.11.txt /tmp/zPov9rP7t1/query.smpl.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.smpl.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -l -S ^/build/reproducible-path/bcftools-1.21/test/query.smpl.11.txt + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.smpl.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -l -S ^/build/reproducible-path/bcftools-1.21/test/query.smpl.11.txt .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f "[%SAMPLE %GT\n]" -S /build/reproducible-path/bcftools-1.21/test/query.smpl.txt /tmp/wj8A4a3te7/query.smpl.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f "[%SAMPLE %GT\n]" -S /build/reproducible-path/bcftools-1.21/test/query.smpl.txt /tmp/zPov9rP7t1/query.smpl.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.smpl.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f "[%SAMPLE %GT\n]" -S /build/reproducible-path/bcftools-1.21/test/query.smpl.txt + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.smpl.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f "[%SAMPLE %GT\n]" -S /build/reproducible-path/bcftools-1.21/test/query.smpl.txt .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -l -S /build/reproducible-path/bcftools-1.21/test/query.smpl.txt /tmp/wj8A4a3te7/query.smpl.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -l -S /build/reproducible-path/bcftools-1.21/test/query.smpl.txt /tmp/zPov9rP7t1/query.smpl.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.smpl.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -l -S /build/reproducible-path/bcftools-1.21/test/query.smpl.txt + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.smpl.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -l -S /build/reproducible-path/bcftools-1.21/test/query.smpl.txt .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID~"s12"' /tmp/wj8A4a3te7/query.filter.id.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID~"s12"' /tmp/zPov9rP7t1/query.filter.id.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.id.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID~"s12"' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.id.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID~"s12"' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID="rs123"' /tmp/wj8A4a3te7/query.filter.id.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID="rs123"' /tmp/zPov9rP7t1/query.filter.id.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.id.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID="rs123"' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.id.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID="rs123"' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID="abc"' /tmp/wj8A4a3te7/query.filter.id.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID="abc"' /tmp/zPov9rP7t1/query.filter.id.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.id.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID="abc"' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.id.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID="abc"' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID=@/build/reproducible-path/bcftools-1.21/test/query.filter.id.3.txt' /tmp/wj8A4a3te7/query.filter.id.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID=@/build/reproducible-path/bcftools-1.21/test/query.filter.id.3.txt' /tmp/zPov9rP7t1/query.filter.id.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.id.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID=@/build/reproducible-path/bcftools-1.21/test/query.filter.id.3.txt' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.id.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID=@/build/reproducible-path/bcftools-1.21/test/query.filter.id.3.txt' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID!="abc"' /tmp/wj8A4a3te7/query.filter.id.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID!="abc"' /tmp/zPov9rP7t1/query.filter.id.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.id.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID!="abc"' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.id.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID!="abc"' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID!=@/build/reproducible-path/bcftools-1.21/test/query.filter.id.3.txt' /tmp/wj8A4a3te7/query.filter.id.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID!=@/build/reproducible-path/bcftools-1.21/test/query.filter.id.3.txt' /tmp/zPov9rP7t1/query.filter.id.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter.id.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID!=@/build/reproducible-path/bcftools-1.21/test/query.filter.id.3.txt' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter.id.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID!=@/build/reproducible-path/bcftools-1.21/test/query.filter.id.3.txt' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER="A"' -f'%FILTER\n' /tmp/wj8A4a3te7/filter.12.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER="A"' -f'%FILTER\n' /tmp/zPov9rP7t1/filter.12.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/filter.12.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER="A"' -f'%FILTER\n' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/filter.12.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER="A"' -f'%FILTER\n' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER~"A"' -f'%FILTER\n' /tmp/wj8A4a3te7/filter.12.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER~"A"' -f'%FILTER\n' /tmp/zPov9rP7t1/filter.12.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/filter.12.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER~"A"' -f'%FILTER\n' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/filter.12.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER~"A"' -f'%FILTER\n' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER="A;B"' -f'%FILTER\n' /tmp/wj8A4a3te7/filter.12.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER="A;B"' -f'%FILTER\n' /tmp/zPov9rP7t1/filter.12.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/filter.12.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER="A;B"' -f'%FILTER\n' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/filter.12.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER="A;B"' -f'%FILTER\n' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER!="A;B"' -f'%FILTER\n' /tmp/wj8A4a3te7/filter.12.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER!="A;B"' -f'%FILTER\n' /tmp/zPov9rP7t1/filter.12.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/filter.12.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER!="A;B"' -f'%FILTER\n' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/filter.12.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER!="A;B"' -f'%FILTER\n' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER~"A;B"' -f'%FILTER\n' /tmp/wj8A4a3te7/filter.12.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER~"A;B"' -f'%FILTER\n' /tmp/zPov9rP7t1/filter.12.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/filter.12.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER~"A;B"' -f'%FILTER\n' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/filter.12.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER~"A;B"' -f'%FILTER\n' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER!~"A;B"' -f'%FILTER\n' /tmp/wj8A4a3te7/filter.12.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER!~"A;B"' -f'%FILTER\n' /tmp/zPov9rP7t1/filter.12.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/filter.12.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER!~"A;B"' -f'%FILTER\n' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/filter.12.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER!~"A;B"' -f'%FILTER\n' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -i'DP%10==2' -f'[ %DP]\n' /tmp/wj8A4a3te7/filter.10.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -i'DP%10==2' -f'[ %DP]\n' /tmp/zPov9rP7t1/filter.10.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/filter.10.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'DP%10==2' -f'[ %DP]\n' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/filter.10.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'DP%10==2' -f'[ %DP]\n' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -i'REF="N"' -f'%CHROM %POS %REF %ALT %QUAL\n' /tmp/wj8A4a3te7/filter.13.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -i'REF="N"' -f'%CHROM %POS %REF %ALT %QUAL\n' /tmp/zPov9rP7t1/filter.13.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/filter.13.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'REF="N"' -f'%CHROM %POS %REF %ALT %QUAL\n' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/filter.13.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'REF="N"' -f'%CHROM %POS %REF %ALT %QUAL\n' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -H -f'[%CHROM %POS %SAMPLE %DP %GT\n]' /tmp/wj8A4a3te7/query.header.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -H -f'[%CHROM %POS %SAMPLE %DP %GT\n]' /tmp/zPov9rP7t1/query.header.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.header.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -H -f'[%CHROM %POS %SAMPLE %DP %GT\n]' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.header.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -H -f'[%CHROM %POS %SAMPLE %DP %GT\n]' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -H -f'[%CHROM %POS %SAMPLE %DP %GT\t]\n' /tmp/wj8A4a3te7/query.header.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -H -f'[%CHROM %POS %SAMPLE %DP %GT\t]\n' /tmp/zPov9rP7t1/query.header.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.header.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -H -f'[%CHROM %POS %SAMPLE %DP %GT\t]\n' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.header.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -H -f'[%CHROM %POS %SAMPLE %DP %GT\t]\n' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]\n' /tmp/wj8A4a3te7/query.header.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]\n' /tmp/zPov9rP7t1/query.header.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.header.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]\n' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.header.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]\n' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]' /tmp/wj8A4a3te7/query.header.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]' /tmp/zPov9rP7t1/query.header.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.header.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.header.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]\n' /tmp/wj8A4a3te7/query.header.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]\n' /tmp/zPov9rP7t1/query.header.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.header.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]\n' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.header.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]\n' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]' /tmp/wj8A4a3te7/query.header.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]' /tmp/zPov9rP7t1/query.header.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.header.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.header.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -HH -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]' /tmp/wj8A4a3te7/query.header.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -HH -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]' /tmp/zPov9rP7t1/query.header.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.header.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -HH -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.header.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -HH -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'[%SAMPLE %DP\n]' -i'DP=1 || DP=2' /tmp/wj8A4a3te7/query.filter-or.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'[%SAMPLE %DP\n]' -i'DP=1 || DP=2' /tmp/zPov9rP7t1/query.filter-or.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter-or.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%SAMPLE %DP\n]' -i'DP=1 || DP=2' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter-or.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%SAMPLE %DP\n]' -i'DP=1 || DP=2' .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools query -f'[%SAMPLE %DP\n]' -i'DP=1 | DP=2' /tmp/wj8A4a3te7/query.filter-or.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'[%SAMPLE %DP\n]' -i'DP=1 | DP=2' /tmp/zPov9rP7t1/query.filter-or.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/query.filter-or.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%SAMPLE %DP\n]' -i'DP=1 | DP=2' + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/query.filter-or.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%SAMPLE %DP\n]' -i'DP=1 | DP=2' .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/wj8A4a3te7/norm.sort.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/zPov9rP7t1/norm.sort.vcf.gz .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/wj8A4a3te7/norm.sort.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/zPov9rP7t1/norm.sort.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - -S lex /tmp/wj8A4a3te7/norm.sort.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - -S lex /tmp/zPov9rP7t1/norm.sort.vcf.gz .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - -S lex /tmp/wj8A4a3te7/norm.sort.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - -S lex /tmp/zPov9rP7t1/norm.sort.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +both /tmp/wj8A4a3te7/norm.join-missing-ploidy.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +both /tmp/zPov9rP7t1/norm.join-missing-ploidy.vcf.gz .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +both /tmp/wj8A4a3te7/norm.join-missing-ploidy.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +both /tmp/zPov9rP7t1/norm.join-missing-ploidy.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - --multi-overlaps . /tmp/wj8A4a3te7/norm.split.5.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - --multi-overlaps . /tmp/zPov9rP7t1/norm.split.5.vcf.gz .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - --multi-overlaps . /tmp/wj8A4a3te7/norm.split.5.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - --multi-overlaps . /tmp/zPov9rP7t1/norm.split.5.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version /tmp/wj8A4a3te7/norm.symbolic.3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.symbolic.3.fa + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version /tmp/zPov9rP7t1/norm.symbolic.3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.symbolic.3.fa .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version /tmp/wj8A4a3te7/norm.symbolic.3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.symbolic.3.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version /tmp/zPov9rP7t1/norm.symbolic.3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.symbolic.3.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -cx /tmp/wj8A4a3te7/norm.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.fa + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -cx /tmp/zPov9rP7t1/norm.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.fa .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -cx /tmp/wj8A4a3te7/norm.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -cx /tmp/zPov9rP7t1/norm.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- /tmp/wj8A4a3te7/norm.split.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- /tmp/zPov9rP7t1/norm.split.vcf.gz .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- /tmp/wj8A4a3te7/norm.split.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- /tmp/zPov9rP7t1/norm.split.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- /tmp/wj8A4a3te7/norm.split.2.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- /tmp/zPov9rP7t1/norm.split.2.vcf.gz .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- /tmp/wj8A4a3te7/norm.split.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- /tmp/zPov9rP7t1/norm.split.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- --force /tmp/wj8A4a3te7/norm.split.3.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- --force /tmp/zPov9rP7t1/norm.split.3.vcf.gz .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- --force /tmp/wj8A4a3te7/norm.split.3.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- --force /tmp/zPov9rP7t1/norm.split.3.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- /tmp/wj8A4a3te7/norm.split.4.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- /tmp/zPov9rP7t1/norm.split.4.vcf.gz .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- /tmp/wj8A4a3te7/norm.split.4.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- /tmp/zPov9rP7t1/norm.split.4.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- --keep-sum AD /tmp/wj8A4a3te7/norm.split.4.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- --keep-sum AD /tmp/zPov9rP7t1/norm.split.4.vcf.gz .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- --keep-sum AD /tmp/wj8A4a3te7/norm.split.4.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- --keep-sum AD /tmp/zPov9rP7t1/norm.split.4.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- /tmp/wj8A4a3te7/norm.split.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.fa + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- /tmp/zPov9rP7t1/norm.split.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.fa .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- /tmp/wj8A4a3te7/norm.split.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- /tmp/zPov9rP7t1/norm.split.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m+ /tmp/wj8A4a3te7/norm.merge.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m+ /tmp/zPov9rP7t1/norm.merge.vcf.gz .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m+ /tmp/wj8A4a3te7/norm.merge.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m+ /tmp/zPov9rP7t1/norm.merge.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m+ /tmp/wj8A4a3te7/norm.merge.2.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m+ /tmp/zPov9rP7t1/norm.merge.2.vcf.gz .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m+ /tmp/wj8A4a3te7/norm.merge.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m+ /tmp/zPov9rP7t1/norm.merge.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m+ /tmp/wj8A4a3te7/norm.merge.3.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m+ /tmp/zPov9rP7t1/norm.merge.3.vcf.gz .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m+ /tmp/wj8A4a3te7/norm.merge.3.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m+ /tmp/zPov9rP7t1/norm.merge.3.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m+ -s /tmp/wj8A4a3te7/norm.merge.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m+ -s /tmp/zPov9rP7t1/norm.merge.vcf.gz .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m+ -s /tmp/wj8A4a3te7/norm.merge.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m+ -s /tmp/zPov9rP7t1/norm.merge.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -Nc s /tmp/wj8A4a3te7/norm.setref.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.fa + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -Nc s /tmp/zPov9rP7t1/norm.setref.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.fa .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -Nc s /tmp/wj8A4a3te7/norm.setref.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -Nc s /tmp/zPov9rP7t1/norm.setref.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version /tmp/wj8A4a3te7/norm.telomere.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.fa + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version /tmp/zPov9rP7t1/norm.telomere.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.fa .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version /tmp/wj8A4a3te7/norm.telomere.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version /tmp/zPov9rP7t1/norm.telomere.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d snps /tmp/wj8A4a3te7/norm.rmdup.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d snps /tmp/zPov9rP7t1/norm.rmdup.vcf.gz .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d snps /tmp/wj8A4a3te7/norm.rmdup.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d snps /tmp/zPov9rP7t1/norm.rmdup.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d indels /tmp/wj8A4a3te7/norm.rmdup.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d indels /tmp/zPov9rP7t1/norm.rmdup.vcf.gz .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d indels /tmp/wj8A4a3te7/norm.rmdup.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d indels /tmp/zPov9rP7t1/norm.rmdup.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d both /tmp/wj8A4a3te7/norm.rmdup.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d both /tmp/zPov9rP7t1/norm.rmdup.vcf.gz .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d both /tmp/wj8A4a3te7/norm.rmdup.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d both /tmp/zPov9rP7t1/norm.rmdup.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d all /tmp/wj8A4a3te7/norm.rmdup.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d all /tmp/zPov9rP7t1/norm.rmdup.vcf.gz .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d all /tmp/wj8A4a3te7/norm.rmdup.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d all /tmp/zPov9rP7t1/norm.rmdup.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d none /tmp/wj8A4a3te7/norm.rmdup.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d none /tmp/zPov9rP7t1/norm.rmdup.vcf.gz .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d none /tmp/wj8A4a3te7/norm.rmdup.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d none /tmp/zPov9rP7t1/norm.rmdup.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d exact /tmp/wj8A4a3te7/norm.rmdup.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d exact /tmp/zPov9rP7t1/norm.rmdup.vcf.gz .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d exact /tmp/wj8A4a3te7/norm.rmdup.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d exact /tmp/zPov9rP7t1/norm.rmdup.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d none /tmp/wj8A4a3te7/norm.rmdup.2.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d none /tmp/zPov9rP7t1/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d none /tmp/wj8A4a3te7/norm.rmdup.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d none /tmp/zPov9rP7t1/norm.rmdup.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d exact /tmp/wj8A4a3te7/norm.rmdup.2.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d exact /tmp/zPov9rP7t1/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d exact /tmp/wj8A4a3te7/norm.rmdup.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d exact /tmp/zPov9rP7t1/norm.rmdup.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d indels /tmp/wj8A4a3te7/norm.rmdup.2.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d indels /tmp/zPov9rP7t1/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d indels /tmp/wj8A4a3te7/norm.rmdup.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d indels /tmp/zPov9rP7t1/norm.rmdup.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d any /tmp/wj8A4a3te7/norm.rmdup.2.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d any /tmp/zPov9rP7t1/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d any /tmp/wj8A4a3te7/norm.rmdup.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d any /tmp/zPov9rP7t1/norm.rmdup.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d both /tmp/wj8A4a3te7/norm.rmdup.2.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d both /tmp/zPov9rP7t1/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d both /tmp/wj8A4a3te7/norm.rmdup.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d both /tmp/zPov9rP7t1/norm.rmdup.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d snps /tmp/wj8A4a3te7/norm.rmdup.2.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d snps /tmp/zPov9rP7t1/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d snps /tmp/wj8A4a3te7/norm.rmdup.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d snps /tmp/zPov9rP7t1/norm.rmdup.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d exact /tmp/wj8A4a3te7/norm.rmdup.3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.rmdup.3.fa + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d exact /tmp/zPov9rP7t1/norm.rmdup.3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.rmdup.3.fa .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d exact /tmp/wj8A4a3te7/norm.rmdup.3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.rmdup.3.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d exact /tmp/zPov9rP7t1/norm.rmdup.3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.rmdup.3.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d all /tmp/wj8A4a3te7/norm.rmdup.3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.rmdup.3.fa + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d all /tmp/zPov9rP7t1/norm.rmdup.3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.rmdup.3.fa .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d all /tmp/wj8A4a3te7/norm.rmdup.3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.rmdup.3.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d all /tmp/zPov9rP7t1/norm.rmdup.3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.rmdup.3.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -c s -a /tmp/wj8A4a3te7/norm.2.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.2.fa + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -c s -a /tmp/zPov9rP7t1/norm.2.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.2.fa .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -c s -a /tmp/wj8A4a3te7/norm.2.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.2.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -c s -a /tmp/zPov9rP7t1/norm.2.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.2.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -c s /tmp/wj8A4a3te7/norm.iupac.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.iupac.fa + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -c s /tmp/zPov9rP7t1/norm.iupac.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.iupac.fa .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -c s /tmp/wj8A4a3te7/norm.iupac.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.iupac.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -c s /tmp/zPov9rP7t1/norm.iupac.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.iupac.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -c s /tmp/wj8A4a3te7/norm.3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.3.fa + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -c s /tmp/zPov9rP7t1/norm.3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.3.fa .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -c s /tmp/wj8A4a3te7/norm.3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.3.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -c s /tmp/zPov9rP7t1/norm.3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.3.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -c s -i'alt="N"' /tmp/wj8A4a3te7/norm.3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.3.fa + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -c s -i'alt="N"' /tmp/zPov9rP7t1/norm.3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.3.fa .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -c s -i'alt="N"' /tmp/wj8A4a3te7/norm.3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.3.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -c s -i'alt="N"' /tmp/zPov9rP7t1/norm.3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.3.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -a --old-rec-tag OLD_REC /tmp/wj8A4a3te7/atomize.split.1.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any --force + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -a --old-rec-tag OLD_REC /tmp/zPov9rP7t1/atomize.split.1.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any --force .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -a --old-rec-tag OLD_REC /tmp/wj8A4a3te7/atomize.split.1.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any --force -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -a --old-rec-tag OLD_REC /tmp/zPov9rP7t1/atomize.split.1.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any --force -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any --old-rec-tag OLD_REC --force /tmp/wj8A4a3te7/atomize.split.1.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -a + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any --old-rec-tag OLD_REC --force /tmp/zPov9rP7t1/atomize.split.1.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -a .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any --old-rec-tag OLD_REC --force /tmp/wj8A4a3te7/atomize.split.1.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -a -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any --old-rec-tag OLD_REC --force /tmp/zPov9rP7t1/atomize.split.1.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -a -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any --old-rec-tag OLD_REC --force -a /tmp/wj8A4a3te7/atomize.split.1.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any --old-rec-tag OLD_REC --force -a /tmp/zPov9rP7t1/atomize.split.1.vcf.gz .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any --old-rec-tag OLD_REC --force -a /tmp/wj8A4a3te7/atomize.split.1.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any --old-rec-tag OLD_REC --force -a /tmp/zPov9rP7t1/atomize.split.1.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/wj8A4a3te7/atomize.split.1.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/zPov9rP7t1/atomize.split.1.vcf.gz .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/wj8A4a3te7/atomize.split.1.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/zPov9rP7t1/atomize.split.1.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/wj8A4a3te7/atomize.split.1.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/zPov9rP7t1/atomize.split.1.vcf.gz .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/wj8A4a3te7/atomize.split.1.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/zPov9rP7t1/atomize.split.1.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/wj8A4a3te7/atomize.split.2.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/zPov9rP7t1/atomize.split.2.vcf.gz .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/wj8A4a3te7/atomize.split.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/zPov9rP7t1/atomize.split.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/wj8A4a3te7/atomize.split.2.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/zPov9rP7t1/atomize.split.2.vcf.gz .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/wj8A4a3te7/atomize.split.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/zPov9rP7t1/atomize.split.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . /tmp/wj8A4a3te7/atomize.split.3.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . /tmp/zPov9rP7t1/atomize.split.3.vcf.gz .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . /tmp/wj8A4a3te7/atomize.split.3.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . /tmp/zPov9rP7t1/atomize.split.3.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/wj8A4a3te7/atomize.split.4.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/zPov9rP7t1/atomize.split.4.vcf.gz .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/wj8A4a3te7/atomize.split.4.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/zPov9rP7t1/atomize.split.4.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC -i 'ILEN=0' /tmp/wj8A4a3te7/atomize.split.4.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC -i 'ILEN=0' /tmp/zPov9rP7t1/atomize.split.4.vcf.gz .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC -i 'ILEN=0' /tmp/wj8A4a3te7/atomize.split.4.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC -i 'ILEN=0' /tmp/zPov9rP7t1/atomize.split.4.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --old-rec-tag OLD_REC --atom-overlaps . /tmp/wj8A4a3te7/atomize.split.5.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --old-rec-tag OLD_REC --atom-overlaps . /tmp/zPov9rP7t1/atomize.split.5.vcf.gz .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --old-rec-tag OLD_REC --atom-overlaps . /tmp/wj8A4a3te7/atomize.split.5.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --old-rec-tag OLD_REC --atom-overlaps . /tmp/zPov9rP7t1/atomize.split.5.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/wj8A4a3te7/atomize.split.5.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/zPov9rP7t1/atomize.split.5.vcf.gz .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/wj8A4a3te7/atomize.split.5.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/zPov9rP7t1/atomize.split.5.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +both /tmp/wj8A4a3te7/norm.4.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +both /tmp/zPov9rP7t1/norm.4.vcf.gz .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +both /tmp/wj8A4a3te7/norm.4.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +both /tmp/zPov9rP7t1/norm.4.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +any /tmp/wj8A4a3te7/norm.4.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +any /tmp/zPov9rP7t1/norm.4.vcf.gz .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +any /tmp/wj8A4a3te7/norm.4.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +any /tmp/zPov9rP7t1/norm.4.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - --multi-overlaps 0 /tmp/wj8A4a3te7/norm.5.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - --multi-overlaps 0 /tmp/zPov9rP7t1/norm.5.vcf.gz .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - --multi-overlaps 0 /tmp/wj8A4a3te7/norm.5.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - --multi-overlaps 0 /tmp/zPov9rP7t1/norm.5.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - --multi-overlaps . /tmp/wj8A4a3te7/norm.5.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - --multi-overlaps . /tmp/zPov9rP7t1/norm.5.vcf.gz .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - --multi-overlaps . /tmp/wj8A4a3te7/norm.5.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - --multi-overlaps . /tmp/zPov9rP7t1/norm.5.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any /tmp/wj8A4a3te7/norm.m-any.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any /tmp/zPov9rP7t1/norm.m-any.vcf.gz .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any /tmp/wj8A4a3te7/norm.m-any.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any /tmp/zPov9rP7t1/norm.m-any.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any /tmp/wj8A4a3te7/norm.phased-split.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any /tmp/zPov9rP7t1/norm.phased-split.vcf.gz .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any /tmp/wj8A4a3te7/norm.phased-split.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any /tmp/zPov9rP7t1/norm.phased-split.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +any /tmp/wj8A4a3te7/norm.phased-join.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +any /tmp/zPov9rP7t1/norm.phased-join.vcf.gz .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +any /tmp/wj8A4a3te7/norm.phased-join.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +any /tmp/zPov9rP7t1/norm.phased-join.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI /tmp/wj8A4a3te7/norm.symbolic.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.symbolic.fa + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI /tmp/zPov9rP7t1/norm.symbolic.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.symbolic.fa .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI /tmp/wj8A4a3te7/norm.symbolic.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.symbolic.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI /tmp/zPov9rP7t1/norm.symbolic.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.symbolic.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI /tmp/wj8A4a3te7/norm.symbolic.2.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.symbolic.fa + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI /tmp/zPov9rP7t1/norm.symbolic.2.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.symbolic.fa .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI /tmp/wj8A4a3te7/norm.symbolic.2.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.symbolic.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI /tmp/zPov9rP7t1/norm.symbolic.2.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.symbolic.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI /tmp/wj8A4a3te7/norm.right-align.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.right-align.fa + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI /tmp/zPov9rP7t1/norm.right-align.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.right-align.fa .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI /tmp/wj8A4a3te7/norm.right-align.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.right-align.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI /tmp/zPov9rP7t1/norm.right-align.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.right-align.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI -g /build/reproducible-path/bcftools-1.21/test/norm.right-align.gff /tmp/wj8A4a3te7/norm.right-align.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.right-align.fa + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI -g /build/reproducible-path/bcftools-1.21/test/norm.right-align.gff /tmp/zPov9rP7t1/norm.right-align.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.right-align.fa .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI -g /build/reproducible-path/bcftools-1.21/test/norm.right-align.gff /tmp/wj8A4a3te7/norm.right-align.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.right-align.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI -g /build/reproducible-path/bcftools-1.21/test/norm.right-align.gff /tmp/zPov9rP7t1/norm.right-align.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.right-align.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI -a -m -any /tmp/wj8A4a3te7/norm.atom-split-norm.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.atom-split-norm.fa + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI -a -m -any /tmp/zPov9rP7t1/norm.atom-split-norm.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.atom-split-norm.fa .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI -a -m -any /tmp/wj8A4a3te7/norm.atom-split-norm.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.atom-split-norm.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI -a -m -any /tmp/zPov9rP7t1/norm.atom-split-norm.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.atom-split-norm.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any /tmp/wj8A4a3te7/norm.string-tags.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any /tmp/zPov9rP7t1/norm.string-tags.vcf.gz .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any /tmp/wj8A4a3te7/norm.string-tags.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any /tmp/zPov9rP7t1/norm.string-tags.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/wj8A4a3te7/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +both + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/zPov9rP7t1/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +both .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/wj8A4a3te7/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +both -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/zPov9rP7t1/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +both -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/wj8A4a3te7/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +indels + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/zPov9rP7t1/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +indels .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/wj8A4a3te7/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +indels -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/zPov9rP7t1/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +indels -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/wj8A4a3te7/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +snps + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/zPov9rP7t1/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +snps .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/wj8A4a3te7/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +snps -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/zPov9rP7t1/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +snps -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/wj8A4a3te7/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +snps + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/zPov9rP7t1/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +snps .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/wj8A4a3te7/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +snps -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/zPov9rP7t1/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +snps -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/wj8A4a3te7/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +any + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/zPov9rP7t1/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +any .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/wj8A4a3te7/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +any -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/zPov9rP7t1/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +any -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - -i 'type="snp"' /tmp/wj8A4a3te7/norm.split.merge.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - -i 'type="snp"' /tmp/zPov9rP7t1/norm.split.merge.vcf.gz .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - -i 'type="snp"' /tmp/wj8A4a3te7/norm.split.merge.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - -i 'type="snp"' /tmp/zPov9rP7t1/norm.split.merge.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +any /tmp/wj8A4a3te7/norm.merge.4.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +any /tmp/zPov9rP7t1/norm.merge.4.vcf.gz .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +any /tmp/wj8A4a3te7/norm.merge.4.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +any /tmp/zPov9rP7t1/norm.merge.4.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +both /tmp/wj8A4a3te7/norm.merge.4.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +both /tmp/zPov9rP7t1/norm.merge.4.vcf.gz .. ok test_vcf_norm: - /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +both /tmp/wj8A4a3te7/norm.merge.4.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +both /tmp/zPov9rP7t1/norm.merge.4.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version -i 'INFO/TAG=@/build/reproducible-path/bcftools-1.21/test/filter.string.1.txt' /tmp/wj8A4a3te7/filter.string.1.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools view --no-version -i 'INFO/TAG=@/build/reproducible-path/bcftools-1.21/test/filter.string.1.txt' /tmp/zPov9rP7t1/filter.string.1.vcf.gz .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob -i 'INFO/TAG=@/build/reproducible-path/bcftools-1.21/test/filter.string.1.txt' /tmp/wj8A4a3te7/filter.string.1.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools view -Ob -i 'INFO/TAG=@/build/reproducible-path/bcftools-1.21/test/filter.string.1.txt' /tmp/zPov9rP7t1/filter.string.1.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version -i 'FMT/TAG=@/build/reproducible-path/bcftools-1.21/test/filter.string.1.txt' /tmp/wj8A4a3te7/filter.string.1.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools view --no-version -i 'FMT/TAG=@/build/reproducible-path/bcftools-1.21/test/filter.string.1.txt' /tmp/zPov9rP7t1/filter.string.1.vcf.gz .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob -i 'FMT/TAG=@/build/reproducible-path/bcftools-1.21/test/filter.string.1.txt' /tmp/wj8A4a3te7/filter.string.1.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools view -Ob -i 'FMT/TAG=@/build/reproducible-path/bcftools-1.21/test/filter.string.1.txt' /tmp/zPov9rP7t1/filter.string.1.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version -HA /tmp/wj8A4a3te7/merge.gvcf.2.a.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools view --no-version -HA /tmp/zPov9rP7t1/merge.gvcf.2.a.vcf.gz .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version -HAA /tmp/wj8A4a3te7/merge.gvcf.2.a.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools view --no-version -HAA /tmp/zPov9rP7t1/merge.gvcf.2.a.vcf.gz .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r 1 + /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/zPov9rP7t1/weird-chr-names.vcf.gz -r 1 .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r 1 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/weird-chr-names.vcf.gz -r 1 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r 1:1-2 + /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/zPov9rP7t1/weird-chr-names.vcf.gz -r 1:1-2 .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r 1:1-2 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/weird-chr-names.vcf.gz -r 1:1-2 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r 1:1,1:2 + /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/zPov9rP7t1/weird-chr-names.vcf.gz -r 1:1,1:2 .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r 1:1,1:2 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/weird-chr-names.vcf.gz -r 1:1,1:2 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r 1:1-1 + /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/zPov9rP7t1/weird-chr-names.vcf.gz -r 1:1-1 .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r 1:1-1 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/weird-chr-names.vcf.gz -r 1:1-1 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r {1:1} + /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/zPov9rP7t1/weird-chr-names.vcf.gz -r {1:1} .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r {1:1} | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/weird-chr-names.vcf.gz -r {1:1} | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r {1:1}:1-2 + /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/zPov9rP7t1/weird-chr-names.vcf.gz -r {1:1}:1-2 .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r {1:1}:1-2 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/weird-chr-names.vcf.gz -r {1:1}:1-2 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r {1:1}:1,{1:1}:2 + /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/zPov9rP7t1/weird-chr-names.vcf.gz -r {1:1}:1,{1:1}:2 .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r {1:1}:1,{1:1}:2 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/weird-chr-names.vcf.gz -r {1:1}:1,{1:1}:2 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r {1:1}:1-1 + /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/zPov9rP7t1/weird-chr-names.vcf.gz -r {1:1}:1-1 .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r {1:1}:1-1 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/weird-chr-names.vcf.gz -r {1:1}:1-1 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r {1:1-1} + /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/zPov9rP7t1/weird-chr-names.vcf.gz -r {1:1-1} .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r {1:1-1} | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/weird-chr-names.vcf.gz -r {1:1-1} | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r {1:1-1}:1-2 + /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/zPov9rP7t1/weird-chr-names.vcf.gz -r {1:1-1}:1-2 .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r {1:1-1}:1-2 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/weird-chr-names.vcf.gz -r {1:1-1}:1-2 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r {1:1-1}:1,{1:1-1}:2 + /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/zPov9rP7t1/weird-chr-names.vcf.gz -r {1:1-1}:1,{1:1-1}:2 .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r {1:1-1}:1,{1:1-1}:2 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/weird-chr-names.vcf.gz -r {1:1-1}:1,{1:1-1}:2 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r {1:1-1}:1-1 + /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/zPov9rP7t1/weird-chr-names.vcf.gz -r {1:1-1}:1-1 .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r {1:1-1}:1-1 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/weird-chr-names.vcf.gz -r {1:1-1}:1-1 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r {1:1-1}-2 + /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/zPov9rP7t1/weird-chr-names.vcf.gz -r {1:1-1}-2 .. ok, expected non-zero status test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/weird-chr-names.vcf.gz -r {1:1-1}-2 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/weird-chr-names.vcf.gz -r {1:1-1}-2 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok, expected non-zero status test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version -aUc1 -C1 -s NA00002 -v snps /tmp/wj8A4a3te7/view.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools view --no-version -aUc1 -C1 -s NA00002 -v snps /tmp/zPov9rP7t1/view.vcf.gz .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/wj8A4a3te7/view.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/zPov9rP7t1/view.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version -f PASS -Xks NA00003 /tmp/wj8A4a3te7/view.vcf.gz -r20,Y + /build/reproducible-path/bcftools-1.21/bcftools view --no-version -f PASS -Xks NA00003 /tmp/zPov9rP7t1/view.vcf.gz -r20,Y .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob -f PASS -Xks NA00003 /tmp/wj8A4a3te7/view.vcf.gz -r20,Y | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools view -Ob -f PASS -Xks NA00003 /tmp/zPov9rP7t1/view.vcf.gz -r20,Y | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version -xs NA00003 /tmp/wj8A4a3te7/view.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools view --no-version -xs NA00003 /tmp/zPov9rP7t1/view.vcf.gz .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob -xs NA00003 /tmp/wj8A4a3te7/view.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools view -Ob -xs NA00003 /tmp/zPov9rP7t1/view.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/wj8A4a3te7/view.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools view --no-version -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/zPov9rP7t1/view.vcf.gz .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/wj8A4a3te7/view.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools view -Ob -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/zPov9rP7t1/view.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version -p /tmp/wj8A4a3te7/view.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools view --no-version -p /tmp/zPov9rP7t1/view.vcf.gz .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob -p /tmp/wj8A4a3te7/view.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools view -Ob -p /tmp/zPov9rP7t1/view.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version -P /tmp/wj8A4a3te7/view.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools view --no-version -P /tmp/zPov9rP7t1/view.vcf.gz .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob -P /tmp/wj8A4a3te7/view.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools view -Ob -P /tmp/zPov9rP7t1/view.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version -hm2 -M2 -q0.3 -Q0.7 /tmp/wj8A4a3te7/view.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools view --no-version -hm2 -M2 -q0.3 -Q0.7 /tmp/zPov9rP7t1/view.vcf.gz .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/wj8A4a3te7/view.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/zPov9rP7t1/view.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version -Hu /tmp/wj8A4a3te7/view.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools view --no-version -Hu /tmp/zPov9rP7t1/view.vcf.gz .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version -GVsnps /tmp/wj8A4a3te7/view.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools view --no-version -GVsnps /tmp/zPov9rP7t1/view.vcf.gz .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob -GVsnps /tmp/wj8A4a3te7/view.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools view -Ob -GVsnps /tmp/zPov9rP7t1/view.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version -ne 'INDEL=1 || PV4[0]<0.006' /tmp/wj8A4a3te7/view.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools view --no-version -ne 'INDEL=1 || PV4[0]<0.006' /tmp/zPov9rP7t1/view.vcf.gz .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/wj8A4a3te7/view.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/zPov9rP7t1/view.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version -s ^NA00003 /tmp/wj8A4a3te7/view.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools view --no-version -s ^NA00003 /tmp/zPov9rP7t1/view.vcf.gz .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob -s ^NA00003 /tmp/wj8A4a3te7/view.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools view -Ob -s ^NA00003 /tmp/zPov9rP7t1/view.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/wj8A4a3te7/view.omitgenotypes.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/zPov9rP7t1/view.omitgenotypes.vcf.gz .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/view.omitgenotypes.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/view.omitgenotypes.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version -G /tmp/wj8A4a3te7/view.omitgenotypes.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools view --no-version -G /tmp/zPov9rP7t1/view.omitgenotypes.vcf.gz .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob -G /tmp/wj8A4a3te7/view.omitgenotypes.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools view -Ob -G /tmp/zPov9rP7t1/view.omitgenotypes.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version -HG /tmp/wj8A4a3te7/view.omitgenotypes.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools view --no-version -HG /tmp/zPov9rP7t1/view.omitgenotypes.vcf.gz .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version -a /tmp/wj8A4a3te7/many.alleles.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools view --no-version -a /tmp/zPov9rP7t1/many.alleles.vcf.gz .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob -a /tmp/wj8A4a3te7/many.alleles.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools view -Ob -a /tmp/zPov9rP7t1/many.alleles.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version -asA /tmp/wj8A4a3te7/view.vectors.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools view --no-version -asA /tmp/zPov9rP7t1/view.vectors.vcf.gz .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob -asA /tmp/wj8A4a3te7/view.vectors.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools view -Ob -asA /tmp/zPov9rP7t1/view.vectors.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version -asB /tmp/wj8A4a3te7/view.vectors.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools view --no-version -asB /tmp/zPov9rP7t1/view.vectors.vcf.gz .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob -asB /tmp/wj8A4a3te7/view.vectors.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools view -Ob -asB /tmp/zPov9rP7t1/view.vectors.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version -asA /tmp/wj8A4a3te7/view.vectors.2.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools view --no-version -asA /tmp/zPov9rP7t1/view.vectors.2.vcf.gz .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob -asA /tmp/wj8A4a3te7/view.vectors.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools view -Ob -asA /tmp/zPov9rP7t1/view.vectors.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -i'FMT/FGS[*:0]="AAAAAA"' /tmp/wj8A4a3te7/view.filter.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -i'FMT/FGS[*:0]="AAAAAA"' /tmp/zPov9rP7t1/view.filter.vcf.gz .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -i'FMT/FGS[*:2]="C"' /tmp/wj8A4a3te7/view.filter.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -i'FMT/FGS[*:2]="C"' /tmp/zPov9rP7t1/view.filter.vcf.gz .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -i'FMT/FGS[*:4]="EE"' /tmp/wj8A4a3te7/view.filter.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -i'FMT/FGS[*:4]="EE"' /tmp/zPov9rP7t1/view.filter.vcf.gz .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -i'FMT/FRS[*:1]="BB"' /tmp/wj8A4a3te7/view.filter.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -i'FMT/FRS[*:1]="BB"' /tmp/zPov9rP7t1/view.filter.vcf.gz .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -i'TXT0="text"' /tmp/wj8A4a3te7/view.filter.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -i'TXT0="text"' /tmp/zPov9rP7t1/view.filter.vcf.gz .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version -T /build/reproducible-path/bcftools-1.21/test/view.chrs.tab /tmp/wj8A4a3te7/view.chrs.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools view --no-version -T /build/reproducible-path/bcftools-1.21/test/view.chrs.tab /tmp/zPov9rP7t1/view.chrs.vcf.gz .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob -T /build/reproducible-path/bcftools-1.21/test/view.chrs.tab /tmp/wj8A4a3te7/view.chrs.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools view -Ob -T /build/reproducible-path/bcftools-1.21/test/view.chrs.tab /tmp/zPov9rP7t1/view.chrs.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version -i 'POS>=3062917' /tmp/wj8A4a3te7/filter.2.vcf.gz 1:3062917-3157410 + /build/reproducible-path/bcftools-1.21/bcftools view --no-version -i 'POS>=3062917' /tmp/zPov9rP7t1/filter.2.vcf.gz 1:3062917-3157410 .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob -i 'POS>=3062917' /tmp/wj8A4a3te7/filter.2.vcf.gz 1:3062917-3157410 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools view -Ob -i 'POS>=3062917' /tmp/zPov9rP7t1/filter.2.vcf.gz 1:3062917-3157410 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -r 1:10,1:12,1:10 /tmp/wj8A4a3te7/idx.1.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -r 1:10,1:12,1:10 /tmp/zPov9rP7t1/idx.1.vcf.gz .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -r 1:1172777-1172804,1:1172806-1172808 /tmp/wj8A4a3te7/idx.2.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -r 1:1172777-1172804,1:1172806-1172808 /tmp/zPov9rP7t1/idx.2.vcf.gz .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -R /build/reproducible-path/bcftools-1.21/test/idx.2.bed /tmp/wj8A4a3te7/idx.2.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -R /build/reproducible-path/bcftools-1.21/test/idx.2.bed /tmp/zPov9rP7t1/idx.2.vcf.gz .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -R /build/reproducible-path/bcftools-1.21/test/idx.3.bed /tmp/wj8A4a3te7/idx.3.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -R /build/reproducible-path/bcftools-1.21/test/idx.3.bed /tmp/zPov9rP7t1/idx.3.vcf.gz .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -R /build/reproducible-path/bcftools-1.21/test/idx.4.bed /tmp/wj8A4a3te7/idx.4.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -R /build/reproducible-path/bcftools-1.21/test/idx.4.bed /tmp/zPov9rP7t1/idx.4.vcf.gz .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version -Ht 2 /tmp/wj8A4a3te7/view-t.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools view --no-version -Ht 2 /tmp/zPov9rP7t1/view-t.vcf.gz .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version -Ht 3 /tmp/wj8A4a3te7/view-t.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools view --no-version -Ht 3 /tmp/zPov9rP7t1/view-t.vcf.gz .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 0 /tmp/wj8A4a3te7/overlap.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 0 /tmp/zPov9rP7t1/overlap.vcf.gz .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 1 /tmp/wj8A4a3te7/overlap.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 1 /tmp/zPov9rP7t1/overlap.vcf.gz .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 2 /tmp/wj8A4a3te7/overlap.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 2 /tmp/zPov9rP7t1/overlap.vcf.gz .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 0 /tmp/wj8A4a3te7/overlap.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 0 /tmp/zPov9rP7t1/overlap.vcf.gz .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 1 /tmp/wj8A4a3te7/overlap.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 1 /tmp/zPov9rP7t1/overlap.vcf.gz .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 2 /tmp/wj8A4a3te7/overlap.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 2 /tmp/zPov9rP7t1/overlap.vcf.gz .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 0 /tmp/wj8A4a3te7/overlap.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 0 /tmp/zPov9rP7t1/overlap.vcf.gz .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 1 /tmp/wj8A4a3te7/overlap.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 1 /tmp/zPov9rP7t1/overlap.vcf.gz .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 2 /tmp/wj8A4a3te7/overlap.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 2 /tmp/zPov9rP7t1/overlap.vcf.gz .. ok test_vcf_64bit: @@ -4095,47 +4131,47 @@ .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -C5:nonmajor /tmp/wj8A4a3te7/view.minmaxac.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -C5:nonmajor /tmp/zPov9rP7t1/view.minmaxac.vcf.gz .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -c6:nonmajor /tmp/wj8A4a3te7/view.minmaxac.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -c6:nonmajor /tmp/zPov9rP7t1/view.minmaxac.vcf.gz .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -q0.3:major /tmp/wj8A4a3te7/view.minmaxac.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -q0.3:major /tmp/zPov9rP7t1/view.minmaxac.vcf.gz .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/wj8A4a3te7/view.filter.annovar.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/zPov9rP7t1/view.filter.annovar.vcf.gz .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -i 'Gene.refGene~"NOD"' /tmp/wj8A4a3te7/view.filter.annovar.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -i 'Gene.refGene~"NOD"' /tmp/zPov9rP7t1/view.filter.annovar.vcf.gz .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -i 'LJB2_MutationTaster=="0.291000"' /tmp/wj8A4a3te7/view.filter.annovar.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -i 'LJB2_MutationTaster=="0.291000"' /tmp/zPov9rP7t1/view.filter.annovar.vcf.gz .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -a /tmp/wj8A4a3te7/view-a.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -a /tmp/zPov9rP7t1/view-a.vcf.gz .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version -T /build/reproducible-path/bcftools-1.21/test/view.sites.txt /tmp/wj8A4a3te7/view.sites.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools view --no-version -T /build/reproducible-path/bcftools-1.21/test/view.sites.txt /tmp/zPov9rP7t1/view.sites.vcf.gz .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob -T /build/reproducible-path/bcftools-1.21/test/view.sites.txt /tmp/wj8A4a3te7/view.sites.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools view -Ob -T /build/reproducible-path/bcftools-1.21/test/view.sites.txt /tmp/zPov9rP7t1/view.sites.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version -T /build/reproducible-path/bcftools-1.21/test/view.sites.txt.gz /tmp/wj8A4a3te7/view.sites.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools view --no-version -T /build/reproducible-path/bcftools-1.21/test/view.sites.txt.gz /tmp/zPov9rP7t1/view.sites.vcf.gz .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob -T /build/reproducible-path/bcftools-1.21/test/view.sites.txt.gz /tmp/wj8A4a3te7/view.sites.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools view -Ob -T /build/reproducible-path/bcftools-1.21/test/view.sites.txt.gz /tmp/zPov9rP7t1/view.sites.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_head: @@ -4179,27 +4215,27 @@ .. ok test_vcf_head2: - /build/reproducible-path/bcftools-1.21/bcftools head -s0 /tmp/wj8A4a3te7/mpileup.2.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools head -s0 /tmp/zPov9rP7t1/mpileup.2.vcf.gz .. ok test_vcf_head2: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version -Ob /tmp/wj8A4a3te7/mpileup.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools head -s0 + /build/reproducible-path/bcftools-1.21/bcftools view --no-version -Ob /tmp/zPov9rP7t1/mpileup.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools head -s0 .. ok test_vcf_head2: - /build/reproducible-path/bcftools-1.21/bcftools head -s1 /tmp/wj8A4a3te7/mpileup.2.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools head -s1 /tmp/zPov9rP7t1/mpileup.2.vcf.gz .. ok test_vcf_head2: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version -Ob /tmp/wj8A4a3te7/mpileup.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools head -s1 + /build/reproducible-path/bcftools-1.21/bcftools view --no-version -Ob /tmp/zPov9rP7t1/mpileup.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools head -s1 .. ok test_vcf_head2: - /build/reproducible-path/bcftools-1.21/bcftools head -s2 -h2 /tmp/wj8A4a3te7/mpileup.2.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools head -s2 -h2 /tmp/zPov9rP7t1/mpileup.2.vcf.gz .. ok test_vcf_head2: - /build/reproducible-path/bcftools-1.21/bcftools view --no-version -Ob /tmp/wj8A4a3te7/mpileup.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools head -s2 -h2 + /build/reproducible-path/bcftools-1.21/bcftools view --no-version -Ob /tmp/zPov9rP7t1/mpileup.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools head -s2 -h2 .. ok test_vcf_call: @@ -4307,75 +4343,75 @@ .. ok test_vcf_call_cAls: - /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/wj8A4a3te7/mpileup.tab.gz /build/reproducible-path/bcftools-1.21/test/mpileup.vcf + /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/zPov9rP7t1/mpileup.tab.gz /build/reproducible-path/bcftools-1.21/test/mpileup.vcf .. ok test_vcf_call_cAls: - /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/wj8A4a3te7/mpileup.tab.gz /build/reproducible-path/bcftools-1.21/test/mpileup.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/zPov9rP7t1/mpileup.tab.gz /build/reproducible-path/bcftools-1.21/test/mpileup.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: - /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/wj8A4a3te7/mpileup.2.tab.gz /build/reproducible-path/bcftools-1.21/test/mpileup.2.vcf + /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/zPov9rP7t1/mpileup.2.tab.gz /build/reproducible-path/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_call_cAls: - /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/wj8A4a3te7/mpileup.2.tab.gz /build/reproducible-path/bcftools-1.21/test/mpileup.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/zPov9rP7t1/mpileup.2.tab.gz /build/reproducible-path/bcftools-1.21/test/mpileup.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: - /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/wj8A4a3te7/mpileup.3.tab.gz -i /build/reproducible-path/bcftools-1.21/test/mpileup.3.vcf + /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/zPov9rP7t1/mpileup.3.tab.gz -i /build/reproducible-path/bcftools-1.21/test/mpileup.3.vcf .. ok test_vcf_call_cAls: - /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/wj8A4a3te7/mpileup.3.tab.gz -i /build/reproducible-path/bcftools-1.21/test/mpileup.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/zPov9rP7t1/mpileup.3.tab.gz -i /build/reproducible-path/bcftools-1.21/test/mpileup.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: - /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/wj8A4a3te7/mpileup.4.tab.gz -i /build/reproducible-path/bcftools-1.21/test/mpileup.3.vcf + /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/zPov9rP7t1/mpileup.4.tab.gz -i /build/reproducible-path/bcftools-1.21/test/mpileup.3.vcf .. ok test_vcf_call_cAls: - /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/wj8A4a3te7/mpileup.4.tab.gz -i /build/reproducible-path/bcftools-1.21/test/mpileup.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/zPov9rP7t1/mpileup.4.tab.gz -i /build/reproducible-path/bcftools-1.21/test/mpileup.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: - /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/wj8A4a3te7/mpileup.5.tab.gz -i /build/reproducible-path/bcftools-1.21/test/mpileup.3.vcf + /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/zPov9rP7t1/mpileup.5.tab.gz -i /build/reproducible-path/bcftools-1.21/test/mpileup.3.vcf .. ok test_vcf_call_cAls: - /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/wj8A4a3te7/mpileup.5.tab.gz -i /build/reproducible-path/bcftools-1.21/test/mpileup.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/zPov9rP7t1/mpileup.5.tab.gz -i /build/reproducible-path/bcftools-1.21/test/mpileup.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: - /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/wj8A4a3te7/mpileup.6.tab.gz -i /build/reproducible-path/bcftools-1.21/test/mpileup.4.vcf + /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/zPov9rP7t1/mpileup.6.tab.gz -i /build/reproducible-path/bcftools-1.21/test/mpileup.4.vcf .. ok test_vcf_call_cAls: - /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/wj8A4a3te7/mpileup.6.tab.gz -i /build/reproducible-path/bcftools-1.21/test/mpileup.4.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/zPov9rP7t1/mpileup.6.tab.gz -i /build/reproducible-path/bcftools-1.21/test/mpileup.4.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: - /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/wj8A4a3te7/mpileup.7.tab.gz -i /build/reproducible-path/bcftools-1.21/test/mpileup.5.vcf + /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/zPov9rP7t1/mpileup.7.tab.gz -i /build/reproducible-path/bcftools-1.21/test/mpileup.5.vcf .. ok test_vcf_call_cAls: - /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/wj8A4a3te7/mpileup.7.tab.gz -i /build/reproducible-path/bcftools-1.21/test/mpileup.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/zPov9rP7t1/mpileup.7.tab.gz -i /build/reproducible-path/bcftools-1.21/test/mpileup.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: - /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/wj8A4a3te7/mpileup.cals.1.tab.gz /build/reproducible-path/bcftools-1.21/test/mpileup.cals.1.vcf + /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/zPov9rP7t1/mpileup.cals.1.tab.gz /build/reproducible-path/bcftools-1.21/test/mpileup.cals.1.vcf .. ok test_vcf_call_cAls: - /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/wj8A4a3te7/mpileup.cals.1.tab.gz /build/reproducible-path/bcftools-1.21/test/mpileup.cals.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/zPov9rP7t1/mpileup.cals.1.tab.gz /build/reproducible-path/bcftools-1.21/test/mpileup.cals.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: - /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/wj8A4a3te7/mpileup.cals.2.tab.gz /build/reproducible-path/bcftools-1.21/test/mpileup.cals.2.vcf + /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/zPov9rP7t1/mpileup.cals.2.tab.gz /build/reproducible-path/bcftools-1.21/test/mpileup.cals.2.vcf .. ok test_vcf_call_cAls: - /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/wj8A4a3te7/mpileup.cals.2.tab.gz /build/reproducible-path/bcftools-1.21/test/mpileup.cals.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/zPov9rP7t1/mpileup.cals.2.tab.gz /build/reproducible-path/bcftools-1.21/test/mpileup.cals.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: @@ -5091,155 +5127,155 @@ .. ok test_vcf_regions: - /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /build/reproducible-path/bcftools-1.21/test/regions.tab /tmp/wj8A4a3te7/regions.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /build/reproducible-path/bcftools-1.21/test/regions.tab /tmp/zPov9rP7t1/regions.vcf.gz .. ok test_vcf_regions: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/regions.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /build/reproducible-path/bcftools-1.21/test/regions.tab + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/regions.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /build/reproducible-path/bcftools-1.21/test/regions.tab .. ok test_vcf_regions: - /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /build/reproducible-path/bcftools-1.21/test/regions.tab /tmp/wj8A4a3te7/regions.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /build/reproducible-path/bcftools-1.21/test/regions.tab /tmp/zPov9rP7t1/regions.vcf.gz .. ok test_vcf_regions: - /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/wj8A4a3te7/regions.tab.gz /tmp/wj8A4a3te7/regions.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/zPov9rP7t1/regions.tab.gz /tmp/zPov9rP7t1/regions.vcf.gz .. ok test_vcf_regions: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/regions.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/wj8A4a3te7/regions.tab.gz + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/regions.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/zPov9rP7t1/regions.tab.gz .. ok test_vcf_regions: - /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/wj8A4a3te7/regions.tab.gz /tmp/wj8A4a3te7/regions.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/zPov9rP7t1/regions.tab.gz /tmp/zPov9rP7t1/regions.vcf.gz .. ok test_vcf_regions: - /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/wj8A4a3te7/regions.bed /tmp/wj8A4a3te7/regions.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/zPov9rP7t1/regions.bed /tmp/zPov9rP7t1/regions.vcf.gz .. ok test_vcf_regions: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/regions.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/wj8A4a3te7/regions.bed + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/regions.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/zPov9rP7t1/regions.bed .. ok test_vcf_regions: - /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/wj8A4a3te7/regions.bed /tmp/wj8A4a3te7/regions.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/zPov9rP7t1/regions.bed /tmp/zPov9rP7t1/regions.vcf.gz .. ok test_vcf_regions: - /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/wj8A4a3te7/regions.bed.gz /tmp/wj8A4a3te7/regions.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/zPov9rP7t1/regions.bed.gz /tmp/zPov9rP7t1/regions.vcf.gz .. ok test_vcf_regions: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/regions.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/wj8A4a3te7/regions.bed.gz + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/regions.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/zPov9rP7t1/regions.bed.gz .. ok test_vcf_regions: - /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/wj8A4a3te7/regions.bed.gz /tmp/wj8A4a3te7/regions.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/zPov9rP7t1/regions.bed.gz /tmp/zPov9rP7t1/regions.vcf.gz .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate.escape.1.tab.gz -c CHROM,POS,ISTR,FMT/FSTR /build/reproducible-path/bcftools-1.21/test/annotate.escape.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate.escape.1.tab.gz -c CHROM,POS,ISTR,FMT/FSTR /build/reproducible-path/bcftools-1.21/test/annotate.escape.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate.escape.1.tab.gz -c CHROM,POS,ISTR,FMT/FSTR /build/reproducible-path/bcftools-1.21/test/annotate.escape.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate.escape.1.tab.gz -c CHROM,POS,ISTR,FMT/FSTR /build/reproducible-path/bcftools-1.21/test/annotate.escape.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate.match.1.tab.gz -c CHROM,POS,-,-,SCORE,~X,-,- -i'STR={X}' /build/reproducible-path/bcftools-1.21/test/annotate.match.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate.match.1.tab.gz -c CHROM,POS,-,-,SCORE,~X,-,- -i'STR={X}' /build/reproducible-path/bcftools-1.21/test/annotate.match.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate.match.1.tab.gz -c CHROM,POS,-,-,SCORE,~X,-,- -i'STR={X}' /build/reproducible-path/bcftools-1.21/test/annotate.match.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate.match.1.tab.gz -c CHROM,POS,-,-,SCORE,~X,-,- -i'STR={X}' /build/reproducible-path/bcftools-1.21/test/annotate.match.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate.match.1.tab.gz -c CHROM,POS,REF,ALT,SCORE,-,~X,- -i'INT={X}' /build/reproducible-path/bcftools-1.21/test/annotate.match.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate.match.1.tab.gz -c CHROM,POS,REF,ALT,SCORE,-,~X,- -i'INT={X}' /build/reproducible-path/bcftools-1.21/test/annotate.match.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate.match.1.tab.gz -c CHROM,POS,REF,ALT,SCORE,-,~X,- -i'INT={X}' /build/reproducible-path/bcftools-1.21/test/annotate.match.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate.match.1.tab.gz -c CHROM,POS,REF,ALT,SCORE,-,~X,- -i'INT={X}' /build/reproducible-path/bcftools-1.21/test/annotate.match.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate.match.1.tab.gz -c CHROM,POS,REF,ALT,SCORE,-,-,~X -i'FLT={X}' /build/reproducible-path/bcftools-1.21/test/annotate.match.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate.match.1.tab.gz -c CHROM,POS,REF,ALT,SCORE,-,-,~X -i'FLT={X}' /build/reproducible-path/bcftools-1.21/test/annotate.match.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate.match.1.tab.gz -c CHROM,POS,REF,ALT,SCORE,-,-,~X -i'FLT={X}' /build/reproducible-path/bcftools-1.21/test/annotate.match.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate.match.1.tab.gz -c CHROM,POS,REF,ALT,SCORE,-,-,~X -i'FLT={X}' /build/reproducible-path/bcftools-1.21/test/annotate.match.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /build/reproducible-path/bcftools-1.21/test/annotate.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /build/reproducible-path/bcftools-1.21/test/annotate.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /build/reproducible-path/bcftools-1.21/test/annotate.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /build/reproducible-path/bcftools-1.21/test/annotate.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate2.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate.hdr -c CHROM,POS,-,T_STR /build/reproducible-path/bcftools-1.21/test/annotate.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate2.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate.hdr -c CHROM,POS,-,T_STR /build/reproducible-path/bcftools-1.21/test/annotate.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate2.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate.hdr -c CHROM,POS,-,T_STR /build/reproducible-path/bcftools-1.21/test/annotate.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate2.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate.hdr -c CHROM,POS,-,T_STR /build/reproducible-path/bcftools-1.21/test/annotate.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate2.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate.hdr -c CHROM,FROM,TO,T_STR /build/reproducible-path/bcftools-1.21/test/annotate.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate2.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate.hdr -c CHROM,FROM,TO,T_STR /build/reproducible-path/bcftools-1.21/test/annotate.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate2.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate.hdr -c CHROM,FROM,TO,T_STR /build/reproducible-path/bcftools-1.21/test/annotate.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate2.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate.hdr -c CHROM,FROM,TO,T_STR /build/reproducible-path/bcftools-1.21/test/annotate.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/wj8A4a3te7/annotate.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/zPov9rP7t1/annotate.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/wj8A4a3te7/annotate.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/zPov9rP7t1/annotate.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/zPov9rP7t1/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/zPov9rP7t1/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/zPov9rP7t1/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/zPov9rP7t1/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/zPov9rP7t1/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/zPov9rP7t1/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/zPov9rP7t1/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/zPov9rP7t1/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/zPov9rP7t1/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/zPov9rP7t1/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: @@ -5259,115 +5295,115 @@ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots4.vcf.gz -c +INFO /tmp/wj8A4a3te7/annotate4.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots4.vcf.gz -c +INFO /tmp/zPov9rP7t1/annotate4.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots4.vcf.gz -c +INFO /tmp/wj8A4a3te7/annotate4.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots4.vcf.gz -c +INFO /tmp/zPov9rP7t1/annotate4.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots4.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /build/reproducible-path/bcftools-1.21/test/annotate4.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots4.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /build/reproducible-path/bcftools-1.21/test/annotate4.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots4.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /build/reproducible-path/bcftools-1.21/test/annotate4.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots4.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /build/reproducible-path/bcftools-1.21/test/annotate4.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots10.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /build/reproducible-path/bcftools-1.21/test/annotate10.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots10.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /build/reproducible-path/bcftools-1.21/test/annotate10.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots10.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /build/reproducible-path/bcftools-1.21/test/annotate10.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots10.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /build/reproducible-path/bcftools-1.21/test/annotate10.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/zPov9rP7t1/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/zPov9rP7t1/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /build/reproducible-path/bcftools-1.21/test/annotate2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /build/reproducible-path/bcftools-1.21/test/annotate2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /build/reproducible-path/bcftools-1.21/test/annotate2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /build/reproducible-path/bcftools-1.21/test/annotate2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/zPov9rP7t1/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/zPov9rP7t1/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/zPov9rP7t1/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/zPov9rP7t1/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/zPov9rP7t1/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/zPov9rP7t1/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots11.vcf.gz -c FMT /tmp/wj8A4a3te7/annotate11.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots11.vcf.gz -c FMT /tmp/zPov9rP7t1/annotate11.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots11.vcf.gz -c FMT /tmp/wj8A4a3te7/annotate11.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots11.vcf.gz -c FMT /tmp/zPov9rP7t1/annotate11.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots2.vcf.gz -c FMT/newGT:=GT /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots2.vcf.gz -c FMT/newGT:=GT /tmp/zPov9rP7t1/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots2.vcf.gz -c FMT/newGT:=GT /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots2.vcf.gz -c FMT/newGT:=GT /tmp/zPov9rP7t1/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots12.vcf.gz -c FMT/GT:=newGT /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots12.vcf.gz -c FMT/GT:=newGT /tmp/zPov9rP7t1/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots12.vcf.gz -c FMT/GT:=newGT /tmp/wj8A4a3te7/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots12.vcf.gz -c FMT/GT:=newGT /tmp/zPov9rP7t1/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots13.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate13.hdr -c CHROM,BEG,END,ABC /build/reproducible-path/bcftools-1.21/test/annotate13.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots13.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate13.hdr -c CHROM,BEG,END,ABC /build/reproducible-path/bcftools-1.21/test/annotate13.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots13.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate13.hdr -c CHROM,BEG,END,ABC /build/reproducible-path/bcftools-1.21/test/annotate13.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots13.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate13.hdr -c CHROM,BEG,END,ABC /build/reproducible-path/bcftools-1.21/test/annotate13.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots13.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:append /build/reproducible-path/bcftools-1.21/test/annotate13.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots13.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:append /build/reproducible-path/bcftools-1.21/test/annotate13.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots13.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:append /build/reproducible-path/bcftools-1.21/test/annotate13.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots13.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:append /build/reproducible-path/bcftools-1.21/test/annotate13.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots13.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:unique /build/reproducible-path/bcftools-1.21/test/annotate13.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots13.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:unique /build/reproducible-path/bcftools-1.21/test/annotate13.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots13.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:unique /build/reproducible-path/bcftools-1.21/test/annotate13.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots13.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:unique /build/reproducible-path/bcftools-1.21/test/annotate13.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: @@ -5379,27 +5415,27 @@ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate15.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate15.hdr -s SAMPLE1 -c CHROM,FROM,TO,FMT/FOO,BAR /build/reproducible-path/bcftools-1.21/test/annotate15.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate15.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate15.hdr -s SAMPLE1 -c CHROM,FROM,TO,FMT/FOO,BAR /build/reproducible-path/bcftools-1.21/test/annotate15.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate15.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate15.hdr -s SAMPLE1 -c CHROM,FROM,TO,FMT/FOO,BAR /build/reproducible-path/bcftools-1.21/test/annotate15.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate15.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate15.hdr -s SAMPLE1 -c CHROM,FROM,TO,FMT/FOO,BAR /build/reproducible-path/bcftools-1.21/test/annotate15.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate15.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate15.hdr -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR /build/reproducible-path/bcftools-1.21/test/annotate15.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate15.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate15.hdr -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR /build/reproducible-path/bcftools-1.21/test/annotate15.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate15.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate15.hdr -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR /build/reproducible-path/bcftools-1.21/test/annotate15.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate15.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate15.hdr -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR /build/reproducible-path/bcftools-1.21/test/annotate15.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate15.tab.gz -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR -H '##FORMAT=' -H '##INFO=' /build/reproducible-path/bcftools-1.21/test/annotate15.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate15.tab.gz -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR -H '##FORMAT=' -H '##INFO=' /build/reproducible-path/bcftools-1.21/test/annotate15.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate15.tab.gz -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR -H '##FORMAT=' -H '##INFO=' /build/reproducible-path/bcftools-1.21/test/annotate15.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate15.tab.gz -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR -H '##FORMAT=' -H '##INFO=' /build/reproducible-path/bcftools-1.21/test/annotate15.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: @@ -5411,67 +5447,67 @@ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/reproducible-path/bcftools-1.21/test/annotate17.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/reproducible-path/bcftools-1.21/test/annotate17.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/reproducible-path/bcftools-1.21/test/annotate17.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/reproducible-path/bcftools-1.21/test/annotate17.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/reproducible-path/bcftools-1.21/test/annotate17.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/reproducible-path/bcftools-1.21/test/annotate17.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/reproducible-path/bcftools-1.21/test/annotate17.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/reproducible-path/bcftools-1.21/test/annotate17.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate17.3.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/reproducible-path/bcftools-1.21/test/annotate17.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate17.3.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/reproducible-path/bcftools-1.21/test/annotate17.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate17.3.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/reproducible-path/bcftools-1.21/test/annotate17.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate17.3.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/reproducible-path/bcftools-1.21/test/annotate17.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate18.1.tab.gz -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /build/reproducible-path/bcftools-1.21/test/annotate18.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate18.1.tab.gz -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /build/reproducible-path/bcftools-1.21/test/annotate18.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate18.1.tab.gz -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /build/reproducible-path/bcftools-1.21/test/annotate18.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate18.1.tab.gz -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /build/reproducible-path/bcftools-1.21/test/annotate18.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate18.2.tab.gz -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /build/reproducible-path/bcftools-1.21/test/annotate18.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate18.2.tab.gz -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /build/reproducible-path/bcftools-1.21/test/annotate18.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate18.2.tab.gz -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /build/reproducible-path/bcftools-1.21/test/annotate18.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate18.2.tab.gz -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /build/reproducible-path/bcftools-1.21/test/annotate18.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/wj8A4a3te7/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/zPov9rP7t1/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/wj8A4a3te7/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/zPov9rP7t1/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/wj8A4a3te7/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/zPov9rP7t1/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/wj8A4a3te7/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/zPov9rP7t1/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/wj8A4a3te7/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/zPov9rP7t1/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/wj8A4a3te7/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/zPov9rP7t1/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: @@ -5483,83 +5519,83 @@ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER /tmp/wj8A4a3te7/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER /tmp/zPov9rP7t1/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER /tmp/wj8A4a3te7/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER /tmp/zPov9rP7t1/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER /tmp/wj8A4a3te7/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER /tmp/zPov9rP7t1/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER /tmp/wj8A4a3te7/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER /tmp/zPov9rP7t1/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER,FILTER /tmp/wj8A4a3te7/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER,FILTER /tmp/zPov9rP7t1/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER,FILTER /tmp/wj8A4a3te7/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER,FILTER /tmp/zPov9rP7t1/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=./FILTER /tmp/wj8A4a3te7/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=./FILTER /tmp/zPov9rP7t1/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=./FILTER /tmp/wj8A4a3te7/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=./FILTER /tmp/zPov9rP7t1/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate20.src.vcf.gz -c FMT/GT /tmp/wj8A4a3te7/annotate20.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate20.src.vcf.gz -c FMT/GT /tmp/zPov9rP7t1/annotate20.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate20.src.vcf.gz -c FMT/GT /tmp/wj8A4a3te7/annotate20.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate20.src.vcf.gz -c FMT/GT /tmp/zPov9rP7t1/annotate20.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate20.src.vcf.gz -c +FMT/GT /tmp/wj8A4a3te7/annotate20.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate20.src.vcf.gz -c +FMT/GT /tmp/zPov9rP7t1/annotate20.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate20.src.vcf.gz -c +FMT/GT /tmp/wj8A4a3te7/annotate20.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate20.src.vcf.gz -c +FMT/GT /tmp/zPov9rP7t1/annotate20.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate20.src.vcf.gz -c -FMT/GT /tmp/wj8A4a3te7/annotate20.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate20.src.vcf.gz -c -FMT/GT /tmp/zPov9rP7t1/annotate20.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate20.src.vcf.gz -c -FMT/GT /tmp/wj8A4a3te7/annotate20.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate20.src.vcf.gz -c -FMT/GT /tmp/zPov9rP7t1/annotate20.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate.multi.tab.gz -c CHROM,POS,REF,ALT,ANN -l ANN:append /build/reproducible-path/bcftools-1.21/test/annotate.multi.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate.multi.tab.gz -c CHROM,POS,REF,ALT,ANN -l ANN:append /build/reproducible-path/bcftools-1.21/test/annotate.multi.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate.multi.tab.gz -c CHROM,POS,REF,ALT,ANN -l ANN:append /build/reproducible-path/bcftools-1.21/test/annotate.multi.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate.multi.tab.gz -c CHROM,POS,REF,ALT,ANN -l ANN:append /build/reproducible-path/bcftools-1.21/test/annotate.multi.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate.missing-append.tab.gz -c CHROM,POS,REF,ALT,STR,INT,FLT -l STR:append-missing,INT:append-missing,FLT:append-missing /build/reproducible-path/bcftools-1.21/test/annotate.missing-append.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate.missing-append.tab.gz -c CHROM,POS,REF,ALT,STR,INT,FLT -l STR:append-missing,INT:append-missing,FLT:append-missing /build/reproducible-path/bcftools-1.21/test/annotate.missing-append.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate.missing-append.tab.gz -c CHROM,POS,REF,ALT,STR,INT,FLT -l STR:append-missing,INT:append-missing,FLT:append-missing /build/reproducible-path/bcftools-1.21/test/annotate.missing-append.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate.missing-append.tab.gz -c CHROM,POS,REF,ALT,STR,INT,FLT -l STR:append-missing,INT:append-missing,FLT:append-missing /build/reproducible-path/bcftools-1.21/test/annotate.missing-append.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /build/reproducible-path/bcftools-1.21/test/annotate9.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /build/reproducible-path/bcftools-1.21/test/annotate9.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /build/reproducible-path/bcftools-1.21/test/annotate9.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /build/reproducible-path/bcftools-1.21/test/annotate9.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: @@ -5579,179 +5615,179 @@ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/wj8A4a3te7/annotate22.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/zPov9rP7t1/annotate22.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/wj8A4a3te7/annotate22.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/zPov9rP7t1/annotate22.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate23.tab.gz -c CHROM,POS,~ID,REF,ALT,INFO/END /build/reproducible-path/bcftools-1.21/test/annotate23.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate23.tab.gz -c CHROM,POS,~ID,REF,ALT,INFO/END /build/reproducible-path/bcftools-1.21/test/annotate23.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate23.tab.gz -c CHROM,POS,~ID,REF,ALT,INFO/END /build/reproducible-path/bcftools-1.21/test/annotate23.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate23.tab.gz -c CHROM,POS,~ID,REF,ALT,INFO/END /build/reproducible-path/bcftools-1.21/test/annotate23.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate24.src.vcf.gz -c XX /tmp/wj8A4a3te7/annotate24.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate24.src.vcf.gz -c XX /tmp/zPov9rP7t1/annotate24.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate24.src.vcf.gz -c XX /tmp/wj8A4a3te7/annotate24.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate24.src.vcf.gz -c XX /tmp/zPov9rP7t1/annotate24.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate25.tab.gz -c CHROM,POS,ID,REF,ALT,~INFO/END /build/reproducible-path/bcftools-1.21/test/annotate25.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate25.tab.gz -c CHROM,POS,ID,REF,ALT,~INFO/END /build/reproducible-path/bcftools-1.21/test/annotate25.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate25.tab.gz -c CHROM,POS,ID,REF,ALT,~INFO/END /build/reproducible-path/bcftools-1.21/test/annotate25.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate25.tab.gz -c CHROM,POS,ID,REF,ALT,~INFO/END /build/reproducible-path/bcftools-1.21/test/annotate25.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate26.tab.gz -c CHROM,POS,-POS /build/reproducible-path/bcftools-1.21/test/annotate26.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate26.tab.gz -c CHROM,POS,-POS /build/reproducible-path/bcftools-1.21/test/annotate26.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate26.tab.gz -c CHROM,POS,-POS /build/reproducible-path/bcftools-1.21/test/annotate26.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate26.tab.gz -c CHROM,POS,-POS /build/reproducible-path/bcftools-1.21/test/annotate26.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,TSTR,TFLT,TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,TSTR,TFLT,TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,TSTR,TFLT,TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,TSTR,TFLT,TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.TSTR,.TFLT,.TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.TSTR,.TFLT,.TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.TSTR,.TFLT,.TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.TSTR,.TFLT,.TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.+TSTR,.+TFLT,.+TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.+TSTR,.+TFLT,.+TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.+TSTR,.+TFLT,.+TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.+TSTR,.+TFLT,.+TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,+TSTR,+TFLT,+TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,+TSTR,+TFLT,+TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,+TSTR,+TFLT,+TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,+TSTR,+TFLT,+TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.=TSTR,.=TFLT,.=TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.=TSTR,.=TFLT,.=TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.=TSTR,.=TFLT,.=TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.=TSTR,.=TFLT,.=TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,=TSTR,=TFLT,=TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,=TSTR,=TFLT,=TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,=TSTR,=TFLT,=TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,=TSTR,=TFLT,=TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique /build/reproducible-path/bcftools-1.21/test/annotate.olap.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique /build/reproducible-path/bcftools-1.21/test/annotate.olap.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique /build/reproducible-path/bcftools-1.21/test/annotate.olap.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique /build/reproducible-path/bcftools-1.21/test/annotate.olap.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique --min-overlap 0.4:0.5 -m XXX /build/reproducible-path/bcftools-1.21/test/annotate.olap.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique --min-overlap 0.4:0.5 -m XXX /build/reproducible-path/bcftools-1.21/test/annotate.olap.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique --min-overlap 0.4:0.5 -m XXX /build/reproducible-path/bcftools-1.21/test/annotate.olap.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique --min-overlap 0.4:0.5 -m XXX /build/reproducible-path/bcftools-1.21/test/annotate.olap.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots.id.vcf.gz -c ALT /tmp/wj8A4a3te7/annotate.id.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots.id.vcf.gz -c ALT /tmp/zPov9rP7t1/annotate.id.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots.id.vcf.gz -c ALT /tmp/wj8A4a3te7/annotate.id.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots.id.vcf.gz -c ALT /tmp/zPov9rP7t1/annotate.id.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots.id.vcf.gz -c +ALT /tmp/wj8A4a3te7/annotate.id.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots.id.vcf.gz -c +ALT /tmp/zPov9rP7t1/annotate.id.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots.id.vcf.gz -c +ALT /tmp/wj8A4a3te7/annotate.id.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots.id.vcf.gz -c +ALT /tmp/zPov9rP7t1/annotate.id.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots.id.2.vcf.gz --pair-logic some -c +ID /tmp/wj8A4a3te7/annotate.id.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots.id.2.vcf.gz --pair-logic some -c +ID /tmp/zPov9rP7t1/annotate.id.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots.id.2.vcf.gz --pair-logic some -c +ID /tmp/wj8A4a3te7/annotate.id.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots.id.2.vcf.gz --pair-logic some -c +ID /tmp/zPov9rP7t1/annotate.id.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots.id.2.vcf.gz --pair-logic any -c +ID /tmp/wj8A4a3te7/annotate.id.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots.id.2.vcf.gz --pair-logic any -c +ID /tmp/zPov9rP7t1/annotate.id.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots.id.2.vcf.gz --pair-logic any -c +ID /tmp/wj8A4a3te7/annotate.id.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots.id.2.vcf.gz --pair-logic any -c +ID /tmp/zPov9rP7t1/annotate.id.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annotate27.tab.gz -c CHROM,POS,REF,ALT,EVIDENCE /build/reproducible-path/bcftools-1.21/test/annotate27.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annotate27.tab.gz -c CHROM,POS,REF,ALT,EVIDENCE /build/reproducible-path/bcftools-1.21/test/annotate27.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annotate27.tab.gz -c CHROM,POS,REF,ALT,EVIDENCE /build/reproducible-path/bcftools-1.21/test/annotate27.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annotate27.tab.gz -c CHROM,POS,REF,ALT,EVIDENCE /build/reproducible-path/bcftools-1.21/test/annotate27.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1,smpl2 /build/reproducible-path/bcftools-1.21/test/annotate28.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1,smpl2 /build/reproducible-path/bcftools-1.21/test/annotate28.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1,smpl2 /build/reproducible-path/bcftools-1.21/test/annotate28.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1,smpl2 /build/reproducible-path/bcftools-1.21/test/annotate28.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2,smpl1 /build/reproducible-path/bcftools-1.21/test/annotate28.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2,smpl1 /build/reproducible-path/bcftools-1.21/test/annotate28.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2,smpl1 /build/reproducible-path/bcftools-1.21/test/annotate28.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2,smpl1 /build/reproducible-path/bcftools-1.21/test/annotate28.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1 /build/reproducible-path/bcftools-1.21/test/annotate28.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1 /build/reproducible-path/bcftools-1.21/test/annotate28.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1 /build/reproducible-path/bcftools-1.21/test/annotate28.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1 /build/reproducible-path/bcftools-1.21/test/annotate28.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2 /build/reproducible-path/bcftools-1.21/test/annotate28.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2 /build/reproducible-path/bcftools-1.21/test/annotate28.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2 /build/reproducible-path/bcftools-1.21/test/annotate28.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2 /build/reproducible-path/bcftools-1.21/test/annotate28.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: @@ -5763,148 +5799,148 @@ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots34.tab.gz -c CHROM,FROM,TO,INFO/END -H '##INFO=' /build/reproducible-path/bcftools-1.21/test/annotate34.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots34.tab.gz -c CHROM,FROM,TO,INFO/END -H '##INFO=' /build/reproducible-path/bcftools-1.21/test/annotate34.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots34.tab.gz -c CHROM,FROM,TO,INFO/END -H '##INFO=' /build/reproducible-path/bcftools-1.21/test/annotate34.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots34.tab.gz -c CHROM,FROM,TO,INFO/END -H '##INFO=' /build/reproducible-path/bcftools-1.21/test/annotate34.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/wj8A4a3te7/annots-mark.bed.gz -c CHROM,FROM,TO -m TAG /build/reproducible-path/bcftools-1.21/test/annots-mark.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/zPov9rP7t1/annots-mark.bed.gz -c CHROM,FROM,TO -m TAG /build/reproducible-path/bcftools-1.21/test/annots-mark.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/wj8A4a3te7/annots-mark.bed.gz -c CHROM,FROM,TO -m TAG /build/reproducible-path/bcftools-1.21/test/annots-mark.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/zPov9rP7t1/annots-mark.bed.gz -c CHROM,FROM,TO -m TAG /build/reproducible-path/bcftools-1.21/test/annots-mark.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: - /build/reproducible-path/bcftools-1.21/bcftools concat --no-version /tmp/wj8A4a3te7/concat.1.a.vcf.gz /tmp/wj8A4a3te7/concat.1.b.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools concat --no-version /tmp/zPov9rP7t1/concat.1.a.vcf.gz /tmp/zPov9rP7t1/concat.1.b.vcf.gz .. ok test_vcf_concat: - /build/reproducible-path/bcftools-1.21/bcftools concat -Ob /tmp/wj8A4a3te7/concat.1.a.vcf.gz /tmp/wj8A4a3te7/concat.1.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools concat -Ob /tmp/zPov9rP7t1/concat.1.a.vcf.gz /tmp/zPov9rP7t1/concat.1.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: - /build/reproducible-path/bcftools-1.21/bcftools concat --no-version /tmp/wj8A4a3te7/concat.1.a.bcf /tmp/wj8A4a3te7/concat.1.b.bcf + /build/reproducible-path/bcftools-1.21/bcftools concat --no-version /tmp/zPov9rP7t1/concat.1.a.bcf /tmp/zPov9rP7t1/concat.1.b.bcf .. ok test_vcf_concat: - /build/reproducible-path/bcftools-1.21/bcftools concat -Ob /tmp/wj8A4a3te7/concat.1.a.bcf /tmp/wj8A4a3te7/concat.1.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools concat -Ob /tmp/zPov9rP7t1/concat.1.a.bcf /tmp/zPov9rP7t1/concat.1.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: - /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -a /tmp/wj8A4a3te7/concat.2.a.vcf.gz /tmp/wj8A4a3te7/concat.2.b.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -a /tmp/zPov9rP7t1/concat.2.a.vcf.gz /tmp/zPov9rP7t1/concat.2.b.vcf.gz .. ok test_vcf_concat: - /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -a /tmp/wj8A4a3te7/concat.2.a.vcf.gz /tmp/wj8A4a3te7/concat.2.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -a /tmp/zPov9rP7t1/concat.2.a.vcf.gz /tmp/zPov9rP7t1/concat.2.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: - /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -a /tmp/wj8A4a3te7/concat.2.a.bcf /tmp/wj8A4a3te7/concat.2.b.bcf + /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -a /tmp/zPov9rP7t1/concat.2.a.bcf /tmp/zPov9rP7t1/concat.2.b.bcf .. ok test_vcf_concat: - /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -a /tmp/wj8A4a3te7/concat.2.a.bcf /tmp/wj8A4a3te7/concat.2.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -a /tmp/zPov9rP7t1/concat.2.a.bcf /tmp/zPov9rP7t1/concat.2.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: - /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -aD /tmp/wj8A4a3te7/concat.2.a.vcf.gz /tmp/wj8A4a3te7/concat.2.b.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -aD /tmp/zPov9rP7t1/concat.2.a.vcf.gz /tmp/zPov9rP7t1/concat.2.b.vcf.gz .. ok test_vcf_concat: - /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -aD /tmp/wj8A4a3te7/concat.2.a.vcf.gz /tmp/wj8A4a3te7/concat.2.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -aD /tmp/zPov9rP7t1/concat.2.a.vcf.gz /tmp/zPov9rP7t1/concat.2.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: - /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -aD /tmp/wj8A4a3te7/concat.2.a.bcf /tmp/wj8A4a3te7/concat.2.b.bcf + /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -aD /tmp/zPov9rP7t1/concat.2.a.bcf /tmp/zPov9rP7t1/concat.2.b.bcf .. ok test_vcf_concat: - /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -aD /tmp/wj8A4a3te7/concat.2.a.bcf /tmp/wj8A4a3te7/concat.2.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -aD /tmp/zPov9rP7t1/concat.2.a.bcf /tmp/zPov9rP7t1/concat.2.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: - /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -l --ligate-warn /tmp/wj8A4a3te7/concat.3.a.vcf.gz /tmp/wj8A4a3te7/concat.3.b.vcf.gz /tmp/wj8A4a3te7/concat.3.0.vcf.gz /tmp/wj8A4a3te7/concat.3.c.vcf.gz /tmp/wj8A4a3te7/concat.3.d.vcf.gz /tmp/wj8A4a3te7/concat.3.e.vcf.gz /tmp/wj8A4a3te7/concat.3.f.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -l --ligate-warn /tmp/zPov9rP7t1/concat.3.a.vcf.gz /tmp/zPov9rP7t1/concat.3.b.vcf.gz /tmp/zPov9rP7t1/concat.3.0.vcf.gz /tmp/zPov9rP7t1/concat.3.c.vcf.gz /tmp/zPov9rP7t1/concat.3.d.vcf.gz /tmp/zPov9rP7t1/concat.3.e.vcf.gz /tmp/zPov9rP7t1/concat.3.f.vcf.gz .. ok test_vcf_concat: - /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -l --ligate-warn /tmp/wj8A4a3te7/concat.3.a.vcf.gz /tmp/wj8A4a3te7/concat.3.b.vcf.gz /tmp/wj8A4a3te7/concat.3.0.vcf.gz /tmp/wj8A4a3te7/concat.3.c.vcf.gz /tmp/wj8A4a3te7/concat.3.d.vcf.gz /tmp/wj8A4a3te7/concat.3.e.vcf.gz /tmp/wj8A4a3te7/concat.3.f.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -l --ligate-warn /tmp/zPov9rP7t1/concat.3.a.vcf.gz /tmp/zPov9rP7t1/concat.3.b.vcf.gz /tmp/zPov9rP7t1/concat.3.0.vcf.gz /tmp/zPov9rP7t1/concat.3.c.vcf.gz /tmp/zPov9rP7t1/concat.3.d.vcf.gz /tmp/zPov9rP7t1/concat.3.e.vcf.gz /tmp/zPov9rP7t1/concat.3.f.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: - /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -l --ligate-warn /tmp/wj8A4a3te7/concat.3.a.bcf /tmp/wj8A4a3te7/concat.3.b.bcf /tmp/wj8A4a3te7/concat.3.0.bcf /tmp/wj8A4a3te7/concat.3.c.bcf /tmp/wj8A4a3te7/concat.3.d.bcf /tmp/wj8A4a3te7/concat.3.e.bcf /tmp/wj8A4a3te7/concat.3.f.bcf + /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -l --ligate-warn /tmp/zPov9rP7t1/concat.3.a.bcf /tmp/zPov9rP7t1/concat.3.b.bcf /tmp/zPov9rP7t1/concat.3.0.bcf /tmp/zPov9rP7t1/concat.3.c.bcf /tmp/zPov9rP7t1/concat.3.d.bcf /tmp/zPov9rP7t1/concat.3.e.bcf /tmp/zPov9rP7t1/concat.3.f.bcf .. ok test_vcf_concat: - /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -l --ligate-warn /tmp/wj8A4a3te7/concat.3.a.bcf /tmp/wj8A4a3te7/concat.3.b.bcf /tmp/wj8A4a3te7/concat.3.0.bcf /tmp/wj8A4a3te7/concat.3.c.bcf /tmp/wj8A4a3te7/concat.3.d.bcf /tmp/wj8A4a3te7/concat.3.e.bcf /tmp/wj8A4a3te7/concat.3.f.bcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ -Random seed for test_naive_concat: 2755974125 + /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -l --ligate-warn /tmp/zPov9rP7t1/concat.3.a.bcf /tmp/zPov9rP7t1/concat.3.b.bcf /tmp/zPov9rP7t1/concat.3.0.bcf /tmp/zPov9rP7t1/concat.3.c.bcf /tmp/zPov9rP7t1/concat.3.d.bcf /tmp/zPov9rP7t1/concat.3.e.bcf /tmp/zPov9rP7t1/concat.3.f.bcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ +Random seed for test_naive_concat: 1061134846 .. ok test_naive_concat: - /build/reproducible-path/bcftools-1.21/bcftools concat --naive-force /tmp/wj8A4a3te7/naive_concat.0.bcf /tmp/wj8A4a3te7/naive_concat.1.bcf /tmp/wj8A4a3te7/naive_concat.2.bcf /tmp/wj8A4a3te7/naive_concat.3.bcf /tmp/wj8A4a3te7/naive_concat.4.bcf /tmp/wj8A4a3te7/naive_concat.5.bcf /tmp/wj8A4a3te7/naive_concat.6.bcf /tmp/wj8A4a3te7/naive_concat.7.bcf /tmp/wj8A4a3te7/naive_concat.8.bcf /tmp/wj8A4a3te7/naive_concat.9.bcf | /build/reproducible-path/bcftools-1.21/bcftools view -H + /build/reproducible-path/bcftools-1.21/bcftools concat --naive-force /tmp/zPov9rP7t1/naive_concat.0.bcf /tmp/zPov9rP7t1/naive_concat.1.bcf /tmp/zPov9rP7t1/naive_concat.2.bcf /tmp/zPov9rP7t1/naive_concat.3.bcf /tmp/zPov9rP7t1/naive_concat.4.bcf /tmp/zPov9rP7t1/naive_concat.5.bcf /tmp/zPov9rP7t1/naive_concat.6.bcf /tmp/zPov9rP7t1/naive_concat.7.bcf /tmp/zPov9rP7t1/naive_concat.8.bcf /tmp/zPov9rP7t1/naive_concat.9.bcf | /build/reproducible-path/bcftools-1.21/bcftools view -H .. ok test_naive_concat: - /build/reproducible-path/bcftools-1.21/bcftools concat --naive /tmp/wj8A4a3te7/naive_concat.0.vcf.gz /tmp/wj8A4a3te7/naive_concat.1.vcf.gz /tmp/wj8A4a3te7/naive_concat.2.vcf.gz /tmp/wj8A4a3te7/naive_concat.3.vcf.gz /tmp/wj8A4a3te7/naive_concat.4.vcf.gz /tmp/wj8A4a3te7/naive_concat.5.vcf.gz /tmp/wj8A4a3te7/naive_concat.6.vcf.gz /tmp/wj8A4a3te7/naive_concat.7.vcf.gz /tmp/wj8A4a3te7/naive_concat.8.vcf.gz /tmp/wj8A4a3te7/naive_concat.9.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view -H + /build/reproducible-path/bcftools-1.21/bcftools concat --naive /tmp/zPov9rP7t1/naive_concat.0.vcf.gz /tmp/zPov9rP7t1/naive_concat.1.vcf.gz /tmp/zPov9rP7t1/naive_concat.2.vcf.gz /tmp/zPov9rP7t1/naive_concat.3.vcf.gz /tmp/zPov9rP7t1/naive_concat.4.vcf.gz /tmp/zPov9rP7t1/naive_concat.5.vcf.gz /tmp/zPov9rP7t1/naive_concat.6.vcf.gz /tmp/zPov9rP7t1/naive_concat.7.vcf.gz /tmp/zPov9rP7t1/naive_concat.8.vcf.gz /tmp/zPov9rP7t1/naive_concat.9.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view -H .. ok test_vcf_concat: - /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -l /tmp/wj8A4a3te7/concat.4.a.vcf.gz /tmp/wj8A4a3te7/concat.4.b.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -l /tmp/zPov9rP7t1/concat.4.a.vcf.gz /tmp/zPov9rP7t1/concat.4.b.vcf.gz .. ok test_vcf_concat: - /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -l /tmp/wj8A4a3te7/concat.4.a.vcf.gz /tmp/wj8A4a3te7/concat.4.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -l /tmp/zPov9rP7t1/concat.4.a.vcf.gz /tmp/zPov9rP7t1/concat.4.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: - /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -l /tmp/wj8A4a3te7/concat.4.a.bcf /tmp/wj8A4a3te7/concat.4.b.bcf + /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -l /tmp/zPov9rP7t1/concat.4.a.bcf /tmp/zPov9rP7t1/concat.4.b.bcf .. ok test_vcf_concat: - /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -l /tmp/wj8A4a3te7/concat.4.a.bcf /tmp/wj8A4a3te7/concat.4.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -l /tmp/zPov9rP7t1/concat.4.a.bcf /tmp/zPov9rP7t1/concat.4.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: - /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -l --ligate-warn /tmp/wj8A4a3te7/concat.5.a.vcf.gz /tmp/wj8A4a3te7/concat.5.b.vcf.gz /tmp/wj8A4a3te7/concat.5.c.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -l --ligate-warn /tmp/zPov9rP7t1/concat.5.a.vcf.gz /tmp/zPov9rP7t1/concat.5.b.vcf.gz /tmp/zPov9rP7t1/concat.5.c.vcf.gz .. ok test_vcf_concat: - /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -l --ligate-warn /tmp/wj8A4a3te7/concat.5.a.vcf.gz /tmp/wj8A4a3te7/concat.5.b.vcf.gz /tmp/wj8A4a3te7/concat.5.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -l --ligate-warn /tmp/zPov9rP7t1/concat.5.a.vcf.gz /tmp/zPov9rP7t1/concat.5.b.vcf.gz /tmp/zPov9rP7t1/concat.5.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: - /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -l --ligate-warn /tmp/wj8A4a3te7/concat.5.a.bcf /tmp/wj8A4a3te7/concat.5.b.bcf /tmp/wj8A4a3te7/concat.5.c.bcf + /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -l --ligate-warn /tmp/zPov9rP7t1/concat.5.a.bcf /tmp/zPov9rP7t1/concat.5.b.bcf /tmp/zPov9rP7t1/concat.5.c.bcf .. ok test_vcf_concat: - /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -l --ligate-warn /tmp/wj8A4a3te7/concat.5.a.bcf /tmp/wj8A4a3te7/concat.5.b.bcf /tmp/wj8A4a3te7/concat.5.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -l --ligate-warn /tmp/zPov9rP7t1/concat.5.a.bcf /tmp/zPov9rP7t1/concat.5.b.bcf /tmp/zPov9rP7t1/concat.5.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: - /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -l --ligate-force /tmp/wj8A4a3te7/concat.5.a.bcf /tmp/wj8A4a3te7/concat.5.b.bcf /tmp/wj8A4a3te7/concat.5.c.bcf + /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -l --ligate-force /tmp/zPov9rP7t1/concat.5.a.bcf /tmp/zPov9rP7t1/concat.5.b.bcf /tmp/zPov9rP7t1/concat.5.c.bcf .. ok test_vcf_concat: - /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -l --ligate-force /tmp/wj8A4a3te7/concat.5.a.bcf /tmp/wj8A4a3te7/concat.5.b.bcf /tmp/wj8A4a3te7/concat.5.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -l --ligate-force /tmp/zPov9rP7t1/concat.5.a.bcf /tmp/zPov9rP7t1/concat.5.b.bcf /tmp/zPov9rP7t1/concat.5.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: - /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -G -a -D /tmp/wj8A4a3te7/concat.5.a.vcf.gz /tmp/wj8A4a3te7/concat.5.b.vcf.gz /tmp/wj8A4a3te7/concat.5.c.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -G -a -D /tmp/zPov9rP7t1/concat.5.a.vcf.gz /tmp/zPov9rP7t1/concat.5.b.vcf.gz /tmp/zPov9rP7t1/concat.5.c.vcf.gz .. ok test_vcf_concat: - /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -G -a -D /tmp/wj8A4a3te7/concat.5.a.vcf.gz /tmp/wj8A4a3te7/concat.5.b.vcf.gz /tmp/wj8A4a3te7/concat.5.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -G -a -D /tmp/zPov9rP7t1/concat.5.a.vcf.gz /tmp/zPov9rP7t1/concat.5.b.vcf.gz /tmp/zPov9rP7t1/concat.5.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: - /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -G -a -D /tmp/wj8A4a3te7/concat.5.a.bcf /tmp/wj8A4a3te7/concat.5.b.bcf /tmp/wj8A4a3te7/concat.5.c.bcf + /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -G -a -D /tmp/zPov9rP7t1/concat.5.a.bcf /tmp/zPov9rP7t1/concat.5.b.bcf /tmp/zPov9rP7t1/concat.5.c.bcf .. ok test_vcf_concat: - /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -G -a -D /tmp/wj8A4a3te7/concat.5.a.bcf /tmp/wj8A4a3te7/concat.5.b.bcf /tmp/wj8A4a3te7/concat.5.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ + /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -G -a -D /tmp/zPov9rP7t1/concat.5.a.bcf /tmp/zPov9rP7t1/concat.5.b.bcf /tmp/zPov9rP7t1/concat.5.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_reheader: @@ -5916,19 +5952,19 @@ .. ok test_vcf_reheader: - /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.hdr /tmp/wj8A4a3te7/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version + /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.hdr /tmp/zPov9rP7t1/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: - cat /tmp/wj8A4a3te7/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.hdr | /build/reproducible-path/bcftools-1.21/bcftools view --no-version + cat /tmp/zPov9rP7t1/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.hdr | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: - /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.hdr /tmp/wj8A4a3te7/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version + /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.hdr /tmp/zPov9rP7t1/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: - cat /tmp/wj8A4a3te7/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.hdr | /build/reproducible-path/bcftools-1.21/bcftools view --no-version + cat /tmp/zPov9rP7t1/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.hdr | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: @@ -5940,19 +5976,19 @@ .. ok test_vcf_reheader: - /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples /tmp/wj8A4a3te7/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version + /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples /tmp/zPov9rP7t1/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: - cat /tmp/wj8A4a3te7/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples | /build/reproducible-path/bcftools-1.21/bcftools view --no-version + cat /tmp/zPov9rP7t1/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: - /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples /tmp/wj8A4a3te7/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version + /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples /tmp/zPov9rP7t1/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: - cat /tmp/wj8A4a3te7/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples | /build/reproducible-path/bcftools-1.21/bcftools view --no-version + cat /tmp/zPov9rP7t1/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: @@ -5964,19 +6000,19 @@ .. ok test_vcf_reheader: - /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples2 /tmp/wj8A4a3te7/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version + /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples2 /tmp/zPov9rP7t1/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: - cat /tmp/wj8A4a3te7/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples2 | /build/reproducible-path/bcftools-1.21/bcftools view --no-version + cat /tmp/zPov9rP7t1/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples2 | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: - /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples2 /tmp/wj8A4a3te7/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version + /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples2 /tmp/zPov9rP7t1/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: - cat /tmp/wj8A4a3te7/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples2 | /build/reproducible-path/bcftools-1.21/bcftools view --no-version + cat /tmp/zPov9rP7t1/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples2 | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: @@ -5988,19 +6024,19 @@ .. ok test_vcf_reheader: - /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples3 /tmp/wj8A4a3te7/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version + /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples3 /tmp/zPov9rP7t1/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: - cat /tmp/wj8A4a3te7/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples3 | /build/reproducible-path/bcftools-1.21/bcftools view --no-version + cat /tmp/zPov9rP7t1/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples3 | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: - /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples3 /tmp/wj8A4a3te7/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version + /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples3 /tmp/zPov9rP7t1/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: - cat /tmp/wj8A4a3te7/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples3 | /build/reproducible-path/bcftools-1.21/bcftools view --no-version + cat /tmp/zPov9rP7t1/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples3 | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: @@ -6012,19 +6048,19 @@ .. ok test_vcf_reheader: - /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples4 /tmp/wj8A4a3te7/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version + /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples4 /tmp/zPov9rP7t1/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: - cat /tmp/wj8A4a3te7/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples4 | /build/reproducible-path/bcftools-1.21/bcftools view --no-version + cat /tmp/zPov9rP7t1/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples4 | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: - /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples4 /tmp/wj8A4a3te7/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version + /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples4 /tmp/zPov9rP7t1/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: - cat /tmp/wj8A4a3te7/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples4 | /build/reproducible-path/bcftools-1.21/bcftools view --no-version + cat /tmp/zPov9rP7t1/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples4 | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: @@ -6036,19 +6072,19 @@ .. ok test_vcf_reheader: - /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.empty.hdr /tmp/wj8A4a3te7/empty.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version + /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.empty.hdr /tmp/zPov9rP7t1/empty.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: - cat /tmp/wj8A4a3te7/empty.bcf | /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.empty.hdr | /build/reproducible-path/bcftools-1.21/bcftools view --no-version + cat /tmp/zPov9rP7t1/empty.bcf | /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.empty.hdr | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: - /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.empty.hdr /tmp/wj8A4a3te7/empty.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version + /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.empty.hdr /tmp/zPov9rP7t1/empty.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: - cat /tmp/wj8A4a3te7/empty.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.empty.hdr | /build/reproducible-path/bcftools-1.21/bcftools view --no-version + cat /tmp/zPov9rP7t1/empty.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.empty.hdr | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: @@ -6056,11 +6092,11 @@ .. ok test_vcf_reheader: - /build/reproducible-path/bcftools-1.21/bcftools reheader -f /build/reproducible-path/bcftools-1.21/test/reheader.fai /tmp/wj8A4a3te7/reheader.2.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version + /build/reproducible-path/bcftools-1.21/bcftools reheader -f /build/reproducible-path/bcftools-1.21/test/reheader.fai /tmp/zPov9rP7t1/reheader.2.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: - /build/reproducible-path/bcftools-1.21/bcftools reheader -f /build/reproducible-path/bcftools-1.21/test/reheader.fai /tmp/wj8A4a3te7/reheader.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version + /build/reproducible-path/bcftools-1.21/bcftools reheader -f /build/reproducible-path/bcftools-1.21/test/reheader.fai /tmp/zPov9rP7t1/reheader.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: @@ -6068,11 +6104,11 @@ .. ok test_vcf_reheader: - /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.2.hdr -f /build/reproducible-path/bcftools-1.21/test/reheader.fai /tmp/wj8A4a3te7/reheader.2.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version + /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.2.hdr -f /build/reproducible-path/bcftools-1.21/test/reheader.fai /tmp/zPov9rP7t1/reheader.2.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: - /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.2.hdr -f /build/reproducible-path/bcftools-1.21/test/reheader.fai /tmp/wj8A4a3te7/reheader.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version + /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.2.hdr -f /build/reproducible-path/bcftools-1.21/test/reheader.fai /tmp/zPov9rP7t1/reheader.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: @@ -6080,59 +6116,59 @@ .. ok test_vcf_reheader: - /build/reproducible-path/bcftools-1.21/bcftools reheader -f /build/reproducible-path/bcftools-1.21/test/reheader.3.fai /tmp/wj8A4a3te7/reheader.3.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version + /build/reproducible-path/bcftools-1.21/bcftools reheader -f /build/reproducible-path/bcftools-1.21/test/reheader.3.fai /tmp/zPov9rP7t1/reheader.3.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: - /build/reproducible-path/bcftools-1.21/bcftools reheader -f /build/reproducible-path/bcftools-1.21/test/reheader.3.fai /tmp/wj8A4a3te7/reheader.3.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version + /build/reproducible-path/bcftools-1.21/bcftools reheader -f /build/reproducible-path/bcftools-1.21/test/reheader.3.fai /tmp/zPov9rP7t1/reheader.3.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_rename_chrs: - /build/reproducible-path/bcftools-1.21/bcftools annotate --rename-chrs /tmp/wj8A4a3te7/rename.map -Ov /tmp/wj8A4a3te7/annotate.bcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM\t%POS\n' + /build/reproducible-path/bcftools-1.21/bcftools annotate --rename-chrs /tmp/zPov9rP7t1/rename.map -Ov /tmp/zPov9rP7t1/annotate.bcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: - /build/reproducible-path/bcftools-1.21/bcftools annotate --rename-chrs /tmp/wj8A4a3te7/rename.map -Ob /tmp/wj8A4a3te7/annotate.bcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM\t%POS\n' + /build/reproducible-path/bcftools-1.21/bcftools annotate --rename-chrs /tmp/zPov9rP7t1/rename.map -Ob /tmp/zPov9rP7t1/annotate.bcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: - /build/reproducible-path/bcftools-1.21/bcftools annotate --rename-chrs /tmp/wj8A4a3te7/rename.map -Ov /build/reproducible-path/bcftools-1.21/test/annotate.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM\t%POS\n' + /build/reproducible-path/bcftools-1.21/bcftools annotate --rename-chrs /tmp/zPov9rP7t1/rename.map -Ov /build/reproducible-path/bcftools-1.21/test/annotate.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: - /build/reproducible-path/bcftools-1.21/bcftools annotate --rename-chrs /tmp/wj8A4a3te7/rename.map -Ob /build/reproducible-path/bcftools-1.21/test/annotate.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM\t%POS\n' + /build/reproducible-path/bcftools-1.21/bcftools annotate --rename-chrs /tmp/zPov9rP7t1/rename.map -Ob /build/reproducible-path/bcftools-1.21/test/annotate.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM\t%POS\n' .. ok test_vcf_convert: - /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. /tmp/wj8A4a3te7/convert.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. /tmp/zPov9rP7t1/convert.vcf.gz .. ok test_vcf_convert: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. .. ok test_vcf_convert: - /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --vcf-ids /tmp/wj8A4a3te7/convert.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --vcf-ids /tmp/zPov9rP7t1/convert.vcf.gz .. ok test_vcf_convert: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --vcf-ids + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --vcf-ids .. ok test_vcf_convert: - /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --vcf-ids --3N6 /tmp/wj8A4a3te7/convert.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --vcf-ids --3N6 /tmp/zPov9rP7t1/convert.vcf.gz .. ok test_vcf_convert: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --vcf-ids --3N6 + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --vcf-ids --3N6 .. ok test_vcf_convert: - /build/reproducible-path/bcftools-1.21/bcftools convert -g .,- /tmp/wj8A4a3te7/convert.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools convert -g .,- /tmp/zPov9rP7t1/convert.vcf.gz .. ok test_vcf_convert: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g .,- + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g .,- .. ok test_vcf_convert_hs2vcf: @@ -6176,99 +6212,99 @@ .. ok test_vcf_convert: - /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --tag PL /tmp/wj8A4a3te7/convert.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --tag PL /tmp/zPov9rP7t1/convert.vcf.gz .. ok test_vcf_convert: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --tag PL + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --tag PL .. ok test_vcf_convert: - /build/reproducible-path/bcftools-1.21/bcftools convert -g .,- --tag PL /tmp/wj8A4a3te7/convert.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools convert -g .,- --tag PL /tmp/zPov9rP7t1/convert.vcf.gz .. ok test_vcf_convert: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g .,- --tag PL + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g .,- --tag PL .. ok test_vcf_convert: - /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --vcf-ids /tmp/wj8A4a3te7/check.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --vcf-ids /tmp/zPov9rP7t1/check.vcf.gz .. ok test_vcf_convert: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/check.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --vcf-ids + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/check.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --vcf-ids .. ok test_vcf_convert: - /build/reproducible-path/bcftools-1.21/bcftools convert -g .,- --vcf-ids /tmp/wj8A4a3te7/check.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools convert -g .,- --vcf-ids /tmp/zPov9rP7t1/check.vcf.gz .. ok test_vcf_convert: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/check.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g .,- --vcf-ids + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/check.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g .,- --vcf-ids .. ok test_vcf_convert: - /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --3N6 /tmp/wj8A4a3te7/check.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --3N6 /tmp/zPov9rP7t1/check.vcf.gz .. ok test_vcf_convert: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/check.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --3N6 + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/check.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --3N6 .. ok test_vcf_convert: - /build/reproducible-path/bcftools-1.21/bcftools convert -g .,- --3N6 /tmp/wj8A4a3te7/check.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools convert -g .,- --3N6 /tmp/zPov9rP7t1/check.vcf.gz .. ok test_vcf_convert: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/check.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g .,- --3N6 + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/check.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g .,- --3N6 .. ok test_vcf_convert: - /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --3N6 --vcf-ids /tmp/wj8A4a3te7/check.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --3N6 --vcf-ids /tmp/zPov9rP7t1/check.vcf.gz .. ok test_vcf_convert: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/check.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --3N6 --vcf-ids + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/check.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --3N6 --vcf-ids .. ok test_vcf_convert: - /build/reproducible-path/bcftools-1.21/bcftools convert -g .,- --3N6 --vcf-ids /tmp/wj8A4a3te7/check.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools convert -g .,- --3N6 --vcf-ids /tmp/zPov9rP7t1/check.vcf.gz .. ok test_vcf_convert: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/check.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g .,- --3N6 --vcf-ids + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/check.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g .,- --3N6 --vcf-ids .. ok test_vcf_convert: - /build/reproducible-path/bcftools-1.21/bcftools convert -h -,.,. /tmp/wj8A4a3te7/convert.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools convert -h -,.,. /tmp/zPov9rP7t1/convert.vcf.gz .. ok test_vcf_convert: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -h -,.,. + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -h -,.,. .. ok test_vcf_convert: - /build/reproducible-path/bcftools-1.21/bcftools convert -h .,-,. /tmp/wj8A4a3te7/convert.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools convert -h .,-,. /tmp/zPov9rP7t1/convert.vcf.gz .. ok test_vcf_convert: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -h .,-,. + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -h .,-,. .. ok test_vcf_convert: - /build/reproducible-path/bcftools-1.21/bcftools convert -h .,-,. --vcf-ids /tmp/wj8A4a3te7/convert.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools convert -h .,-,. --vcf-ids /tmp/zPov9rP7t1/convert.vcf.gz .. ok test_vcf_convert: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -h .,-,. --vcf-ids + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -h .,-,. --vcf-ids .. ok test_vcf_convert: - /build/reproducible-path/bcftools-1.21/bcftools convert -h .,.,- /tmp/wj8A4a3te7/convert.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools convert -h .,.,- /tmp/zPov9rP7t1/convert.vcf.gz .. ok test_vcf_convert: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -h .,.,- + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -h .,.,- .. ok test_vcf_convert_hls2vcf: @@ -6280,35 +6316,35 @@ .. ok test_vcf_convert: - /build/reproducible-path/bcftools-1.21/bcftools convert --haplegendsample -,.,. /tmp/wj8A4a3te7/convert.hap-missing.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools convert --haplegendsample -,.,. /tmp/zPov9rP7t1/convert.hap-missing.vcf.gz .. ok test_vcf_convert: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/convert.hap-missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert --haplegendsample -,.,. + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/convert.hap-missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert --haplegendsample -,.,. .. ok test_vcf_convert: - /build/reproducible-path/bcftools-1.21/bcftools convert --hapsample -,. /tmp/wj8A4a3te7/convert.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools convert --hapsample -,. /tmp/zPov9rP7t1/convert.vcf.gz .. ok test_vcf_convert: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert --hapsample -,. + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert --hapsample -,. .. ok test_vcf_convert: - /build/reproducible-path/bcftools-1.21/bcftools convert --hapsample -,. --vcf-ids /tmp/wj8A4a3te7/convert.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools convert --hapsample -,. --vcf-ids /tmp/zPov9rP7t1/convert.vcf.gz .. ok test_vcf_convert: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert --hapsample -,. --vcf-ids + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert --hapsample -,. --vcf-ids .. ok test_vcf_convert: - /build/reproducible-path/bcftools-1.21/bcftools convert --hapsample .,- /tmp/wj8A4a3te7/convert.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools convert --hapsample .,- /tmp/zPov9rP7t1/convert.vcf.gz .. ok test_vcf_convert: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert --hapsample .,- + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert --hapsample .,- .. ok test_vcf_convert_hs2vcf: @@ -6328,11 +6364,11 @@ .. ok test_vcf_convert_gvcf: - /build/reproducible-path/bcftools-1.21/bcftools convert --no-version --gvcf2vcf -i'FILTER="PASS"' -f /build/reproducible-path/bcftools-1.21/test/gvcf.fa /tmp/wj8A4a3te7/convert.gvcf.vcf.gz + /build/reproducible-path/bcftools-1.21/bcftools convert --no-version --gvcf2vcf -i'FILTER="PASS"' -f /build/reproducible-path/bcftools-1.21/test/gvcf.fa /tmp/zPov9rP7t1/convert.gvcf.vcf.gz .. ok test_vcf_convert_gvcf: - /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/wj8A4a3te7/convert.gvcf.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert --gvcf2vcf -i'FILTER="PASS"' -f /build/reproducible-path/bcftools-1.21/test/gvcf.fa | grep -v ^##bcftools + /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/zPov9rP7t1/convert.gvcf.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert --gvcf2vcf -i'FILTER="PASS"' -f /build/reproducible-path/bcftools-1.21/test/gvcf.fa | grep -v ^##bcftools .. ok test_vcf_convert_tsv2vcf: @@ -6352,499 +6388,499 @@ .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.overlaps.1.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.overlaps.1.fa -s A + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.overlaps.1.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.overlaps.1.fa -s A .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.overlaps.1.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.overlaps.1.fa -s A + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.overlaps.1.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.overlaps.1.fa -s A .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.overlaps.1.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.overlaps.1.fa -s B + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.overlaps.1.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.overlaps.1.fa -s B .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.overlaps.1.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.overlaps.1.fa -s B + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.overlaps.1.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.overlaps.1.fa -s B .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.overlaps.1.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.overlaps.1.fa -s A -a N + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.overlaps.1.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.overlaps.1.fa -s A -a N .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.overlaps.1.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.overlaps.1.fa -s A -a N + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.overlaps.1.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.overlaps.1.fa -s A -a N .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.overlaps.1.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.overlaps.1.fa -s B -a N + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.overlaps.1.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.overlaps.1.fa -s B -a N .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.overlaps.1.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.overlaps.1.fa -s B -a N + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.overlaps.1.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.overlaps.1.fa -s B -a N .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.beyond.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.beyond.fa + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.beyond.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.beyond.fa .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.beyond.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.beyond.fa + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.beyond.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.beyond.fa .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -m /build/reproducible-path/bcftools-1.21/test/consensus.tab + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -m /build/reproducible-path/bcftools-1.21/test/consensus.tab .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -m /build/reproducible-path/bcftools-1.21/test/consensus.tab + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -m /build/reproducible-path/bcftools-1.21/test/consensus.tab .. ok test_vcf_consensus_chain: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -m /build/reproducible-path/bcftools-1.21/test/consensus.tab -c /tmp/wj8A4a3te7/consensus.1.chain.new >/dev/null; cat /tmp/wj8A4a3te7/consensus.1.chain.new + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -m /build/reproducible-path/bcftools-1.21/test/consensus.tab -c /tmp/zPov9rP7t1/consensus.1.chain.new >/dev/null; cat /tmp/zPov9rP7t1/consensus.1.chain.new .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -H 1 -m /build/reproducible-path/bcftools-1.21/test/consensus.tab + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -H 1 -m /build/reproducible-path/bcftools-1.21/test/consensus.tab .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -H 1 -m /build/reproducible-path/bcftools-1.21/test/consensus.tab + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -H 1 -m /build/reproducible-path/bcftools-1.21/test/consensus.tab .. ok test_vcf_consensus_chain: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -H 1 -m /build/reproducible-path/bcftools-1.21/test/consensus.tab -c /tmp/wj8A4a3te7/consensus.2.chain.new >/dev/null; cat /tmp/wj8A4a3te7/consensus.2.chain.new + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -H 1 -m /build/reproducible-path/bcftools-1.21/test/consensus.tab -c /tmp/zPov9rP7t1/consensus.2.chain.new >/dev/null; cat /tmp/zPov9rP7t1/consensus.2.chain.new .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -I -s - -m /build/reproducible-path/bcftools-1.21/test/consensus.tab + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -I -s - -m /build/reproducible-path/bcftools-1.21/test/consensus.tab .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -I -s - -m /build/reproducible-path/bcftools-1.21/test/consensus.tab + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -I -s - -m /build/reproducible-path/bcftools-1.21/test/consensus.tab .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -I -m /build/reproducible-path/bcftools-1.21/test/consensus.tab --mask-with X -m /build/reproducible-path/bcftools-1.21/test/consensus.tab --mask-with lc + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -I -m /build/reproducible-path/bcftools-1.21/test/consensus.tab --mask-with X -m /build/reproducible-path/bcftools-1.21/test/consensus.tab --mask-with lc .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -I -m /build/reproducible-path/bcftools-1.21/test/consensus.tab --mask-with X -m /build/reproducible-path/bcftools-1.21/test/consensus.tab --mask-with lc + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -I -m /build/reproducible-path/bcftools-1.21/test/consensus.tab --mask-with X -m /build/reproducible-path/bcftools-1.21/test/consensus.tab --mask-with lc .. ok test_vcf_consensus_chain: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -I -m /build/reproducible-path/bcftools-1.21/test/consensus.tab -c /tmp/wj8A4a3te7/consensus.3.chain.new >/dev/null; cat /tmp/wj8A4a3te7/consensus.3.chain.new + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -I -m /build/reproducible-path/bcftools-1.21/test/consensus.tab -c /tmp/zPov9rP7t1/consensus.3.chain.new >/dev/null; cat /tmp/zPov9rP7t1/consensus.3.chain.new .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -H 1 + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -H 1 .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -H 1 + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -H 1 .. ok test_vcf_consensus_chain: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -H 1 -c /tmp/wj8A4a3te7/consensus.4.chain.new >/dev/null; cat /tmp/wj8A4a3te7/consensus.4.chain.new + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -H 1 -c /tmp/zPov9rP7t1/consensus.4.chain.new >/dev/null; cat /tmp/zPov9rP7t1/consensus.4.chain.new .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus2.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -H 1 + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus2.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -H 1 .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus2.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -H 1 + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus2.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -H 1 .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus2.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -H 2 + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus2.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -H 2 .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus2.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -H 2 + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus2.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -H 2 .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/empty.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/empty.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/empty.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/empty.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -H 2 -M "?" + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -H 2 -M "?" .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus3.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -H 2 -M "?" + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus3.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -H 2 -M "?" .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -H 2 -M "?" -p xx_ + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -H 2 -M "?" -p xx_ .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus3.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -H 2 -M "?" -p xx_ + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus3.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -H 2 -M "?" -p xx_ .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus4.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -s - + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus4.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -s - .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus4.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -s - + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus4.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -s - .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus5.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus5.fa --haplotype LA + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus5.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus5.fa --haplotype LA .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus5.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus5.fa --haplotype LA + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus5.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus5.fa --haplotype LA .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus6.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus6.fa -s - + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus6.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus6.fa -s - .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus6.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus6.fa -s - + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus6.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus6.fa -s - .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus7.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 2 + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus7.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 2 .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus7.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 2 + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus7.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 2 .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus7.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 4 + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus7.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 4 .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus7.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 4 + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus7.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 4 .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus7.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 2pIu + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus7.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 2pIu .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus7.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 2pIu + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus7.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 2pIu .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus7.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 4pIu + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus7.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 4pIu .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus7.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 4pIu + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus7.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 4pIu .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus7.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 1 + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus7.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 1 .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus7.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 1 + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus7.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 1 .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus7.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 3 + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus7.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 3 .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus7.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 3 + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus7.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 3 .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus7.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 1pIu + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus7.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 1pIu .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus7.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 1pIu + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus7.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 1pIu .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus7.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 3pIu + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus7.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 3pIu .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus7.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 3pIu + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus7.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 3pIu .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus8.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus8.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus8.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus8.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus8.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -a . + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus8.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -a . .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus8.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -a . + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus8.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -a . .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus8.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -a . -i 'type="snp" || type="ref"' + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus8.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -a . -i 'type="snp" || type="ref"' .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus8.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -a . -i 'type="snp" || type="ref"' + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus8.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -a . -i 'type="snp" || type="ref"' .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus8.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -a . -i 'ALT!=""' + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus8.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -a . -i 'ALT!=""' .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus8.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -a . -i 'ALT!=""' + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus8.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -a . -i 'ALT!=""' .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus8.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -a . -e 'MinDP>15' + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus8.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -a . -e 'MinDP>15' .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus8.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -a . -e 'MinDP>15' + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus8.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -a . -e 'MinDP>15' .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus8.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -a . -e 'MinDP<15' + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus8.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -a . -e 'MinDP<15' .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus8.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -a . -e 'MinDP<15' + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus8.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -a . -e 'MinDP<15' .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.9.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.9.1.fa -H A + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.9.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.9.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.9.1.fa -H A + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.9.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.9.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.9.2.fa -H A + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.9.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.9.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.9.2.fa -H A + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.9.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.10.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.9.1.fa -H A + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.10.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.10.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.9.1.fa -H A + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.10.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.10.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.9.2.fa -H A + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.10.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.10.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.9.2.fa -H A + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.10.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.11.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.11.fa -s smpl + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.11.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.11.fa -s smpl .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.11.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.11.fa -s smpl + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.11.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.11.fa -s smpl .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.11.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.11.fa -s smpl -a N + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.11.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.11.fa -s smpl -a N .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.11.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.11.fa -s smpl -a N + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.11.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.11.fa -s smpl -a N .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.12.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.12.fa -s - + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.12.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.12.fa -s - .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.12.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.12.fa -s - + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.12.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.12.fa -s - .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.13.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.13.fa -s - + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.13.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.13.fa -s - .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.13.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.13.fa -s - + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.13.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.13.fa -s - .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.14.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.14.fa -s - + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.14.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.14.fa -s - .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.14.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.14.fa -s - + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.14.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.14.fa -s - .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.12.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.12.fa -s - --mark-del - --mark-ins uc --mark-snv uc + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.12.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.12.fa -s - --mark-del - --mark-ins uc --mark-snv uc .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.12.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.12.fa -s - --mark-del - --mark-ins uc --mark-snv uc + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.12.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.12.fa -s - --mark-del - --mark-ins uc --mark-snv uc .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.12.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.12.fa -s - --mark-del - --mark-ins + --mark-snv : + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.12.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.12.fa -s - --mark-del - --mark-ins + --mark-snv : .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.12.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.12.fa -s - --mark-del - --mark-ins + --mark-snv : + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.12.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.12.fa -s - --mark-del - --mark-ins + --mark-snv : .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.15.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.15.fa -H I --mark-ins lc --mark-snv lc + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.15.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.15.fa -H I --mark-ins lc --mark-snv lc .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.15.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.15.fa -H I --mark-ins lc --mark-snv lc + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.15.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.15.fa -H I --mark-ins lc --mark-snv lc .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.16.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -I + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.16.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -I .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.16.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -I + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.16.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -I .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.16.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -H I + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.16.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -H I .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.16.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -H I + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.16.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -H I .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.17.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -s - -M N -m /build/reproducible-path/bcftools-1.21/test/consensus.17.bed + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.17.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -s - -M N -m /build/reproducible-path/bcftools-1.21/test/consensus.17.bed .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.17.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -s - -M N -m /build/reproducible-path/bcftools-1.21/test/consensus.17.bed + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.17.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -s - -M N -m /build/reproducible-path/bcftools-1.21/test/consensus.17.bed .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.18.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.18.fa -s - + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.18.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.18.fa -s - .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.18.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.18.fa -s - + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.18.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.18.fa -s - .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.19.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.19.fa -s - + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.19.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.19.fa -s - .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.19.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.19.fa -s - + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.19.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.19.fa -s - .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.20.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.20.fa -s - + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.20.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.20.fa -s - .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.20.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.20.fa -s - + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.20.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.20.fa -s - .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.20.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.20.fa + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.20.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.20.fa .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.20.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.20.fa + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.20.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.20.fa .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.20.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.20.fa -M . -s b + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.20.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.20.fa -M . -s b .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.20.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.20.fa -M . -s b + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.20.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.20.fa -M . -s b .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.20.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.20.fa -M . -s a + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.20.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.20.fa -M . -s a .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.20.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.20.fa -M . -s a + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.20.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.20.fa -M . -s a .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.21.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.21.fa + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.21.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.21.fa .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.21.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.21.fa + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.21.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.21.fa .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.22.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 0 --mark-del . + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.22.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 0 --mark-del . .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.22.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 0 --mark-del . + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.22.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 0 --mark-del . .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.22.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 1 --mark-del . + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.22.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 1 --mark-del . .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.22.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 1 --mark-del . + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.22.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 1 --mark-del . .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.22.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 2 --mark-del . + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.22.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 2 --mark-del . .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.22.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 2 --mark-del . + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.22.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 2 --mark-del . .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.22.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 0 + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.22.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 0 .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.22.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 0 + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.22.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 0 .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.22.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 1 + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.22.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 1 .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.22.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 1 + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.22.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 1 .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.22.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 2 + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.22.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 2 .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/wj8A4a3te7/consensus.22.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 2 + /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/zPov9rP7t1/consensus.22.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 2 .. ok test_mpileup: @@ -6856,11 +6892,11 @@ .. ok test_mpileup: - /build/reproducible-path/bcftools-1.21/bcftools mpileup -r17:100-150 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -b /tmp/wj8A4a3te7/mpileup.bam.list --no-version | grep -v ^##reference + /build/reproducible-path/bcftools-1.21/bcftools mpileup -r17:100-150 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -b /tmp/zPov9rP7t1/mpileup.bam.list --no-version | grep -v ^##reference .. ok test_mpileup: - /build/reproducible-path/bcftools-1.21/bcftools mpileup -r17:100-150 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob -b /tmp/wj8A4a3te7/mpileup.bam.urllist | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference + /build/reproducible-path/bcftools-1.21/bcftools mpileup -r17:100-150 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob -b /tmp/zPov9rP7t1/mpileup.bam.urllist | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: @@ -6872,11 +6908,11 @@ .. ok test_mpileup: - /build/reproducible-path/bcftools-1.21/bcftools mpileup -r17:100-150 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -b /tmp/wj8A4a3te7/mpileup.cram.list --no-version | grep -v ^##reference + /build/reproducible-path/bcftools-1.21/bcftools mpileup -r17:100-150 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -b /tmp/zPov9rP7t1/mpileup.cram.list --no-version | grep -v ^##reference .. ok test_mpileup: - /build/reproducible-path/bcftools-1.21/bcftools mpileup -r17:100-150 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob -b /tmp/wj8A4a3te7/mpileup.cram.urllist | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference + /build/reproducible-path/bcftools-1.21/bcftools mpileup -r17:100-150 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob -b /tmp/zPov9rP7t1/mpileup.cram.urllist | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: @@ -7424,111 +7460,107 @@ .. ok test_csq_real: - cd /build/reproducible-path/bcftools-1.21/test/csq/ENST00000410009 && /build/reproducible-path/bcftools-1.21/bcftools csq -lb -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' -.. ok - -test_csq_real: - cd /build/reproducible-path/bcftools-1.21/test/csq/ENST00000410009 && /build/reproducible-path/bcftools-1.21/bcftools csq -B 5 -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000420670/ENST00000420670.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000420670/ENST00000420670.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000420670/start-stop-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000410009/ENST00000410009.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000410009/ENST00000410009.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000410009/frameshift.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000420670/ENST00000420670.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000420670/ENST00000420670.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000420670/segfault.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - cd /build/reproducible-path/bcftools-1.21/test/csq/ENST00000410009 && /build/reproducible-path/bcftools-1.21/bcftools csq -b -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/frame2.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000557788/ENST00000557788.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000557788/ENST00000557788.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000557788/long-overlap-del.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/frame2.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - cd /build/reproducible-path/bcftools-1.21/test/csq/ENSMUST00000133836 && /build/reproducible-path/bcftools-1.21/bcftools csq -f ENSMUST00000133836.fa -g ENSMUST00000133836.gff filter-problem.vcf -i 'FILTER="PASS"' --phase m | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000420190/ENST00000420190.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000420190/ENST00000420190.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000420190/abort-in-csq-push.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000448695/ENST00000448695.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000448695/ENST00000448695.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000448695/syn-and-splice-reg.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000520868/ENST00000520868.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000520868/ENST00000520868.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000520868/long-deletion.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000373833/ENST00000373833.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000373833/ENST00000373833.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000373833/boundary-insertion.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/frame3.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000373833/ENST00000373833.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000373833/ENST00000373833.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000373833/boundary-insertion.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/frame3.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000518414/ENST00000518414.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000518414/ENST00000518414.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000518414/incorrect-inframe-del.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000571540/ENST00000571540.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000571540/ENST00000571540.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000571540/nmd.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000318249/ENST00000318249.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000318249/ENST00000318249.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000318249/start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000318249/ENST00000318249.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000318249/ENST00000318249.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000318249/start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000218032/ENST00000218032.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000218032/ENST00000218032.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000218032/start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000218032/ENST00000218032.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000218032/ENST00000218032.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000218032/start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000218032/ENST00000218032.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000218032/ENST00000218032.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000218032/start-lost-del.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/frame1.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000329454/ENST00000329454.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000329454/ENST00000329454.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000329454/boundary-deletion.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/frame1.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000329454/ENST00000329454.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000329454/ENST00000329454.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000329454/boundary-deletion.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0002/EDUMMY0002.fa -g /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0002/EDUMMY0002.gff /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0002/boundaries.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0001/EDUMMY0001.fa -g /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0001/EDUMMY0001.gff /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0001/starts-with-1.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0001/EDUMMY0001.fa -g /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0001/EDUMMY0001.gff /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0001/starts-with-1.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/frame2.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/frame2.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: @@ -7540,99 +7572,99 @@ .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000375992/ENST00000375992.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000375992/ENST00000375992.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000375992/incorrect-synon-del-not-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000373833/ENST00000373833.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000373833/ENST00000373833.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000373833/boundary-insertion.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000373833/ENST00000373833.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000373833/ENST00000373833.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000373833/boundary-insertion.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000218032/ENST00000218032.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000218032/ENST00000218032.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000218032/start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/frame1.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000218032/ENST00000218032.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000218032/ENST00000218032.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000218032/start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/frame1.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000218032/ENST00000218032.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000218032/ENST00000218032.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000218032/start-lost-del.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0002/EDUMMY0002.fa -g /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0002/EDUMMY0002.gff /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0002/boundaries.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000420190/ENST00000420190.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000420190/ENST00000420190.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000420190/abort-in-csq-push.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000378322/ENST00000378322.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000378322/ENST00000378322.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000378322/end-overlap-tscript.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000378322/ENST00000378322.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000378322/ENST00000378322.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000378322/end-overlap-tscript.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/frame3.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000230048/ENST00000230048.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000230048/ENST00000230048.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000230048/start-del.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/frame3.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000400151/ENST00000400151.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000400151/ENST00000400151.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000400151/long-del.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000390520/ENST00000390520.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000390520/ENST00000390520.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000390520/deletion-overlap.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000542803/ENST00000542803.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000542803/ENST00000542803.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000542803/splice-region.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000542803/ENST00000542803.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000542803/ENST00000542803.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000542803/splice-region.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0003/EDUMMY0003.fa -g /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0003/EDUMMY0003.gff /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0003/long-del.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000545279/ENST00000545279.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000545279/ENST00000545279.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000545279/splice-region-insert.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + cd /build/reproducible-path/bcftools-1.21/test/csq/ENSMUST00000121418 && /build/reproducible-path/bcftools-1.21/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25496' --phase m | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + cd /build/reproducible-path/bcftools-1.21/test/csq/ENSMUST00000121418 && /build/reproducible-path/bcftools-1.21/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25500' --phase m | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + cd /build/reproducible-path/bcftools-1.21/test/csq/ENSMUST00000121418 && /build/reproducible-path/bcftools-1.21/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25105' --phase m | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000382647/ENST00000382647.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000382647/ENST00000382647.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000382647/synon-splice-region-insert.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000520795/ENST00000520795.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000520795/ENST00000520795.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000520795/long-inside-del.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000303039/ENST00000303039.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000303039/ENST00000303039.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000303039/not-a-stop.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000520795/ENST00000520795.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000520795/ENST00000520795.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000520795/long-inside-del.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000303039/ENST00000303039.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000303039/ENST00000303039.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000303039/not-a-stop.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000528237/ENST00000528237.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000528237/ENST00000528237.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000528237/retained-stop-incomplete-cds.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000409523/ENST00000409523.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000409523/ENST00000409523.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000409523/long-overlapping-del.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000436063/ENST00000436063.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000436063/ENST00000436063.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000436063/insert-before-utr.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: @@ -7644,135 +7676,139 @@ .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000230048/ENST00000230048.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000230048/ENST00000230048.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000230048/start-del.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000285021/ENST00000285021.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000285021/ENST00000285021.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000285021/stop-gained-inframe-indel.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/snps.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000382647/ENST00000382647.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000382647/ENST00000382647.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000382647/synon-splice-region-insert.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/snps.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000571540/ENST00000571540.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000571540/ENST00000571540.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000571540/nmd.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/insert3.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000413103/ENST00000413103.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000413103/ENST00000413103.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000413103/long-deletion.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/insert3.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000536784/ENST00000536784.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000536784/ENST00000536784.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000536784/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0003/EDUMMY0003.fa -g /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0003/EDUMMY0003.gff /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0003/long-del.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000536784/ENST00000536784.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000536784/ENST00000536784.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000536784/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000375992/ENST00000375992.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000375992/ENST00000375992.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000375992/incorrect-synon-del-not-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/snps.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000263103-INS/ENST00000263103-INS.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000263103-INS/ENST00000263103-INS.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000263103-INS/insertions.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/snps.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000413103/ENST00000413103.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000413103/ENST00000413103.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000413103/long-deletion.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/insert3.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000295641/ENST00000295641.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000295641/ENST00000295641.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000295641/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/insert3.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000295641/ENST00000295641.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000295641/ENST00000295641.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000295641/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + cd /build/reproducible-path/bcftools-1.21/test/csq/ENSMUST00000133836 && /build/reproducible-path/bcftools-1.21/bcftools csq -f ENSMUST00000133836.fa -g ENSMUST00000133836.gff filter-problem.vcf -i 'FILTER="PASS"' --phase m | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000378322/ENST00000378322.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000378322/ENST00000378322.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000378322/end-overlap-tscript.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + cd /build/reproducible-path/bcftools-1.21/test/csq/ENST00000000000 && /build/reproducible-path/bcftools-1.21/bcftools csq -p a -f ENST00000000000.fa -g ENST00000000000.gff upstream-stop.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%REF\t%ALT\t%SAMPLE\t%GT\t%TBCSQ\n]' | ../sort-csq -q .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000378322/ENST00000378322.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000378322/ENST00000378322.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000378322/end-overlap-tscript.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + cd /build/reproducible-path/bcftools-1.21/test/csq/ENST00000422159 && /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000422159.fa -g ENST00000422159.gff multiallelic.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%REF\t%ALT\t%GT\t%TBCSQ\n]' | ../sort-csq -q ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000422159.fa -g short.gff multiallelic.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%REF\t%ALT\t%GT\t%TBCSQ\n]' | ../sort-csq -q .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000542803/ENST00000542803.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000542803/ENST00000542803.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000542803/splice-region.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000479739/ENST00000479739.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000479739/ENST00000479739.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000479739/short-cds-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000542803/ENST00000542803.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000542803/ENST00000542803.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000542803/splice-region.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000479739/ENST00000479739.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000479739/ENST00000479739.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000479739/short-cds-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000271583/ENST00000271583.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000271583/ENST00000271583.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000271583/splice-acceptor.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000557788/ENST00000557788.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000557788/ENST00000557788.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000557788/long-overlap-del.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000294661/ENST00000294661.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000294661/ENST00000294661.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000294661/non-coding-boundary.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + cd /build/reproducible-path/bcftools-1.21/test/csq/ENST00000410009 && /build/reproducible-path/bcftools-1.21/bcftools csq -B 5 -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000294661/ENST00000294661.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000294661/ENST00000294661.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000294661/non-coding-boundary.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000410009/ENST00000410009.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000410009/ENST00000410009.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000410009/frameshift.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000360372/ENST00000360372.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000360372/ENST00000360372.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000360372/mnp.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + cd /build/reproducible-path/bcftools-1.21/test/csq/ENST00000410009 && /build/reproducible-path/bcftools-1.21/bcftools csq -lb -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: - cd /build/reproducible-path/bcftools-1.21/test/csq/ENST00000422159 && /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000422159.fa -g ENST00000422159.gff multiallelic.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%REF\t%ALT\t%GT\t%TBCSQ\n]' | ../sort-csq -q ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000422159.fa -g short.gff multiallelic.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%REF\t%ALT\t%GT\t%TBCSQ\n]' | ../sort-csq -q + cd /build/reproducible-path/bcftools-1.21/test/csq/ENST00000410009 && /build/reproducible-path/bcftools-1.21/bcftools csq -b -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000518414-ENST00000521270/valgrind.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000269081/ENST00000269081.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000269081/ENST00000269081.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000269081/stop-gained-not-inframe-insertion.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000528237/ENST00000528237.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000528237/ENST00000528237.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000528237/retained-stop-incomplete-cds.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000573035-bt2212/ENST00000573035-bt2212.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000573035-bt2212/ENST00000573035-bt2212.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000573035-bt2212/complex-event.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - cd /build/reproducible-path/bcftools-1.21/test/csq/ENST00000379416 && /build/reproducible-path/bcftools-1.21/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.del-snp.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-del.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-ins.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-snp.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff single.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000520868/ENST00000520868.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000520868/ENST00000520868.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000520868/long-deletion.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000536784/ENST00000536784.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000536784/ENST00000536784.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000536784/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + cd /build/reproducible-path/bcftools-1.21/test/csq/EMN908947 && /build/reproducible-path/bcftools-1.21/bcftools csq -f EMN908947.fa -g simple.gff simple.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000536784/ENST00000536784.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000536784/ENST00000536784.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000536784/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + cd /build/reproducible-path/bcftools-1.21/test/csq/EMN908947 && /build/reproducible-path/bcftools-1.21/bcftools csq -f EMN908947.fa -g ribosomal-slippage.gff ribosomal-slippage.vcf --force | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000436063/ENST00000436063.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000436063/ENST00000436063.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000436063/insert-before-utr.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000409523/ENST00000409523.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000409523/ENST00000409523.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000409523/long-overlapping-del.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - cd /build/reproducible-path/bcftools-1.21/test/csq/EMN908947 && /build/reproducible-path/bcftools-1.21/bcftools csq -f EMN908947.fa -g ribosomal-slippage.gff ribosomal-slippage.vcf --force | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000368801.2/ENST00000368801.2.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000368801.2/ENST00000368801.2.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000368801.2/start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - cd /build/reproducible-path/bcftools-1.21/test/csq/EMN908947 && /build/reproducible-path/bcftools-1.21/bcftools csq -f EMN908947.fa -g simple.gff simple.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000357367/ENST00000357367.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000357367/ENST00000357367.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000357367/stop-retained.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000357367/ENST00000357367.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000357367/ENST00000357367.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000357367/stop-retained.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000519442/ENST00000519442.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000519442/ENST00000519442.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000519442/synon-splice-region-del.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000573035-bt2212/ENST00000573035-bt2212.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000573035-bt2212/ENST00000573035-bt2212.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000573035-bt2212/complex-event.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000256452/ENST00000256452.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000256452/ENST00000256452.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000256452/intron.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000318249.2/ENST00000318249.2.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000318249.2/ENST00000318249.2.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000318249.2/synonymous-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000518414-ENST00000521270/valgrind.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000545279/ENST00000545279.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000545279/ENST00000545279.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000545279/splice-region-insert.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + cd /build/reproducible-path/bcftools-1.21/test/csq/ENST00000580206 && /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.ins-snv.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g short.gff compound.ins-snv.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff single.ins-snv.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g short.gff single.ins-snv.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.del-snv.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g short.gff compound.del-snv.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g short.gff single.del-snv.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.del-ins.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g short.gff compound.del-ins.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g short.gff single.del-ins.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000368801/ENST00000368801.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000368801/ENST00000368801.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000368801/compound-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + cd /build/reproducible-path/bcftools-1.21/test/csq/ENST00000379416 && /build/reproducible-path/bcftools-1.21/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.del-snp.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-del.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-ins.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-snp.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff single.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' +.. ok + +test_csq_real: + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000263103-INS/ENST00000263103-INS.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000263103-INS/ENST00000263103-INS.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000263103-INS/insertions.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: @@ -7780,103 +7816,103 @@ .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000285021/ENST00000285021.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000285021/ENST00000285021.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000285021/stop-gained-inframe-indel.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000543077/ENST00000543077.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000543077/ENST00000543077.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000543077/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000400151/ENST00000400151.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000400151/ENST00000400151.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000400151/long-del.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000543077/ENST00000543077.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000543077/ENST00000543077.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000543077/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000420670/ENST00000420670.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000420670/ENST00000420670.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000420670/start-stop-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENSG00000173376/ENSG00000173376.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENSG00000173376/ENSG00000173376.gff /build/reproducible-path/bcftools-1.21/test/csq/ENSG00000173376/synon.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000420670/ENST00000420670.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000420670/ENST00000420670.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000420670/segfault.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000318249.2/ENST00000318249.2.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000318249.2/ENST00000318249.2.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000318249.2/synonymous-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - cd /build/reproducible-path/bcftools-1.21/test/csq/ENST00000580206 && /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.ins-snv.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g short.gff compound.ins-snv.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff single.ins-snv.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g short.gff single.ins-snv.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.del-snv.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g short.gff compound.del-snv.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g short.gff single.del-snv.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.del-ins.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g short.gff compound.del-ins.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g short.gff single.del-ins.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000518414/ENST00000518414.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000518414/ENST00000518414.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000518414/incorrect-inframe-del.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000256452/ENST00000256452.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000256452/ENST00000256452.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000256452/intron.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000360372/ENST00000360372.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000360372/ENST00000360372.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000360372/mnp.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENSG00000173376/ENSG00000173376.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENSG00000173376/ENSG00000173376.gff /build/reproducible-path/bcftools-1.21/test/csq/ENSG00000173376/synon.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000593942/ENST00000593942.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000593942/ENST00000593942.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000593942/last-codon-deletion.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000519442/ENST00000519442.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000519442/ENST00000519442.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000519442/synon-splice-region-del.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000448695/ENST00000448695.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000448695/ENST00000448695.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000448695/syn-and-splice-reg.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000390520/ENST00000390520.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000390520/ENST00000390520.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000390520/deletion-overlap.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000227471/ENST00000227471.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000227471/ENST00000227471.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000227471/insert-splice-vs-frameshift.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - cd /build/reproducible-path/bcftools-1.21/test/csq/ENST00000000000 && /build/reproducible-path/bcftools-1.21/bcftools csq -p a -f ENST00000000000.fa -g ENST00000000000.gff upstream-stop.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%REF\t%ALT\t%SAMPLE\t%GT\t%TBCSQ\n]' | ../sort-csq -q + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000624631/ENST00000624631.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000624631/ENST00000624631.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000624631/ambiguous.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000269081/ENST00000269081.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000269081/ENST00000269081.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000269081/stop-gained-not-inframe-insertion.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000295641/ENST00000295641.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000295641/ENST00000295641.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000295641/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000543077/ENST00000543077.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000543077/ENST00000543077.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000543077/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000295641/ENST00000295641.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000295641/ENST00000295641.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000295641/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000543077/ENST00000543077.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000543077/ENST00000543077.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000543077/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000294661/ENST00000294661.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000294661/ENST00000294661.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000294661/non-coding-boundary.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000624631/ENST00000624631.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000624631/ENST00000624631.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000624631/ambiguous.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000294661/ENST00000294661.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000294661/ENST00000294661.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000294661/non-coding-boundary.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000479739/ENST00000479739.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000479739/ENST00000479739.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000479739/short-cds-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000303039/ENST00000303039.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000303039/ENST00000303039.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000303039/not-a-stop.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000479739/ENST00000479739.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000479739/ENST00000479739.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000479739/short-cds-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000303039/ENST00000303039.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000303039/ENST00000303039.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000303039/not-a-stop.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000301246/ENST00000301246.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000301246/ENST00000301246.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000301246/15bp-insert.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000318249/ENST00000318249.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000318249/ENST00000318249.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000318249/start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000368801.2/ENST00000368801.2.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000368801.2/ENST00000368801.2.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000368801.2/start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000318249/ENST00000318249.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000318249/ENST00000318249.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000318249/start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - cd /build/reproducible-path/bcftools-1.21/test/csq/ENSMUST00000121418 && /build/reproducible-path/bcftools-1.21/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25500' --phase m | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000368801/ENST00000368801.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000368801/ENST00000368801.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000368801/compound-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - cd /build/reproducible-path/bcftools-1.21/test/csq/ENSMUST00000121418 && /build/reproducible-path/bcftools-1.21/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25496' --phase m | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000329454/ENST00000329454.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000329454/ENST00000329454.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000329454/boundary-deletion.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - cd /build/reproducible-path/bcftools-1.21/test/csq/ENSMUST00000121418 && /build/reproducible-path/bcftools-1.21/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25105' --phase m | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000329454/ENST00000329454.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000329454/ENST00000329454.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000329454/boundary-deletion.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000593942/ENST00000593942.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000593942/ENST00000593942.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000593942/last-codon-deletion.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000271583/ENST00000271583.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000271583/ENST00000271583.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000271583/splice-acceptor.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000520795/ENST00000520795.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000520795/ENST00000520795.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000520795/long-inside-del.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000301246/ENST00000301246.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000301246/ENST00000301246.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000301246/15bp-insert.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000520795/ENST00000520795.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000520795/ENST00000520795.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000520795/long-inside-del.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0001/EDUMMY0001.fa -g /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0001/EDUMMY0001.gff /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0001/starts-with-1.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: - /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000227471/ENST00000227471.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000227471/ENST00000227471.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000227471/insert-splice-vs-frameshift.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' + /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0001/EDUMMY0001.fa -g /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0001/EDUMMY0001.gff /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0001/starts-with-1.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_roh: @@ -7908,139 +7944,139 @@ .. ok test_gtcheck: - /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 --no-HWE-prob /tmp/wj8A4a3te7/gtcheck.1.vcf.gz -g /tmp/wj8A4a3te7/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO + /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 --no-HWE-prob /tmp/zPov9rP7t1/gtcheck.1.vcf.gz -g /tmp/zPov9rP7t1/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: - /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 /tmp/wj8A4a3te7/gtcheck.1.vcf.gz -g /tmp/wj8A4a3te7/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO + /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 /tmp/zPov9rP7t1/gtcheck.1.vcf.gz -g /tmp/zPov9rP7t1/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: - /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -u GT,GT /tmp/wj8A4a3te7/gtcheck.1.vcf.gz -g /tmp/wj8A4a3te7/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO + /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -u GT,GT /tmp/zPov9rP7t1/gtcheck.1.vcf.gz -g /tmp/zPov9rP7t1/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: - /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -u GT,PL /tmp/wj8A4a3te7/gtcheck.1.vcf.gz -g /tmp/wj8A4a3te7/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO + /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -u GT,PL /tmp/zPov9rP7t1/gtcheck.1.vcf.gz -g /tmp/zPov9rP7t1/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: - /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -u PL,GT /tmp/wj8A4a3te7/gtcheck.1.vcf.gz -g /tmp/wj8A4a3te7/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO + /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -u PL,GT /tmp/zPov9rP7t1/gtcheck.1.vcf.gz -g /tmp/zPov9rP7t1/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: - /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -u PL,PL /tmp/wj8A4a3te7/gtcheck.1.vcf.gz -g /tmp/wj8A4a3te7/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO + /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -u PL,PL /tmp/zPov9rP7t1/gtcheck.1.vcf.gz -g /tmp/zPov9rP7t1/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: - /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -p s1,s1 /tmp/wj8A4a3te7/gtcheck.1.vcf.gz -g /tmp/wj8A4a3te7/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO + /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -p s1,s1 /tmp/zPov9rP7t1/gtcheck.1.vcf.gz -g /tmp/zPov9rP7t1/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: - /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 /tmp/wj8A4a3te7/gtcheck.2.vcf.gz -g /tmp/wj8A4a3te7/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO + /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 /tmp/zPov9rP7t1/gtcheck.2.vcf.gz -g /tmp/zPov9rP7t1/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: - /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 /tmp/wj8A4a3te7/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO + /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 /tmp/zPov9rP7t1/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: - /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -p B,A,C,A,C,B,D,A,D,B,D,C,E,A,E,B,E,C,E,D /tmp/wj8A4a3te7/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO + /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -p B,A,C,A,C,B,D,A,D,B,D,C,E,A,E,B,E,C,E,D /tmp/zPov9rP7t1/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: - /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -P /build/reproducible-path/bcftools-1.21/test/gtcheck.3.pairs /tmp/wj8A4a3te7/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO + /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -P /build/reproducible-path/bcftools-1.21/test/gtcheck.3.pairs /tmp/zPov9rP7t1/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: - /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -u PL /tmp/wj8A4a3te7/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO + /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -u PL /tmp/zPov9rP7t1/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: - /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 --n-matches 4 /tmp/wj8A4a3te7/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO | sort + /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 --n-matches 4 /tmp/zPov9rP7t1/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO | sort .. ok test_gtcheck: - /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -s qry:E,D,C /tmp/wj8A4a3te7/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO + /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -s qry:E,D,C /tmp/zPov9rP7t1/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: - /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -s qry:E,D,C -u PL /tmp/wj8A4a3te7/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO + /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -s qry:E,D,C -u PL /tmp/zPov9rP7t1/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: - /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -s qry:B -s gt:D /tmp/wj8A4a3te7/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO + /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -s qry:B -s gt:D /tmp/zPov9rP7t1/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: - /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -s qry:B -s gt:D -u PL /tmp/wj8A4a3te7/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO + /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -s qry:B -s gt:D -u PL /tmp/zPov9rP7t1/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: - /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -s qry:B -s gt:D,C /tmp/wj8A4a3te7/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO + /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -s qry:B -s gt:D,C /tmp/zPov9rP7t1/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: - /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -p B,C,B,D /tmp/wj8A4a3te7/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO + /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -p B,C,B,D /tmp/zPov9rP7t1/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: - /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -u GT,GT -H /tmp/wj8A4a3te7/gtcheck.1.vcf.gz -g /tmp/wj8A4a3te7/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO + /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -u GT,GT -H /tmp/zPov9rP7t1/gtcheck.1.vcf.gz -g /tmp/zPov9rP7t1/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: - /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -u GT,PL -H /tmp/wj8A4a3te7/gtcheck.1.vcf.gz -g /tmp/wj8A4a3te7/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO + /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -u GT,PL -H /tmp/zPov9rP7t1/gtcheck.1.vcf.gz -g /tmp/zPov9rP7t1/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: - /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -u PL,GT -H /tmp/wj8A4a3te7/gtcheck.1.vcf.gz -g /tmp/wj8A4a3te7/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO + /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -u PL,GT -H /tmp/zPov9rP7t1/gtcheck.1.vcf.gz -g /tmp/zPov9rP7t1/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: - /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -u PL,PL -H /tmp/wj8A4a3te7/gtcheck.1.vcf.gz -g /tmp/wj8A4a3te7/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO + /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -u PL,PL -H /tmp/zPov9rP7t1/gtcheck.1.vcf.gz -g /tmp/zPov9rP7t1/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: - /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -P /build/reproducible-path/bcftools-1.21/test/gtcheck.4.pairs --distinctive-sites 3 /tmp/wj8A4a3te7/gtcheck.4.vcf.gz | grep -v ^# | grep -v ^INFO + /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -P /build/reproducible-path/bcftools-1.21/test/gtcheck.4.pairs --distinctive-sites 3 /tmp/zPov9rP7t1/gtcheck.4.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: - /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -P /build/reproducible-path/bcftools-1.21/test/gtcheck.4.pairs --distinctive-sites 3,1 /tmp/wj8A4a3te7/gtcheck.4.vcf.gz | grep -v ^# | grep -v ^INFO + /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -P /build/reproducible-path/bcftools-1.21/test/gtcheck.4.pairs --distinctive-sites 3,1 /tmp/zPov9rP7t1/gtcheck.4.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: - /build/reproducible-path/bcftools-1.21/bcftools gtcheck -u GT -e 30 /tmp/wj8A4a3te7/gtcheck.1.vcf.gz -g /tmp/wj8A4a3te7/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO + /build/reproducible-path/bcftools-1.21/bcftools gtcheck -u GT -e 30 /tmp/zPov9rP7t1/gtcheck.1.vcf.gz -g /tmp/zPov9rP7t1/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: - /build/reproducible-path/bcftools-1.21/bcftools gtcheck -u GT -e 30 -p s1,s1 /tmp/wj8A4a3te7/gtcheck.1.vcf.gz -g /tmp/wj8A4a3te7/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO + /build/reproducible-path/bcftools-1.21/bcftools gtcheck -u GT -e 30 -p s1,s1 /tmp/zPov9rP7t1/gtcheck.1.vcf.gz -g /tmp/zPov9rP7t1/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: - /build/reproducible-path/bcftools-1.21/bcftools gtcheck -u GT -e 300 /tmp/wj8A4a3te7/gtcheck.1.vcf.gz -g /tmp/wj8A4a3te7/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO + /build/reproducible-path/bcftools-1.21/bcftools gtcheck -u GT -e 300 /tmp/zPov9rP7t1/gtcheck.1.vcf.gz -g /tmp/zPov9rP7t1/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: - /build/reproducible-path/bcftools-1.21/bcftools gtcheck -u PL -e 30 /tmp/wj8A4a3te7/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO + /build/reproducible-path/bcftools-1.21/bcftools gtcheck -u PL -e 30 /tmp/zPov9rP7t1/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: - /build/reproducible-path/bcftools-1.21/bcftools gtcheck /tmp/wj8A4a3te7/gtcheck.ntop.vcf.gz -g /tmp/wj8A4a3te7/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO + /build/reproducible-path/bcftools-1.21/bcftools gtcheck /tmp/zPov9rP7t1/gtcheck.ntop.vcf.gz -g /tmp/zPov9rP7t1/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: - /build/reproducible-path/bcftools-1.21/bcftools gtcheck --n-matches 2 /tmp/wj8A4a3te7/gtcheck.ntop.vcf.gz -g /tmp/wj8A4a3te7/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO + /build/reproducible-path/bcftools-1.21/bcftools gtcheck --n-matches 2 /tmp/zPov9rP7t1/gtcheck.ntop.vcf.gz -g /tmp/zPov9rP7t1/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: - /build/reproducible-path/bcftools-1.21/bcftools gtcheck /tmp/wj8A4a3te7/gtcheck.5.vcf.gz -g /tmp/wj8A4a3te7/gtcheck.5.gts.vcf.gz | grep -v ^# | grep -v Time + /build/reproducible-path/bcftools-1.21/bcftools gtcheck /tmp/zPov9rP7t1/gtcheck.5.vcf.gz -g /tmp/zPov9rP7t1/gtcheck.5.gts.vcf.gz | grep -v ^# | grep -v Time .. ok test_gtcheck: - /build/reproducible-path/bcftools-1.21/bcftools gtcheck -p A,B,B,C /tmp/wj8A4a3te7/gtcheck.6.vcf.gz | grep -v ^# | grep -v ^INFO + /build/reproducible-path/bcftools-1.21/bcftools gtcheck -p A,B,B,C /tmp/zPov9rP7t1/gtcheck.6.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: - /build/reproducible-path/bcftools-1.21/bcftools gtcheck -t 11:33 -p A,D,A,E,D,E -u GT -e 10 /tmp/wj8A4a3te7/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO + /build/reproducible-path/bcftools-1.21/bcftools gtcheck -t 11:33 -p A,D,A,E,D,E -u GT -e 10 /tmp/zPov9rP7t1/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok @@ -8054,7 +8090,7 @@ create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/bcftools/ - make -j40 install DESTDIR=/build/reproducible-path/bcftools-1.21/debian/bcftools AM_UPDATE_INFO_DIR=no + make -j42 install DESTDIR=/build/reproducible-path/bcftools-1.21/debian/bcftools AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/bcftools-1.21' mkdir -p -m 755 /build/reproducible-path/bcftools-1.21/debian/bcftools/usr/bin /build/reproducible-path/bcftools-1.21/debian/bcftools/usr/share/man/man1 /build/reproducible-path/bcftools-1.21/debian/bcftools/usr/lib/x86_64-linux-gnu/bcftools install -p bcftools /build/reproducible-path/bcftools-1.21/debian/bcftools/usr/bin @@ -8093,8 +8129,8 @@ dpkg-gencontrol: warning: package bcftools: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb -dpkg-deb: building package 'bcftools-dbgsym' in '../bcftools-dbgsym_1.21-1_amd64.deb'. dpkg-deb: building package 'bcftools' in '../bcftools_1.21-1_amd64.deb'. +dpkg-deb: building package 'bcftools-dbgsym' in '../bcftools-dbgsym_1.21-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../bcftools_1.21-1_amd64.buildinfo dpkg-genchanges --build=binary -O../bcftools_1.21-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -8102,12 +8138,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/95539/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/95539/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/712482 and its subdirectories -I: Current time: Sat Jul 5 06:05:45 -12 2025 -I: pbuilder-time-stamp: 1751738745 +I: removing directory /srv/workspace/pbuilder/95539 and its subdirectories +I: Current time: Sat Aug 8 14:30:29 +14 2026 +I: pbuilder-time-stamp: 1786149029 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/bcftools_1.21-1.diff: 95.9% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/bcftools_1.21-1.diff.gz b2/build.log: 94.5% -- replaced with stdout Compressing the 1st log... b1/build.log: 94.6% -- replaced with stdout Sat Jul 5 18:07:31 UTC 2025 I: diffoscope 300 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_bcftools_unstable_amd64_1751738851 + touch /var/log/reproducible-builds/diffoscope_stamp_bcftools_unstable_amd64_1751738851 + RESULT=0 + systemd-run '--description=diffoscope on bcftools/1.21-1 in unstable/amd64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-amd64_31-48025 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.k066tCUN --run-session -c jenkins-reproducible-unstable-diffoscope-fdbf788b-b82d-46e9-8ccc-a0586ac9e8c3 -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.k066tCUN/dbd-tmp-jQv7X7j ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.k066tCUN/bcftools_1.21-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.k066tCUN/bcftools_1.21-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.k066tCUN/bcftools_1.21-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.k066tCUN/b1/bcftools_1.21-1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.k066tCUN/b2/bcftools_1.21-1_amd64.changes' + false + set +x Running as unit: rb-diffoscope-amd64_31-48025.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.k066tCUN/bcftools_1.21-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.k066tCUN/bcftools_1.21-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.k066tCUN/bcftools_1.21-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.k066tCUN/b1/bcftools_1.21-1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.k066tCUN/b2/bcftools_1.21-1_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.003s) 0.003s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 157ms CPU time consumed: 159ms _ __ _ _ | |__ ___ / _| |_ ___ ___ | |___ | '_ \ / __| |_| __/ _ \ / _ \| / __| | |_) | (__| _| || (_) | (_) | \__ \ |_.__/ \___|_| \__\___/ \___/|_|___/ Sat Jul 5 18:07:31 UTC 2025 I: diffoscope 300 found no differences in the changes files, and a .buildinfo file also exists. Sat Jul 5 18:07:31 UTC 2025 I: bcftools from unstable built successfully and reproducibly on amd64. INSERT 0 1 INSERT 0 1 DELETE 1 [2025-07-05 18:07:31] INFO: Starting at 2025-07-05 18:07:31.904941 [2025-07-05 18:07:31] INFO: Generating the pages of 1 package(s) [2025-07-05 18:07:32] CRITICAL: https://tests.reproducible-builds.org/debian/unstable/amd64/bcftools didn't produce a buildlog, even though it has been built. [2025-07-05 18:07:32] INFO: Finished at 2025-07-05 18:07:32.214454, took: 0:00:00.309517 Sat Jul 5 18:07:32 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/bcftools.html Sat Jul 5 18:07:32 UTC 2025 I: Removing signed bcftools_1.21-1_amd64.buildinfo.asc files: removed './b1/bcftools_1.21-1_amd64.buildinfo.asc' removed './b2/bcftools_1.21-1_amd64.buildinfo.asc' 1751738852 amd64 unstable bcftools Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/bcftools_1.21-1.rbuild.log: 94.1% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/bcftools_1.21-1.rbuild.log.gz [2025-07-05 18:07:32] INFO: Starting at 2025-07-05 18:07:32.479937 [2025-07-05 18:07:32] INFO: Generating the pages of 1 package(s) [2025-07-05 18:07:32] INFO: Finished at 2025-07-05 18:07:32.781417, took: 0:00:00.301486 All cleanup done. Sat Jul 5 18:07:32 UTC 2025 - total duration: 0h 6m 21s. Sat Jul 5 18:07:32 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-3cZdgF0o, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 6min 21.985s CPU time consumed: 5.499s