Thu Mar 13 00:54:04 UTC 2025 I: starting to build bcftools/trixie/amd64 on jenkins on '2025-03-13 00:53' Thu Mar 13 00:54:04 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_31/35522/console.log Thu Mar 13 00:54:04 UTC 2025 I: Downloading source for trixie/bcftools=1.21-1 --2025-03-13 00:54:04-- 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% 368M=0s 2025-03-13 00:54:04 (368 MB/s) - ‘bcftools_1.21-1.dsc’ saved [2267/2267] Thu Mar 13 00:54:04 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----- Thu Mar 13 00:54:04 UTC 2025 I: Checking whether the package is not for us Thu Mar 13 00:54:04 UTC 2025 I: Starting 1st build on remote node ionos11-amd64.debian.net. Thu Mar 13 00:54:04 UTC 2025 I: Preparing to do remote build '1' on ionos11-amd64.debian.net. Thu Mar 13 01:01:14 UTC 2025 I: Deleting $TMPDIR on ionos11-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Mar 12 12:54:07 -12 2025 I: pbuilder-time-stamp: 1741827247 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-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: unsupported subcommand 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/1091695/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=20 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='ba94f66aa11d49afbe76c2fe64df7d3d' 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='1091695' 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.haxgeckP/pbuilderrc_K59r --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.haxgeckP/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 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1091695/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 ... 19801 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} libicu72{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, 99 newly installed, 0 to remove and 0 not upgraded. Need to get 42.9 MB of archives. After unpacking 158 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.23.1-1 [243 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.4-5 [92.4 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-7 [294 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.17-3 [862 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.23.1-1 [770 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.2-1 [24.0 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 comerr-dev amd64 2.1-1.47.2-1 [55.7 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-4 [539 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 24 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-1 [476 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-6 [9421 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b2 [699 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.23.1-1 [1680 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.1 [920 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-4 [32.8 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-4 [80.9 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 36 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-4 [326 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-4 [138 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 libgssrpc4t64 amd64 1.21.3-4 [60.0 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libkadm5clnt-mit12 amd64 1.21.3-4 [42.2 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libkdb5-10t64 amd64 1.21.3-4 [42.4 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 libkadm5srv-mit12 amd64 1.21.3-4 [54.2 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 krb5-multidev amd64 1.21.3-4 [126 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 libbrotli-dev amd64 1.1.0-2+b7 [316 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 libidn2-0 amd64 2.3.8-1 [109 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 libffi8 amd64 3.4.7-1 [23.9 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 libgnutls30t64 amd64 3.8.9-2 [1464 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 libldap2 amd64 2.6.9+dfsg-1 [192 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 libnghttp3-9 amd64 1.8.0-1 [67.7 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 libngtcp2-16 amd64 1.11.0-1 [131 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 libngtcp2-crypto-gnutls8 amd64 1.11.0-1 [29.3 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 libcurl3t64-gnutls amd64 8.12.1-3 [365 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 libunbound8 amd64 1.22.0-1+b1 [598 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 libgnutls-dane0t64 amd64 3.8.9-2 [455 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 libgnutls-openssl27t64 amd64 3.8.9-2 [455 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 libidn2-dev amd64 2.3.8-1 [102 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 libp11-kit-dev amd64 0.25.5-3 [208 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 libtasn1-6-dev amd64 4.20.0-2 [99.2 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-3 [329 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-3 [642 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 nettle-dev amd64 3.10.1-1 [1318 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 libgnutls28-dev amd64 3.8.9-2 [1401 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 libkrb5-dev amd64 1.21.3-4 [15.9 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 libldap-dev amd64 2.6.9+dfsg-1 [307 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 libnghttp2-dev amd64 1.64.0-1 [115 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 libnghttp3-dev amd64 1.8.0-1 [91.3 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.11.0-1 [34.0 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 libngtcp2-dev amd64 1.11.0-1 [179 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 libpsl-dev amd64 0.21.2-1.1+b1 [77.6 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-2+b5 [68.0 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 libssl-dev amd64 3.4.1-1 [2787 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 libssh2-1-dev amd64 1.11.1-1 [393 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 libzstd-dev amd64 1.5.6+dfsg-2 [365 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 libcurl4-gnutls-dev amd64 8.12.1-3 [480 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.23-1+b1 [47.5 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 libdeflate-dev amd64 1.23-1+b1 [56.0 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 libgslcblas0 amd64 2.8+dfsg-5 [116 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 libgsl28 amd64 2.8+dfsg-5 [994 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 libgsl-dev amd64 2.8+dfsg-5 [1222 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 libhtscodecs2 amd64 1.6.1-2 [95.8 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 libhts3t64 amd64 1.21+ds-1 [463 kB] Get: 96 http://deb.debian.org/debian trixie/main amd64 liblzma-dev amd64 5.6.4-1 [323 kB] Get: 97 http://deb.debian.org/debian trixie/main amd64 libhts-dev amd64 1.21+ds-1 [1733 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 libio-pty-perl amd64 1:1.20-1+b3 [34.3 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 tabix amd64 1.21+ds-1 [496 kB] Fetched 42.9 MB in 3s (15.0 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 ... 19801 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:amd64. 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Selecting previously unselected package libkrb5-dev:amd64. Preparing to unpack .../72-libkrb5-dev_1.21.3-4_amd64.deb ... Unpacking libkrb5-dev:amd64 (1.21.3-4) ... Selecting previously unselected package libldap-dev:amd64. Preparing to unpack .../73-libldap-dev_2.6.9+dfsg-1_amd64.deb ... Unpacking libldap-dev:amd64 (2.6.9+dfsg-1) ... Selecting previously unselected package libpkgconf3:amd64. Preparing to unpack .../74-libpkgconf3_1.8.1-4_amd64.deb ... Unpacking libpkgconf3:amd64 (1.8.1-4) ... Selecting previously unselected package pkgconf-bin. Preparing to unpack .../75-pkgconf-bin_1.8.1-4_amd64.deb ... Unpacking pkgconf-bin (1.8.1-4) ... Selecting previously unselected package pkgconf:amd64. Preparing to unpack .../76-pkgconf_1.8.1-4_amd64.deb ... Unpacking pkgconf:amd64 (1.8.1-4) ... Selecting previously unselected package libnghttp2-dev:amd64. Preparing to unpack .../77-libnghttp2-dev_1.64.0-1_amd64.deb ... Unpacking libnghttp2-dev:amd64 (1.64.0-1) ... 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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 -j20 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 -f test/*.unsorted.hex test/*.unsorted.tsv rm -rf plugins/*.dSYM 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 gcc option to enable large file support... 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 -j20 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 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-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/UuhxTXGXNz/merge.a.vcf.gz 2:3199812-3199812 .. ok test_tabix: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/UuhxTXGXNz/merge.a.bcf 2:3199812-3199812 .. ok test_tabix: tabix /tmp/UuhxTXGXNz/merge.a.vcf.gz 1:3000151-3000151 .. ok test_tabix: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/UuhxTXGXNz/merge.a.bcf 1:3000151-3000151 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/UuhxTXGXNz/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/UuhxTXGXNz/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/UuhxTXGXNz/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/UuhxTXGXNz/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/UuhxTXGXNz/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/UuhxTXGXNz/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/UuhxTXGXNz/large_chrom_csi_limit.bcf chr20 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/UuhxTXGXNz/large_chrom_csi_limit.bcf chr20 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/UuhxTXGXNz/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/UuhxTXGXNz/large_chrom_csi_limit.bcf chr20 .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -s /tmp/UuhxTXGXNz/idx.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -s /tmp/UuhxTXGXNz/idx.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -s /tmp/UuhxTXGXNz/idx.bcf .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/UuhxTXGXNz/idx.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/UuhxTXGXNz/idx.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/UuhxTXGXNz/idx.vcf.gz.csi .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/UuhxTXGXNz/idx.bcf .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/UuhxTXGXNz/idx.bcf.csi .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -s /tmp/UuhxTXGXNz/empty.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -s /tmp/UuhxTXGXNz/empty.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -s /tmp/UuhxTXGXNz/empty.bcf .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/UuhxTXGXNz/empty.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/UuhxTXGXNz/empty.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/UuhxTXGXNz/empty.vcf.gz.csi .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/UuhxTXGXNz/empty.bcf .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/UuhxTXGXNz/empty.bcf.csi .. ok test_vcf_check: /build/reproducible-path/bcftools-1.21/bcftools stats -s - /tmp/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/check.1.chk /tmp/UuhxTXGXNz/check.2.chk /tmp/UuhxTXGXNz/check.3.chk /tmp/UuhxTXGXNz/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/UuhxTXGXNz/stats.a.vcf.gz /tmp/UuhxTXGXNz/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/reproducible-path/bcftools-1.21/bcftools stats -s B /tmp/UuhxTXGXNz/stats.a.vcf.gz /tmp/UuhxTXGXNz/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/reproducible-path/bcftools-1.21/bcftools stats -s - /tmp/UuhxTXGXNz/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/UuhxTXGXNz/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/reproducible-path/bcftools-1.21/bcftools stats -s - /tmp/UuhxTXGXNz/stats.vaf.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -n =2 /tmp/UuhxTXGXNz/isec.a.vcf.gz /tmp/UuhxTXGXNz/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -n =2 /tmp/UuhxTXGXNz/isec.a.vcf.gz /tmp/UuhxTXGXNz/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/UuhxTXGXNz/isec.a.vcf.gz /tmp/UuhxTXGXNz/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -n =2 -i"STRLEN(REF)==2" /tmp/UuhxTXGXNz/isec.a.vcf.gz /tmp/UuhxTXGXNz/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -n =2 -c both /tmp/UuhxTXGXNz/isec.a.vcf.gz /tmp/UuhxTXGXNz/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -n =2 -c both /tmp/UuhxTXGXNz/isec.a.vcf.gz /tmp/UuhxTXGXNz/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -n =2 -c any /tmp/UuhxTXGXNz/isec.a.vcf.gz /tmp/UuhxTXGXNz/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -n =2 -c any /tmp/UuhxTXGXNz/isec.a.vcf.gz /tmp/UuhxTXGXNz/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -C -c any /tmp/UuhxTXGXNz/isec.a.vcf.gz /tmp/UuhxTXGXNz/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -C -c any /tmp/UuhxTXGXNz/isec.a.vcf.gz /tmp/UuhxTXGXNz/isec.b.vcf.gz .. ok test_vcf_isec2: /build/reproducible-path/bcftools-1.21/bcftools isec --no-version -T /tmp/UuhxTXGXNz/isec.tab.gz /tmp/UuhxTXGXNz/isec.a.vcf.gz .. ok test_vcf_isec2: /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -T /tmp/UuhxTXGXNz/isec.tab.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/isec-miss.1.1.vcf.gz /tmp/UuhxTXGXNz/isec-miss.1.2.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/isec-miss.1.1.vcf.gz /tmp/UuhxTXGXNz/isec-miss.1.2.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/isec-miss.1.1.vcf.gz /tmp/UuhxTXGXNz/isec-miss.1.2.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/isec-miss.1.1.vcf.gz /tmp/UuhxTXGXNz/isec-miss.1.2.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/isec-miss.2.1.vcf.gz /tmp/UuhxTXGXNz/isec-miss.2.2.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/isec-miss.2.1.vcf.gz /tmp/UuhxTXGXNz/isec-miss.2.2.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/isec-miss.2.1.vcf.gz /tmp/UuhxTXGXNz/isec-miss.2.2.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/isec-miss.2.1.vcf.gz /tmp/UuhxTXGXNz/isec-miss.2.2.vcf.gz /tmp/UuhxTXGXNz/isec-miss.2.3.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/UuhxTXGXNz/merge.11.a.vcf.gz /tmp/UuhxTXGXNz/merge.11.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/UuhxTXGXNz/merge.11.a.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.11.a.bcf /tmp/UuhxTXGXNz/merge.11.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/UuhxTXGXNz/merge.11.a.bcf /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.join.a.vcf.gz /tmp/UuhxTXGXNz/merge.join.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -i AF:join /tmp/UuhxTXGXNz/merge.join.a.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.join.a.bcf /tmp/UuhxTXGXNz/merge.join.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -i AF:join /tmp/UuhxTXGXNz/merge.join.a.bcf /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.LPL.a.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-single /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.LPL.a.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-single /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.LPL.a.vcf.gz /tmp/UuhxTXGXNz/merge.LPL.b.vcf.gz /tmp/UuhxTXGXNz/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/UuhxTXGXNz/merge.LPL.a.vcf.gz /tmp/UuhxTXGXNz/merge.LPL.b.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.LPL.a.bcf /tmp/UuhxTXGXNz/merge.LPL.b.bcf /tmp/UuhxTXGXNz/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/UuhxTXGXNz/merge.LPL.a.bcf /tmp/UuhxTXGXNz/merge.LPL.b.bcf /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.LPL.a.vcf.gz /tmp/UuhxTXGXNz/merge.LPL.b.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.LPL.a.vcf.gz /tmp/UuhxTXGXNz/merge.LPL.b.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.LPL.a.bcf /tmp/UuhxTXGXNz/merge.LPL.b.bcf /tmp/UuhxTXGXNz/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 1 /tmp/UuhxTXGXNz/merge.LPL.a.bcf /tmp/UuhxTXGXNz/merge.LPL.b.bcf /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.LPL.a.vcf.gz /tmp/UuhxTXGXNz/merge.LPL.b.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.LPL.a.vcf.gz /tmp/UuhxTXGXNz/merge.LPL.b.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.LPL.a.bcf /tmp/UuhxTXGXNz/merge.LPL.b.bcf /tmp/UuhxTXGXNz/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 2 /tmp/UuhxTXGXNz/merge.LPL.a.bcf /tmp/UuhxTXGXNz/merge.LPL.b.bcf /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.LPL.a.vcf.gz /tmp/UuhxTXGXNz/merge.LPL.b.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.LPL.a.vcf.gz /tmp/UuhxTXGXNz/merge.LPL.b.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.LPL.a.bcf /tmp/UuhxTXGXNz/merge.LPL.b.bcf /tmp/UuhxTXGXNz/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 3 /tmp/UuhxTXGXNz/merge.LPL.a.bcf /tmp/UuhxTXGXNz/merge.LPL.b.bcf /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.LPL.a.vcf.gz /tmp/UuhxTXGXNz/merge.LPL.b.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.LPL.a.vcf.gz /tmp/UuhxTXGXNz/merge.LPL.b.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.LPL.a.bcf /tmp/UuhxTXGXNz/merge.LPL.b.bcf /tmp/UuhxTXGXNz/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 4 /tmp/UuhxTXGXNz/merge.LPL.a.bcf /tmp/UuhxTXGXNz/merge.LPL.b.bcf /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.LPL.a.vcf.gz /tmp/UuhxTXGXNz/merge.LPL.b.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.LPL.a.vcf.gz /tmp/UuhxTXGXNz/merge.LPL.b.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.LPL.a.bcf /tmp/UuhxTXGXNz/merge.LPL.b.bcf /tmp/UuhxTXGXNz/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 5 /tmp/UuhxTXGXNz/merge.LPL.a.bcf /tmp/UuhxTXGXNz/merge.LPL.b.bcf /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.a.vcf.gz /tmp/UuhxTXGXNz/merge.b.vcf.gz /tmp/UuhxTXGXNz/merge.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/UuhxTXGXNz/merge.a.vcf.gz /tmp/UuhxTXGXNz/merge.b.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.a.bcf /tmp/UuhxTXGXNz/merge.b.bcf /tmp/UuhxTXGXNz/merge.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/UuhxTXGXNz/merge.a.bcf /tmp/UuhxTXGXNz/merge.b.bcf /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.a.vcf.gz /tmp/UuhxTXGXNz/merge.b.vcf.gz /tmp/UuhxTXGXNz/merge.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -Fx /tmp/UuhxTXGXNz/merge.a.vcf.gz /tmp/UuhxTXGXNz/merge.b.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.a.bcf /tmp/UuhxTXGXNz/merge.b.bcf /tmp/UuhxTXGXNz/merge.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -Fx /tmp/UuhxTXGXNz/merge.a.bcf /tmp/UuhxTXGXNz/merge.b.bcf /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.a.vcf.gz /tmp/UuhxTXGXNz/merge.b.vcf.gz /tmp/UuhxTXGXNz/merge.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -0 /tmp/UuhxTXGXNz/merge.a.vcf.gz /tmp/UuhxTXGXNz/merge.b.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.a.bcf /tmp/UuhxTXGXNz/merge.b.bcf /tmp/UuhxTXGXNz/merge.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -0 /tmp/UuhxTXGXNz/merge.a.bcf /tmp/UuhxTXGXNz/merge.b.bcf /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.2.a.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.2.a.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.2.a.bcf /tmp/UuhxTXGXNz/merge.2.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m none /tmp/UuhxTXGXNz/merge.2.a.bcf /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.2.a.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.2.a.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.2.a.bcf /tmp/UuhxTXGXNz/merge.2.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m both /tmp/UuhxTXGXNz/merge.2.a.bcf /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.2.a.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.2.a.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.2.a.bcf /tmp/UuhxTXGXNz/merge.2.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m all /tmp/UuhxTXGXNz/merge.2.a.bcf /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.3.a.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.3.a.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.3.a.bcf /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.3.a.bcf /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.4.a.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.4.a.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.4.a.bcf /tmp/UuhxTXGXNz/merge.4.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m id /tmp/UuhxTXGXNz/merge.4.a.bcf /tmp/UuhxTXGXNz/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/UuhxTXGXNz/gvcf.merge.1.vcf.gz /tmp/UuhxTXGXNz/gvcf.merge.2.vcf.gz /tmp/UuhxTXGXNz/gvcf.merge.3.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/UuhxTXGXNz/gvcf.merge.1.vcf.gz /tmp/UuhxTXGXNz/gvcf.merge.2.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/gvcf.merge.1.bcf /tmp/UuhxTXGXNz/gvcf.merge.2.bcf /tmp/UuhxTXGXNz/gvcf.merge.3.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/UuhxTXGXNz/gvcf.merge.1.bcf /tmp/UuhxTXGXNz/gvcf.merge.2.bcf /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.gvcf.2.a.vcf.gz /tmp/UuhxTXGXNz/merge.gvcf.2.b.vcf.gz /tmp/UuhxTXGXNz/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/UuhxTXGXNz/merge.gvcf.2.a.vcf.gz /tmp/UuhxTXGXNz/merge.gvcf.2.b.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.gvcf.2.a.vcf.gz /tmp/UuhxTXGXNz/merge.gvcf.2.b.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.gvcf.2.a.vcf.gz /tmp/UuhxTXGXNz/merge.gvcf.2.b.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.gvcf.2.a.vcf.gz /tmp/UuhxTXGXNz/merge.gvcf.2.b.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.gvcf.2.a.vcf.gz /tmp/UuhxTXGXNz/merge.gvcf.2.b.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.gvcf.3.a.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.gvcf.3.a.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.gvcf.4.a.vcf.gz /tmp/UuhxTXGXNz/merge.gvcf.4.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/UuhxTXGXNz/merge.gvcf.4.a.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.gvcf.4.a.bcf /tmp/UuhxTXGXNz/merge.gvcf.4.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/UuhxTXGXNz/merge.gvcf.4.a.bcf /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.5.a.vcf.gz /tmp/UuhxTXGXNz/merge.5.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/UuhxTXGXNz/merge.5.a.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.5.a.bcf /tmp/UuhxTXGXNz/merge.5.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/UuhxTXGXNz/merge.5.a.bcf /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.6.a.vcf.gz /tmp/UuhxTXGXNz/merge.6.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/UuhxTXGXNz/merge.6.a.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.6.a.bcf /tmp/UuhxTXGXNz/merge.6.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/UuhxTXGXNz/merge.6.a.bcf /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.gvcf.7.a.vcf.gz /tmp/UuhxTXGXNz/merge.gvcf.7.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/UuhxTXGXNz/merge.gvcf.7.a.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.gvcf.7.a.bcf /tmp/UuhxTXGXNz/merge.gvcf.7.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/UuhxTXGXNz/merge.gvcf.7.a.bcf /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.gvcf.8.a.vcf.gz /tmp/UuhxTXGXNz/merge.gvcf.8.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/UuhxTXGXNz/merge.gvcf.8.a.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.gvcf.8.a.bcf /tmp/UuhxTXGXNz/merge.gvcf.8.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/UuhxTXGXNz/merge.gvcf.8.a.bcf /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.7.a.vcf.gz /tmp/UuhxTXGXNz/merge.7.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/UuhxTXGXNz/merge.7.a.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.7.a.bcf /tmp/UuhxTXGXNz/merge.7.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/UuhxTXGXNz/merge.7.a.bcf /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.gvcf.9a.vcf.gz /tmp/UuhxTXGXNz/merge.gvcf.9b.vcf.gz /tmp/UuhxTXGXNz/merge.gvcf.9c.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.gvcf.9a.vcf.gz /tmp/UuhxTXGXNz/merge.gvcf.9b.vcf.gz /tmp/UuhxTXGXNz/merge.gvcf.9c.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.gvcf.9a.bcf /tmp/UuhxTXGXNz/merge.gvcf.9b.bcf /tmp/UuhxTXGXNz/merge.gvcf.9c.bcf /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.gvcf.9a.bcf /tmp/UuhxTXGXNz/merge.gvcf.9b.bcf /tmp/UuhxTXGXNz/merge.gvcf.9c.bcf /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.gvcf.9a.vcf.gz /tmp/UuhxTXGXNz/merge.gvcf.9b.vcf.gz /tmp/UuhxTXGXNz/merge.gvcf.9c.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.gvcf.9a.vcf.gz /tmp/UuhxTXGXNz/merge.gvcf.9b.vcf.gz /tmp/UuhxTXGXNz/merge.gvcf.9c.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.gvcf.9a.bcf /tmp/UuhxTXGXNz/merge.gvcf.9b.bcf /tmp/UuhxTXGXNz/merge.gvcf.9c.bcf /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.gvcf.9a.bcf /tmp/UuhxTXGXNz/merge.gvcf.9b.bcf /tmp/UuhxTXGXNz/merge.gvcf.9c.bcf /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.gvcf.9a.vcf.gz /tmp/UuhxTXGXNz/merge.gvcf.9b.vcf.gz /tmp/UuhxTXGXNz/merge.gvcf.9c.vcf.gz /tmp/UuhxTXGXNz/merge.gvcf.9d.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.gvcf.9a.vcf.gz /tmp/UuhxTXGXNz/merge.gvcf.9b.vcf.gz /tmp/UuhxTXGXNz/merge.gvcf.9c.vcf.gz /tmp/UuhxTXGXNz/merge.gvcf.9d.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.gvcf.9a.bcf /tmp/UuhxTXGXNz/merge.gvcf.9b.bcf /tmp/UuhxTXGXNz/merge.gvcf.9c.bcf /tmp/UuhxTXGXNz/merge.gvcf.9d.bcf /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.gvcf.9a.bcf /tmp/UuhxTXGXNz/merge.gvcf.9b.bcf /tmp/UuhxTXGXNz/merge.gvcf.9c.bcf /tmp/UuhxTXGXNz/merge.gvcf.9d.bcf /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.gvcf.9a.vcf.gz /tmp/UuhxTXGXNz/merge.gvcf.9b.vcf.gz /tmp/UuhxTXGXNz/merge.gvcf.9c.vcf.gz /tmp/UuhxTXGXNz/merge.gvcf.9d.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.gvcf.9a.vcf.gz /tmp/UuhxTXGXNz/merge.gvcf.9b.vcf.gz /tmp/UuhxTXGXNz/merge.gvcf.9c.vcf.gz /tmp/UuhxTXGXNz/merge.gvcf.9d.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.gvcf.9a.bcf /tmp/UuhxTXGXNz/merge.gvcf.9b.bcf /tmp/UuhxTXGXNz/merge.gvcf.9c.bcf /tmp/UuhxTXGXNz/merge.gvcf.9d.bcf /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.gvcf.9a.bcf /tmp/UuhxTXGXNz/merge.gvcf.9b.bcf /tmp/UuhxTXGXNz/merge.gvcf.9c.bcf /tmp/UuhxTXGXNz/merge.gvcf.9d.bcf /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.gvcf.10.a.vcf.gz /tmp/UuhxTXGXNz/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/UuhxTXGXNz/merge.gvcf.10.a.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.gvcf.10.a.bcf /tmp/UuhxTXGXNz/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/UuhxTXGXNz/merge.gvcf.10.a.bcf /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.gvcf.10.a.vcf.gz /tmp/UuhxTXGXNz/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m none /tmp/UuhxTXGXNz/merge.gvcf.10.a.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.gvcf.10.a.bcf /tmp/UuhxTXGXNz/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m none /tmp/UuhxTXGXNz/merge.gvcf.10.a.bcf /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.gvcf.10.a.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.gvcf.10.a.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.gvcf.10.a.bcf /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.gvcf.10.a.bcf /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.gvcf.10.a.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.gvcf.10.a.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.gvcf.10.a.bcf /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.gvcf.10.a.bcf /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.noidx.a.vcf.gz /tmp/UuhxTXGXNz/merge.noidx.b.vcf.gz /tmp/UuhxTXGXNz/merge.noidx.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/UuhxTXGXNz/merge.noidx.a.vcf.gz /tmp/UuhxTXGXNz/merge.noidx.b.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.noidx.a.bcf /tmp/UuhxTXGXNz/merge.noidx.b.bcf /tmp/UuhxTXGXNz/merge.noidx.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/UuhxTXGXNz/merge.noidx.a.bcf /tmp/UuhxTXGXNz/merge.noidx.b.bcf /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.noidx.a.bcf /tmp/UuhxTXGXNz/merge.noidx.b.bcf /tmp/UuhxTXGXNz/merge.noidx.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --no-index /tmp/UuhxTXGXNz/merge.noidx.a.bcf /tmp/UuhxTXGXNz/merge.noidx.b.bcf /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.8.a.vcf.gz /tmp/UuhxTXGXNz/merge.8.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/UuhxTXGXNz/merge.8.a.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.8.a.bcf /tmp/UuhxTXGXNz/merge.8.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/UuhxTXGXNz/merge.8.a.bcf /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.8.a.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.8.a.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.8.a.bcf /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.8.a.bcf /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.9.a.vcf.gz /tmp/UuhxTXGXNz/merge.9.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/UuhxTXGXNz/merge.9.a.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.9.a.bcf /tmp/UuhxTXGXNz/merge.9.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/UuhxTXGXNz/merge.9.a.bcf /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.9.a.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.9.a.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.9.a.bcf /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.9.a.bcf /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.10.a.vcf.gz /tmp/UuhxTXGXNz/merge.10.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m none /tmp/UuhxTXGXNz/merge.10.a.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.10.a.bcf /tmp/UuhxTXGXNz/merge.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m none /tmp/UuhxTXGXNz/merge.10.a.bcf /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.10.a.vcf.gz /tmp/UuhxTXGXNz/merge.10.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m both /tmp/UuhxTXGXNz/merge.10.a.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.10.a.bcf /tmp/UuhxTXGXNz/merge.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m both /tmp/UuhxTXGXNz/merge.10.a.bcf /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.10.a.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.10.a.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.10.a.bcf /tmp/UuhxTXGXNz/merge.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m snp-ins-del /tmp/UuhxTXGXNz/merge.10.a.bcf /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.mrules.1.a.vcf.gz /tmp/UuhxTXGXNz/merge.mrules.1.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/UuhxTXGXNz/merge.mrules.1.a.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.mrules.1.a.bcf /tmp/UuhxTXGXNz/merge.mrules.1.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/UuhxTXGXNz/merge.mrules.1.a.bcf /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.mrules.1.a.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.mrules.1.a.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.mrules.1.a.bcf /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.mrules.1.a.bcf /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.gvcf.5.a.vcf.gz /tmp/UuhxTXGXNz/merge.gvcf.5.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/UuhxTXGXNz/merge.gvcf.5.a.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.gvcf.5.a.bcf /tmp/UuhxTXGXNz/merge.gvcf.5.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/UuhxTXGXNz/merge.gvcf.5.a.bcf /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.gvcf.5.a.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.gvcf.5.a.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.gvcf.5.a.bcf /tmp/UuhxTXGXNz/merge.gvcf.5.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - --merge none /tmp/UuhxTXGXNz/merge.gvcf.5.a.bcf /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.gvcf.11.a.vcf.gz /tmp/UuhxTXGXNz/merge.gvcf.11.b.vcf.gz /tmp/UuhxTXGXNz/merge.gvcf.11.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/UuhxTXGXNz/merge.gvcf.11.a.vcf.gz /tmp/UuhxTXGXNz/merge.gvcf.11.b.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/merge.gvcf.11.a.bcf /tmp/UuhxTXGXNz/merge.gvcf.11.b.bcf /tmp/UuhxTXGXNz/merge.gvcf.11.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/UuhxTXGXNz/merge.gvcf.11.a.bcf /tmp/UuhxTXGXNz/merge.gvcf.11.b.bcf /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.string.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.string.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.string.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.string.2.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.string.2.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.variantkey.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/view.vectors.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.2.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.filter-type.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.filter-type.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.filter-type.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.filter-type.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.filter-type.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/filter-missing-floats.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/filter-missing-floats.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.filter.2.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.filter.3.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.filter.3.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.filter.3.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.filter.4.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/view.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.negative.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.negative.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.negative.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.negative.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.filter.6.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.filter.8.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.filter.8.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.filter.9.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.filter.9.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.filter.13.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.filter.10.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.filter.10.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.filter.id.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.filter.id.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.filter.id.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.filter.id.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.filter.id.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.filter.id.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/filter.10.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/filter.13.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.filter-or.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/query.filter-or.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/norm.sort.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/UuhxTXGXNz/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/UuhxTXGXNz/norm.sort.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - -S lex /tmp/UuhxTXGXNz/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/UuhxTXGXNz/norm.join-missing-ploidy.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +both /tmp/UuhxTXGXNz/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/UuhxTXGXNz/norm.split.5.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - --multi-overlaps . /tmp/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/norm.split.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- /tmp/UuhxTXGXNz/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/UuhxTXGXNz/norm.split.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- /tmp/UuhxTXGXNz/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/UuhxTXGXNz/norm.split.3.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- --force /tmp/UuhxTXGXNz/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/UuhxTXGXNz/norm.split.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- /tmp/UuhxTXGXNz/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/UuhxTXGXNz/norm.split.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- --keep-sum AD /tmp/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/norm.merge.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m+ /tmp/UuhxTXGXNz/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/UuhxTXGXNz/norm.merge.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m+ /tmp/UuhxTXGXNz/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/UuhxTXGXNz/norm.merge.3.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m+ /tmp/UuhxTXGXNz/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/UuhxTXGXNz/norm.merge.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m+ -s /tmp/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d snps /tmp/UuhxTXGXNz/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/UuhxTXGXNz/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d indels /tmp/UuhxTXGXNz/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/UuhxTXGXNz/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d both /tmp/UuhxTXGXNz/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/UuhxTXGXNz/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d all /tmp/UuhxTXGXNz/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/UuhxTXGXNz/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d none /tmp/UuhxTXGXNz/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/UuhxTXGXNz/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d exact /tmp/UuhxTXGXNz/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/UuhxTXGXNz/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d none /tmp/UuhxTXGXNz/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/UuhxTXGXNz/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d exact /tmp/UuhxTXGXNz/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/UuhxTXGXNz/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d indels /tmp/UuhxTXGXNz/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/UuhxTXGXNz/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d any /tmp/UuhxTXGXNz/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/UuhxTXGXNz/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d both /tmp/UuhxTXGXNz/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/UuhxTXGXNz/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d snps /tmp/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/atomize.split.3.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . /tmp/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/norm.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +both /tmp/UuhxTXGXNz/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/UuhxTXGXNz/norm.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +any /tmp/UuhxTXGXNz/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/UuhxTXGXNz/norm.5.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - --multi-overlaps 0 /tmp/UuhxTXGXNz/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/UuhxTXGXNz/norm.5.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - --multi-overlaps . /tmp/UuhxTXGXNz/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/UuhxTXGXNz/norm.m-any.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any /tmp/UuhxTXGXNz/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/UuhxTXGXNz/norm.phased-split.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any /tmp/UuhxTXGXNz/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/UuhxTXGXNz/norm.phased-join.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +any /tmp/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/norm.string-tags.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any /tmp/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/norm.split.merge.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - -i 'type="snp"' /tmp/UuhxTXGXNz/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/UuhxTXGXNz/norm.merge.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +any /tmp/UuhxTXGXNz/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/UuhxTXGXNz/norm.merge.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +both /tmp/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/merge.gvcf.2.a.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -HAA /tmp/UuhxTXGXNz/merge.gvcf.2.a.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/UuhxTXGXNz/weird-chr-names.vcf.gz -r 1 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/weird-chr-names.vcf.gz -r 1:1-2 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/weird-chr-names.vcf.gz -r 1:1,1:2 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/weird-chr-names.vcf.gz -r 1:1-1 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/weird-chr-names.vcf.gz -r {1:1} .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/weird-chr-names.vcf.gz -r {1:1}:1-2 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/weird-chr-names.vcf.gz -r {1:1}:1-1 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/weird-chr-names.vcf.gz -r {1:1-1} .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/UuhxTXGXNz/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/UuhxTXGXNz/view.vcf.gz -r20,Y .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -f PASS -Xks NA00003 /tmp/UuhxTXGXNz/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/UuhxTXGXNz/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -xs NA00003 /tmp/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -p /tmp/UuhxTXGXNz/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/UuhxTXGXNz/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -P /tmp/UuhxTXGXNz/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/UuhxTXGXNz/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/UuhxTXGXNz/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/UuhxTXGXNz/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -GVsnps /tmp/UuhxTXGXNz/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -GVsnps /tmp/UuhxTXGXNz/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/UuhxTXGXNz/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/UuhxTXGXNz/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/UuhxTXGXNz/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -s ^NA00003 /tmp/UuhxTXGXNz/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/UuhxTXGXNz/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -G /tmp/UuhxTXGXNz/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/UuhxTXGXNz/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -a /tmp/UuhxTXGXNz/many.alleles.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -a /tmp/UuhxTXGXNz/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/UuhxTXGXNz/view.vectors.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -asA /tmp/UuhxTXGXNz/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/UuhxTXGXNz/view.vectors.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -asB /tmp/UuhxTXGXNz/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/UuhxTXGXNz/view.vectors.2.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -asA /tmp/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/view.filter.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -i'TXT0="text"' /tmp/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/filter.2.vcf.gz 1:3062917-3157410 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -i 'POS>=3062917' /tmp/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/idx.4.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -Ht 2 /tmp/UuhxTXGXNz/view-t.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -Ht 3 /tmp/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -c6:nonmajor /tmp/UuhxTXGXNz/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -q0.3:major /tmp/UuhxTXGXNz/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/view.filter.annovar.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -a /tmp/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/mpileup.2.vcf.gz .. ok test_vcf_head2: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/mpileup.2.vcf.gz .. ok test_vcf_head2: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/mpileup.2.vcf.gz .. ok test_vcf_head2: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/UuhxTXGXNz/regions.tab.gz /tmp/UuhxTXGXNz/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/regions.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/UuhxTXGXNz/regions.tab.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/UuhxTXGXNz/regions.tab.gz /tmp/UuhxTXGXNz/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/UuhxTXGXNz/regions.bed /tmp/UuhxTXGXNz/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/regions.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/UuhxTXGXNz/regions.bed .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/UuhxTXGXNz/regions.bed /tmp/UuhxTXGXNz/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/UuhxTXGXNz/regions.bed.gz /tmp/UuhxTXGXNz/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/regions.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/UuhxTXGXNz/regions.bed.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/UuhxTXGXNz/regions.bed.gz /tmp/UuhxTXGXNz/regions.vcf.gz .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/UuhxTXGXNz/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/UuhxTXGXNz/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/UuhxTXGXNz/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/UuhxTXGXNz/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/UuhxTXGXNz/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/UuhxTXGXNz/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/UuhxTXGXNz/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/UuhxTXGXNz/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/UuhxTXGXNz/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/UuhxTXGXNz/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/UuhxTXGXNz/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/UuhxTXGXNz/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/UuhxTXGXNz/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/UuhxTXGXNz/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/UuhxTXGXNz/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/UuhxTXGXNz/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/UuhxTXGXNz/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/UuhxTXGXNz/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/UuhxTXGXNz/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/UuhxTXGXNz/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/UuhxTXGXNz/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/UuhxTXGXNz/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/UuhxTXGXNz/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/UuhxTXGXNz/annots4.vcf.gz -c +INFO /tmp/UuhxTXGXNz/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/UuhxTXGXNz/annots4.vcf.gz -c +INFO /tmp/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/UuhxTXGXNz/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/UuhxTXGXNz/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/UuhxTXGXNz/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/UuhxTXGXNz/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/UuhxTXGXNz/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/UuhxTXGXNz/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/UuhxTXGXNz/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/UuhxTXGXNz/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/UuhxTXGXNz/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/UuhxTXGXNz/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/UuhxTXGXNz/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/UuhxTXGXNz/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/UuhxTXGXNz/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/UuhxTXGXNz/annots11.vcf.gz -c FMT /tmp/UuhxTXGXNz/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/UuhxTXGXNz/annots11.vcf.gz -c FMT /tmp/UuhxTXGXNz/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/UuhxTXGXNz/annots2.vcf.gz -c FMT/newGT:=GT /tmp/UuhxTXGXNz/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/UuhxTXGXNz/annots2.vcf.gz -c FMT/newGT:=GT /tmp/UuhxTXGXNz/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/UuhxTXGXNz/annots12.vcf.gz -c FMT/GT:=newGT /tmp/UuhxTXGXNz/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/UuhxTXGXNz/annots12.vcf.gz -c FMT/GT:=newGT /tmp/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/UuhxTXGXNz/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/UuhxTXGXNz/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/UuhxTXGXNz/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/UuhxTXGXNz/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/UuhxTXGXNz/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/UuhxTXGXNz/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/UuhxTXGXNz/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/UuhxTXGXNz/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/UuhxTXGXNz/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/UuhxTXGXNz/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/UuhxTXGXNz/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/UuhxTXGXNz/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER /tmp/UuhxTXGXNz/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/UuhxTXGXNz/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER /tmp/UuhxTXGXNz/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/UuhxTXGXNz/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER /tmp/UuhxTXGXNz/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/UuhxTXGXNz/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER /tmp/UuhxTXGXNz/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/UuhxTXGXNz/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER,FILTER /tmp/UuhxTXGXNz/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/UuhxTXGXNz/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER,FILTER /tmp/UuhxTXGXNz/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/UuhxTXGXNz/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=./FILTER /tmp/UuhxTXGXNz/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/UuhxTXGXNz/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=./FILTER /tmp/UuhxTXGXNz/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/UuhxTXGXNz/annotate20.src.vcf.gz -c FMT/GT /tmp/UuhxTXGXNz/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/UuhxTXGXNz/annotate20.src.vcf.gz -c FMT/GT /tmp/UuhxTXGXNz/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/UuhxTXGXNz/annotate20.src.vcf.gz -c +FMT/GT /tmp/UuhxTXGXNz/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/UuhxTXGXNz/annotate20.src.vcf.gz -c +FMT/GT /tmp/UuhxTXGXNz/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/UuhxTXGXNz/annotate20.src.vcf.gz -c -FMT/GT /tmp/UuhxTXGXNz/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/UuhxTXGXNz/annotate20.src.vcf.gz -c -FMT/GT /tmp/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/UuhxTXGXNz/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/UuhxTXGXNz/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/annotate24.src.vcf.gz -c XX /tmp/UuhxTXGXNz/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/UuhxTXGXNz/annotate24.src.vcf.gz -c XX /tmp/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/annots.id.vcf.gz -c ALT /tmp/UuhxTXGXNz/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/UuhxTXGXNz/annots.id.vcf.gz -c ALT /tmp/UuhxTXGXNz/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/UuhxTXGXNz/annots.id.vcf.gz -c +ALT /tmp/UuhxTXGXNz/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/UuhxTXGXNz/annots.id.vcf.gz -c +ALT /tmp/UuhxTXGXNz/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/UuhxTXGXNz/annots.id.2.vcf.gz --pair-logic some -c +ID /tmp/UuhxTXGXNz/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/UuhxTXGXNz/annots.id.2.vcf.gz --pair-logic some -c +ID /tmp/UuhxTXGXNz/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/UuhxTXGXNz/annots.id.2.vcf.gz --pair-logic any -c +ID /tmp/UuhxTXGXNz/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/UuhxTXGXNz/annots.id.2.vcf.gz --pair-logic any -c +ID /tmp/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/concat.1.a.vcf.gz /tmp/UuhxTXGXNz/concat.1.b.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob /tmp/UuhxTXGXNz/concat.1.a.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/concat.1.a.bcf /tmp/UuhxTXGXNz/concat.1.b.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob /tmp/UuhxTXGXNz/concat.1.a.bcf /tmp/UuhxTXGXNz/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/UuhxTXGXNz/concat.2.a.vcf.gz /tmp/UuhxTXGXNz/concat.2.b.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -a /tmp/UuhxTXGXNz/concat.2.a.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/concat.2.a.bcf /tmp/UuhxTXGXNz/concat.2.b.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -a /tmp/UuhxTXGXNz/concat.2.a.bcf /tmp/UuhxTXGXNz/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/UuhxTXGXNz/concat.2.a.vcf.gz /tmp/UuhxTXGXNz/concat.2.b.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -aD /tmp/UuhxTXGXNz/concat.2.a.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/concat.2.a.bcf /tmp/UuhxTXGXNz/concat.2.b.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -aD /tmp/UuhxTXGXNz/concat.2.a.bcf /tmp/UuhxTXGXNz/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/UuhxTXGXNz/concat.3.a.vcf.gz /tmp/UuhxTXGXNz/concat.3.b.vcf.gz /tmp/UuhxTXGXNz/concat.3.0.vcf.gz /tmp/UuhxTXGXNz/concat.3.c.vcf.gz /tmp/UuhxTXGXNz/concat.3.d.vcf.gz /tmp/UuhxTXGXNz/concat.3.e.vcf.gz /tmp/UuhxTXGXNz/concat.3.f.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -l --ligate-warn /tmp/UuhxTXGXNz/concat.3.a.vcf.gz /tmp/UuhxTXGXNz/concat.3.b.vcf.gz /tmp/UuhxTXGXNz/concat.3.0.vcf.gz /tmp/UuhxTXGXNz/concat.3.c.vcf.gz /tmp/UuhxTXGXNz/concat.3.d.vcf.gz /tmp/UuhxTXGXNz/concat.3.e.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/concat.3.a.bcf /tmp/UuhxTXGXNz/concat.3.b.bcf /tmp/UuhxTXGXNz/concat.3.0.bcf /tmp/UuhxTXGXNz/concat.3.c.bcf /tmp/UuhxTXGXNz/concat.3.d.bcf /tmp/UuhxTXGXNz/concat.3.e.bcf /tmp/UuhxTXGXNz/concat.3.f.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -l --ligate-warn /tmp/UuhxTXGXNz/concat.3.a.bcf /tmp/UuhxTXGXNz/concat.3.b.bcf /tmp/UuhxTXGXNz/concat.3.0.bcf /tmp/UuhxTXGXNz/concat.3.c.bcf /tmp/UuhxTXGXNz/concat.3.d.bcf /tmp/UuhxTXGXNz/concat.3.e.bcf /tmp/UuhxTXGXNz/concat.3.f.bcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ Random seed for test_naive_concat: 3260046851 .. ok test_naive_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --naive-force /tmp/UuhxTXGXNz/naive_concat.0.bcf /tmp/UuhxTXGXNz/naive_concat.1.bcf /tmp/UuhxTXGXNz/naive_concat.2.bcf /tmp/UuhxTXGXNz/naive_concat.3.bcf /tmp/UuhxTXGXNz/naive_concat.4.bcf /tmp/UuhxTXGXNz/naive_concat.5.bcf /tmp/UuhxTXGXNz/naive_concat.6.bcf /tmp/UuhxTXGXNz/naive_concat.7.bcf /tmp/UuhxTXGXNz/naive_concat.8.bcf /tmp/UuhxTXGXNz/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/UuhxTXGXNz/naive_concat.0.vcf.gz /tmp/UuhxTXGXNz/naive_concat.1.vcf.gz /tmp/UuhxTXGXNz/naive_concat.2.vcf.gz /tmp/UuhxTXGXNz/naive_concat.3.vcf.gz /tmp/UuhxTXGXNz/naive_concat.4.vcf.gz /tmp/UuhxTXGXNz/naive_concat.5.vcf.gz /tmp/UuhxTXGXNz/naive_concat.6.vcf.gz /tmp/UuhxTXGXNz/naive_concat.7.vcf.gz /tmp/UuhxTXGXNz/naive_concat.8.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/concat.4.a.vcf.gz /tmp/UuhxTXGXNz/concat.4.b.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -l /tmp/UuhxTXGXNz/concat.4.a.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/concat.4.a.bcf /tmp/UuhxTXGXNz/concat.4.b.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -l /tmp/UuhxTXGXNz/concat.4.a.bcf /tmp/UuhxTXGXNz/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/UuhxTXGXNz/concat.5.a.vcf.gz /tmp/UuhxTXGXNz/concat.5.b.vcf.gz /tmp/UuhxTXGXNz/concat.5.c.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -l --ligate-warn /tmp/UuhxTXGXNz/concat.5.a.vcf.gz /tmp/UuhxTXGXNz/concat.5.b.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/concat.5.a.bcf /tmp/UuhxTXGXNz/concat.5.b.bcf /tmp/UuhxTXGXNz/concat.5.c.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -l --ligate-warn /tmp/UuhxTXGXNz/concat.5.a.bcf /tmp/UuhxTXGXNz/concat.5.b.bcf /tmp/UuhxTXGXNz/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/UuhxTXGXNz/concat.5.a.bcf /tmp/UuhxTXGXNz/concat.5.b.bcf /tmp/UuhxTXGXNz/concat.5.c.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -l --ligate-force /tmp/UuhxTXGXNz/concat.5.a.bcf /tmp/UuhxTXGXNz/concat.5.b.bcf /tmp/UuhxTXGXNz/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/UuhxTXGXNz/concat.5.a.vcf.gz /tmp/UuhxTXGXNz/concat.5.b.vcf.gz /tmp/UuhxTXGXNz/concat.5.c.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -G -a -D /tmp/UuhxTXGXNz/concat.5.a.vcf.gz /tmp/UuhxTXGXNz/concat.5.b.vcf.gz /tmp/UuhxTXGXNz/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/UuhxTXGXNz/concat.5.a.bcf /tmp/UuhxTXGXNz/concat.5.b.bcf /tmp/UuhxTXGXNz/concat.5.c.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -G -a -D /tmp/UuhxTXGXNz/concat.5.a.bcf /tmp/UuhxTXGXNz/concat.5.b.bcf /tmp/UuhxTXGXNz/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/UuhxTXGXNz/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/UuhxTXGXNz/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/UuhxTXGXNz/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/UuhxTXGXNz/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/UuhxTXGXNz/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/UuhxTXGXNz/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/UuhxTXGXNz/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/UuhxTXGXNz/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/UuhxTXGXNz/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/UuhxTXGXNz/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/UuhxTXGXNz/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/UuhxTXGXNz/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/UuhxTXGXNz/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/UuhxTXGXNz/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/UuhxTXGXNz/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/UuhxTXGXNz/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/UuhxTXGXNz/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/UuhxTXGXNz/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/UuhxTXGXNz/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/UuhxTXGXNz/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/UuhxTXGXNz/empty.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/UuhxTXGXNz/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/UuhxTXGXNz/empty.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/rename.map -Ov /tmp/UuhxTXGXNz/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/UuhxTXGXNz/rename.map -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/convert.hap-missing.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/convert.gvcf.vcf.gz .. ok test_vcf_convert_gvcf: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/consensus.1.chain.new >/dev/null; cat /tmp/UuhxTXGXNz/consensus.1.chain.new .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/consensus.2.chain.new >/dev/null; cat /tmp/UuhxTXGXNz/consensus.2.chain.new .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/consensus.3.chain.new >/dev/null; cat /tmp/UuhxTXGXNz/consensus.3.chain.new .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -H 1 -c /tmp/UuhxTXGXNz/consensus.4.chain.new >/dev/null; cat /tmp/UuhxTXGXNz/consensus.4.chain.new .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/gtcheck.1.vcf.gz -g /tmp/UuhxTXGXNz/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 /tmp/UuhxTXGXNz/gtcheck.1.vcf.gz -g /tmp/UuhxTXGXNz/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/UuhxTXGXNz/gtcheck.1.vcf.gz -g /tmp/UuhxTXGXNz/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/UuhxTXGXNz/gtcheck.1.vcf.gz -g /tmp/UuhxTXGXNz/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/UuhxTXGXNz/gtcheck.1.vcf.gz -g /tmp/UuhxTXGXNz/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/UuhxTXGXNz/gtcheck.1.vcf.gz -g /tmp/UuhxTXGXNz/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/UuhxTXGXNz/gtcheck.1.vcf.gz -g /tmp/UuhxTXGXNz/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 /tmp/UuhxTXGXNz/gtcheck.2.vcf.gz -g /tmp/UuhxTXGXNz/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 /tmp/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/gtcheck.1.vcf.gz -g /tmp/UuhxTXGXNz/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/UuhxTXGXNz/gtcheck.1.vcf.gz -g /tmp/UuhxTXGXNz/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/UuhxTXGXNz/gtcheck.1.vcf.gz -g /tmp/UuhxTXGXNz/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/UuhxTXGXNz/gtcheck.1.vcf.gz -g /tmp/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/gtcheck.1.vcf.gz -g /tmp/UuhxTXGXNz/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/UuhxTXGXNz/gtcheck.1.vcf.gz -g /tmp/UuhxTXGXNz/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/UuhxTXGXNz/gtcheck.1.vcf.gz -g /tmp/UuhxTXGXNz/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/UuhxTXGXNz/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck /tmp/UuhxTXGXNz/gtcheck.ntop.vcf.gz -g /tmp/UuhxTXGXNz/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/UuhxTXGXNz/gtcheck.ntop.vcf.gz -g /tmp/UuhxTXGXNz/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck /tmp/UuhxTXGXNz/gtcheck.5.vcf.gz -g /tmp/UuhxTXGXNz/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/UuhxTXGXNz/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/UuhxTXGXNz/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 -j20 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/1091695 and its subdirectories I: Current time: Wed Mar 12 13:01:12 -12 2025 I: pbuilder-time-stamp: 1741827672 Thu Mar 13 01:01:14 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos5-amd64.debian.net. Thu Mar 13 01:01:14 UTC 2025 I: Preparing to do remote build '2' on ionos5-amd64.debian.net. Thu Mar 13 01:02:42 UTC 2025 I: Deleting $TMPDIR on ionos5-amd64.debian.net. Thu Mar 13 01:02:43 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: 6241e524330f42f5b1cfc633ba3ab02b054ed843 2232296 bcftools-dbgsym_1.21-1_amd64.deb 29f731ac94599b7baa84228c3f35e28b07f17833 7022 bcftools_1.21-1_amd64.buildinfo 3e62bb38fd452788eccf35219cd7280e947c3a0a 784568 bcftools_1.21-1_amd64.deb Checksums-Sha256: 6ac02eed61881077c6b08733481d0bf3c1d674da7d82bc30696cc946a4d94ba4 2232296 bcftools-dbgsym_1.21-1_amd64.deb 04aa0424b4cf4013f046b8ac00690603900129129852de3fd73700b6d5558ac6 7022 bcftools_1.21-1_amd64.buildinfo 9b751bf33705e01981594c329886926b5291e0d73e49eedc87f99fc0c434e726 784568 bcftools_1.21-1_amd64.deb Files: 52a954f1c7e5550d6ecddc39ffe1cabe 2232296 debug optional bcftools-dbgsym_1.21-1_amd64.deb 19a8055a1bec1ce6c27a8be774992a58 7022 science optional bcftools_1.21-1_amd64.buildinfo d8e1fb79f49016b093a07eade50a8d4c 784568 science optional bcftools_1.21-1_amd64.deb Thu Mar 13 01:02:44 UTC 2025 I: diffoscope 289 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_31-35522.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.haxgeckP/bcftools_1.21-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.haxgeckP/bcftools_1.21-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.haxgeckP/bcftools_1.21-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.haxgeckP/b1/bcftools_1.21-1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.haxgeckP/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: 230ms CPU time consumed: 231ms Thu Mar 13 01:03:43 UTC 2025 I: diffoscope 289 found no differences in the changes files, and a .buildinfo file also exists. Thu Mar 13 01:03:43 UTC 2025 I: bcftools from trixie built successfully and reproducibly on amd64. Thu Mar 13 01:03:45 UTC 2025 I: Submitting .buildinfo files to external archives: Thu Mar 13 01:03:45 UTC 2025 I: Submitting 8.0K b1/bcftools_1.21-1_amd64.buildinfo.asc Thu Mar 13 01:03:47 UTC 2025 I: Submitting 8.0K b2/bcftools_1.21-1_amd64.buildinfo.asc Thu Mar 13 01:03:50 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu Mar 13 01:03:50 UTC 2025 I: Done submitting .buildinfo files. Thu Mar 13 01:03:50 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'