Mon Feb 17 16:42:42 UTC 2025 I: starting to build bcftools/trixie/arm64 on jenkins on '2025-02-17 16:42' Mon Feb 17 16:42:43 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_4/57719/console.log Mon Feb 17 16:42:43 UTC 2025 I: Downloading source for trixie/bcftools=1.21-1 --2025-02-17 16:42:43-- 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% 302M=0s 2025-02-17 16:42:43 (302 MB/s) - ‘bcftools_1.21-1.dsc’ saved [2267/2267] Mon Feb 17 16:42:43 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----- Mon Feb 17 16:42:43 UTC 2025 I: Checking whether the package is not for us Mon Feb 17 16:42:43 UTC 2025 I: Starting 1st build on remote node codethink03-arm64.debian.net. Mon Feb 17 16:42:43 UTC 2025 I: Preparing to do remote build '1' on codethink03-arm64.debian.net. Mon Feb 17 16:46:32 UTC 2025 I: Deleting $TMPDIR on codethink03-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Mar 22 11:05:45 -12 2026 I: pbuilder-time-stamp: 1774220745 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/3400892/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='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='0b355be2058b4b619a4a9b72fdbc325a' 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='3400892' 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.YKtOyVzv/pbuilderrc_Ja0I --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.YKtOyVzv/b1 --logfile b1/build.log bcftools_1.21-1.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink03-arm64 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3400892/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: arm64 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 ... 19923 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 42.0 MB of archives. After unpacking 162 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.23.1-1 [241 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-7 [1129 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.4-3 [92.0 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-5 [284 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.17-3 [862 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.23.1-1 [770 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 libcom-err2 arm64 1.47.2-1 [23.9 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 comerr-dev arm64 2.1-1.47.2-1 [55.9 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 libtool all 2.5.4-3 [539 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 24 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 libunistring5 arm64 1.3-1 [449 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-6 [9239 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.23.1-1 [1610 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.24.1 [920 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 libkrb5support0 arm64 1.21.3-4 [32.2 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 libk5crypto3 arm64 1.21.3-4 [81.5 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 libkeyutils1 arm64 1.6.3-4 [9352 B] Get: 36 http://deb.debian.org/debian trixie/main arm64 libkrb5-3 arm64 1.21.3-4 [308 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 libgssapi-krb5-2 arm64 1.21.3-4 [127 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 libgssrpc4t64 arm64 1.21.3-4 [56.9 kB] Get: 39 http://deb.debian.org/debian trixie/main arm64 libkadm5clnt-mit12 arm64 1.21.3-4 [41.0 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 libkdb5-10t64 arm64 1.21.3-4 [41.0 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 libkadm5srv-mit12 arm64 1.21.3-4 [53.1 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 krb5-multidev arm64 1.21.3-4 [126 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 libbrotli1 arm64 1.1.0-2+b6 [297 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 libbrotli-dev arm64 1.1.0-2+b6 [308 kB] Get: 45 http://deb.debian.org/debian trixie/main arm64 libbz2-dev arm64 1.0.8-6 [31.9 kB] Get: 46 http://deb.debian.org/debian trixie/main arm64 libidn2-0 arm64 2.3.7-2+b1 [127 kB] Get: 47 http://deb.debian.org/debian trixie/main arm64 libffi8 arm64 3.4.6-1 [20.9 kB] Get: 48 http://deb.debian.org/debian trixie/main arm64 libp11-kit0 arm64 0.25.5-3 [409 kB] Get: 49 http://deb.debian.org/debian trixie/main arm64 libtasn1-6 arm64 4.20.0-2 [47.3 kB] Get: 50 http://deb.debian.org/debian trixie/main arm64 libgnutls30t64 arm64 3.8.9-2 [1374 kB] Get: 51 http://deb.debian.org/debian trixie/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-8+b1 [20.3 kB] Get: 52 http://deb.debian.org/debian trixie/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-8+b1 [55.7 kB] Get: 53 http://deb.debian.org/debian trixie/main arm64 libldap2 arm64 2.6.9+dfsg-1 [179 kB] Get: 54 http://deb.debian.org/debian trixie/main arm64 libnghttp2-14 arm64 1.64.0-1 [71.3 kB] Get: 55 http://deb.debian.org/debian trixie/main arm64 libnghttp3-9 arm64 1.6.0-2 [60.5 kB] Get: 56 http://deb.debian.org/debian trixie/main arm64 libngtcp2-16 arm64 1.9.1-1 [109 kB] Get: 57 http://deb.debian.org/debian trixie/main arm64 libngtcp2-crypto-gnutls8 arm64 1.9.1-1 [17.3 kB] Get: 58 http://deb.debian.org/debian trixie/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get: 59 http://deb.debian.org/debian trixie/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b5 [56.8 kB] Get: 60 http://deb.debian.org/debian trixie/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get: 61 http://deb.debian.org/debian trixie/main arm64 libcurl3t64-gnutls arm64 8.12.0+git20250209.89ed161+ds-1 [336 kB] Get: 62 http://deb.debian.org/debian trixie/main arm64 libevent-2.1-7t64 arm64 2.1.12-stable-10+b1 [170 kB] Get: 63 http://deb.debian.org/debian trixie/main arm64 libunbound8 arm64 1.22.0-1+b1 [553 kB] Get: 64 http://deb.debian.org/debian trixie/main arm64 libgnutls-dane0t64 arm64 3.8.9-2 [452 kB] Get: 65 http://deb.debian.org/debian trixie/main arm64 libgnutls-openssl27t64 arm64 3.8.9-2 [452 kB] Get: 66 http://deb.debian.org/debian trixie/main arm64 libidn2-dev arm64 2.3.7-2+b1 [122 kB] Get: 67 http://deb.debian.org/debian trixie/main arm64 libp11-kit-dev arm64 0.25.5-3 [208 kB] Get: 68 http://deb.debian.org/debian trixie/main arm64 libtasn1-6-dev arm64 4.20.0-2 [96.7 kB] Get: 69 http://deb.debian.org/debian trixie/main arm64 libgmpxx4ldbl arm64 2:6.3.0+dfsg-3 [329 kB] Get: 70 http://deb.debian.org/debian trixie/main arm64 libgmp-dev arm64 2:6.3.0+dfsg-3 [621 kB] Get: 71 http://deb.debian.org/debian trixie/main arm64 nettle-dev arm64 3.10-1+b1 [1324 kB] Get: 72 http://deb.debian.org/debian trixie/main arm64 libgnutls28-dev arm64 3.8.9-2 [1419 kB] Get: 73 http://deb.debian.org/debian trixie/main arm64 libkrb5-dev arm64 1.21.3-4 [15.9 kB] Get: 74 http://deb.debian.org/debian trixie/main arm64 libldap-dev arm64 2.6.9+dfsg-1 [305 kB] Get: 75 http://deb.debian.org/debian trixie/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB] Get: 76 http://deb.debian.org/debian trixie/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB] Get: 77 http://deb.debian.org/debian trixie/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB] Get: 78 http://deb.debian.org/debian trixie/main arm64 libnghttp2-dev arm64 1.64.0-1 [112 kB] Get: 79 http://deb.debian.org/debian trixie/main arm64 libnghttp3-dev arm64 1.6.0-2 [86.5 kB] Get: 80 http://deb.debian.org/debian trixie/main arm64 libngtcp2-crypto-gnutls-dev arm64 1.9.1-1 [23.0 kB] Get: 81 http://deb.debian.org/debian trixie/main arm64 libngtcp2-dev arm64 1.9.1-1 [162 kB] Get: 82 http://deb.debian.org/debian trixie/main arm64 libpsl-dev arm64 0.21.2-1.1+b1 [77.9 kB] Get: 83 http://deb.debian.org/debian trixie/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 84 http://deb.debian.org/debian trixie/main arm64 librtmp-dev arm64 2.4+20151223.gitfa8646d.1-2+b5 [67.5 kB] Get: 85 http://deb.debian.org/debian trixie/main arm64 libssl-dev arm64 3.4.0-2 [3234 kB] Get: 86 http://deb.debian.org/debian trixie/main arm64 libssh2-1-dev arm64 1.11.1-1 [388 kB] Get: 87 http://deb.debian.org/debian trixie/main arm64 libzstd-dev arm64 1.5.6+dfsg-2 [329 kB] Get: 88 http://deb.debian.org/debian trixie/main arm64 libcurl4-gnutls-dev arm64 8.12.0+git20250209.89ed161+ds-1 [465 kB] Get: 89 http://deb.debian.org/debian trixie/main arm64 libdeflate0 arm64 1.23-1+b1 [42.5 kB] Get: 90 http://deb.debian.org/debian trixie/main arm64 libdeflate-dev arm64 1.23-1+b1 [51.4 kB] Get: 91 http://deb.debian.org/debian trixie/main arm64 libgslcblas0 arm64 2.8+dfsg-5 [84.1 kB] Get: 92 http://deb.debian.org/debian trixie/main arm64 libgsl28 arm64 2.8+dfsg-5 [881 kB] Get: 93 http://deb.debian.org/debian trixie/main arm64 libgsl-dev arm64 2.8+dfsg-5 [1118 kB] Get: 94 http://deb.debian.org/debian trixie/main arm64 libhtscodecs2 arm64 1.6.1-1 [74.6 kB] Get: 95 http://deb.debian.org/debian trixie/main arm64 libhts3t64 arm64 1.21+ds-1 [426 kB] Get: 96 http://deb.debian.org/debian trixie/main arm64 liblzma-dev arm64 5.6.3-1+b1 [312 kB] Get: 97 http://deb.debian.org/debian trixie/main arm64 libhts-dev arm64 1.21+ds-1 [1658 kB] Get: 98 http://deb.debian.org/debian trixie/main arm64 libio-pty-perl arm64 1:1.20-1+b2 [34.0 kB] Get: 99 http://deb.debian.org/debian trixie/main arm64 tabix arm64 1.21+ds-1 [461 kB] Fetched 42.0 MB in 0s (90.7 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 ... 19923 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_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3+b1_arm64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-1_arm64.deb ... Unpacking gettext-base (0.23.1-1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-7_arm64.deb ... Unpacking groff-base (1.23.0-7) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.4-3_arm64.deb ... Unpacking bsdextrautils (2.40.4-3) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../08-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-5_arm64.deb ... Unpacking m4 (1.4.19-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.17-3_all.deb ... Unpacking automake (1:1.17-3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.23.1-1_all.deb ... Unpacking autopoint (0.23.1-1) ... Selecting previously unselected package libcom-err2:arm64. Preparing to unpack .../15-libcom-err2_1.47.2-1_arm64.deb ... Unpacking libcom-err2:arm64 (1.47.2-1) ... Selecting previously unselected package comerr-dev:arm64. Preparing to unpack .../16-comerr-dev_2.1-1.47.2-1_arm64.deb ... Unpacking comerr-dev:arm64 (2.1-1.47.2-1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../17-libdebhelper-perl_13.24.1_all.deb ... Unpacking libdebhelper-perl (13.24.1) ... Selecting previously unselected package libtool. Preparing to unpack .../18-libtool_2.5.4-3_all.deb ... Unpacking libtool (2.5.4-3) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../19-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../20-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../21-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../22-dh-strip-nondeterminism_1.14.1-2_all.deb ... Unpacking dh-strip-nondeterminism (1.14.1-2) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../23-libelf1t64_0.192-4_arm64.deb ... Unpacking libelf1t64:arm64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../24-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libunistring5:arm64. Preparing to unpack .../25-libunistring5_1.3-1_arm64.deb ... Unpacking libunistring5:arm64 (1.3-1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../26-libicu72_72.1-6_arm64.deb ... Unpacking libicu72:arm64 (72.1-6) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../27-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../28-gettext_0.23.1-1_arm64.deb ... Unpacking gettext (0.23.1-1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../29-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../30-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../31-debhelper_13.24.1_all.deb ... Unpacking debhelper (13.24.1) ... Selecting previously unselected package libkrb5support0:arm64. Preparing to unpack .../32-libkrb5support0_1.21.3-4_arm64.deb ... Unpacking libkrb5support0:arm64 (1.21.3-4) ... Selecting previously unselected package libk5crypto3:arm64. Preparing to unpack .../33-libk5crypto3_1.21.3-4_arm64.deb ... Unpacking libk5crypto3:arm64 (1.21.3-4) ... Selecting previously unselected package libkeyutils1:arm64. Preparing to unpack .../34-libkeyutils1_1.6.3-4_arm64.deb ... Unpacking libkeyutils1:arm64 (1.6.3-4) ... Selecting previously unselected package libkrb5-3:arm64. Preparing to unpack .../35-libkrb5-3_1.21.3-4_arm64.deb ... Unpacking libkrb5-3:arm64 (1.21.3-4) ... Selecting previously unselected package libgssapi-krb5-2:arm64. Preparing to unpack .../36-libgssapi-krb5-2_1.21.3-4_arm64.deb ... Unpacking libgssapi-krb5-2:arm64 (1.21.3-4) ... Selecting previously unselected package libgssrpc4t64:arm64. Preparing to unpack .../37-libgssrpc4t64_1.21.3-4_arm64.deb ... Unpacking libgssrpc4t64:arm64 (1.21.3-4) ... Selecting previously unselected package libkadm5clnt-mit12:arm64. Preparing to unpack .../38-libkadm5clnt-mit12_1.21.3-4_arm64.deb ... Unpacking libkadm5clnt-mit12:arm64 (1.21.3-4) ... Selecting previously unselected package libkdb5-10t64:arm64. Preparing to unpack .../39-libkdb5-10t64_1.21.3-4_arm64.deb ... Unpacking libkdb5-10t64:arm64 (1.21.3-4) ... Selecting previously unselected package libkadm5srv-mit12:arm64. Preparing to unpack .../40-libkadm5srv-mit12_1.21.3-4_arm64.deb ... Unpacking libkadm5srv-mit12:arm64 (1.21.3-4) ... Selecting previously unselected package krb5-multidev:arm64. Preparing to unpack .../41-krb5-multidev_1.21.3-4_arm64.deb ... Unpacking krb5-multidev:arm64 (1.21.3-4) ... Selecting previously unselected package libbrotli1:arm64. Preparing to unpack .../42-libbrotli1_1.1.0-2+b6_arm64.deb ... Unpacking libbrotli1:arm64 (1.1.0-2+b6) ... Selecting previously unselected package libbrotli-dev:arm64. Preparing to unpack .../43-libbrotli-dev_1.1.0-2+b6_arm64.deb ... Unpacking libbrotli-dev:arm64 (1.1.0-2+b6) ... Selecting previously unselected package libbz2-dev:arm64. Preparing to unpack .../44-libbz2-dev_1.0.8-6_arm64.deb ... Unpacking libbz2-dev:arm64 (1.0.8-6) ... Selecting previously unselected package libidn2-0:arm64. Preparing to unpack .../45-libidn2-0_2.3.7-2+b1_arm64.deb ... Unpacking libidn2-0:arm64 (2.3.7-2+b1) ... Selecting previously unselected package libffi8:arm64. Preparing to unpack .../46-libffi8_3.4.6-1_arm64.deb ... Unpacking libffi8:arm64 (3.4.6-1) ... Selecting previously unselected package libp11-kit0:arm64. Preparing to unpack .../47-libp11-kit0_0.25.5-3_arm64.deb ... Unpacking libp11-kit0:arm64 (0.25.5-3) ... Selecting previously unselected package libtasn1-6:arm64. Preparing to unpack .../48-libtasn1-6_4.20.0-2_arm64.deb ... Unpacking libtasn1-6:arm64 (4.20.0-2) ... Selecting previously unselected package libgnutls30t64:arm64. Preparing to unpack .../49-libgnutls30t64_3.8.9-2_arm64.deb ... Unpacking libgnutls30t64:arm64 (3.8.9-2) ... Selecting previously unselected package libsasl2-modules-db:arm64. Preparing to unpack .../50-libsasl2-modules-db_2.1.28+dfsg1-8+b1_arm64.deb ... Unpacking libsasl2-modules-db:arm64 (2.1.28+dfsg1-8+b1) ... Selecting previously unselected package libsasl2-2:arm64. Preparing to unpack .../51-libsasl2-2_2.1.28+dfsg1-8+b1_arm64.deb ... Unpacking libsasl2-2:arm64 (2.1.28+dfsg1-8+b1) ... Selecting previously unselected package libldap2:arm64. Preparing to unpack .../52-libldap2_2.6.9+dfsg-1_arm64.deb ... Unpacking libldap2:arm64 (2.6.9+dfsg-1) ... Selecting previously unselected package libnghttp2-14:arm64. Preparing to unpack .../53-libnghttp2-14_1.64.0-1_arm64.deb ... Unpacking libnghttp2-14:arm64 (1.64.0-1) ... Selecting previously unselected package libnghttp3-9:arm64. Preparing to unpack .../54-libnghttp3-9_1.6.0-2_arm64.deb ... Unpacking libnghttp3-9:arm64 (1.6.0-2) ... Selecting previously unselected package libngtcp2-16:arm64. Preparing to unpack .../55-libngtcp2-16_1.9.1-1_arm64.deb ... Unpacking libngtcp2-16:arm64 (1.9.1-1) ... Selecting previously unselected package libngtcp2-crypto-gnutls8:arm64. Preparing to unpack .../56-libngtcp2-crypto-gnutls8_1.9.1-1_arm64.deb ... Unpacking libngtcp2-crypto-gnutls8:arm64 (1.9.1-1) ... Selecting previously unselected package libpsl5t64:arm64. Preparing to unpack .../57-libpsl5t64_0.21.2-1.1+b1_arm64.deb ... Unpacking libpsl5t64:arm64 (0.21.2-1.1+b1) ... Selecting previously unselected package librtmp1:arm64. Preparing to unpack .../58-librtmp1_2.4+20151223.gitfa8646d.1-2+b5_arm64.deb ... Unpacking librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b5) ... Selecting previously unselected package libssh2-1t64:arm64. Preparing to unpack .../59-libssh2-1t64_1.11.1-1_arm64.deb ... Unpacking libssh2-1t64:arm64 (1.11.1-1) ... Selecting previously unselected package libcurl3t64-gnutls:arm64. Preparing to unpack .../60-libcurl3t64-gnutls_8.12.0+git20250209.89ed161+ds-1_arm64.deb ... Unpacking libcurl3t64-gnutls:arm64 (8.12.0+git20250209.89ed161+ds-1) ... Selecting previously unselected package libevent-2.1-7t64:arm64. Preparing to unpack .../61-libevent-2.1-7t64_2.1.12-stable-10+b1_arm64.deb ... Unpacking libevent-2.1-7t64:arm64 (2.1.12-stable-10+b1) ... Selecting previously unselected package libunbound8:arm64. Preparing to unpack .../62-libunbound8_1.22.0-1+b1_arm64.deb ... Unpacking libunbound8:arm64 (1.22.0-1+b1) ... Selecting previously unselected package libgnutls-dane0t64:arm64. Preparing to unpack .../63-libgnutls-dane0t64_3.8.9-2_arm64.deb ... Unpacking libgnutls-dane0t64:arm64 (3.8.9-2) ... Selecting previously unselected package libgnutls-openssl27t64:arm64. Preparing to unpack .../64-libgnutls-openssl27t64_3.8.9-2_arm64.deb ... Unpacking libgnutls-openssl27t64:arm64 (3.8.9-2) ... Selecting previously unselected package libidn2-dev:arm64. Preparing to unpack .../65-libidn2-dev_2.3.7-2+b1_arm64.deb ... Unpacking libidn2-dev:arm64 (2.3.7-2+b1) ... Selecting previously unselected package libp11-kit-dev:arm64. Preparing to unpack .../66-libp11-kit-dev_0.25.5-3_arm64.deb ... Unpacking libp11-kit-dev:arm64 (0.25.5-3) ... Selecting previously unselected package libtasn1-6-dev:arm64. Preparing to unpack .../67-libtasn1-6-dev_4.20.0-2_arm64.deb ... Unpacking libtasn1-6-dev:arm64 (4.20.0-2) ... Selecting previously unselected package libgmpxx4ldbl:arm64. Preparing to unpack .../68-libgmpxx4ldbl_2%3a6.3.0+dfsg-3_arm64.deb ... Unpacking libgmpxx4ldbl:arm64 (2:6.3.0+dfsg-3) ... Selecting previously unselected package libgmp-dev:arm64. Preparing to unpack .../69-libgmp-dev_2%3a6.3.0+dfsg-3_arm64.deb ... Unpacking libgmp-dev:arm64 (2:6.3.0+dfsg-3) ... Selecting previously unselected package nettle-dev:arm64. Preparing to unpack .../70-nettle-dev_3.10-1+b1_arm64.deb ... Unpacking nettle-dev:arm64 (3.10-1+b1) ... Selecting previously unselected package libgnutls28-dev:arm64. Preparing to unpack .../71-libgnutls28-dev_3.8.9-2_arm64.deb ... Unpacking libgnutls28-dev:arm64 (3.8.9-2) ... Selecting previously unselected package libkrb5-dev:arm64. Preparing to unpack .../72-libkrb5-dev_1.21.3-4_arm64.deb ... Unpacking libkrb5-dev:arm64 (1.21.3-4) ... Selecting previously unselected package libldap-dev:arm64. Preparing to unpack .../73-libldap-dev_2.6.9+dfsg-1_arm64.deb ... Unpacking libldap-dev:arm64 (2.6.9+dfsg-1) ... Selecting previously unselected package libpkgconf3:arm64. Preparing to unpack .../74-libpkgconf3_1.8.1-4_arm64.deb ... Unpacking libpkgconf3:arm64 (1.8.1-4) ... Selecting previously unselected package pkgconf-bin. Preparing to unpack .../75-pkgconf-bin_1.8.1-4_arm64.deb ... Unpacking pkgconf-bin (1.8.1-4) ... Selecting previously unselected package pkgconf:arm64. Preparing to unpack .../76-pkgconf_1.8.1-4_arm64.deb ... Unpacking pkgconf:arm64 (1.8.1-4) ... Selecting previously unselected package libnghttp2-dev:arm64. Preparing to unpack .../77-libnghttp2-dev_1.64.0-1_arm64.deb ... Unpacking libnghttp2-dev:arm64 (1.64.0-1) ... Selecting previously unselected package libnghttp3-dev:arm64. Preparing to unpack .../78-libnghttp3-dev_1.6.0-2_arm64.deb ... Unpacking libnghttp3-dev:arm64 (1.6.0-2) ... Selecting previously unselected package libngtcp2-crypto-gnutls-dev:arm64. Preparing to unpack .../79-libngtcp2-crypto-gnutls-dev_1.9.1-1_arm64.deb ... Unpacking libngtcp2-crypto-gnutls-dev:arm64 (1.9.1-1) ... Selecting previously unselected package libngtcp2-dev:arm64. Preparing to unpack .../80-libngtcp2-dev_1.9.1-1_arm64.deb ... Unpacking libngtcp2-dev:arm64 (1.9.1-1) ... Selecting previously unselected package libpsl-dev:arm64. Preparing to unpack .../81-libpsl-dev_0.21.2-1.1+b1_arm64.deb ... Unpacking libpsl-dev:arm64 (0.21.2-1.1+b1) ... Selecting previously unselected package zlib1g-dev:arm64. Preparing to unpack .../82-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_arm64.deb ... Unpacking zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ... Selecting previously unselected package librtmp-dev:arm64. Preparing to unpack .../83-librtmp-dev_2.4+20151223.gitfa8646d.1-2+b5_arm64.deb ... Unpacking librtmp-dev:arm64 (2.4+20151223.gitfa8646d.1-2+b5) ... Selecting previously unselected package libssl-dev:arm64. Preparing to unpack .../84-libssl-dev_3.4.0-2_arm64.deb ... Unpacking libssl-dev:arm64 (3.4.0-2) ... Selecting previously unselected package libssh2-1-dev:arm64. Preparing to unpack .../85-libssh2-1-dev_1.11.1-1_arm64.deb ... Unpacking libssh2-1-dev:arm64 (1.11.1-1) ... Selecting previously unselected package libzstd-dev:arm64. Preparing to unpack .../86-libzstd-dev_1.5.6+dfsg-2_arm64.deb ... Unpacking libzstd-dev:arm64 (1.5.6+dfsg-2) ... Selecting previously unselected package libcurl4-gnutls-dev:arm64. Preparing to unpack .../87-libcurl4-gnutls-dev_8.12.0+git20250209.89ed161+ds-1_arm64.deb ... Unpacking libcurl4-gnutls-dev:arm64 (8.12.0+git20250209.89ed161+ds-1) ... Selecting previously unselected package libdeflate0:arm64. Preparing to unpack .../88-libdeflate0_1.23-1+b1_arm64.deb ... Unpacking libdeflate0:arm64 (1.23-1+b1) ... Selecting previously unselected package libdeflate-dev:arm64. Preparing to unpack .../89-libdeflate-dev_1.23-1+b1_arm64.deb ... Unpacking libdeflate-dev:arm64 (1.23-1+b1) ... Selecting previously unselected package libgslcblas0:arm64. Preparing to unpack .../90-libgslcblas0_2.8+dfsg-5_arm64.deb ... Unpacking libgslcblas0:arm64 (2.8+dfsg-5) ... Selecting previously unselected package libgsl28:arm64. Preparing to unpack .../91-libgsl28_2.8+dfsg-5_arm64.deb ... Unpacking libgsl28:arm64 (2.8+dfsg-5) ... Selecting previously unselected package libgsl-dev. Preparing to unpack .../92-libgsl-dev_2.8+dfsg-5_arm64.deb ... Unpacking libgsl-dev (2.8+dfsg-5) ... Selecting previously unselected package libhtscodecs2:arm64. Preparing to unpack .../93-libhtscodecs2_1.6.1-1_arm64.deb ... Unpacking libhtscodecs2:arm64 (1.6.1-1) ... Selecting previously unselected package libhts3t64:arm64. Preparing to unpack .../94-libhts3t64_1.21+ds-1_arm64.deb ... Unpacking libhts3t64:arm64 (1.21+ds-1) ... Selecting previously unselected package liblzma-dev:arm64. Preparing to unpack .../95-liblzma-dev_5.6.3-1+b1_arm64.deb ... Unpacking liblzma-dev:arm64 (5.6.3-1+b1) ... Selecting previously unselected package libhts-dev:arm64. Preparing to unpack .../96-libhts-dev_1.21+ds-1_arm64.deb ... Unpacking libhts-dev:arm64 (1.21+ds-1) ... Selecting previously unselected package libio-pty-perl. Preparing to unpack .../97-libio-pty-perl_1%3a1.20-1+b2_arm64.deb ... Unpacking libio-pty-perl (1:1.20-1+b2) ... Selecting previously unselected package tabix. Preparing to unpack .../98-tabix_1.21+ds-1_arm64.deb ... Unpacking tabix (1.21+ds-1) ... Setting up libhtscodecs2:arm64 (1.6.1-1) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up libkeyutils1:arm64 (1.6.3-4) ... Setting up libicu72:arm64 (72.1-6) ... Setting up libzstd-dev:arm64 (1.5.6+dfsg-2) ... Setting up bsdextrautils (2.40.4-3) ... Setting up libgslcblas0:arm64 (2.8+dfsg-5) ... Setting up libio-pty-perl (1:1.20-1+b2) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.24.1) ... Setting up libbrotli1:arm64 (1.1.0-2+b6) ... Setting up libmagic1t64:arm64 (1:5.45-3+b1) ... Setting up libnghttp2-14:arm64 (1.64.0-1) ... Setting up libdeflate0:arm64 (1.23-1+b1) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-5) ... Setting up libevent-2.1-7t64:arm64 (2.1.12-stable-10+b1) ... Setting up libcom-err2:arm64 (1.47.2-1) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up libkrb5support0:arm64 (1.21.3-4) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-8+b1) ... Setting up autotools-dev (20220109.1) ... Setting up libunbound8:arm64 (1.22.0-1+b1) ... Setting up libpkgconf3:arm64 (1.8.1-4) ... Setting up libgmpxx4ldbl:arm64 (2:6.3.0+dfsg-3) ... Setting up comerr-dev:arm64 (2.1-1.47.2-1) ... Setting up libunistring5:arm64 (1.3-1) ... Setting up libssl-dev:arm64 (3.4.0-2) ... Setting up autopoint (0.23.1-1) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libk5crypto3:arm64 (1.21.3-4) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg1-8+b1) ... Setting up autoconf (2.72-3) ... Setting up libnghttp3-9:arm64 (1.6.0-2) ... Setting up libnghttp3-dev:arm64 (1.6.0-2) ... Setting up liblzma-dev:arm64 (5.6.3-1+b1) ... Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libffi8:arm64 (3.4.6-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up libtasn1-6:arm64 (4.20.0-2) ... Setting up libngtcp2-16:arm64 (1.9.1-1) ... Setting up libkrb5-3:arm64 (1.21.3-4) ... Setting up libssh2-1t64:arm64 (1.11.1-1) ... Setting up libgsl28:arm64 (2.8+dfsg-5) ... Setting up libtasn1-6-dev:arm64 (4.20.0-2) ... Setting up libdeflate-dev:arm64 (1.23-1+b1) ... Setting up tabix (1.21+ds-1) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up libldap2:arm64 (2.6.9+dfsg-1) ... Setting up libbrotli-dev:arm64 (1.1.0-2+b6) ... Setting up libbz2-dev:arm64 (1.0.8-6) ... Setting up automake (1:1.17-3) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up gettext (0.23.1-1) ... Setting up libgsl-dev (2.8+dfsg-5) ... Setting up libgmp-dev:arm64 (2:6.3.0+dfsg-3) ... Setting up nettle-dev:arm64 (3.10-1+b1) ... Setting up libtool (2.5.4-3) ... Setting up libidn2-0:arm64 (2.3.7-2+b1) ... Setting up libngtcp2-dev:arm64 (1.9.1-1) ... Setting up pkgconf:arm64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libldap-dev:arm64 (2.6.9+dfsg-1) ... Setting up libp11-kit0:arm64 (0.25.5-3) ... Setting up libgssapi-krb5-2:arm64 (1.21.3-4) ... Setting up libssh2-1-dev:arm64 (1.11.1-1) ... Setting up libidn2-dev:arm64 (2.3.7-2+b1) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-7) ... Setting up libp11-kit-dev:arm64 (0.25.5-3) ... Setting up libgnutls30t64:arm64 (3.8.9-2) ... Setting up libgnutls-openssl27t64:arm64 (3.8.9-2) ... Setting up libnghttp2-dev:arm64 (1.64.0-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpsl5t64:arm64 (0.21.2-1.1+b1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libpsl-dev:arm64 (0.21.2-1.1+b1) ... Setting up libgnutls-dane0t64:arm64 (3.8.9-2) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libgssrpc4t64:arm64 (1.21.3-4) ... Setting up libngtcp2-crypto-gnutls8:arm64 (1.9.1-1) ... Setting up libkadm5clnt-mit12:arm64 (1.21.3-4) ... Setting up libgnutls28-dev:arm64 (3.8.9-2) ... Setting up libkdb5-10t64:arm64 (1.21.3-4) ... Setting up libcurl3t64-gnutls:arm64 (8.12.0+git20250209.89ed161+ds-1) ... Setting up debhelper (13.24.1) ... Setting up libngtcp2-crypto-gnutls-dev:arm64 (1.9.1-1) ... Setting up librtmp-dev:arm64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libkadm5srv-mit12:arm64 (1.21.3-4) ... Setting up libhts3t64:arm64 (1.21+ds-1) ... Setting up krb5-multidev:arm64 (1.21.3-4) ... Setting up libkrb5-dev:arm64 (1.21.3-4) ... Setting up libcurl4-gnutls-dev:arm64 (8.12.0+git20250209.89ed161+ds-1) ... Setting up libhts-dev:arm64 (1.21+ds-1) ... Processing triggers for libc-bin (2.40-6) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/bcftools-1.21/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../bcftools_1.21-1_source.changes dpkg-buildpackage: info: source package bcftools dpkg-buildpackage: info: source version 1.21-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 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 -j12 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 test/*.unsorted.hex test/*.unsorted.tsv rm -f plugins/*.so plugins/*.P 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/aarch64-linux-gnu/bcftools ./configure --build=aarch64-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/aarch64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system --enable-gsl --with-cblas=gslcblas --with-bcf-plugin-dir=/usr/lib/aarch64-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 -j12 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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfstats.o vcfstats.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfisec.o vcfisec.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfmerge.o vcfmerge.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfquery.o vcfquery.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcffilter.o vcffilter.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o filter.o filter.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfsom.o vcfsom.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfnorm.o vcfnorm.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfgtcheck.o vcfgtcheck.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfview.o vcfview.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfannotate.o vcfannotate.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfroh.o vcfroh.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfconcat.o vcfconcat.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcall.o vcfcall.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mcall.o mcall.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcmp.o vcmp.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DPLUGINPATH='"/usr/lib/aarch64-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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/3cu4rA6rcP/merge.a.vcf.gz 2:3199812-3199812 .. ok test_tabix: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/3cu4rA6rcP/merge.a.bcf 2:3199812-3199812 .. ok test_tabix: tabix /tmp/3cu4rA6rcP/merge.a.vcf.gz 1:3000151-3000151 .. ok test_tabix: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/3cu4rA6rcP/merge.a.bcf 1:3000151-3000151 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/3cu4rA6rcP/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/3cu4rA6rcP/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/3cu4rA6rcP/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/3cu4rA6rcP/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/3cu4rA6rcP/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/3cu4rA6rcP/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/3cu4rA6rcP/large_chrom_csi_limit.bcf chr20 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/3cu4rA6rcP/large_chrom_csi_limit.bcf chr20 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/3cu4rA6rcP/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/3cu4rA6rcP/large_chrom_csi_limit.bcf chr20 .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -s /tmp/3cu4rA6rcP/idx.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -s /tmp/3cu4rA6rcP/idx.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -s /tmp/3cu4rA6rcP/idx.bcf .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/3cu4rA6rcP/idx.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/3cu4rA6rcP/idx.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/3cu4rA6rcP/idx.vcf.gz.csi .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/3cu4rA6rcP/idx.bcf .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/3cu4rA6rcP/idx.bcf.csi .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -s /tmp/3cu4rA6rcP/empty.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -s /tmp/3cu4rA6rcP/empty.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -s /tmp/3cu4rA6rcP/empty.bcf .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/3cu4rA6rcP/empty.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/3cu4rA6rcP/empty.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/3cu4rA6rcP/empty.vcf.gz.csi .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/3cu4rA6rcP/empty.bcf .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/3cu4rA6rcP/empty.bcf.csi .. ok test_vcf_check: /build/reproducible-path/bcftools-1.21/bcftools stats -s - /tmp/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/check.1.chk /tmp/3cu4rA6rcP/check.2.chk /tmp/3cu4rA6rcP/check.3.chk /tmp/3cu4rA6rcP/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/3cu4rA6rcP/stats.a.vcf.gz /tmp/3cu4rA6rcP/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/reproducible-path/bcftools-1.21/bcftools stats -s B /tmp/3cu4rA6rcP/stats.a.vcf.gz /tmp/3cu4rA6rcP/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/reproducible-path/bcftools-1.21/bcftools stats -s - /tmp/3cu4rA6rcP/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/3cu4rA6rcP/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/reproducible-path/bcftools-1.21/bcftools stats -s - /tmp/3cu4rA6rcP/stats.vaf.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -n =2 /tmp/3cu4rA6rcP/isec.a.vcf.gz /tmp/3cu4rA6rcP/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -n =2 /tmp/3cu4rA6rcP/isec.a.vcf.gz /tmp/3cu4rA6rcP/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/3cu4rA6rcP/isec.a.vcf.gz /tmp/3cu4rA6rcP/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -n =2 -i"STRLEN(REF)==2" /tmp/3cu4rA6rcP/isec.a.vcf.gz /tmp/3cu4rA6rcP/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -n =2 -c both /tmp/3cu4rA6rcP/isec.a.vcf.gz /tmp/3cu4rA6rcP/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -n =2 -c both /tmp/3cu4rA6rcP/isec.a.vcf.gz /tmp/3cu4rA6rcP/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -n =2 -c any /tmp/3cu4rA6rcP/isec.a.vcf.gz /tmp/3cu4rA6rcP/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -n =2 -c any /tmp/3cu4rA6rcP/isec.a.vcf.gz /tmp/3cu4rA6rcP/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -C -c any /tmp/3cu4rA6rcP/isec.a.vcf.gz /tmp/3cu4rA6rcP/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -C -c any /tmp/3cu4rA6rcP/isec.a.vcf.gz /tmp/3cu4rA6rcP/isec.b.vcf.gz .. ok test_vcf_isec2: /build/reproducible-path/bcftools-1.21/bcftools isec --no-version -T /tmp/3cu4rA6rcP/isec.tab.gz /tmp/3cu4rA6rcP/isec.a.vcf.gz .. ok test_vcf_isec2: /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -T /tmp/3cu4rA6rcP/isec.tab.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/isec-miss.1.1.vcf.gz /tmp/3cu4rA6rcP/isec-miss.1.2.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/isec-miss.1.1.vcf.gz /tmp/3cu4rA6rcP/isec-miss.1.2.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/isec-miss.1.1.vcf.gz /tmp/3cu4rA6rcP/isec-miss.1.2.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/isec-miss.1.1.vcf.gz /tmp/3cu4rA6rcP/isec-miss.1.2.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/isec-miss.2.1.vcf.gz /tmp/3cu4rA6rcP/isec-miss.2.2.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/isec-miss.2.1.vcf.gz /tmp/3cu4rA6rcP/isec-miss.2.2.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/isec-miss.2.1.vcf.gz /tmp/3cu4rA6rcP/isec-miss.2.2.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/isec-miss.2.1.vcf.gz /tmp/3cu4rA6rcP/isec-miss.2.2.vcf.gz /tmp/3cu4rA6rcP/isec-miss.2.3.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/3cu4rA6rcP/merge.11.a.vcf.gz /tmp/3cu4rA6rcP/merge.11.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/3cu4rA6rcP/merge.11.a.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.11.a.bcf /tmp/3cu4rA6rcP/merge.11.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/3cu4rA6rcP/merge.11.a.bcf /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.join.a.vcf.gz /tmp/3cu4rA6rcP/merge.join.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -i AF:join /tmp/3cu4rA6rcP/merge.join.a.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.join.a.bcf /tmp/3cu4rA6rcP/merge.join.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -i AF:join /tmp/3cu4rA6rcP/merge.join.a.bcf /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.LPL.a.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-single /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.LPL.a.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-single /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.LPL.a.vcf.gz /tmp/3cu4rA6rcP/merge.LPL.b.vcf.gz /tmp/3cu4rA6rcP/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/3cu4rA6rcP/merge.LPL.a.vcf.gz /tmp/3cu4rA6rcP/merge.LPL.b.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.LPL.a.bcf /tmp/3cu4rA6rcP/merge.LPL.b.bcf /tmp/3cu4rA6rcP/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/3cu4rA6rcP/merge.LPL.a.bcf /tmp/3cu4rA6rcP/merge.LPL.b.bcf /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.LPL.a.vcf.gz /tmp/3cu4rA6rcP/merge.LPL.b.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.LPL.a.vcf.gz /tmp/3cu4rA6rcP/merge.LPL.b.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.LPL.a.bcf /tmp/3cu4rA6rcP/merge.LPL.b.bcf /tmp/3cu4rA6rcP/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 1 /tmp/3cu4rA6rcP/merge.LPL.a.bcf /tmp/3cu4rA6rcP/merge.LPL.b.bcf /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.LPL.a.vcf.gz /tmp/3cu4rA6rcP/merge.LPL.b.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.LPL.a.vcf.gz /tmp/3cu4rA6rcP/merge.LPL.b.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.LPL.a.bcf /tmp/3cu4rA6rcP/merge.LPL.b.bcf /tmp/3cu4rA6rcP/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 2 /tmp/3cu4rA6rcP/merge.LPL.a.bcf /tmp/3cu4rA6rcP/merge.LPL.b.bcf /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.LPL.a.vcf.gz /tmp/3cu4rA6rcP/merge.LPL.b.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.LPL.a.vcf.gz /tmp/3cu4rA6rcP/merge.LPL.b.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.LPL.a.bcf /tmp/3cu4rA6rcP/merge.LPL.b.bcf /tmp/3cu4rA6rcP/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 3 /tmp/3cu4rA6rcP/merge.LPL.a.bcf /tmp/3cu4rA6rcP/merge.LPL.b.bcf /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.LPL.a.vcf.gz /tmp/3cu4rA6rcP/merge.LPL.b.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.LPL.a.vcf.gz /tmp/3cu4rA6rcP/merge.LPL.b.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.LPL.a.bcf /tmp/3cu4rA6rcP/merge.LPL.b.bcf /tmp/3cu4rA6rcP/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 4 /tmp/3cu4rA6rcP/merge.LPL.a.bcf /tmp/3cu4rA6rcP/merge.LPL.b.bcf /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.LPL.a.vcf.gz /tmp/3cu4rA6rcP/merge.LPL.b.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.LPL.a.vcf.gz /tmp/3cu4rA6rcP/merge.LPL.b.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.LPL.a.bcf /tmp/3cu4rA6rcP/merge.LPL.b.bcf /tmp/3cu4rA6rcP/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 5 /tmp/3cu4rA6rcP/merge.LPL.a.bcf /tmp/3cu4rA6rcP/merge.LPL.b.bcf /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.a.vcf.gz /tmp/3cu4rA6rcP/merge.b.vcf.gz /tmp/3cu4rA6rcP/merge.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/3cu4rA6rcP/merge.a.vcf.gz /tmp/3cu4rA6rcP/merge.b.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.a.bcf /tmp/3cu4rA6rcP/merge.b.bcf /tmp/3cu4rA6rcP/merge.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/3cu4rA6rcP/merge.a.bcf /tmp/3cu4rA6rcP/merge.b.bcf /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.a.vcf.gz /tmp/3cu4rA6rcP/merge.b.vcf.gz /tmp/3cu4rA6rcP/merge.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -Fx /tmp/3cu4rA6rcP/merge.a.vcf.gz /tmp/3cu4rA6rcP/merge.b.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.a.bcf /tmp/3cu4rA6rcP/merge.b.bcf /tmp/3cu4rA6rcP/merge.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -Fx /tmp/3cu4rA6rcP/merge.a.bcf /tmp/3cu4rA6rcP/merge.b.bcf /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.a.vcf.gz /tmp/3cu4rA6rcP/merge.b.vcf.gz /tmp/3cu4rA6rcP/merge.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -0 /tmp/3cu4rA6rcP/merge.a.vcf.gz /tmp/3cu4rA6rcP/merge.b.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.a.bcf /tmp/3cu4rA6rcP/merge.b.bcf /tmp/3cu4rA6rcP/merge.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -0 /tmp/3cu4rA6rcP/merge.a.bcf /tmp/3cu4rA6rcP/merge.b.bcf /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.2.a.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.2.a.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.2.a.bcf /tmp/3cu4rA6rcP/merge.2.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m none /tmp/3cu4rA6rcP/merge.2.a.bcf /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.2.a.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.2.a.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.2.a.bcf /tmp/3cu4rA6rcP/merge.2.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m both /tmp/3cu4rA6rcP/merge.2.a.bcf /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.2.a.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.2.a.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.2.a.bcf /tmp/3cu4rA6rcP/merge.2.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m all /tmp/3cu4rA6rcP/merge.2.a.bcf /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.3.a.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.3.a.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.3.a.bcf /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.3.a.bcf /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.4.a.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.4.a.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.4.a.bcf /tmp/3cu4rA6rcP/merge.4.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m id /tmp/3cu4rA6rcP/merge.4.a.bcf /tmp/3cu4rA6rcP/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/3cu4rA6rcP/gvcf.merge.1.vcf.gz /tmp/3cu4rA6rcP/gvcf.merge.2.vcf.gz /tmp/3cu4rA6rcP/gvcf.merge.3.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/3cu4rA6rcP/gvcf.merge.1.vcf.gz /tmp/3cu4rA6rcP/gvcf.merge.2.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/gvcf.merge.1.bcf /tmp/3cu4rA6rcP/gvcf.merge.2.bcf /tmp/3cu4rA6rcP/gvcf.merge.3.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/3cu4rA6rcP/gvcf.merge.1.bcf /tmp/3cu4rA6rcP/gvcf.merge.2.bcf /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.gvcf.2.a.vcf.gz /tmp/3cu4rA6rcP/merge.gvcf.2.b.vcf.gz /tmp/3cu4rA6rcP/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/3cu4rA6rcP/merge.gvcf.2.a.vcf.gz /tmp/3cu4rA6rcP/merge.gvcf.2.b.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.gvcf.2.a.vcf.gz /tmp/3cu4rA6rcP/merge.gvcf.2.b.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.gvcf.2.a.vcf.gz /tmp/3cu4rA6rcP/merge.gvcf.2.b.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.gvcf.2.a.vcf.gz /tmp/3cu4rA6rcP/merge.gvcf.2.b.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.gvcf.2.a.vcf.gz /tmp/3cu4rA6rcP/merge.gvcf.2.b.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.gvcf.3.a.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.gvcf.3.a.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.gvcf.4.a.vcf.gz /tmp/3cu4rA6rcP/merge.gvcf.4.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/3cu4rA6rcP/merge.gvcf.4.a.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.gvcf.4.a.bcf /tmp/3cu4rA6rcP/merge.gvcf.4.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/3cu4rA6rcP/merge.gvcf.4.a.bcf /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.5.a.vcf.gz /tmp/3cu4rA6rcP/merge.5.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/3cu4rA6rcP/merge.5.a.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.5.a.bcf /tmp/3cu4rA6rcP/merge.5.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/3cu4rA6rcP/merge.5.a.bcf /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.6.a.vcf.gz /tmp/3cu4rA6rcP/merge.6.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/3cu4rA6rcP/merge.6.a.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.6.a.bcf /tmp/3cu4rA6rcP/merge.6.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/3cu4rA6rcP/merge.6.a.bcf /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.gvcf.7.a.vcf.gz /tmp/3cu4rA6rcP/merge.gvcf.7.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/3cu4rA6rcP/merge.gvcf.7.a.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.gvcf.7.a.bcf /tmp/3cu4rA6rcP/merge.gvcf.7.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/3cu4rA6rcP/merge.gvcf.7.a.bcf /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.gvcf.8.a.vcf.gz /tmp/3cu4rA6rcP/merge.gvcf.8.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/3cu4rA6rcP/merge.gvcf.8.a.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.gvcf.8.a.bcf /tmp/3cu4rA6rcP/merge.gvcf.8.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/3cu4rA6rcP/merge.gvcf.8.a.bcf /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.7.a.vcf.gz /tmp/3cu4rA6rcP/merge.7.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/3cu4rA6rcP/merge.7.a.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.7.a.bcf /tmp/3cu4rA6rcP/merge.7.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/3cu4rA6rcP/merge.7.a.bcf /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.gvcf.9a.vcf.gz /tmp/3cu4rA6rcP/merge.gvcf.9b.vcf.gz /tmp/3cu4rA6rcP/merge.gvcf.9c.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.gvcf.9a.vcf.gz /tmp/3cu4rA6rcP/merge.gvcf.9b.vcf.gz /tmp/3cu4rA6rcP/merge.gvcf.9c.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.gvcf.9a.bcf /tmp/3cu4rA6rcP/merge.gvcf.9b.bcf /tmp/3cu4rA6rcP/merge.gvcf.9c.bcf /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.gvcf.9a.bcf /tmp/3cu4rA6rcP/merge.gvcf.9b.bcf /tmp/3cu4rA6rcP/merge.gvcf.9c.bcf /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.gvcf.9a.vcf.gz /tmp/3cu4rA6rcP/merge.gvcf.9b.vcf.gz /tmp/3cu4rA6rcP/merge.gvcf.9c.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.gvcf.9a.vcf.gz /tmp/3cu4rA6rcP/merge.gvcf.9b.vcf.gz /tmp/3cu4rA6rcP/merge.gvcf.9c.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.gvcf.9a.bcf /tmp/3cu4rA6rcP/merge.gvcf.9b.bcf /tmp/3cu4rA6rcP/merge.gvcf.9c.bcf /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.gvcf.9a.bcf /tmp/3cu4rA6rcP/merge.gvcf.9b.bcf /tmp/3cu4rA6rcP/merge.gvcf.9c.bcf /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.gvcf.9a.vcf.gz /tmp/3cu4rA6rcP/merge.gvcf.9b.vcf.gz /tmp/3cu4rA6rcP/merge.gvcf.9c.vcf.gz /tmp/3cu4rA6rcP/merge.gvcf.9d.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.gvcf.9a.vcf.gz /tmp/3cu4rA6rcP/merge.gvcf.9b.vcf.gz /tmp/3cu4rA6rcP/merge.gvcf.9c.vcf.gz /tmp/3cu4rA6rcP/merge.gvcf.9d.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.gvcf.9a.bcf /tmp/3cu4rA6rcP/merge.gvcf.9b.bcf /tmp/3cu4rA6rcP/merge.gvcf.9c.bcf /tmp/3cu4rA6rcP/merge.gvcf.9d.bcf /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.gvcf.9a.bcf /tmp/3cu4rA6rcP/merge.gvcf.9b.bcf /tmp/3cu4rA6rcP/merge.gvcf.9c.bcf /tmp/3cu4rA6rcP/merge.gvcf.9d.bcf /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.gvcf.9a.vcf.gz /tmp/3cu4rA6rcP/merge.gvcf.9b.vcf.gz /tmp/3cu4rA6rcP/merge.gvcf.9c.vcf.gz /tmp/3cu4rA6rcP/merge.gvcf.9d.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.gvcf.9a.vcf.gz /tmp/3cu4rA6rcP/merge.gvcf.9b.vcf.gz /tmp/3cu4rA6rcP/merge.gvcf.9c.vcf.gz /tmp/3cu4rA6rcP/merge.gvcf.9d.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.gvcf.9a.bcf /tmp/3cu4rA6rcP/merge.gvcf.9b.bcf /tmp/3cu4rA6rcP/merge.gvcf.9c.bcf /tmp/3cu4rA6rcP/merge.gvcf.9d.bcf /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.gvcf.9a.bcf /tmp/3cu4rA6rcP/merge.gvcf.9b.bcf /tmp/3cu4rA6rcP/merge.gvcf.9c.bcf /tmp/3cu4rA6rcP/merge.gvcf.9d.bcf /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.gvcf.10.a.vcf.gz /tmp/3cu4rA6rcP/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/3cu4rA6rcP/merge.gvcf.10.a.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.gvcf.10.a.bcf /tmp/3cu4rA6rcP/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/3cu4rA6rcP/merge.gvcf.10.a.bcf /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.gvcf.10.a.vcf.gz /tmp/3cu4rA6rcP/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m none /tmp/3cu4rA6rcP/merge.gvcf.10.a.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.gvcf.10.a.bcf /tmp/3cu4rA6rcP/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m none /tmp/3cu4rA6rcP/merge.gvcf.10.a.bcf /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.gvcf.10.a.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.gvcf.10.a.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.gvcf.10.a.bcf /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.gvcf.10.a.bcf /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.gvcf.10.a.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.gvcf.10.a.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.gvcf.10.a.bcf /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.gvcf.10.a.bcf /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.noidx.a.vcf.gz /tmp/3cu4rA6rcP/merge.noidx.b.vcf.gz /tmp/3cu4rA6rcP/merge.noidx.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/3cu4rA6rcP/merge.noidx.a.vcf.gz /tmp/3cu4rA6rcP/merge.noidx.b.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.noidx.a.bcf /tmp/3cu4rA6rcP/merge.noidx.b.bcf /tmp/3cu4rA6rcP/merge.noidx.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/3cu4rA6rcP/merge.noidx.a.bcf /tmp/3cu4rA6rcP/merge.noidx.b.bcf /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.noidx.a.bcf /tmp/3cu4rA6rcP/merge.noidx.b.bcf /tmp/3cu4rA6rcP/merge.noidx.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --no-index /tmp/3cu4rA6rcP/merge.noidx.a.bcf /tmp/3cu4rA6rcP/merge.noidx.b.bcf /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.8.a.vcf.gz /tmp/3cu4rA6rcP/merge.8.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/3cu4rA6rcP/merge.8.a.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.8.a.bcf /tmp/3cu4rA6rcP/merge.8.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/3cu4rA6rcP/merge.8.a.bcf /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.8.a.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.8.a.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.8.a.bcf /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.8.a.bcf /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.9.a.vcf.gz /tmp/3cu4rA6rcP/merge.9.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/3cu4rA6rcP/merge.9.a.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.9.a.bcf /tmp/3cu4rA6rcP/merge.9.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/3cu4rA6rcP/merge.9.a.bcf /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.9.a.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.9.a.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.9.a.bcf /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.9.a.bcf /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.10.a.vcf.gz /tmp/3cu4rA6rcP/merge.10.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m none /tmp/3cu4rA6rcP/merge.10.a.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.10.a.bcf /tmp/3cu4rA6rcP/merge.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m none /tmp/3cu4rA6rcP/merge.10.a.bcf /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.10.a.vcf.gz /tmp/3cu4rA6rcP/merge.10.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m both /tmp/3cu4rA6rcP/merge.10.a.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.10.a.bcf /tmp/3cu4rA6rcP/merge.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m both /tmp/3cu4rA6rcP/merge.10.a.bcf /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.10.a.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.10.a.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.10.a.bcf /tmp/3cu4rA6rcP/merge.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m snp-ins-del /tmp/3cu4rA6rcP/merge.10.a.bcf /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.mrules.1.a.vcf.gz /tmp/3cu4rA6rcP/merge.mrules.1.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/3cu4rA6rcP/merge.mrules.1.a.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.mrules.1.a.bcf /tmp/3cu4rA6rcP/merge.mrules.1.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/3cu4rA6rcP/merge.mrules.1.a.bcf /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.mrules.1.a.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.mrules.1.a.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.mrules.1.a.bcf /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.mrules.1.a.bcf /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.gvcf.5.a.vcf.gz /tmp/3cu4rA6rcP/merge.gvcf.5.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/3cu4rA6rcP/merge.gvcf.5.a.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.gvcf.5.a.bcf /tmp/3cu4rA6rcP/merge.gvcf.5.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/3cu4rA6rcP/merge.gvcf.5.a.bcf /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.gvcf.5.a.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.gvcf.5.a.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.gvcf.5.a.bcf /tmp/3cu4rA6rcP/merge.gvcf.5.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - --merge none /tmp/3cu4rA6rcP/merge.gvcf.5.a.bcf /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.gvcf.11.a.vcf.gz /tmp/3cu4rA6rcP/merge.gvcf.11.b.vcf.gz /tmp/3cu4rA6rcP/merge.gvcf.11.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/3cu4rA6rcP/merge.gvcf.11.a.vcf.gz /tmp/3cu4rA6rcP/merge.gvcf.11.b.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/merge.gvcf.11.a.bcf /tmp/3cu4rA6rcP/merge.gvcf.11.b.bcf /tmp/3cu4rA6rcP/merge.gvcf.11.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/3cu4rA6rcP/merge.gvcf.11.a.bcf /tmp/3cu4rA6rcP/merge.gvcf.11.b.bcf /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.string.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.string.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.string.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.string.2.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.string.2.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.variantkey.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/view.vectors.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.2.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.filter-type.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.filter-type.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.filter-type.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.filter-type.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.filter-type.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/filter-missing-floats.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/filter-missing-floats.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.filter.2.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.filter.3.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.filter.3.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.filter.3.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.filter.4.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/view.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.negative.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.negative.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.negative.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.negative.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.filter.6.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.filter.8.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.filter.8.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.filter.9.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.filter.9.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.filter.13.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.filter.10.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.filter.10.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.filter.id.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.filter.id.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.filter.id.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.filter.id.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.filter.id.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.filter.id.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/filter.10.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/filter.13.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.filter-or.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/query.filter-or.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/norm.sort.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/3cu4rA6rcP/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/3cu4rA6rcP/norm.sort.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - -S lex /tmp/3cu4rA6rcP/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/3cu4rA6rcP/norm.join-missing-ploidy.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +both /tmp/3cu4rA6rcP/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/3cu4rA6rcP/norm.split.5.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - --multi-overlaps . /tmp/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/norm.split.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- /tmp/3cu4rA6rcP/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/3cu4rA6rcP/norm.split.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- /tmp/3cu4rA6rcP/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/3cu4rA6rcP/norm.split.3.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- --force /tmp/3cu4rA6rcP/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/3cu4rA6rcP/norm.split.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- /tmp/3cu4rA6rcP/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/3cu4rA6rcP/norm.split.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- --keep-sum AD /tmp/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/norm.merge.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m+ /tmp/3cu4rA6rcP/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/3cu4rA6rcP/norm.merge.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m+ /tmp/3cu4rA6rcP/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/3cu4rA6rcP/norm.merge.3.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m+ /tmp/3cu4rA6rcP/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/3cu4rA6rcP/norm.merge.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m+ -s /tmp/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d snps /tmp/3cu4rA6rcP/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/3cu4rA6rcP/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d indels /tmp/3cu4rA6rcP/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/3cu4rA6rcP/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d both /tmp/3cu4rA6rcP/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/3cu4rA6rcP/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d all /tmp/3cu4rA6rcP/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/3cu4rA6rcP/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d none /tmp/3cu4rA6rcP/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/3cu4rA6rcP/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d exact /tmp/3cu4rA6rcP/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/3cu4rA6rcP/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d none /tmp/3cu4rA6rcP/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/3cu4rA6rcP/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d exact /tmp/3cu4rA6rcP/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/3cu4rA6rcP/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d indels /tmp/3cu4rA6rcP/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/3cu4rA6rcP/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d any /tmp/3cu4rA6rcP/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/3cu4rA6rcP/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d both /tmp/3cu4rA6rcP/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/3cu4rA6rcP/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d snps /tmp/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/atomize.split.3.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . /tmp/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/norm.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +both /tmp/3cu4rA6rcP/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/3cu4rA6rcP/norm.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +any /tmp/3cu4rA6rcP/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/3cu4rA6rcP/norm.5.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - --multi-overlaps 0 /tmp/3cu4rA6rcP/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/3cu4rA6rcP/norm.5.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - --multi-overlaps . /tmp/3cu4rA6rcP/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/3cu4rA6rcP/norm.m-any.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any /tmp/3cu4rA6rcP/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/3cu4rA6rcP/norm.phased-split.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any /tmp/3cu4rA6rcP/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/3cu4rA6rcP/norm.phased-join.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +any /tmp/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/norm.string-tags.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any /tmp/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/norm.split.merge.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - -i 'type="snp"' /tmp/3cu4rA6rcP/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/3cu4rA6rcP/norm.merge.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +any /tmp/3cu4rA6rcP/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/3cu4rA6rcP/norm.merge.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +both /tmp/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/merge.gvcf.2.a.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -HAA /tmp/3cu4rA6rcP/merge.gvcf.2.a.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/3cu4rA6rcP/weird-chr-names.vcf.gz -r 1 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/weird-chr-names.vcf.gz -r 1:1-2 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/weird-chr-names.vcf.gz -r 1:1,1:2 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/weird-chr-names.vcf.gz -r 1:1-1 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/weird-chr-names.vcf.gz -r {1:1} .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/weird-chr-names.vcf.gz -r {1:1}:1-2 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/weird-chr-names.vcf.gz -r {1:1}:1-1 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/weird-chr-names.vcf.gz -r {1:1-1} .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/3cu4rA6rcP/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/3cu4rA6rcP/view.vcf.gz -r20,Y .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -f PASS -Xks NA00003 /tmp/3cu4rA6rcP/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/3cu4rA6rcP/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -xs NA00003 /tmp/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -p /tmp/3cu4rA6rcP/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/3cu4rA6rcP/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -P /tmp/3cu4rA6rcP/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/3cu4rA6rcP/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/3cu4rA6rcP/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/3cu4rA6rcP/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -GVsnps /tmp/3cu4rA6rcP/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -GVsnps /tmp/3cu4rA6rcP/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/3cu4rA6rcP/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/3cu4rA6rcP/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/3cu4rA6rcP/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -s ^NA00003 /tmp/3cu4rA6rcP/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/3cu4rA6rcP/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -G /tmp/3cu4rA6rcP/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/3cu4rA6rcP/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -a /tmp/3cu4rA6rcP/many.alleles.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -a /tmp/3cu4rA6rcP/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/3cu4rA6rcP/view.vectors.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -asA /tmp/3cu4rA6rcP/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/3cu4rA6rcP/view.vectors.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -asB /tmp/3cu4rA6rcP/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/3cu4rA6rcP/view.vectors.2.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -asA /tmp/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/view.filter.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -i'TXT0="text"' /tmp/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/filter.2.vcf.gz 1:3062917-3157410 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -i 'POS>=3062917' /tmp/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/idx.4.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -Ht 2 /tmp/3cu4rA6rcP/view-t.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -Ht 3 /tmp/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -c6:nonmajor /tmp/3cu4rA6rcP/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -q0.3:major /tmp/3cu4rA6rcP/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/view.filter.annovar.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -a /tmp/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/mpileup.2.vcf.gz .. ok test_vcf_head2: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/mpileup.2.vcf.gz .. ok test_vcf_head2: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/mpileup.2.vcf.gz .. ok test_vcf_head2: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/3cu4rA6rcP/regions.tab.gz /tmp/3cu4rA6rcP/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/regions.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/3cu4rA6rcP/regions.tab.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/3cu4rA6rcP/regions.tab.gz /tmp/3cu4rA6rcP/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/3cu4rA6rcP/regions.bed /tmp/3cu4rA6rcP/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/regions.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/3cu4rA6rcP/regions.bed .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/3cu4rA6rcP/regions.bed /tmp/3cu4rA6rcP/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/3cu4rA6rcP/regions.bed.gz /tmp/3cu4rA6rcP/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/regions.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/3cu4rA6rcP/regions.bed.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/3cu4rA6rcP/regions.bed.gz /tmp/3cu4rA6rcP/regions.vcf.gz .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/3cu4rA6rcP/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/3cu4rA6rcP/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/3cu4rA6rcP/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/3cu4rA6rcP/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/3cu4rA6rcP/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/3cu4rA6rcP/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/3cu4rA6rcP/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/3cu4rA6rcP/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/3cu4rA6rcP/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/3cu4rA6rcP/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/3cu4rA6rcP/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/3cu4rA6rcP/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/3cu4rA6rcP/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/3cu4rA6rcP/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/3cu4rA6rcP/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/3cu4rA6rcP/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/3cu4rA6rcP/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/3cu4rA6rcP/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/3cu4rA6rcP/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/3cu4rA6rcP/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/3cu4rA6rcP/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/3cu4rA6rcP/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/3cu4rA6rcP/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/3cu4rA6rcP/annots4.vcf.gz -c +INFO /tmp/3cu4rA6rcP/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/3cu4rA6rcP/annots4.vcf.gz -c +INFO /tmp/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/3cu4rA6rcP/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/3cu4rA6rcP/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/3cu4rA6rcP/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/3cu4rA6rcP/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/3cu4rA6rcP/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/3cu4rA6rcP/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/3cu4rA6rcP/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/3cu4rA6rcP/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/3cu4rA6rcP/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/3cu4rA6rcP/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/3cu4rA6rcP/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/3cu4rA6rcP/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/3cu4rA6rcP/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/3cu4rA6rcP/annots11.vcf.gz -c FMT /tmp/3cu4rA6rcP/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/3cu4rA6rcP/annots11.vcf.gz -c FMT /tmp/3cu4rA6rcP/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/3cu4rA6rcP/annots2.vcf.gz -c FMT/newGT:=GT /tmp/3cu4rA6rcP/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/3cu4rA6rcP/annots2.vcf.gz -c FMT/newGT:=GT /tmp/3cu4rA6rcP/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/3cu4rA6rcP/annots12.vcf.gz -c FMT/GT:=newGT /tmp/3cu4rA6rcP/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/3cu4rA6rcP/annots12.vcf.gz -c FMT/GT:=newGT /tmp/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/3cu4rA6rcP/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/3cu4rA6rcP/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/3cu4rA6rcP/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/3cu4rA6rcP/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/3cu4rA6rcP/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/3cu4rA6rcP/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/3cu4rA6rcP/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/3cu4rA6rcP/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/3cu4rA6rcP/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/3cu4rA6rcP/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/3cu4rA6rcP/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/3cu4rA6rcP/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER /tmp/3cu4rA6rcP/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/3cu4rA6rcP/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER /tmp/3cu4rA6rcP/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/3cu4rA6rcP/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER /tmp/3cu4rA6rcP/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/3cu4rA6rcP/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER /tmp/3cu4rA6rcP/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/3cu4rA6rcP/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER,FILTER /tmp/3cu4rA6rcP/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/3cu4rA6rcP/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER,FILTER /tmp/3cu4rA6rcP/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/3cu4rA6rcP/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=./FILTER /tmp/3cu4rA6rcP/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/3cu4rA6rcP/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=./FILTER /tmp/3cu4rA6rcP/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/3cu4rA6rcP/annotate20.src.vcf.gz -c FMT/GT /tmp/3cu4rA6rcP/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/3cu4rA6rcP/annotate20.src.vcf.gz -c FMT/GT /tmp/3cu4rA6rcP/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/3cu4rA6rcP/annotate20.src.vcf.gz -c +FMT/GT /tmp/3cu4rA6rcP/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/3cu4rA6rcP/annotate20.src.vcf.gz -c +FMT/GT /tmp/3cu4rA6rcP/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/3cu4rA6rcP/annotate20.src.vcf.gz -c -FMT/GT /tmp/3cu4rA6rcP/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/3cu4rA6rcP/annotate20.src.vcf.gz -c -FMT/GT /tmp/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/3cu4rA6rcP/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/3cu4rA6rcP/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/annotate24.src.vcf.gz -c XX /tmp/3cu4rA6rcP/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/3cu4rA6rcP/annotate24.src.vcf.gz -c XX /tmp/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/annots.id.vcf.gz -c ALT /tmp/3cu4rA6rcP/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/3cu4rA6rcP/annots.id.vcf.gz -c ALT /tmp/3cu4rA6rcP/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/3cu4rA6rcP/annots.id.vcf.gz -c +ALT /tmp/3cu4rA6rcP/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/3cu4rA6rcP/annots.id.vcf.gz -c +ALT /tmp/3cu4rA6rcP/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/3cu4rA6rcP/annots.id.2.vcf.gz --pair-logic some -c +ID /tmp/3cu4rA6rcP/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/3cu4rA6rcP/annots.id.2.vcf.gz --pair-logic some -c +ID /tmp/3cu4rA6rcP/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/3cu4rA6rcP/annots.id.2.vcf.gz --pair-logic any -c +ID /tmp/3cu4rA6rcP/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/3cu4rA6rcP/annots.id.2.vcf.gz --pair-logic any -c +ID /tmp/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/concat.1.a.vcf.gz /tmp/3cu4rA6rcP/concat.1.b.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob /tmp/3cu4rA6rcP/concat.1.a.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/concat.1.a.bcf /tmp/3cu4rA6rcP/concat.1.b.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob /tmp/3cu4rA6rcP/concat.1.a.bcf /tmp/3cu4rA6rcP/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/3cu4rA6rcP/concat.2.a.vcf.gz /tmp/3cu4rA6rcP/concat.2.b.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -a /tmp/3cu4rA6rcP/concat.2.a.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/concat.2.a.bcf /tmp/3cu4rA6rcP/concat.2.b.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -a /tmp/3cu4rA6rcP/concat.2.a.bcf /tmp/3cu4rA6rcP/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/3cu4rA6rcP/concat.2.a.vcf.gz /tmp/3cu4rA6rcP/concat.2.b.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -aD /tmp/3cu4rA6rcP/concat.2.a.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/concat.2.a.bcf /tmp/3cu4rA6rcP/concat.2.b.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -aD /tmp/3cu4rA6rcP/concat.2.a.bcf /tmp/3cu4rA6rcP/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/3cu4rA6rcP/concat.3.a.vcf.gz /tmp/3cu4rA6rcP/concat.3.b.vcf.gz /tmp/3cu4rA6rcP/concat.3.0.vcf.gz /tmp/3cu4rA6rcP/concat.3.c.vcf.gz /tmp/3cu4rA6rcP/concat.3.d.vcf.gz /tmp/3cu4rA6rcP/concat.3.e.vcf.gz /tmp/3cu4rA6rcP/concat.3.f.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -l --ligate-warn /tmp/3cu4rA6rcP/concat.3.a.vcf.gz /tmp/3cu4rA6rcP/concat.3.b.vcf.gz /tmp/3cu4rA6rcP/concat.3.0.vcf.gz /tmp/3cu4rA6rcP/concat.3.c.vcf.gz /tmp/3cu4rA6rcP/concat.3.d.vcf.gz /tmp/3cu4rA6rcP/concat.3.e.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/concat.3.a.bcf /tmp/3cu4rA6rcP/concat.3.b.bcf /tmp/3cu4rA6rcP/concat.3.0.bcf /tmp/3cu4rA6rcP/concat.3.c.bcf /tmp/3cu4rA6rcP/concat.3.d.bcf /tmp/3cu4rA6rcP/concat.3.e.bcf /tmp/3cu4rA6rcP/concat.3.f.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -l --ligate-warn /tmp/3cu4rA6rcP/concat.3.a.bcf /tmp/3cu4rA6rcP/concat.3.b.bcf /tmp/3cu4rA6rcP/concat.3.0.bcf /tmp/3cu4rA6rcP/concat.3.c.bcf /tmp/3cu4rA6rcP/concat.3.d.bcf /tmp/3cu4rA6rcP/concat.3.e.bcf /tmp/3cu4rA6rcP/concat.3.f.bcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ Random seed for test_naive_concat: 3702862440 .. ok test_naive_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --naive-force /tmp/3cu4rA6rcP/naive_concat.0.bcf /tmp/3cu4rA6rcP/naive_concat.1.bcf /tmp/3cu4rA6rcP/naive_concat.2.bcf /tmp/3cu4rA6rcP/naive_concat.3.bcf /tmp/3cu4rA6rcP/naive_concat.4.bcf /tmp/3cu4rA6rcP/naive_concat.5.bcf /tmp/3cu4rA6rcP/naive_concat.6.bcf /tmp/3cu4rA6rcP/naive_concat.7.bcf /tmp/3cu4rA6rcP/naive_concat.8.bcf /tmp/3cu4rA6rcP/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/3cu4rA6rcP/naive_concat.0.vcf.gz /tmp/3cu4rA6rcP/naive_concat.1.vcf.gz /tmp/3cu4rA6rcP/naive_concat.2.vcf.gz /tmp/3cu4rA6rcP/naive_concat.3.vcf.gz /tmp/3cu4rA6rcP/naive_concat.4.vcf.gz /tmp/3cu4rA6rcP/naive_concat.5.vcf.gz /tmp/3cu4rA6rcP/naive_concat.6.vcf.gz /tmp/3cu4rA6rcP/naive_concat.7.vcf.gz /tmp/3cu4rA6rcP/naive_concat.8.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/concat.4.a.vcf.gz /tmp/3cu4rA6rcP/concat.4.b.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -l /tmp/3cu4rA6rcP/concat.4.a.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/concat.4.a.bcf /tmp/3cu4rA6rcP/concat.4.b.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -l /tmp/3cu4rA6rcP/concat.4.a.bcf /tmp/3cu4rA6rcP/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/3cu4rA6rcP/concat.5.a.vcf.gz /tmp/3cu4rA6rcP/concat.5.b.vcf.gz /tmp/3cu4rA6rcP/concat.5.c.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -l --ligate-warn /tmp/3cu4rA6rcP/concat.5.a.vcf.gz /tmp/3cu4rA6rcP/concat.5.b.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/concat.5.a.bcf /tmp/3cu4rA6rcP/concat.5.b.bcf /tmp/3cu4rA6rcP/concat.5.c.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -l --ligate-warn /tmp/3cu4rA6rcP/concat.5.a.bcf /tmp/3cu4rA6rcP/concat.5.b.bcf /tmp/3cu4rA6rcP/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/3cu4rA6rcP/concat.5.a.bcf /tmp/3cu4rA6rcP/concat.5.b.bcf /tmp/3cu4rA6rcP/concat.5.c.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -l --ligate-force /tmp/3cu4rA6rcP/concat.5.a.bcf /tmp/3cu4rA6rcP/concat.5.b.bcf /tmp/3cu4rA6rcP/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/3cu4rA6rcP/concat.5.a.vcf.gz /tmp/3cu4rA6rcP/concat.5.b.vcf.gz /tmp/3cu4rA6rcP/concat.5.c.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -G -a -D /tmp/3cu4rA6rcP/concat.5.a.vcf.gz /tmp/3cu4rA6rcP/concat.5.b.vcf.gz /tmp/3cu4rA6rcP/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/3cu4rA6rcP/concat.5.a.bcf /tmp/3cu4rA6rcP/concat.5.b.bcf /tmp/3cu4rA6rcP/concat.5.c.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -G -a -D /tmp/3cu4rA6rcP/concat.5.a.bcf /tmp/3cu4rA6rcP/concat.5.b.bcf /tmp/3cu4rA6rcP/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/3cu4rA6rcP/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/3cu4rA6rcP/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/3cu4rA6rcP/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/3cu4rA6rcP/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/3cu4rA6rcP/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/3cu4rA6rcP/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/3cu4rA6rcP/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/3cu4rA6rcP/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/3cu4rA6rcP/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/3cu4rA6rcP/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/3cu4rA6rcP/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/3cu4rA6rcP/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/3cu4rA6rcP/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/3cu4rA6rcP/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/3cu4rA6rcP/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/3cu4rA6rcP/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/3cu4rA6rcP/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/3cu4rA6rcP/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/3cu4rA6rcP/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/3cu4rA6rcP/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/3cu4rA6rcP/empty.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/3cu4rA6rcP/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/3cu4rA6rcP/empty.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/rename.map -Ov /tmp/3cu4rA6rcP/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/3cu4rA6rcP/rename.map -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/convert.hap-missing.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/convert.gvcf.vcf.gz .. ok test_vcf_convert_gvcf: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/consensus.1.chain.new >/dev/null; cat /tmp/3cu4rA6rcP/consensus.1.chain.new .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/consensus.2.chain.new >/dev/null; cat /tmp/3cu4rA6rcP/consensus.2.chain.new .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/consensus.3.chain.new >/dev/null; cat /tmp/3cu4rA6rcP/consensus.3.chain.new .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -H 1 -c /tmp/3cu4rA6rcP/consensus.4.chain.new >/dev/null; cat /tmp/3cu4rA6rcP/consensus.4.chain.new .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/mpileup.cram.urllist | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DV -r17:100-600 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DV -r17:100-600 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DV -r17:100-600 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DV -r17:100-600 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP,-AD -r17:100-600 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP,-AD -r17:100-600 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP,-AD -r17:100-600 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP,-AD -r17:100-600 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DV,-AD -r17:100-600 --gvcf 0,2,5 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DV,-AD -r17:100-600 --gvcf 0,2,5 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DV,-AD -r17:100-600 --gvcf 0,2,5 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DV,-AD -r17:100-600 --gvcf 0,2,5 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DV,-AD -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DV,-AD -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DV,-AD -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DV,-AD -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -s HG00101,HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -s HG00101,HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -s HG00101,HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -s HG00101,HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -S /build/reproducible-path/bcftools-1.21/test/mplp.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -S /build/reproducible-path/bcftools-1.21/test/mplp.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -S /build/reproducible-path/bcftools-1.21/test/mplp.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -S /build/reproducible-path/bcftools-1.21/test/mplp.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -s ^HG00101,HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -s ^HG00101,HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -s ^HG00101,HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -s ^HG00101,HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -S ^/build/reproducible-path/bcftools-1.21/test/mplp.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -S ^/build/reproducible-path/bcftools-1.21/test/mplp.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -S ^/build/reproducible-path/bcftools-1.21/test/mplp.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -S ^/build/reproducible-path/bcftools-1.21/test/mplp.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -S /build/reproducible-path/bcftools-1.21/test/mplp.9.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -S /build/reproducible-path/bcftools-1.21/test/mplp.9.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -S /build/reproducible-path/bcftools-1.21/test/mplp.9.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -S /build/reproducible-path/bcftools-1.21/test/mplp.9.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -S /build/reproducible-path/bcftools-1.21/test/mplp.9.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -S /build/reproducible-path/bcftools-1.21/test/mplp.9.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -G /build/reproducible-path/bcftools-1.21/test/mplp.10.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -G /build/reproducible-path/bcftools-1.21/test/mplp.10.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -G /build/reproducible-path/bcftools-1.21/test/mplp.10.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -G /build/reproducible-path/bcftools-1.21/test/mplp.10.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -G /build/reproducible-path/bcftools-1.21/test/mplp.10.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -G /build/reproducible-path/bcftools-1.21/test/mplp.10.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -s HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -s HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.sam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -s HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -s HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -s HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -s HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -s ^HG99999 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -s ^HG99999 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.sam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -s ^HG99999 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -s ^HG99999 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -s ^HG99999 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -s ^HG99999 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -G /build/reproducible-path/bcftools-1.21/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -G /build/reproducible-path/bcftools-1.21/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.sam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -G /build/reproducible-path/bcftools-1.21/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -G /build/reproducible-path/bcftools-1.21/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -G /build/reproducible-path/bcftools-1.21/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -G /build/reproducible-path/bcftools-1.21/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -G /build/reproducible-path/bcftools-1.21/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -G /build/reproducible-path/bcftools-1.21/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.sam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -G /build/reproducible-path/bcftools-1.21/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -G /build/reproducible-path/bcftools-1.21/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -G /build/reproducible-path/bcftools-1.21/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -G /build/reproducible-path/bcftools-1.21/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.fa /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.sam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.fa /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.fa /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD --indels-cns -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.fa /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD --indels-cns -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.sam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD --indels-cns -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.fa /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD --indels-cns -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD --indels-cns -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.fa /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD --indels-cns -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -r 11:75 -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.fa /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -r 11:75 -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -r 11:75 -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.fa /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -r 11:75 -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.fa /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.fa /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.fa /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.fa /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD,INFO/SCR,FMT/SCR -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD,INFO/SCR,FMT/SCR -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD,INFO/SCR,FMT/SCR -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD,INFO/SCR,FMT/SCR -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t 1:100 --skip-all-set PAIRED,PROPER_PAIR,MREVERSE -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t 1:100 --skip-all-set PAIRED,PROPER_PAIR,MREVERSE -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-filter.sam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t 1:100 --skip-any-set READ1 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t 1:100 --skip-any-set READ1 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-filter.sam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t 1:100 --skip-all-unset READ1 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t 1:100 --skip-all-unset READ1 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-filter.sam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t 1:100 --skip-any-unset READ1 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t 1:100 --skip-any-unset READ1 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-filter.sam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD,INFO/NMBZ -r chr19:69-99 -f /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.1.fa /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD,INFO/NMBZ -r chr19:69-99 -f /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.1.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.1.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD,INFO/NMBZ -r chr6:75 -f /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.2.fa /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD,INFO/NMBZ -r chr6:75 -f /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.2.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.2.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD,INFO/NMBZ -r chr16:75 -f /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.3.fa /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.3.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.3.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD,INFO/NMBZ -r chr16:75 -f /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.3.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.3.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.3.2.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_csq: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq.fa -g /build/reproducible-path/bcftools-1.21/test/csq.gff3 /build/reproducible-path/bcftools-1.21/test/csq.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq.fa -g /build/reproducible-path/bcftools-1.21/test/csq.chr.gff3 /build/reproducible-path/bcftools-1.21/test/csq.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq.fa -g /build/reproducible-path/bcftools-1.21/test/csq.2.gff /build/reproducible-path/bcftools-1.21/test/csq.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq.fa -g /build/reproducible-path/bcftools-1.21/test/csq.2.gff --ncsq 64 /build/reproducible-path/bcftools-1.21/test/csq.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq.nchr.fa -g /build/reproducible-path/bcftools-1.21/test/csq.nchr.gff /build/reproducible-path/bcftools-1.21/test/csq.nchr.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq.ychr.fa -g /build/reproducible-path/bcftools-1.21/test/csq.nchr.gff /build/reproducible-path/bcftools-1.21/test/csq.nchr.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq.nchr.fa -g /build/reproducible-path/bcftools-1.21/test/csq.ychr.gff /build/reproducible-path/bcftools-1.21/test/csq.nchr.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq.ychr.fa -g /build/reproducible-path/bcftools-1.21/test/csq.ychr.gff /build/reproducible-path/bcftools-1.21/test/csq.nchr.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq.ychr.fa -g /build/reproducible-path/bcftools-1.21/test/csq.ychr.gff /build/reproducible-path/bcftools-1.21/test/csq.ychr.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq.ychr.fa -g /build/reproducible-path/bcftools-1.21/test/csq.nchr.gff /build/reproducible-path/bcftools-1.21/test/csq.ychr.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq.nchr.fa -g /build/reproducible-path/bcftools-1.21/test/csq.ychr.gff /build/reproducible-path/bcftools-1.21/test/csq.ychr.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq.nchr.fa -g /build/reproducible-path/bcftools-1.21/test/csq.nchr.gff /build/reproducible-path/bcftools-1.21/test/csq.ychr.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/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/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: 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/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/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/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/ENST00000557788/ENST00000557788.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000557788/ENST00000557788.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000557788/long-overlap-del.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/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/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/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/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/ENST00000528237/ENST00000528237.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000528237/ENST00000528237.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000528237/retained-stop-incomplete-cds.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/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/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/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/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/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/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/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/ENST00000436063/ENST00000436063.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000436063/ENST00000436063.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000436063/insert-before-utr.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/snps.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/snps.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/insert3.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/insert3.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.21/test/csq/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/ENST00000420670/ENST00000420670.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000420670/ENST00000420670.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000420670/start-stop-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000420670/ENST00000420670.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000420670/ENST00000420670.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000420670/segfault.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/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/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/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 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: cd /build/reproducible-path/bcftools-1.21/test/csq/ENST00000410009 && /build/reproducible-path/bcftools-1.21/bcftools csq -lb -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.21/test/csq/ENST00000410009 && /build/reproducible-path/bcftools-1.21/bcftools csq -b -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/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/ENST00000400151/ENST00000400151.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000400151/ENST00000400151.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000400151/long-del.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000390520/ENST00000390520.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000390520/ENST00000390520.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000390520/deletion-overlap.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/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/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: 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/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/ENST00000375992/ENST00000375992.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000375992/ENST00000375992.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000375992/incorrect-synon-del-not-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000373833/ENST00000373833.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000373833/ENST00000373833.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000373833/boundary-insertion.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000373833/ENST00000373833.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000373833/ENST00000373833.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000373833/boundary-insertion.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/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/ENST00000368801.2/ENST00000368801.2.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000368801.2/ENST00000368801.2.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000368801.2/start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000360372/ENST00000360372.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000360372/ENST00000360372.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000360372/mnp.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/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/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-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-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-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/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-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-donor3.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/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/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/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/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/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/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/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/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/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/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/ENST00000295641/ENST00000295641.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000295641/ENST00000295641.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000295641/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000295641/ENST00000295641.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000295641/ENST00000295641.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000295641/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000294661/ENST00000294661.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000294661/ENST00000294661.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000294661/non-coding-boundary.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000294661/ENST00000294661.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000294661/ENST00000294661.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000294661/non-coding-boundary.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/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/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/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/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/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/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/ENST00000227471/ENST00000227471.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000227471/ENST00000227471.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000227471/insert-splice-vs-frameshift.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/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: cd /build/reproducible-path/bcftools-1.21/test/csq/ENST00000000000 && /build/reproducible-path/bcftools-1.21/bcftools csq -p a -f ENST00000000000.fa -g ENST00000000000.gff upstream-stop.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%REF\t%ALT\t%SAMPLE\t%GT\t%TBCSQ\n]' | ../sort-csq -q .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.21/test/csq/ENSMUST00000133836 && /build/reproducible-path/bcftools-1.21/bcftools csq -f ENSMUST00000133836.fa -g ENSMUST00000133836.gff filter-problem.vcf -i 'FILTER="PASS"' --phase m | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.21/test/csq/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/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: cd /build/reproducible-path/bcftools-1.21/test/csq/EMN908947 && /build/reproducible-path/bcftools-1.21/bcftools csq -f EMN908947.fa -g simple.gff simple.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.21/test/csq/EMN908947 && /build/reproducible-path/bcftools-1.21/bcftools csq -f EMN908947.fa -g ribosomal-slippage.gff ribosomal-slippage.vcf --force | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/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/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_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/3cu4rA6rcP/gtcheck.1.vcf.gz -g /tmp/3cu4rA6rcP/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 /tmp/3cu4rA6rcP/gtcheck.1.vcf.gz -g /tmp/3cu4rA6rcP/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/3cu4rA6rcP/gtcheck.1.vcf.gz -g /tmp/3cu4rA6rcP/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/3cu4rA6rcP/gtcheck.1.vcf.gz -g /tmp/3cu4rA6rcP/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/3cu4rA6rcP/gtcheck.1.vcf.gz -g /tmp/3cu4rA6rcP/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/3cu4rA6rcP/gtcheck.1.vcf.gz -g /tmp/3cu4rA6rcP/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/3cu4rA6rcP/gtcheck.1.vcf.gz -g /tmp/3cu4rA6rcP/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 /tmp/3cu4rA6rcP/gtcheck.2.vcf.gz -g /tmp/3cu4rA6rcP/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 /tmp/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/gtcheck.1.vcf.gz -g /tmp/3cu4rA6rcP/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/3cu4rA6rcP/gtcheck.1.vcf.gz -g /tmp/3cu4rA6rcP/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/3cu4rA6rcP/gtcheck.1.vcf.gz -g /tmp/3cu4rA6rcP/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/3cu4rA6rcP/gtcheck.1.vcf.gz -g /tmp/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/gtcheck.1.vcf.gz -g /tmp/3cu4rA6rcP/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/3cu4rA6rcP/gtcheck.1.vcf.gz -g /tmp/3cu4rA6rcP/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/3cu4rA6rcP/gtcheck.1.vcf.gz -g /tmp/3cu4rA6rcP/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/3cu4rA6rcP/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck /tmp/3cu4rA6rcP/gtcheck.ntop.vcf.gz -g /tmp/3cu4rA6rcP/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/3cu4rA6rcP/gtcheck.ntop.vcf.gz -g /tmp/3cu4rA6rcP/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck /tmp/3cu4rA6rcP/gtcheck.5.vcf.gz -g /tmp/3cu4rA6rcP/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/3cu4rA6rcP/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/3cu4rA6rcP/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 -j12 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/aarch64-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/aarch64-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 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb dh_gencontrol dpkg-gencontrol: warning: package bcftools: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package bcftools: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'bcftools' in '../bcftools_1.21-1_arm64.deb'. dpkg-deb: building package 'bcftools-dbgsym' in '../bcftools-dbgsym_1.21-1_arm64.deb'. dpkg-genbuildinfo --build=binary -O../bcftools_1.21-1_arm64.buildinfo dpkg-genchanges --build=binary -O../bcftools_1.21-1_arm64.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/3400892 and its subdirectories I: Current time: Sun Mar 22 11:09:30 -12 2026 I: pbuilder-time-stamp: 1774220970 Mon Feb 17 16:46:33 UTC 2025 I: 1st build successful. Starting 2nd build on remote node codethink04-arm64.debian.net. Mon Feb 17 16:46:33 UTC 2025 I: Preparing to do remote build '2' on codethink04-arm64.debian.net. Mon Feb 17 16:49:45 UTC 2025 I: Deleting $TMPDIR on codethink04-arm64.debian.net. Mon Feb 17 16:49:45 UTC 2025 I: bcftools_1.21-1_arm64.changes: Format: 1.8 Date: Thu, 13 Feb 2025 21:42:57 +0100 Source: bcftools Binary: bcftools bcftools-dbgsym Architecture: arm64 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: 9523862f3abc430ba79d4206abf3e919aeacf677 2175136 bcftools-dbgsym_1.21-1_arm64.deb 227596ade1e1af0a3b982fe0feab95061b4f01b9 7062 bcftools_1.21-1_arm64.buildinfo 315409be768263c3c0b087859ef008e41e26df68 706228 bcftools_1.21-1_arm64.deb Checksums-Sha256: b1a30870dfbb0c5e490a1293a277f97a90b215dfc546ad2f87e32f28b1d1e28d 2175136 bcftools-dbgsym_1.21-1_arm64.deb d9d58165c72e12e3c1630bce1fdcc0313ed9928230b678311ca1b16b07ef70ce 7062 bcftools_1.21-1_arm64.buildinfo 7d436e7b2aec25928914d9c437701a8dda173abd2a533372b96a171aab57ea93 706228 bcftools_1.21-1_arm64.deb Files: 7063f439360662fa656841275107cacd 2175136 debug optional bcftools-dbgsym_1.21-1_arm64.deb 48006f7e919efa8bd57a9f43d0094241 7062 science optional bcftools_1.21-1_arm64.buildinfo b40533288b01fb9ad799ffa0d4fadfa5 706228 science optional bcftools_1.21-1_arm64.deb Mon Feb 17 16:49:47 UTC 2025 I: diffoscope 288 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_4-57719.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.YKtOyVzv/bcftools_1.21-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.YKtOyVzv/bcftools_1.21-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.YKtOyVzv/bcftools_1.21-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.YKtOyVzv/b1/bcftools_1.21-1_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.YKtOyVzv/b2/bcftools_1.21-1_arm64.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: 241ms CPU time consumed: 242ms Mon Feb 17 16:49:47 UTC 2025 I: diffoscope 288 found no differences in the changes files, and a .buildinfo file also exists. Mon Feb 17 16:49:47 UTC 2025 I: bcftools from trixie built successfully and reproducibly on arm64. Mon Feb 17 16:49:48 UTC 2025 I: Submitting .buildinfo files to external archives: Mon Feb 17 16:49:48 UTC 2025 I: Submitting 8.0K b1/bcftools_1.21-1_arm64.buildinfo.asc Mon Feb 17 16:49:49 UTC 2025 I: Submitting 8.0K b2/bcftools_1.21-1_arm64.buildinfo.asc Mon Feb 17 16:49:50 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Mon Feb 17 16:49:50 UTC 2025 I: Done submitting .buildinfo files. Mon Feb 17 16:49:50 UTC 2025 I: Removing signed bcftools_1.21-1_arm64.buildinfo.asc files: removed './b1/bcftools_1.21-1_arm64.buildinfo.asc' removed './b2/bcftools_1.21-1_arm64.buildinfo.asc'