I: pbuilder: network access will be disabled during build I: Current time: Wed Jan 10 12:18:37 +14 2024 I: pbuilder-time-stamp: 1704838717 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-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: using eatmydata during job I: Copying source file I: copying [bcftools_1.11-1.dsc] I: copying [./bcftools_1.11.orig.tar.gz] I: copying [./bcftools_1.11-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.hF6_tYaW/trustedkeys.kbx': General error gpgv: Signature made Thu Oct 1 13:48:11 2020 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./bcftools_1.11-1.dsc dpkg-source: info: extracting bcftools in bcftools-1.11 dpkg-source: info: unpacking bcftools_1.11.orig.tar.gz dpkg-source: info: unpacking bcftools_1.11-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying tests-pluginpath.patch 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/4959/tmp/hooks/D01_modify_environment starting debug: Running on ionos12-i386. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Jan 9 22:18 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/4959/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/4959/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") BASH_VERSION='5.1.4(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=i386 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=7 ' DIRSTACK=() DISTRIBUTION=bullseye EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=i686 HOST_ARCH=i386 IFS=' ' INVOCATION_ID=fea2a2df89b94447934e372ba883c769 LANG=C LANGUAGE=de_CH:de LC_ALL=C LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so MACHTYPE=i686-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=4959 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.Zw39VFPA/pbuilderrc_zqBW --distribution bullseye --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Zw39VFPA/b2 --logfile b2/build.log bcftools_1.11-1.dsc' SUDO_GID=112 SUDO_UID=107 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://78.137.99.97:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-17-686-pae #1 SMP PREEMPT_DYNAMIC Debian 6.1.69-1 (2023-12-30) i686 GNU/Linux I: ls -l /bin total 5776 -rwxr-xr-x 1 root root 1367848 Mar 27 2022 bash -rwxr-xr-x 3 root root 38280 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 17768 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 38824 Sep 22 2020 cat -rwxr-xr-x 1 root root 71624 Sep 22 2020 chgrp -rwxr-xr-x 1 root root 67528 Sep 22 2020 chmod -rwxr-xr-x 1 root root 75752 Sep 22 2020 chown -rwxr-xr-x 1 root root 157960 Sep 22 2020 cp -rwxr-xr-x 1 root root 128724 Dec 10 2020 dash -rwxr-xr-x 1 root root 124904 Sep 22 2020 date -rwxr-xr-x 1 root root 92172 Sep 22 2020 dd -rwxr-xr-x 1 root root 100752 Sep 22 2020 df -rwxr-xr-x 1 root root 153964 Sep 22 2020 dir -rwxr-xr-x 1 root root 83644 Jan 20 2022 dmesg lrwxrwxrwx 1 root root 8 Nov 7 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 7 2019 domainname -> hostname -rwxr-xr-x 1 root root 34664 Sep 22 2020 echo -rwxr-xr-x 1 root root 28 Jan 25 2023 egrep -rwxr-xr-x 1 root root 34664 Sep 22 2020 false -rwxr-xr-x 1 root root 28 Jan 25 2023 fgrep -rwxr-xr-x 1 root root 71928 Jan 20 2022 findmnt -rwsr-xr-x 1 root root 30112 Feb 26 2021 fusermount -rwxr-xr-x 1 root root 210488 Jan 25 2023 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 100952 Apr 10 2022 gzip -rwxr-xr-x 1 root root 21916 Nov 7 2019 hostname -rwxr-xr-x 1 root root 83980 Sep 22 2020 ln -rwxr-xr-x 1 root root 55572 Feb 7 2020 login -rwxr-xr-x 1 root root 153964 Sep 22 2020 ls -rwxr-xr-x 1 root root 153124 Jan 20 2022 lsblk -rwxr-xr-x 1 root root 96328 Sep 22 2020 mkdir -rwxr-xr-x 1 root root 79912 Sep 22 2020 mknod -rwxr-xr-x 1 root root 47048 Sep 22 2020 mktemp -rwxr-xr-x 1 root root 58920 Jan 20 2022 more -rwsr-xr-x 1 root root 50720 Jan 20 2022 mount -rwxr-xr-x 1 root root 13856 Jan 20 2022 mountpoint -rwxr-xr-x 1 root root 157996 Sep 22 2020 mv lrwxrwxrwx 1 root root 8 Nov 7 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Dec 16 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 38824 Sep 22 2020 pwd lrwxrwxrwx 1 root root 4 Mar 27 2022 rbash -> bash -rwxr-xr-x 1 root root 46984 Sep 22 2020 readlink -rwxr-xr-x 1 root root 75720 Sep 22 2020 rm -rwxr-xr-x 1 root root 46984 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 22292 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 125036 Dec 22 2018 sed lrwxrwxrwx 1 root root 9 Jan 9 22:18 sh -> /bin/bash -rwxr-xr-x 1 root root 34696 Sep 22 2020 sleep -rwxr-xr-x 1 root root 83880 Sep 22 2020 stty -rwsr-xr-x 1 root root 79396 Jan 20 2022 su -rwxr-xr-x 1 root root 34696 Sep 22 2020 sync -rwxr-xr-x 1 root root 602584 Feb 17 2021 tar -rwxr-xr-x 1 root root 13860 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 108520 Sep 22 2020 touch -rwxr-xr-x 1 root root 34664 Sep 22 2020 true -rwxr-xr-x 1 root root 17768 Feb 26 2021 ulockmgr_server -rwsr-xr-x 1 root root 30236 Jan 20 2022 umount -rwxr-xr-x 1 root root 34664 Sep 22 2020 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 153964 Sep 22 2020 vdir -rwxr-xr-x 1 root root 63024 Jan 20 2022 wdctl lrwxrwxrwx 1 root root 8 Nov 7 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 5898 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8049 Apr 10 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew I: user script /srv/workspace/pbuilder/4959/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: i386 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 (>= 1.11), 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 ... 17763 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 (>= 1.11); 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} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbrotli1{a} libbz2-dev{a} libcurl3-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1{a} libfile-stripnondeterminism-perl{a} libgsl-dev{a} libgsl25{a} libgslcblas0{a} libhts-dev{a} libhts3{a} libicu67{a} libio-pty-perl{a} libldap-2.4-2{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libnghttp2-14{a} libpipeline1{a} libpsl5{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libssh2-1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{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 libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix wget 0 packages upgraded, 53 newly installed, 0 to remove and 0 not upgraded. Need to get 27.8 MB of archives. After unpacking 91.6 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main i386 bsdextrautils i386 2.36.1-8+deb11u1 [149 kB] Get: 2 http://deb.debian.org/debian bullseye/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB] Get: 3 http://deb.debian.org/debian bullseye/main i386 groff-base i386 1.22.4-6 [952 kB] Get: 4 http://deb.debian.org/debian bullseye/main i386 libpipeline1 i386 1.5.3-1 [36.8 kB] Get: 5 http://deb.debian.org/debian bullseye/main i386 man-db i386 2.9.4-2 [1367 kB] Get: 6 http://deb.debian.org/debian bullseye/main i386 sensible-utils all 0.0.14 [14.8 kB] Get: 7 http://deb.debian.org/debian bullseye/main i386 libmagic-mgc i386 1:5.39-3+deb11u1 [273 kB] Get: 8 http://deb.debian.org/debian bullseye/main i386 libmagic1 i386 1:5.39-3+deb11u1 [135 kB] Get: 9 http://deb.debian.org/debian bullseye/main i386 file i386 1:5.39-3+deb11u1 [69.2 kB] Get: 10 http://deb.debian.org/debian bullseye/main i386 gettext-base i386 0.21-4 [176 kB] Get: 11 http://deb.debian.org/debian bullseye/main i386 libsigsegv2 i386 2.13-1 [35.1 kB] Get: 12 http://deb.debian.org/debian bullseye/main i386 m4 i386 1.4.18-5 [206 kB] Get: 13 http://deb.debian.org/debian bullseye/main i386 autoconf all 2.69-14 [313 kB] Get: 14 http://deb.debian.org/debian bullseye/main i386 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 15 http://deb.debian.org/debian bullseye/main i386 automake all 1:1.16.3-2 [814 kB] Get: 16 http://deb.debian.org/debian bullseye/main i386 autopoint all 0.21-4 [510 kB] Get: 17 http://deb.debian.org/debian bullseye/main i386 libdebhelper-perl all 13.3.4 [189 kB] Get: 18 http://deb.debian.org/debian bullseye/main i386 libtool all 2.4.6-15 [513 kB] Get: 19 http://deb.debian.org/debian bullseye/main i386 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian bullseye/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian bullseye/main i386 libsub-override-perl all 0.09-2 [10.2 kB] Get: 22 http://deb.debian.org/debian bullseye/main i386 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 23 http://deb.debian.org/debian bullseye/main i386 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 24 http://deb.debian.org/debian bullseye/main i386 libelf1 i386 0.183-1 [171 kB] Get: 25 http://deb.debian.org/debian bullseye/main i386 dwz i386 0.13+20210201-1 [179 kB] Get: 26 http://deb.debian.org/debian bullseye/main i386 libicu67 i386 67.1-7 [8775 kB] Get: 27 http://deb.debian.org/debian bullseye/main i386 libxml2 i386 2.9.10+dfsg-6.7+deb11u4 [728 kB] Get: 28 http://deb.debian.org/debian bullseye/main i386 gettext i386 0.21-4 [1322 kB] Get: 29 http://deb.debian.org/debian bullseye/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 30 http://deb.debian.org/debian bullseye/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian bullseye/main i386 debhelper all 13.3.4 [1049 kB] Get: 32 http://deb.debian.org/debian bullseye/main i386 libbrotli1 i386 1.0.9-2+b2 [286 kB] Get: 33 http://deb.debian.org/debian bullseye/main i386 libbz2-dev i386 1.0.8-4 [31.3 kB] Get: 34 http://deb.debian.org/debian bullseye/main i386 libsasl2-modules-db i386 2.1.27+dfsg-2.1+deb11u1 [70.1 kB] Get: 35 http://deb.debian.org/debian bullseye/main i386 libsasl2-2 i386 2.1.27+dfsg-2.1+deb11u1 [110 kB] Get: 36 http://deb.debian.org/debian bullseye/main i386 libldap-2.4-2 i386 2.4.57+dfsg-3+deb11u1 [244 kB] Get: 37 http://deb.debian.org/debian bullseye/main i386 libnghttp2-14 i386 1.43.0-1 [85.7 kB] Get: 38 http://deb.debian.org/debian bullseye/main i386 libpsl5 i386 0.21.0-1.2 [57.9 kB] Get: 39 http://deb.debian.org/debian bullseye/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b2 [64.3 kB] Get: 40 http://deb.debian.org/debian bullseye/main i386 libssh2-1 i386 1.9.0-2 [164 kB] Get: 41 http://deb.debian.org/debian bullseye/main i386 libcurl3-gnutls i386 7.74.0-1.3+deb11u9 [374 kB] Get: 42 http://deb.debian.org/debian bullseye/main i386 libcurl4-gnutls-dev i386 7.74.0-1.3+deb11u9 [477 kB] Get: 43 http://deb.debian.org/debian bullseye/main i386 libdeflate0 i386 1.7-1 [48.4 kB] Get: 44 http://deb.debian.org/debian bullseye/main i386 libdeflate-dev i386 1.7-1 [44.4 kB] Get: 45 http://deb.debian.org/debian bullseye/main i386 libgslcblas0 i386 2.6+dfsg-2 [99.2 kB] Get: 46 http://deb.debian.org/debian bullseye/main i386 libgsl25 i386 2.6+dfsg-2 [911 kB] Get: 47 http://deb.debian.org/debian bullseye/main i386 libgsl-dev i386 2.6+dfsg-2 [1146 kB] Get: 48 http://deb.debian.org/debian bullseye/main i386 libhts3 i386 1.11-4 [408 kB] Get: 49 http://deb.debian.org/debian bullseye/main i386 liblzma-dev i386 5.2.5-2.1~deb11u1 [240 kB] Get: 50 http://deb.debian.org/debian bullseye/main i386 zlib1g-dev i386 1:1.2.11.dfsg-2+deb11u2 [194 kB] Get: 51 http://deb.debian.org/debian bullseye/main i386 libhts-dev i386 1.11-4 [3817 kB] Get: 52 http://deb.debian.org/debian bullseye/main i386 libio-pty-perl i386 1:1.15-2 [37.8 kB] Get: 53 http://deb.debian.org/debian bullseye/main i386 tabix i386 1.11-4 [369 kB] Fetched 27.8 MB in 6s (4357 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 17763 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-8+deb11u1_i386.deb ... Unpacking bsdextrautils (2.36.1-8+deb11u1) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../01-libuchardet0_0.0.7-1_i386.deb ... Unpacking libuchardet0:i386 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-6_i386.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../03-libpipeline1_1.5.3-1_i386.deb ... Unpacking libpipeline1:i386 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.4-2_i386.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../05-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../06-libmagic-mgc_1%3a5.39-3+deb11u1_i386.deb ... Unpacking libmagic-mgc (1:5.39-3+deb11u1) ... Selecting previously unselected package libmagic1:i386. Preparing to unpack .../07-libmagic1_1%3a5.39-3+deb11u1_i386.deb ... Unpacking libmagic1:i386 (1:5.39-3+deb11u1) ... Selecting previously unselected package file. Preparing to unpack .../08-file_1%3a5.39-3+deb11u1_i386.deb ... Unpacking file (1:5.39-3+deb11u1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../09-gettext-base_0.21-4_i386.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package libsigsegv2:i386. Preparing to unpack .../10-libsigsegv2_2.13-1_i386.deb ... Unpacking libsigsegv2:i386 (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.18-5_i386.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.69-14_all.deb ... Unpacking autoconf (2.69-14) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../13-autotools-dev_20180224.1+nmu1_all.deb ... Unpacking autotools-dev (20180224.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../14-automake_1%3a1.16.3-2_all.deb ... Unpacking automake (1:1.16.3-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../15-autopoint_0.21-4_all.deb ... Unpacking autopoint (0.21-4) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../16-libdebhelper-perl_13.3.4_all.deb ... Unpacking libdebhelper-perl (13.3.4) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.4.6-15_all.deb ... Unpacking libtool (2.4.6-15) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../19-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../20-libsub-override-perl_0.09-2_all.deb ... Unpacking libsub-override-perl (0.09-2) ... 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Unpacking zlib1g-dev:i386 (1:1.2.11.dfsg-2+deb11u2) ... Selecting previously unselected package libhts-dev:i386. Preparing to unpack .../50-libhts-dev_1.11-4_i386.deb ... Unpacking libhts-dev:i386 (1.11-4) ... Selecting previously unselected package libio-pty-perl. Preparing to unpack .../51-libio-pty-perl_1%3a1.15-2_i386.deb ... Unpacking libio-pty-perl (1:1.15-2) ... Selecting previously unselected package tabix. Preparing to unpack .../52-tabix_1.11-4_i386.deb ... Unpacking tabix (1.11-4) ... Setting up libpipeline1:i386 (1.5.3-1) ... Setting up libpsl5:i386 (0.21.0-1.2) ... Setting up bsdextrautils (2.36.1-8+deb11u1) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libicu67:i386 (67.1-7) ... Setting up libgslcblas0:i386 (2.6+dfsg-2) ... Setting up libio-pty-perl (1:1.15-2) ... Setting up libmagic-mgc (1:5.39-3+deb11u1) ... Setting up libgsl25:i386 (2.6+dfsg-2) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.3.4) ... Setting up libbrotli1:i386 (1.0.9-2+b2) ... Setting up libnghttp2-14:i386 (1.43.0-1) ... Setting up libmagic1:i386 (1:5.39-3+deb11u1) ... Setting up libdeflate0:i386 (1.7-1) ... Setting up gettext-base (0.21-4) ... Setting up file (1:5.39-3+deb11u1) ... Setting up libsasl2-modules-db:i386 (2.1.27+dfsg-2.1+deb11u1) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up librtmp1:i386 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libsigsegv2:i386 (2.13-1) ... Setting up autopoint (0.21-4) ... Setting up libsasl2-2:i386 (2.1.27+dfsg-2.1+deb11u1) ... Setting up liblzma-dev:i386 (5.2.5-2.1~deb11u1) ... Setting up zlib1g-dev:i386 (1:1.2.11.dfsg-2+deb11u2) ... Setting up sensible-utils (0.0.14) ... Setting up libuchardet0:i386 (0.0.7-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libssh2-1:i386 (1.9.0-2) ... Setting up libdeflate-dev:i386 (1.7-1) ... Setting up tabix (1.11-4) ... Setting up libelf1:i386 (0.183-1) ... Setting up libxml2:i386 (2.9.10+dfsg-6.7+deb11u4) ... Setting up libbz2-dev:i386 (1.0.8-4) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up gettext (0.21-4) ... Setting up libgsl-dev (2.6+dfsg-2) ... Setting up libtool (2.4.6-15) ... Setting up libldap-2.4-2:i386 (2.4.57+dfsg-3+deb11u1) ... Setting up m4 (1.4.18-5) ... Setting up libcurl3-gnutls:i386 (7.74.0-1.3+deb11u9) ... Setting up libcurl4-gnutls-dev:i386 (7.74.0-1.3+deb11u9) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.12.0-1) ... Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libhts3:i386 (1.11-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhts-dev:i386 (1.11-4) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up dh-autoreconf (20) ... Setting up debhelper (13.3.4) ... Processing triggers for libc-bin (2.31-13+deb11u6) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/4959/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for bullseye I: user script /srv/workspace/pbuilder/4959/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/bcftools-1.11/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../bcftools_1.11-1_source.changes dpkg-buildpackage: info: source package bcftools dpkg-buildpackage: info: source version 1.11-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean rm -f config.mk && touch config.mk dh clean dh_auto_clean make -j7 distclean make[1]: Entering directory '/build/reproducible-path/bcftools-1.11' rm -f test/*.o test/*~ test/test-rbuf test/test-regidx rm -f plugins/*.so plugins/*.P rm -rf plugins/*.dSYM rm -f test/*.hex 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[1]: Leaving directory '/build/reproducible-path/bcftools-1.11' dh_clean debian/rules binary dh binary dh_update_autotools_config debian/rules override_dh_autoreconf make[1]: Entering directory '/build/reproducible-path/bcftools-1.11' 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.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:94: the top level configure.ac:94: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:94: the top level configure.ac:94: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:94: the top level configure.ac:94: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: 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-1.11' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/bcftools-1.11' dh_auto_configure -- \ --with-htslib=system \ --enable-gsl \ --with-cblas=gslcblas \ --with-bcf-plugin-dir=/usr/lib/i386-linux-gnu/bcftools ./configure --build=i686-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/i386-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system --enable-gsl --with-cblas=gslcblas --with-bcf-plugin-dir=/usr/lib/i386-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 we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for grep that handles long lines and -e... /bin/grep checking for C compiler warning flags... -Wall checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... 64 checking for htslib/sam.h... yes checking for hts_version in -lhts... yes checking shared library type... plain .so checking for library containing dlopen... -ldl 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-1.11' dh_auto_build make -j7 make[1]: Entering directory '/build/reproducible-path/bcftools-1.11' echo '#define BCFTOOLS_VERSION "1.11"' > version.h gcc -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfindex.o vcfindex.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tabix.o tabix.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfstats.o vcfstats.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfisec.o vcfisec.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfmerge.o vcfmerge.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfquery.o vcfquery.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcffilter.o vcffilter.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o filter.o filter.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfsom.o vcfsom.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfnorm.o vcfnorm.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfgtcheck.o vcfgtcheck.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfview.o vcfview.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfannotate.o vcfannotate.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfroh.o vcfroh.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfconcat.o vcfconcat.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcall.o vcfcall.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mcall.o mcall.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcmp.o vcmp.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gvcf.o gvcf.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o reheader.o reheader.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o convert.o convert.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfconvert.o vcfconvert.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tsv2vcf.o tsv2vcf.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcnv.o vcfcnv.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o HMM.o HMM.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o consensus.o consensus.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ploidy.o ploidy.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bin.o bin.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hclust.o hclust.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o version.o version.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o regidx.o regidx.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o smpl_ilist.o smpl_ilist.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o csq.o csq.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfbuf.o vcfbuf.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mpileup.o mpileup.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sample.o bam_sample.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfsort.o vcfsort.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cols.o cols.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o extsort.o extsort.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ccall.o ccall.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o em.o em.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o prob1.o prob1.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kmin.o kmin.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DPLUGINPATH='"/usr/lib/i386-linux-gnu/bcftools"' -c -o vcfplugin.o vcfplugin.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-rbuf.o test/test-rbuf.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-regidx.o test/test-regidx.c gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/GTisec.so version.c plugins/GTisec.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/GTsubset.so version.c plugins/GTsubset.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/ad-bias.so convert.c version.c plugins/ad-bias.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/add-variantkey.so version.c plugins/add-variantkey.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/af-dist.so bin.c version.c plugins/af-dist.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/allele-length.so version.c plugins/allele-length.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/check-ploidy.so version.c plugins/check-ploidy.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/check-sparsity.so version.c plugins/check-sparsity.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/color-chrs.so HMM.c version.c plugins/color-chrs.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/contrast.so version.c plugins/contrast.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/counts.so version.c plugins/counts.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/dosage.so version.c plugins/dosage.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fill-AN-AC.so version.c plugins/fill-AN-AC.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fill-from-fasta.so filter.c version.c plugins/fill-from-fasta.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fill-tags.so version.c plugins/fill-tags.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fixploidy.so ploidy.c regidx.c version.c plugins/fixploidy.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fixref.so version.c plugins/fixref.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/frameshifts.so version.c plugins/frameshifts.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/guess-ploidy.so version.c plugins/guess-ploidy.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/gvcfz.so version.c plugins/gvcfz.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/impute-info.so version.c plugins/impute-info.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/indel-stats.so version.c plugins/indel-stats.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/isecGT.so smpl_ilist.c version.c plugins/isecGT.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/mendelian.so version.c plugins/mendelian.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/missing2ref.so version.c plugins/missing2ref.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/parental-origin.so version.c plugins/parental-origin.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/prune.so version.c plugins/prune.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/remove-overlaps.so version.c plugins/remove-overlaps.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/scatter.so version.c plugins/scatter.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/setGT.so version.c plugins/setGT.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/smpl-stats.so version.c plugins/smpl-stats.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/split-vep.so version.c plugins/split-vep.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/split.so version.c plugins/split.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/tag2tag.so version.c plugins/tag2tag.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/trio-dnm.so version.c plugins/trio-dnm.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/trio-stats.so version.c plugins/trio-stats.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/trio-switch-rate.so version.c plugins/trio-switch-rate.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/variantkey-hex.so version.c plugins/variantkey-hex.c -ldl gcc -Wall -g -O2 -fdebug-prefix-map=/build/reproducible-path/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o main.o main.c gcc -Wl,-z,relro -o test/test-rbuf test/test-rbuf.o -lz -ldl gcc -Wl,-z,relro -o test/test-regidx test/test-regidx.o regidx.o -lhts -lpthread -lz -ldl gcc -rdynamic -Wl,-z,relro -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 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 bam_sample.o vcfsort.o cols.o extsort.o ccall.o em.o prob1.o kmin.o vcfplugin.o -lhts -lm -lz -ldl -lpthread make[1]: Leaving directory '/build/reproducible-path/bcftools-1.11' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/bcftools-1.11' make test-no-plugins VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/bcftools-1.11' ./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 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/vQp5weZwFe/merge.a.vcf.gz 2:3199812-3199812 .. ok test_tabix: /build/reproducible-path/bcftools-1.11/bcftools view -H /tmp/vQp5weZwFe/merge.a.bcf 2:3199812-3199812 .. ok test_tabix: tabix /tmp/vQp5weZwFe/merge.a.vcf.gz 1:3000151-3000151 .. ok test_tabix: /build/reproducible-path/bcftools-1.11/bcftools view -H /tmp/vQp5weZwFe/merge.a.bcf 1:3000151-3000151 .. ok test_index: /build/reproducible-path/bcftools-1.11/bcftools view -H /tmp/vQp5weZwFe/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /build/reproducible-path/bcftools-1.11/bcftools view -H /tmp/vQp5weZwFe/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/reproducible-path/bcftools-1.11/bcftools view -H /tmp/vQp5weZwFe/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/reproducible-path/bcftools-1.11/bcftools view -H /tmp/vQp5weZwFe/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /build/reproducible-path/bcftools-1.11/bcftools view -H /tmp/vQp5weZwFe/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/reproducible-path/bcftools-1.11/bcftools view -H /tmp/vQp5weZwFe/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /build/reproducible-path/bcftools-1.11/bcftools view -H /tmp/vQp5weZwFe/large_chrom_csi_limit.bcf chr20 .. ok test_index: /build/reproducible-path/bcftools-1.11/bcftools view -H /tmp/vQp5weZwFe/large_chrom_csi_limit.bcf chr20 .. ok test_index: /build/reproducible-path/bcftools-1.11/bcftools view -H /tmp/vQp5weZwFe/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /build/reproducible-path/bcftools-1.11/bcftools view -H /tmp/vQp5weZwFe/large_chrom_csi_limit.bcf chr20 .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.11/bcftools index -s /tmp/vQp5weZwFe/idx.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.11/bcftools index -s /tmp/vQp5weZwFe/idx.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.11/bcftools index -s /tmp/vQp5weZwFe/idx.bcf .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.11/bcftools index -n /tmp/vQp5weZwFe/idx.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.11/bcftools index -n /tmp/vQp5weZwFe/idx.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.11/bcftools index -n /tmp/vQp5weZwFe/idx.bcf .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.11/bcftools index -s /tmp/vQp5weZwFe/empty.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.11/bcftools index -s /tmp/vQp5weZwFe/empty.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.11/bcftools index -s /tmp/vQp5weZwFe/empty.bcf .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.11/bcftools index -n /tmp/vQp5weZwFe/empty.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.11/bcftools index -n /tmp/vQp5weZwFe/empty.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.11/bcftools index -n /tmp/vQp5weZwFe/empty.bcf .. ok test_vcf_check: /build/reproducible-path/bcftools-1.11/bcftools stats -s - /tmp/vQp5weZwFe/check.vcf.gz | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/check.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools stats -s - | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check_merge: /build/reproducible-path/bcftools-1.11/misc/plot-vcfstats -m /tmp/vQp5weZwFe/check.1.chk /tmp/vQp5weZwFe/check.2.chk /tmp/vQp5weZwFe/check.3.chk /tmp/vQp5weZwFe/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-1.11/bcftools stats -s - /tmp/vQp5weZwFe/stats.a.vcf.gz /tmp/vQp5weZwFe/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/reproducible-path/bcftools-1.11/bcftools stats -s B /tmp/vQp5weZwFe/stats.a.vcf.gz /tmp/vQp5weZwFe/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/reproducible-path/bcftools-1.11/bcftools stats -s - /tmp/vQp5weZwFe/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.11/bcftools isec -n =2 /tmp/vQp5weZwFe/isec.a.vcf.gz /tmp/vQp5weZwFe/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.11/bcftools isec -Ob -n =2 /tmp/vQp5weZwFe/isec.a.vcf.gz /tmp/vQp5weZwFe/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.11/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/vQp5weZwFe/isec.a.vcf.gz /tmp/vQp5weZwFe/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.11/bcftools isec -Ob -n =2 -i"STRLEN(REF)==2" /tmp/vQp5weZwFe/isec.a.vcf.gz /tmp/vQp5weZwFe/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.11/bcftools isec -n =2 -c both /tmp/vQp5weZwFe/isec.a.vcf.gz /tmp/vQp5weZwFe/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.11/bcftools isec -Ob -n =2 -c both /tmp/vQp5weZwFe/isec.a.vcf.gz /tmp/vQp5weZwFe/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.11/bcftools isec -n =2 -c any /tmp/vQp5weZwFe/isec.a.vcf.gz /tmp/vQp5weZwFe/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.11/bcftools isec -Ob -n =2 -c any /tmp/vQp5weZwFe/isec.a.vcf.gz /tmp/vQp5weZwFe/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.11/bcftools isec -C -c any /tmp/vQp5weZwFe/isec.a.vcf.gz /tmp/vQp5weZwFe/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.11/bcftools isec -Ob -C -c any /tmp/vQp5weZwFe/isec.a.vcf.gz /tmp/vQp5weZwFe/isec.b.vcf.gz .. ok test_vcf_isec2: /build/reproducible-path/bcftools-1.11/bcftools isec --no-version -T /tmp/vQp5weZwFe/isec.tab.gz /tmp/vQp5weZwFe/isec.a.vcf.gz .. ok test_vcf_isec2: /build/reproducible-path/bcftools-1.11/bcftools isec -Ob -T /tmp/vQp5weZwFe/isec.tab.gz /tmp/vQp5weZwFe/isec.a.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.11/bcftools isec -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/vQp5weZwFe/isec-miss.1.1.vcf.gz /tmp/vQp5weZwFe/isec-miss.1.2.vcf.gz /tmp/vQp5weZwFe/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.11/bcftools isec -Ob -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/vQp5weZwFe/isec-miss.1.1.vcf.gz /tmp/vQp5weZwFe/isec-miss.1.2.vcf.gz /tmp/vQp5weZwFe/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.11/bcftools isec -R /build/reproducible-path/bcftools-1.11/test/isec-miss.1.regs.txt -n +1 /tmp/vQp5weZwFe/isec-miss.1.1.vcf.gz /tmp/vQp5weZwFe/isec-miss.1.2.vcf.gz /tmp/vQp5weZwFe/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.11/bcftools isec -Ob -R /build/reproducible-path/bcftools-1.11/test/isec-miss.1.regs.txt -n +1 /tmp/vQp5weZwFe/isec-miss.1.1.vcf.gz /tmp/vQp5weZwFe/isec-miss.1.2.vcf.gz /tmp/vQp5weZwFe/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.11/bcftools isec -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/vQp5weZwFe/isec-miss.2.1.vcf.gz /tmp/vQp5weZwFe/isec-miss.2.2.vcf.gz /tmp/vQp5weZwFe/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.11/bcftools isec -Ob -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/vQp5weZwFe/isec-miss.2.1.vcf.gz /tmp/vQp5weZwFe/isec-miss.2.2.vcf.gz /tmp/vQp5weZwFe/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.11/bcftools isec -R /build/reproducible-path/bcftools-1.11/test/isec-miss.1.regs.txt -n +1 /tmp/vQp5weZwFe/isec-miss.2.1.vcf.gz /tmp/vQp5weZwFe/isec-miss.2.2.vcf.gz /tmp/vQp5weZwFe/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.11/bcftools isec -Ob -R /build/reproducible-path/bcftools-1.11/test/isec-miss.1.regs.txt -n +1 /tmp/vQp5weZwFe/isec-miss.2.1.vcf.gz /tmp/vQp5weZwFe/isec-miss.2.2.vcf.gz /tmp/vQp5weZwFe/isec-miss.2.3.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version -i AF:join /tmp/vQp5weZwFe/merge.join.a.vcf.gz /tmp/vQp5weZwFe/merge.join.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob -i AF:join /tmp/vQp5weZwFe/merge.join.a.vcf.gz /tmp/vQp5weZwFe/merge.join.b.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version -i AF:join /tmp/vQp5weZwFe/merge.join.a.bcf /tmp/vQp5weZwFe/merge.join.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob -i AF:join /tmp/vQp5weZwFe/merge.join.a.bcf /tmp/vQp5weZwFe/merge.join.b.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version --force-samples /tmp/vQp5weZwFe/merge.LPL.a.vcf.gz /tmp/vQp5weZwFe/merge.LPL.b.vcf.gz /tmp/vQp5weZwFe/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob --force-samples /tmp/vQp5weZwFe/merge.LPL.a.vcf.gz /tmp/vQp5weZwFe/merge.LPL.b.vcf.gz /tmp/vQp5weZwFe/merge.LPL.c.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version --force-samples /tmp/vQp5weZwFe/merge.LPL.a.bcf /tmp/vQp5weZwFe/merge.LPL.b.bcf /tmp/vQp5weZwFe/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob --force-samples /tmp/vQp5weZwFe/merge.LPL.a.bcf /tmp/vQp5weZwFe/merge.LPL.b.bcf /tmp/vQp5weZwFe/merge.LPL.c.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version --force-samples -L 1 /tmp/vQp5weZwFe/merge.LPL.a.vcf.gz /tmp/vQp5weZwFe/merge.LPL.b.vcf.gz /tmp/vQp5weZwFe/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob --force-samples -L 1 /tmp/vQp5weZwFe/merge.LPL.a.vcf.gz /tmp/vQp5weZwFe/merge.LPL.b.vcf.gz /tmp/vQp5weZwFe/merge.LPL.c.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version --force-samples -L 1 /tmp/vQp5weZwFe/merge.LPL.a.bcf /tmp/vQp5weZwFe/merge.LPL.b.bcf /tmp/vQp5weZwFe/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob --force-samples -L 1 /tmp/vQp5weZwFe/merge.LPL.a.bcf /tmp/vQp5weZwFe/merge.LPL.b.bcf /tmp/vQp5weZwFe/merge.LPL.c.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version --force-samples -L 2 /tmp/vQp5weZwFe/merge.LPL.a.vcf.gz /tmp/vQp5weZwFe/merge.LPL.b.vcf.gz /tmp/vQp5weZwFe/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob --force-samples -L 2 /tmp/vQp5weZwFe/merge.LPL.a.vcf.gz /tmp/vQp5weZwFe/merge.LPL.b.vcf.gz /tmp/vQp5weZwFe/merge.LPL.c.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version --force-samples -L 2 /tmp/vQp5weZwFe/merge.LPL.a.bcf /tmp/vQp5weZwFe/merge.LPL.b.bcf /tmp/vQp5weZwFe/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob --force-samples -L 2 /tmp/vQp5weZwFe/merge.LPL.a.bcf /tmp/vQp5weZwFe/merge.LPL.b.bcf /tmp/vQp5weZwFe/merge.LPL.c.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version --force-samples -L 3 /tmp/vQp5weZwFe/merge.LPL.a.vcf.gz /tmp/vQp5weZwFe/merge.LPL.b.vcf.gz /tmp/vQp5weZwFe/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob --force-samples -L 3 /tmp/vQp5weZwFe/merge.LPL.a.vcf.gz /tmp/vQp5weZwFe/merge.LPL.b.vcf.gz /tmp/vQp5weZwFe/merge.LPL.c.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version --force-samples -L 3 /tmp/vQp5weZwFe/merge.LPL.a.bcf /tmp/vQp5weZwFe/merge.LPL.b.bcf /tmp/vQp5weZwFe/merge.LPL.c.bcf The outputs differ: /build/reproducible-path/bcftools-1.11/test/merge.LPL.4.out /build/reproducible-path/bcftools-1.11/test/merge.LPL.4.out.new 19c19 < 1 30001 . C CA,CC,CG . . . GT:PL:GL:AD:DF:DD 0/1:10,0,10,.,.,.,.,.,.,.:10,0,10,.,.,.,.,.,.,.:1,2,.,.:0.1,0.2,.,.:1,.,. 0/2:10,.,.,0,.,10,.,.,.,.:10,.,.,0,.,10,.,.,.,.:1,.,2,.:0.1,.,0.2,.:.,1,. 0/3:10,.,.,.,.,.,0,.,.,10:10,.,.,.,.,.,0,.,.,10:1,.,.,2:0.1,.,.,0.2:.,.,1 --- > 1 30001 . C CA,CC,CG . . . GT:PL:GL:AD:DF:DD 0/1:10,0,10,.,.,.,.,.,.,.:10,0,10,.,.,.,.,.,.,.:1,2,.,.:0.1,0.2,.,.:1,.,. 0/2:10,.,.,0,.,10,.,.,.,.:10,.,.,0,.,10,.,.,.,.:1,.,2,.:0.1,.,0.2,.:. 0/3:10,.,.,.,.,.,0,.,.,10:10,.,.,.,.,.,0,.,.,10:1,.,.,2:0.1,.,.,0.2:.,.,1 .. failed ... test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob --force-samples -L 3 /tmp/vQp5weZwFe/merge.LPL.a.bcf /tmp/vQp5weZwFe/merge.LPL.b.bcf /tmp/vQp5weZwFe/merge.LPL.c.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version --force-samples -L 4 /tmp/vQp5weZwFe/merge.LPL.a.vcf.gz /tmp/vQp5weZwFe/merge.LPL.b.vcf.gz /tmp/vQp5weZwFe/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob --force-samples -L 4 /tmp/vQp5weZwFe/merge.LPL.a.vcf.gz /tmp/vQp5weZwFe/merge.LPL.b.vcf.gz /tmp/vQp5weZwFe/merge.LPL.c.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version --force-samples -L 4 /tmp/vQp5weZwFe/merge.LPL.a.bcf /tmp/vQp5weZwFe/merge.LPL.b.bcf /tmp/vQp5weZwFe/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob --force-samples -L 4 /tmp/vQp5weZwFe/merge.LPL.a.bcf /tmp/vQp5weZwFe/merge.LPL.b.bcf /tmp/vQp5weZwFe/merge.LPL.c.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version --force-samples -L 5 /tmp/vQp5weZwFe/merge.LPL.a.vcf.gz /tmp/vQp5weZwFe/merge.LPL.b.vcf.gz /tmp/vQp5weZwFe/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob --force-samples -L 5 /tmp/vQp5weZwFe/merge.LPL.a.vcf.gz /tmp/vQp5weZwFe/merge.LPL.b.vcf.gz /tmp/vQp5weZwFe/merge.LPL.c.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version --force-samples -L 5 /tmp/vQp5weZwFe/merge.LPL.a.bcf /tmp/vQp5weZwFe/merge.LPL.b.bcf /tmp/vQp5weZwFe/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob --force-samples -L 5 /tmp/vQp5weZwFe/merge.LPL.a.bcf /tmp/vQp5weZwFe/merge.LPL.b.bcf /tmp/vQp5weZwFe/merge.LPL.c.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version --force-samples /tmp/vQp5weZwFe/merge.a.vcf.gz /tmp/vQp5weZwFe/merge.b.vcf.gz /tmp/vQp5weZwFe/merge.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob --force-samples /tmp/vQp5weZwFe/merge.a.vcf.gz /tmp/vQp5weZwFe/merge.b.vcf.gz /tmp/vQp5weZwFe/merge.c.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version --force-samples /tmp/vQp5weZwFe/merge.a.bcf /tmp/vQp5weZwFe/merge.b.bcf /tmp/vQp5weZwFe/merge.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob --force-samples /tmp/vQp5weZwFe/merge.a.bcf /tmp/vQp5weZwFe/merge.b.bcf /tmp/vQp5weZwFe/merge.c.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version --force-samples -Fx /tmp/vQp5weZwFe/merge.a.vcf.gz /tmp/vQp5weZwFe/merge.b.vcf.gz /tmp/vQp5weZwFe/merge.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob --force-samples -Fx /tmp/vQp5weZwFe/merge.a.vcf.gz /tmp/vQp5weZwFe/merge.b.vcf.gz /tmp/vQp5weZwFe/merge.c.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version --force-samples -Fx /tmp/vQp5weZwFe/merge.a.bcf /tmp/vQp5weZwFe/merge.b.bcf /tmp/vQp5weZwFe/merge.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob --force-samples -Fx /tmp/vQp5weZwFe/merge.a.bcf /tmp/vQp5weZwFe/merge.b.bcf /tmp/vQp5weZwFe/merge.c.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version --force-samples -0 /tmp/vQp5weZwFe/merge.a.vcf.gz /tmp/vQp5weZwFe/merge.b.vcf.gz /tmp/vQp5weZwFe/merge.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob --force-samples -0 /tmp/vQp5weZwFe/merge.a.vcf.gz /tmp/vQp5weZwFe/merge.b.vcf.gz /tmp/vQp5weZwFe/merge.c.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version --force-samples -0 /tmp/vQp5weZwFe/merge.a.bcf /tmp/vQp5weZwFe/merge.b.bcf /tmp/vQp5weZwFe/merge.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob --force-samples -0 /tmp/vQp5weZwFe/merge.a.bcf /tmp/vQp5weZwFe/merge.b.bcf /tmp/vQp5weZwFe/merge.c.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version --force-samples -m none /tmp/vQp5weZwFe/merge.2.a.vcf.gz /tmp/vQp5weZwFe/merge.2.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob --force-samples -m none /tmp/vQp5weZwFe/merge.2.a.vcf.gz /tmp/vQp5weZwFe/merge.2.b.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version --force-samples -m none /tmp/vQp5weZwFe/merge.2.a.bcf /tmp/vQp5weZwFe/merge.2.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob --force-samples -m none /tmp/vQp5weZwFe/merge.2.a.bcf /tmp/vQp5weZwFe/merge.2.b.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version --force-samples -m both /tmp/vQp5weZwFe/merge.2.a.vcf.gz /tmp/vQp5weZwFe/merge.2.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob --force-samples -m both /tmp/vQp5weZwFe/merge.2.a.vcf.gz /tmp/vQp5weZwFe/merge.2.b.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version --force-samples -m both /tmp/vQp5weZwFe/merge.2.a.bcf /tmp/vQp5weZwFe/merge.2.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob --force-samples -m both /tmp/vQp5weZwFe/merge.2.a.bcf /tmp/vQp5weZwFe/merge.2.b.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version --force-samples -m all /tmp/vQp5weZwFe/merge.2.a.vcf.gz /tmp/vQp5weZwFe/merge.2.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob --force-samples -m all /tmp/vQp5weZwFe/merge.2.a.vcf.gz /tmp/vQp5weZwFe/merge.2.b.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version --force-samples -m all /tmp/vQp5weZwFe/merge.2.a.bcf /tmp/vQp5weZwFe/merge.2.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob --force-samples -m all /tmp/vQp5weZwFe/merge.2.a.bcf /tmp/vQp5weZwFe/merge.2.b.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/vQp5weZwFe/merge.3.a.vcf.gz /tmp/vQp5weZwFe/merge.3.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/vQp5weZwFe/merge.3.a.vcf.gz /tmp/vQp5weZwFe/merge.3.b.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/vQp5weZwFe/merge.3.a.bcf /tmp/vQp5weZwFe/merge.3.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/vQp5weZwFe/merge.3.a.bcf /tmp/vQp5weZwFe/merge.3.b.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version --force-samples -m id /tmp/vQp5weZwFe/merge.4.a.vcf.gz /tmp/vQp5weZwFe/merge.4.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob --force-samples -m id /tmp/vQp5weZwFe/merge.4.a.vcf.gz /tmp/vQp5weZwFe/merge.4.b.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version --force-samples -m id /tmp/vQp5weZwFe/merge.4.a.bcf /tmp/vQp5weZwFe/merge.4.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob --force-samples -m id /tmp/vQp5weZwFe/merge.4.a.bcf /tmp/vQp5weZwFe/merge.4.b.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version --gvcf - /tmp/vQp5weZwFe/gvcf.merge.1.vcf.gz /tmp/vQp5weZwFe/gvcf.merge.2.vcf.gz /tmp/vQp5weZwFe/gvcf.merge.3.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob --gvcf - /tmp/vQp5weZwFe/gvcf.merge.1.vcf.gz /tmp/vQp5weZwFe/gvcf.merge.2.vcf.gz /tmp/vQp5weZwFe/gvcf.merge.3.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version --gvcf - /tmp/vQp5weZwFe/gvcf.merge.1.bcf /tmp/vQp5weZwFe/gvcf.merge.2.bcf /tmp/vQp5weZwFe/gvcf.merge.3.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob --gvcf - /tmp/vQp5weZwFe/gvcf.merge.1.bcf /tmp/vQp5weZwFe/gvcf.merge.2.bcf /tmp/vQp5weZwFe/gvcf.merge.3.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version --gvcf - /tmp/vQp5weZwFe/merge.gvcf.2.a.vcf.gz /tmp/vQp5weZwFe/merge.gvcf.2.b.vcf.gz /tmp/vQp5weZwFe/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob --gvcf - /tmp/vQp5weZwFe/merge.gvcf.2.a.vcf.gz /tmp/vQp5weZwFe/merge.gvcf.2.b.vcf.gz /tmp/vQp5weZwFe/merge.gvcf.2.c.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version --gvcf - -i SRC:join /tmp/vQp5weZwFe/merge.gvcf.3.a.vcf.gz /tmp/vQp5weZwFe/merge.gvcf.3.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob --gvcf - -i SRC:join /tmp/vQp5weZwFe/merge.gvcf.3.a.vcf.gz /tmp/vQp5weZwFe/merge.gvcf.3.b.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version --gvcf - /tmp/vQp5weZwFe/merge.gvcf.4.a.vcf.gz /tmp/vQp5weZwFe/merge.gvcf.4.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob --gvcf - /tmp/vQp5weZwFe/merge.gvcf.4.a.vcf.gz /tmp/vQp5weZwFe/merge.gvcf.4.b.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version --gvcf - /tmp/vQp5weZwFe/merge.gvcf.4.a.bcf /tmp/vQp5weZwFe/merge.gvcf.4.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob --gvcf - /tmp/vQp5weZwFe/merge.gvcf.4.a.bcf /tmp/vQp5weZwFe/merge.gvcf.4.b.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version /tmp/vQp5weZwFe/merge.5.a.vcf.gz /tmp/vQp5weZwFe/merge.5.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob /tmp/vQp5weZwFe/merge.5.a.vcf.gz /tmp/vQp5weZwFe/merge.5.b.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version /tmp/vQp5weZwFe/merge.5.a.bcf /tmp/vQp5weZwFe/merge.5.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob /tmp/vQp5weZwFe/merge.5.a.bcf /tmp/vQp5weZwFe/merge.5.b.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version /tmp/vQp5weZwFe/merge.6.a.vcf.gz /tmp/vQp5weZwFe/merge.6.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob /tmp/vQp5weZwFe/merge.6.a.vcf.gz /tmp/vQp5weZwFe/merge.6.b.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version /tmp/vQp5weZwFe/merge.6.a.bcf /tmp/vQp5weZwFe/merge.6.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob /tmp/vQp5weZwFe/merge.6.a.bcf /tmp/vQp5weZwFe/merge.6.b.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version --gvcf - /tmp/vQp5weZwFe/merge.gvcf.7.a.vcf.gz /tmp/vQp5weZwFe/merge.gvcf.7.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob --gvcf - /tmp/vQp5weZwFe/merge.gvcf.7.a.vcf.gz /tmp/vQp5weZwFe/merge.gvcf.7.b.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version --gvcf - /tmp/vQp5weZwFe/merge.gvcf.7.a.bcf /tmp/vQp5weZwFe/merge.gvcf.7.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob --gvcf - /tmp/vQp5weZwFe/merge.gvcf.7.a.bcf /tmp/vQp5weZwFe/merge.gvcf.7.b.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version --gvcf - /tmp/vQp5weZwFe/merge.gvcf.8.a.vcf.gz /tmp/vQp5weZwFe/merge.gvcf.8.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob --gvcf - /tmp/vQp5weZwFe/merge.gvcf.8.a.vcf.gz /tmp/vQp5weZwFe/merge.gvcf.8.b.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version --gvcf - /tmp/vQp5weZwFe/merge.gvcf.8.a.bcf /tmp/vQp5weZwFe/merge.gvcf.8.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob --gvcf - /tmp/vQp5weZwFe/merge.gvcf.8.a.bcf /tmp/vQp5weZwFe/merge.gvcf.8.b.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version --force-samples /tmp/vQp5weZwFe/merge.7.a.vcf.gz /tmp/vQp5weZwFe/merge.7.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob --force-samples /tmp/vQp5weZwFe/merge.7.a.vcf.gz /tmp/vQp5weZwFe/merge.7.b.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version --force-samples /tmp/vQp5weZwFe/merge.7.a.bcf /tmp/vQp5weZwFe/merge.7.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob --force-samples /tmp/vQp5weZwFe/merge.7.a.bcf /tmp/vQp5weZwFe/merge.7.b.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version --gvcf /build/reproducible-path/bcftools-1.11/test/gvcf.fa /tmp/vQp5weZwFe/merge.gvcf.9a.vcf.gz /tmp/vQp5weZwFe/merge.gvcf.9b.vcf.gz /tmp/vQp5weZwFe/merge.gvcf.9c.vcf.gz /tmp/vQp5weZwFe/merge.gvcf.9d.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob --gvcf /build/reproducible-path/bcftools-1.11/test/gvcf.fa /tmp/vQp5weZwFe/merge.gvcf.9a.vcf.gz /tmp/vQp5weZwFe/merge.gvcf.9b.vcf.gz /tmp/vQp5weZwFe/merge.gvcf.9c.vcf.gz /tmp/vQp5weZwFe/merge.gvcf.9d.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version --gvcf /build/reproducible-path/bcftools-1.11/test/gvcf.fa /tmp/vQp5weZwFe/merge.gvcf.9a.bcf /tmp/vQp5weZwFe/merge.gvcf.9b.bcf /tmp/vQp5weZwFe/merge.gvcf.9c.bcf /tmp/vQp5weZwFe/merge.gvcf.9d.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob --gvcf /build/reproducible-path/bcftools-1.11/test/gvcf.fa /tmp/vQp5weZwFe/merge.gvcf.9a.bcf /tmp/vQp5weZwFe/merge.gvcf.9b.bcf /tmp/vQp5weZwFe/merge.gvcf.9c.bcf /tmp/vQp5weZwFe/merge.gvcf.9d.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version --gvcf /build/reproducible-path/bcftools-1.11/test/gvcf.fa -r 22:21-23 /tmp/vQp5weZwFe/merge.gvcf.9a.vcf.gz /tmp/vQp5weZwFe/merge.gvcf.9b.vcf.gz /tmp/vQp5weZwFe/merge.gvcf.9c.vcf.gz /tmp/vQp5weZwFe/merge.gvcf.9d.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob --gvcf /build/reproducible-path/bcftools-1.11/test/gvcf.fa -r 22:21-23 /tmp/vQp5weZwFe/merge.gvcf.9a.vcf.gz /tmp/vQp5weZwFe/merge.gvcf.9b.vcf.gz /tmp/vQp5weZwFe/merge.gvcf.9c.vcf.gz /tmp/vQp5weZwFe/merge.gvcf.9d.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version --gvcf /build/reproducible-path/bcftools-1.11/test/gvcf.fa -r 22:21-23 /tmp/vQp5weZwFe/merge.gvcf.9a.bcf /tmp/vQp5weZwFe/merge.gvcf.9b.bcf /tmp/vQp5weZwFe/merge.gvcf.9c.bcf /tmp/vQp5weZwFe/merge.gvcf.9d.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob --gvcf /build/reproducible-path/bcftools-1.11/test/gvcf.fa -r 22:21-23 /tmp/vQp5weZwFe/merge.gvcf.9a.bcf /tmp/vQp5weZwFe/merge.gvcf.9b.bcf /tmp/vQp5weZwFe/merge.gvcf.9c.bcf /tmp/vQp5weZwFe/merge.gvcf.9d.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version --gvcf /build/reproducible-path/bcftools-1.11/test/gvcf.fa /tmp/vQp5weZwFe/merge.gvcf.9a.vcf.gz /tmp/vQp5weZwFe/merge.gvcf.9b.vcf.gz /tmp/vQp5weZwFe/merge.gvcf.9c.vcf.gz /tmp/vQp5weZwFe/merge.gvcf.9d.vcf.gz /tmp/vQp5weZwFe/merge.gvcf.9e.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob --gvcf /build/reproducible-path/bcftools-1.11/test/gvcf.fa /tmp/vQp5weZwFe/merge.gvcf.9a.vcf.gz /tmp/vQp5weZwFe/merge.gvcf.9b.vcf.gz /tmp/vQp5weZwFe/merge.gvcf.9c.vcf.gz /tmp/vQp5weZwFe/merge.gvcf.9d.vcf.gz /tmp/vQp5weZwFe/merge.gvcf.9e.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version --gvcf /build/reproducible-path/bcftools-1.11/test/gvcf.fa /tmp/vQp5weZwFe/merge.gvcf.9a.bcf /tmp/vQp5weZwFe/merge.gvcf.9b.bcf /tmp/vQp5weZwFe/merge.gvcf.9c.bcf /tmp/vQp5weZwFe/merge.gvcf.9d.bcf /tmp/vQp5weZwFe/merge.gvcf.9e.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob --gvcf /build/reproducible-path/bcftools-1.11/test/gvcf.fa /tmp/vQp5weZwFe/merge.gvcf.9a.bcf /tmp/vQp5weZwFe/merge.gvcf.9b.bcf /tmp/vQp5weZwFe/merge.gvcf.9c.bcf /tmp/vQp5weZwFe/merge.gvcf.9d.bcf /tmp/vQp5weZwFe/merge.gvcf.9e.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version --gvcf /build/reproducible-path/bcftools-1.11/test/gvcf.fa -r 22:21-23 /tmp/vQp5weZwFe/merge.gvcf.9a.vcf.gz /tmp/vQp5weZwFe/merge.gvcf.9b.vcf.gz /tmp/vQp5weZwFe/merge.gvcf.9c.vcf.gz /tmp/vQp5weZwFe/merge.gvcf.9d.vcf.gz /tmp/vQp5weZwFe/merge.gvcf.9e.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob --gvcf /build/reproducible-path/bcftools-1.11/test/gvcf.fa -r 22:21-23 /tmp/vQp5weZwFe/merge.gvcf.9a.vcf.gz /tmp/vQp5weZwFe/merge.gvcf.9b.vcf.gz /tmp/vQp5weZwFe/merge.gvcf.9c.vcf.gz /tmp/vQp5weZwFe/merge.gvcf.9d.vcf.gz /tmp/vQp5weZwFe/merge.gvcf.9e.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version --gvcf /build/reproducible-path/bcftools-1.11/test/gvcf.fa -r 22:21-23 /tmp/vQp5weZwFe/merge.gvcf.9a.bcf /tmp/vQp5weZwFe/merge.gvcf.9b.bcf /tmp/vQp5weZwFe/merge.gvcf.9c.bcf /tmp/vQp5weZwFe/merge.gvcf.9d.bcf /tmp/vQp5weZwFe/merge.gvcf.9e.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob --gvcf /build/reproducible-path/bcftools-1.11/test/gvcf.fa -r 22:21-23 /tmp/vQp5weZwFe/merge.gvcf.9a.bcf /tmp/vQp5weZwFe/merge.gvcf.9b.bcf /tmp/vQp5weZwFe/merge.gvcf.9c.bcf /tmp/vQp5weZwFe/merge.gvcf.9d.bcf /tmp/vQp5weZwFe/merge.gvcf.9e.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version /tmp/vQp5weZwFe/merge.gvcf.10.a.vcf.gz /tmp/vQp5weZwFe/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob /tmp/vQp5weZwFe/merge.gvcf.10.a.vcf.gz /tmp/vQp5weZwFe/merge.gvcf.10.b.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version /tmp/vQp5weZwFe/merge.gvcf.10.a.bcf /tmp/vQp5weZwFe/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob /tmp/vQp5weZwFe/merge.gvcf.10.a.bcf /tmp/vQp5weZwFe/merge.gvcf.10.b.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version -m none /tmp/vQp5weZwFe/merge.gvcf.10.a.vcf.gz /tmp/vQp5weZwFe/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob -m none /tmp/vQp5weZwFe/merge.gvcf.10.a.vcf.gz /tmp/vQp5weZwFe/merge.gvcf.10.b.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version -m none /tmp/vQp5weZwFe/merge.gvcf.10.a.bcf /tmp/vQp5weZwFe/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob -m none /tmp/vQp5weZwFe/merge.gvcf.10.a.bcf /tmp/vQp5weZwFe/merge.gvcf.10.b.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version -g /build/reproducible-path/bcftools-1.11/test/merge.gvcf.10.fa /tmp/vQp5weZwFe/merge.gvcf.10.a.vcf.gz /tmp/vQp5weZwFe/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob -g /build/reproducible-path/bcftools-1.11/test/merge.gvcf.10.fa /tmp/vQp5weZwFe/merge.gvcf.10.a.vcf.gz /tmp/vQp5weZwFe/merge.gvcf.10.b.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version -g /build/reproducible-path/bcftools-1.11/test/merge.gvcf.10.fa /tmp/vQp5weZwFe/merge.gvcf.10.a.bcf /tmp/vQp5weZwFe/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob -g /build/reproducible-path/bcftools-1.11/test/merge.gvcf.10.fa /tmp/vQp5weZwFe/merge.gvcf.10.a.bcf /tmp/vQp5weZwFe/merge.gvcf.10.b.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version -g /build/reproducible-path/bcftools-1.11/test/merge.gvcf.10.fa -m none /tmp/vQp5weZwFe/merge.gvcf.10.a.vcf.gz /tmp/vQp5weZwFe/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob -g /build/reproducible-path/bcftools-1.11/test/merge.gvcf.10.fa -m none /tmp/vQp5weZwFe/merge.gvcf.10.a.vcf.gz /tmp/vQp5weZwFe/merge.gvcf.10.b.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version -g /build/reproducible-path/bcftools-1.11/test/merge.gvcf.10.fa -m none /tmp/vQp5weZwFe/merge.gvcf.10.a.bcf /tmp/vQp5weZwFe/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob -g /build/reproducible-path/bcftools-1.11/test/merge.gvcf.10.fa -m none /tmp/vQp5weZwFe/merge.gvcf.10.a.bcf /tmp/vQp5weZwFe/merge.gvcf.10.b.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version -g /build/reproducible-path/bcftools-1.11/test/merge.gvcf.10.fa /tmp/vQp5weZwFe/merge.gvcf.10.b.vcf.gz /tmp/vQp5weZwFe/merge.gvcf.10.a.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob -g /build/reproducible-path/bcftools-1.11/test/merge.gvcf.10.fa /tmp/vQp5weZwFe/merge.gvcf.10.b.vcf.gz /tmp/vQp5weZwFe/merge.gvcf.10.a.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version -g /build/reproducible-path/bcftools-1.11/test/merge.gvcf.10.fa /tmp/vQp5weZwFe/merge.gvcf.10.b.bcf /tmp/vQp5weZwFe/merge.gvcf.10.a.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob -g /build/reproducible-path/bcftools-1.11/test/merge.gvcf.10.fa /tmp/vQp5weZwFe/merge.gvcf.10.b.bcf /tmp/vQp5weZwFe/merge.gvcf.10.a.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version -g /build/reproducible-path/bcftools-1.11/test/merge.gvcf.10.fa -m none /tmp/vQp5weZwFe/merge.gvcf.10.b.vcf.gz /tmp/vQp5weZwFe/merge.gvcf.10.a.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob -g /build/reproducible-path/bcftools-1.11/test/merge.gvcf.10.fa -m none /tmp/vQp5weZwFe/merge.gvcf.10.b.vcf.gz /tmp/vQp5weZwFe/merge.gvcf.10.a.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version -g /build/reproducible-path/bcftools-1.11/test/merge.gvcf.10.fa -m none /tmp/vQp5weZwFe/merge.gvcf.10.b.bcf /tmp/vQp5weZwFe/merge.gvcf.10.a.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob -g /build/reproducible-path/bcftools-1.11/test/merge.gvcf.10.fa -m none /tmp/vQp5weZwFe/merge.gvcf.10.b.bcf /tmp/vQp5weZwFe/merge.gvcf.10.a.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version /tmp/vQp5weZwFe/merge.noidx.a.vcf.gz /tmp/vQp5weZwFe/merge.noidx.b.vcf.gz /tmp/vQp5weZwFe/merge.noidx.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob /tmp/vQp5weZwFe/merge.noidx.a.vcf.gz /tmp/vQp5weZwFe/merge.noidx.b.vcf.gz /tmp/vQp5weZwFe/merge.noidx.c.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version /tmp/vQp5weZwFe/merge.noidx.a.bcf /tmp/vQp5weZwFe/merge.noidx.b.bcf /tmp/vQp5weZwFe/merge.noidx.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob /tmp/vQp5weZwFe/merge.noidx.a.bcf /tmp/vQp5weZwFe/merge.noidx.b.bcf /tmp/vQp5weZwFe/merge.noidx.c.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version --no-index /build/reproducible-path/bcftools-1.11/test/merge.noidx.a.vcf /build/reproducible-path/bcftools-1.11/test/merge.noidx.b.vcf /build/reproducible-path/bcftools-1.11/test/merge.noidx.c.vcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob --no-index /build/reproducible-path/bcftools-1.11/test/merge.noidx.a.vcf /build/reproducible-path/bcftools-1.11/test/merge.noidx.b.vcf /build/reproducible-path/bcftools-1.11/test/merge.noidx.c.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge --no-version --no-index /tmp/vQp5weZwFe/merge.noidx.a.bcf /tmp/vQp5weZwFe/merge.noidx.b.bcf /tmp/vQp5weZwFe/merge.noidx.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.11/bcftools merge -Ob --no-index /tmp/vQp5weZwFe/merge.noidx.a.bcf /tmp/vQp5weZwFe/merge.noidx.b.bcf /tmp/vQp5weZwFe/merge.noidx.c.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided,_conflicting_interpretations"' /tmp/vQp5weZwFe/query.string.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/query.string.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided,_conflicting_interpretations"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" || CLNREVSTAT="_conflicting_interpretations"' /tmp/vQp5weZwFe/query.string.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/query.string.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" || CLNREVSTAT="_conflicting_interpretations"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" && CLNREVSTAT="_conflicting_interpretations"' /tmp/vQp5weZwFe/query.string.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/query.string.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" && CLNREVSTAT="_conflicting_interpretations"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' /tmp/vQp5weZwFe/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/query.vcf.gz | /build/reproducible-path/bcftools-1.11/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-1.11/bcftools query -f '%RSX\t%VKX\n' /tmp/vQp5weZwFe/query.variantkey.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/query.variantkey.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f '%RSX\t%VKX\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'%XRI\n' -i'XRI[*]>1111' /tmp/vQp5weZwFe/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%XRI\n' -i'XRI[*]>1111' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' /tmp/vQp5weZwFe/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' /tmp/vQp5weZwFe/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' /tmp/vQp5weZwFe/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' /tmp/vQp5weZwFe/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' /tmp/vQp5weZwFe/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' /tmp/vQp5weZwFe/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' /tmp/vQp5weZwFe/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/query.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' /tmp/vQp5weZwFe/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/query.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' /tmp/vQp5weZwFe/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/query.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' /tmp/vQp5weZwFe/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/query.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' /tmp/vQp5weZwFe/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' /tmp/vQp5weZwFe/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/query.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' /tmp/vQp5weZwFe/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/query.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' /tmp/vQp5weZwFe/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/query.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' /tmp/vQp5weZwFe/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/query.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/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/vQp5weZwFe/view.vectors.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/view.vectors.vcf.gz | /build/reproducible-path/bcftools-1.11/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-1.11/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' /tmp/vQp5weZwFe/query.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/query.filter.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' /tmp/vQp5weZwFe/query.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/query.filter.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' /tmp/vQp5weZwFe/query.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/query.filter.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' /tmp/vQp5weZwFe/query.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/query.filter.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' /tmp/vQp5weZwFe/query.2.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/query.2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -i'IINT="."' -f'%POS %IINT\n' /tmp/vQp5weZwFe/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/missing.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -i'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -i'IINT!="."' -f'%POS %IINT\n' /tmp/vQp5weZwFe/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/missing.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -i'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -e'IINT!="."' -f'%POS %IINT\n' /tmp/vQp5weZwFe/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/missing.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -e'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -e'IINT="."' -f'%POS %IINT\n' /tmp/vQp5weZwFe/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/missing.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -e'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' /tmp/vQp5weZwFe/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/missing.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' /tmp/vQp5weZwFe/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/missing.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' /tmp/vQp5weZwFe/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/missing.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' /tmp/vQp5weZwFe/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/missing.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' /tmp/vQp5weZwFe/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/missing.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' /tmp/vQp5weZwFe/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/missing.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' /tmp/vQp5weZwFe/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/missing.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' /tmp/vQp5weZwFe/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/missing.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' /tmp/vQp5weZwFe/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/missing.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -i'FILTER="A"' -f'%POS %FILTER\n' /tmp/vQp5weZwFe/filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/filter.11.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -i'FILTER="A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -i'FILTER!="A"' -f'%POS %FILTER\n' /tmp/vQp5weZwFe/filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/filter.11.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -i'FILTER!="A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -i'FILTER~"A"' -f'%POS %FILTER\n' /tmp/vQp5weZwFe/filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/filter.11.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -i'FILTER~"A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n' /tmp/vQp5weZwFe/filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/filter.11.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'%LINE' /tmp/vQp5weZwFe/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/query.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%LINE' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' /tmp/vQp5weZwFe/query.filter-type.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/query.filter-type.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' /tmp/vQp5weZwFe/query.filter-type.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/query.filter-type.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' /tmp/vQp5weZwFe/query.filter-type.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/query.filter-type.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' /tmp/vQp5weZwFe/query.filter-type.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/query.filter-type.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\n' -i'INFO/TYPE="xxx"' /tmp/vQp5weZwFe/query.filter-type.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/query.filter-type.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\n' -i'INFO/TYPE="xxx"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/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/vQp5weZwFe/filter-missing-floats.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/filter-missing-floats.vcf.gz | /build/reproducible-path/bcftools-1.11/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-1.11/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/vQp5weZwFe/filter-missing-floats.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/filter-missing-floats.vcf.gz | /build/reproducible-path/bcftools-1.11/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-1.11/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' /tmp/vQp5weZwFe/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/missing.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' /tmp/vQp5weZwFe/query.filter.2.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/query.filter.2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' /tmp/vQp5weZwFe/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' /tmp/vQp5weZwFe/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' /tmp/vQp5weZwFe/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' /tmp/vQp5weZwFe/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' /tmp/vQp5weZwFe/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' /tmp/vQp5weZwFe/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' /tmp/vQp5weZwFe/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' /tmp/vQp5weZwFe/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' /tmp/vQp5weZwFe/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' /tmp/vQp5weZwFe/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' /tmp/vQp5weZwFe/filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/filter.5.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' /tmp/vQp5weZwFe/filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/filter.5.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' /tmp/vQp5weZwFe/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' /tmp/vQp5weZwFe/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' /tmp/vQp5weZwFe/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' /tmp/vQp5weZwFe/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' /tmp/vQp5weZwFe/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 & FMT/GQ=589' /tmp/vQp5weZwFe/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 & FMT/GQ=589' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' /tmp/vQp5weZwFe/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' /tmp/vQp5weZwFe/query.filter.3.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/query.filter.3.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"' /tmp/vQp5weZwFe/query.filter.3.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/query.filter.3.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' /tmp/vQp5weZwFe/query.filter.3.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/query.filter.3.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %AD\n]\n' -i'AD[:0]+AD[:1] > 12' /tmp/vQp5weZwFe/filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/filter.5.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %AD\n]\n' -i'AD[:0]+AD[:1] > 12' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' /tmp/vQp5weZwFe/query.filter.4.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/query.filter.4.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'%ID\n' -i 'ID=@/build/reproducible-path/bcftools-1.11/test/query.56.out' /tmp/vQp5weZwFe/view.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/view.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%ID\n' -i 'ID=@/build/reproducible-path/bcftools-1.11/test/query.56.out' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD)>0.01' /tmp/vQp5weZwFe/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/query.filter.5.vcf.gz | /build/reproducible-path/bcftools-1.11/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-1.11/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD[:0],FMT/AD[:1])>0.01' /tmp/vQp5weZwFe/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/query.filter.5.vcf.gz | /build/reproducible-path/bcftools-1.11/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-1.11/bcftools query -f'%POS\t%AD\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01' /tmp/vQp5weZwFe/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/query.filter.5.vcf.gz | /build/reproducible-path/bcftools-1.11/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-1.11/bcftools query -f'%CHROM %POS\n' -i'CHROM="4"' /tmp/vQp5weZwFe/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/query.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%CHROM %POS\n' -i'CHROM="4"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%TAG1\n' -i'(TAG1>=-129 && TAG1<=-120) || (TAG1>=-32769 && TAG1<=-32760)' /tmp/vQp5weZwFe/query.negative.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/query.negative.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%TAG1\n' -i'(TAG1>=-129 && TAG1<=-120) || (TAG1>=-32769 && TAG1<=-32760)' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%TAGV1\n' -i'(TAGV1>=-129 && TAGV1<=-120) || (TAGV1>=-32769 && TAGV1<=-32760)' /tmp/vQp5weZwFe/query.negative.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/query.negative.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%TAGV1\n' -i'(TAGV1>=-129 && TAGV1<=-120) || (TAGV1>=-32769 && TAGV1<=-32760)' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%TAG2\n' -i'(TAG2>=-129 && TAG2<=-120) || (TAG2>=-32769 && TAG2<=-32760)' /tmp/vQp5weZwFe/query.negative.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/query.negative.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%TAG2\n' -i'(TAG2>=-129 && TAG2<=-120) || (TAG2>=-32769 && TAG2<=-32760)' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%TAGV2\n' -i'(TAGV2>=-129 && TAGV2<=-120) || (TAGV2>=-32769 && TAGV2<=-32760)' /tmp/vQp5weZwFe/query.negative.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/query.negative.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%TAGV2\n' -i'(TAGV2>=-129 && TAGV2<=-120) || (TAGV2>=-32769 && TAGV2<=-32760)' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS\t%SAMPLE\t%GQ\n]' -i'N_PASS(GQ<20)==1' /tmp/vQp5weZwFe/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/query.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS\t%SAMPLE\t%GQ\n]' -i'N_PASS(GQ<20)==1' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'%CHROM\t%POS\t%INFO\t%FORMAT\n' -s D,C /tmp/vQp5weZwFe/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/query.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%CHROM\t%POS\t%INFO\t%FORMAT\n' -s D,C .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\n' -i'POS==16777217 || POS==33554432 || POS=118673904' /tmp/vQp5weZwFe/query.filter.6.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/query.filter.6.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\n' -i'POS==16777217 || POS==33554432 || POS=118673904' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(II)==6' /tmp/vQp5weZwFe/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(II)==6' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(FORMAT/FI)==7' /tmp/vQp5weZwFe/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(FORMAT/FI)==7' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(II)==2' /tmp/vQp5weZwFe/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(II)==2' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(FORMAT/FI)==1.75' /tmp/vQp5weZwFe/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(FORMAT/FI)==1.75' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(II)==2' /tmp/vQp5weZwFe/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(II)==2' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(FORMAT/FI)==1.75' /tmp/vQp5weZwFe/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(FORMAT/FI)==1.75' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(II)==2' /tmp/vQp5weZwFe/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(II)==2' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(FORMAT/FI)==1.5' /tmp/vQp5weZwFe/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(FORMAT/FI)==1.5' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'%ILEN==1' /tmp/vQp5weZwFe/query.filter.8.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/query.filter.8.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'%ILEN==1' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'ILEN==1' /tmp/vQp5weZwFe/query.filter.8.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/query.filter.8.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'ILEN==1' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] < FMT/AD[:1]' /tmp/vQp5weZwFe/query.filter.9.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/query.filter.9.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] < FMT/AD[:1]' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] > FMT/AD[:1]' /tmp/vQp5weZwFe/query.filter.9.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/query.filter.9.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] > FMT/AD[:1]' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS %NUM_TAG\n' -i'COUNT(INFO/NUM_TAG)=2' /tmp/vQp5weZwFe/query.filter.10.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/query.filter.10.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS %NUM_TAG\n' -i'COUNT(INFO/NUM_TAG)=2' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2' /tmp/vQp5weZwFe/query.filter.10.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/query.filter.10.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools query -f '%CHROM:%POS\t%N_PASS(GT="alt" & GQ>110)\t[\t%GT]\t[\t%GQ]\n' /tmp/vQp5weZwFe/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/query.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f '%CHROM:%POS\t%N_PASS(GT="alt" & GQ>110)\t[\t%GT]\t[\t%GQ]\n' .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.11/bcftools norm --no-version -cx -f /build/reproducible-path/bcftools-1.11/test/norm.fa /tmp/vQp5weZwFe/norm.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.11/bcftools norm -Ob -cx -f /build/reproducible-path/bcftools-1.11/test/norm.fa /tmp/vQp5weZwFe/norm.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.11/bcftools norm --no-version -m- /tmp/vQp5weZwFe/norm.split.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.11/bcftools norm -Ob -m- /tmp/vQp5weZwFe/norm.split.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.11/bcftools norm --no-version -m- /tmp/vQp5weZwFe/norm.split.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.11/bcftools norm -Ob -m- /tmp/vQp5weZwFe/norm.split.2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.11/bcftools norm --no-version -m- --force /tmp/vQp5weZwFe/norm.split.3.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.11/bcftools norm -Ob -m- --force /tmp/vQp5weZwFe/norm.split.3.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.11/bcftools norm --no-version -m- /tmp/vQp5weZwFe/norm.split.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.11/bcftools norm -Ob -m- /tmp/vQp5weZwFe/norm.split.4.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.11/bcftools norm --no-version -m- --keep-sum AD /tmp/vQp5weZwFe/norm.split.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.11/bcftools norm -Ob -m- --keep-sum AD /tmp/vQp5weZwFe/norm.split.4.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.11/bcftools norm --no-version -m- -f /build/reproducible-path/bcftools-1.11/test/norm.fa /tmp/vQp5weZwFe/norm.split.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.11/bcftools norm -Ob -m- -f /build/reproducible-path/bcftools-1.11/test/norm.fa /tmp/vQp5weZwFe/norm.split.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.11/bcftools norm --no-version -m+ /tmp/vQp5weZwFe/norm.merge.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.11/bcftools norm -Ob -m+ /tmp/vQp5weZwFe/norm.merge.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.11/bcftools norm --no-version -m+ /tmp/vQp5weZwFe/norm.merge.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.11/bcftools norm -Ob -m+ /tmp/vQp5weZwFe/norm.merge.2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.11/bcftools norm --no-version -m+ /tmp/vQp5weZwFe/norm.merge.3.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.11/bcftools norm -Ob -m+ /tmp/vQp5weZwFe/norm.merge.3.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.11/bcftools norm --no-version -m+ -s /tmp/vQp5weZwFe/norm.merge.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.11/bcftools norm -Ob -m+ -s /tmp/vQp5weZwFe/norm.merge.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.11/bcftools norm --no-version -Nc s -f /build/reproducible-path/bcftools-1.11/test/norm.fa /tmp/vQp5weZwFe/norm.setref.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.11/bcftools norm -Ob -Nc s -f /build/reproducible-path/bcftools-1.11/test/norm.fa /tmp/vQp5weZwFe/norm.setref.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.11/bcftools norm --no-version -f /build/reproducible-path/bcftools-1.11/test/norm.fa /tmp/vQp5weZwFe/norm.telomere.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.11/bcftools norm -Ob -f /build/reproducible-path/bcftools-1.11/test/norm.fa /tmp/vQp5weZwFe/norm.telomere.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.11/bcftools norm --no-version -d snps /tmp/vQp5weZwFe/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.11/bcftools norm -Ob -d snps /tmp/vQp5weZwFe/norm.rmdup.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.11/bcftools norm --no-version -d indels /tmp/vQp5weZwFe/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.11/bcftools norm -Ob -d indels /tmp/vQp5weZwFe/norm.rmdup.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.11/bcftools norm --no-version -d both /tmp/vQp5weZwFe/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.11/bcftools norm -Ob -d both /tmp/vQp5weZwFe/norm.rmdup.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.11/bcftools norm --no-version -d all /tmp/vQp5weZwFe/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.11/bcftools norm -Ob -d all /tmp/vQp5weZwFe/norm.rmdup.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.11/bcftools norm --no-version -d none /tmp/vQp5weZwFe/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.11/bcftools norm -Ob -d none /tmp/vQp5weZwFe/norm.rmdup.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.11/bcftools norm --no-version -d exact /tmp/vQp5weZwFe/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.11/bcftools norm -Ob -d exact /tmp/vQp5weZwFe/norm.rmdup.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.11/bcftools norm --no-version -d none /tmp/vQp5weZwFe/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.11/bcftools norm -Ob -d none /tmp/vQp5weZwFe/norm.rmdup.2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.11/bcftools norm --no-version -d exact /tmp/vQp5weZwFe/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.11/bcftools norm -Ob -d exact /tmp/vQp5weZwFe/norm.rmdup.2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.11/bcftools norm --no-version -d indels /tmp/vQp5weZwFe/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.11/bcftools norm -Ob -d indels /tmp/vQp5weZwFe/norm.rmdup.2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.11/bcftools norm --no-version -d any /tmp/vQp5weZwFe/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.11/bcftools norm -Ob -d any /tmp/vQp5weZwFe/norm.rmdup.2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.11/bcftools norm --no-version -d both /tmp/vQp5weZwFe/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.11/bcftools norm -Ob -d both /tmp/vQp5weZwFe/norm.rmdup.2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.11/bcftools norm --no-version -d snps /tmp/vQp5weZwFe/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.11/bcftools norm -Ob -d snps /tmp/vQp5weZwFe/norm.rmdup.2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.11/bcftools norm --no-version -f /build/reproducible-path/bcftools-1.11/test/norm.2.fa /tmp/vQp5weZwFe/norm.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.11/bcftools norm -Ob -f /build/reproducible-path/bcftools-1.11/test/norm.2.fa /tmp/vQp5weZwFe/norm.2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.11/bcftools norm --no-version -c s -f /build/reproducible-path/bcftools-1.11/test/norm.iupac.fa /tmp/vQp5weZwFe/norm.iupac.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.11/bcftools norm -Ob -c s -f /build/reproducible-path/bcftools-1.11/test/norm.iupac.fa /tmp/vQp5weZwFe/norm.iupac.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.11/bcftools norm --no-version -c s -f /build/reproducible-path/bcftools-1.11/test/norm.3.fa /tmp/vQp5weZwFe/norm.3.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.11/bcftools norm -Ob -c s -f /build/reproducible-path/bcftools-1.11/test/norm.3.fa /tmp/vQp5weZwFe/norm.3.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.11/bcftools view --no-version -aUc1 -C1 -s NA00002 -v snps /tmp/vQp5weZwFe/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.11/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/vQp5weZwFe/view.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.11/bcftools view --no-version -f PASS -Xks NA00003 /tmp/vQp5weZwFe/view.vcf.gz -r20,Y .. ok test_vcf_view: /build/reproducible-path/bcftools-1.11/bcftools view -Ob -f PASS -Xks NA00003 /tmp/vQp5weZwFe/view.vcf.gz -r20,Y | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.11/bcftools view --no-version -xs NA00003 /tmp/vQp5weZwFe/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.11/bcftools view -Ob -xs NA00003 /tmp/vQp5weZwFe/view.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.11/bcftools view --no-version -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/vQp5weZwFe/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.11/bcftools view -Ob -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/vQp5weZwFe/view.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.11/bcftools view --no-version -p /tmp/vQp5weZwFe/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.11/bcftools view -Ob -p /tmp/vQp5weZwFe/view.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.11/bcftools view --no-version -P /tmp/vQp5weZwFe/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.11/bcftools view -Ob -P /tmp/vQp5weZwFe/view.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.11/bcftools view --no-version -hm2 -M2 -q0.3 -Q0.7 /tmp/vQp5weZwFe/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.11/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/vQp5weZwFe/view.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.11/bcftools view --no-version -Hu /tmp/vQp5weZwFe/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.11/bcftools view --no-version -GVsnps /tmp/vQp5weZwFe/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.11/bcftools view -Ob -GVsnps /tmp/vQp5weZwFe/view.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.11/bcftools view --no-version -ne 'INDEL=1 || PV4[0]<0.006' /tmp/vQp5weZwFe/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.11/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/vQp5weZwFe/view.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.11/bcftools view --no-version -s ^NA00003 /tmp/vQp5weZwFe/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.11/bcftools view -Ob -s ^NA00003 /tmp/vQp5weZwFe/view.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.11/bcftools view --no-version /tmp/vQp5weZwFe/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/view.omitgenotypes.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.11/bcftools view --no-version -G /tmp/vQp5weZwFe/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.11/bcftools view -Ob -G /tmp/vQp5weZwFe/view.omitgenotypes.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.11/bcftools view --no-version -HG /tmp/vQp5weZwFe/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.11/bcftools view --no-version -a /tmp/vQp5weZwFe/many.alleles.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.11/bcftools view -Ob -a /tmp/vQp5weZwFe/many.alleles.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.11/bcftools view --no-version -asA /tmp/vQp5weZwFe/view.vectors.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.11/bcftools view -Ob -asA /tmp/vQp5weZwFe/view.vectors.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.11/bcftools view --no-version -asB /tmp/vQp5weZwFe/view.vectors.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.11/bcftools view -Ob -asB /tmp/vQp5weZwFe/view.vectors.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.11/bcftools view --no-version -asA /tmp/vQp5weZwFe/view.vectors.2.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.11/bcftools view -Ob -asA /tmp/vQp5weZwFe/view.vectors.2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.11/bcftools view --no-version -H -i'FMT/FGS[*:0]="AAAAAA"' /tmp/vQp5weZwFe/view.filter.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.11/bcftools view --no-version -H -i'FMT/FGS[*:2]="C"' /tmp/vQp5weZwFe/view.filter.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.11/bcftools view --no-version -H -i'FMT/FGS[*:4]="EE"' /tmp/vQp5weZwFe/view.filter.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.11/bcftools view --no-version -H -i'FMT/FRS[*:1]="BB"' /tmp/vQp5weZwFe/view.filter.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.11/bcftools view --no-version -H -i'TXT0="text"' /tmp/vQp5weZwFe/view.filter.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.11/bcftools view --no-version -T /build/reproducible-path/bcftools-1.11/test/view.chrs.tab /tmp/vQp5weZwFe/view.chrs.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.11/bcftools view -Ob -T /build/reproducible-path/bcftools-1.11/test/view.chrs.tab /tmp/vQp5weZwFe/view.chrs.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.11/bcftools view --no-version -i 'POS>=3062917' /tmp/vQp5weZwFe/filter.2.vcf.gz 1:3062917-3157410 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.11/bcftools view -Ob -i 'POS>=3062917' /tmp/vQp5weZwFe/filter.2.vcf.gz 1:3062917-3157410 | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.11/bcftools view --no-version -H -r 1:10,1:12,1:10 /tmp/vQp5weZwFe/idx.1.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.11/bcftools view --no-version -H -r 1:1172777-1172804,1:1172806-1172808 /tmp/vQp5weZwFe/idx.2.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.11/bcftools view --no-version -H -R /build/reproducible-path/bcftools-1.11/test/idx.2.bed /tmp/vQp5weZwFe/idx.2.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.11/bcftools view --no-version -H -R /build/reproducible-path/bcftools-1.11/test/idx.3.bed /tmp/vQp5weZwFe/idx.3.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.11/bcftools view --no-version -H -R /build/reproducible-path/bcftools-1.11/test/idx.4.bed /tmp/vQp5weZwFe/idx.4.vcf.gz .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.11/bcftools view /build/reproducible-path/bcftools-1.11/test/view64bit.1.vcf -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.11/bcftools view /build/reproducible-path/bcftools-1.11/test/view64bit.1.vcf | /build/reproducible-path/bcftools-1.11/bcftools view -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.11/bcftools view /build/reproducible-path/bcftools-1.11/test/view64bit.1.vcf -Ou | /build/reproducible-path/bcftools-1.11/bcftools view -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.11/bcftools view /build/reproducible-path/bcftools-1.11/test/view64bit.2.vcf -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.11/bcftools view /build/reproducible-path/bcftools-1.11/test/view64bit.2.vcf | /build/reproducible-path/bcftools-1.11/bcftools view -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.11/bcftools view /build/reproducible-path/bcftools-1.11/test/view64bit.2.vcf -Ou | /build/reproducible-path/bcftools-1.11/bcftools view -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.11/bcftools view /build/reproducible-path/bcftools-1.11/test/view64bit.3.vcf -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.11/bcftools view /build/reproducible-path/bcftools-1.11/test/view64bit.3.vcf | /build/reproducible-path/bcftools-1.11/bcftools view -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.11/bcftools view /build/reproducible-path/bcftools-1.11/test/view64bit.4.vcf -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.11/bcftools view /build/reproducible-path/bcftools-1.11/test/view64bit.4.vcf | /build/reproducible-path/bcftools-1.11/bcftools view -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.11/bcftools view /build/reproducible-path/bcftools-1.11/test/view64bit.4.vcf -Ou | /build/reproducible-path/bcftools-1.11/bcftools view -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.11/bcftools view /build/reproducible-path/bcftools-1.11/test/view64bit.5.vcf -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.11/bcftools view /build/reproducible-path/bcftools-1.11/test/view64bit.5.vcf | /build/reproducible-path/bcftools-1.11/bcftools view -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.11/bcftools view /build/reproducible-path/bcftools-1.11/test/view64bit.5.vcf -Ou | /build/reproducible-path/bcftools-1.11/bcftools view -H .. ok test_vcf_view: /build/reproducible-path/bcftools-1.11/bcftools view --no-version -H -C5:nonmajor /tmp/vQp5weZwFe/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.11/bcftools view --no-version -H -c6:nonmajor /tmp/vQp5weZwFe/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.11/bcftools view --no-version -H -q0.3:major /tmp/vQp5weZwFe/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.11/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/vQp5weZwFe/view.filter.annovar.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.11/bcftools view --no-version -H -i 'Gene.refGene~"NOD"' /tmp/vQp5weZwFe/view.filter.annovar.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.11/bcftools view --no-version -H -i 'LJB2_MutationTaster=="0.291000"' /tmp/vQp5weZwFe/view.filter.annovar.vcf.gz .. ok test_vcf_call: /build/reproducible-path/bcftools-1.11/bcftools call --no-version -mv /build/reproducible-path/bcftools-1.11/test/mpileup.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.11/bcftools call -Ob -mv /build/reproducible-path/bcftools-1.11/test/mpileup.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.11/bcftools call --no-version -mg0 /build/reproducible-path/bcftools-1.11/test/mpileup.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.11/bcftools call -Ob -mg0 /build/reproducible-path/bcftools-1.11/test/mpileup.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.11/bcftools call --no-version -mv -S /build/reproducible-path/bcftools-1.11/test/mpileup.3.samples /build/reproducible-path/bcftools-1.11/test/mpileup.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.11/bcftools call -Ob -mv -S /build/reproducible-path/bcftools-1.11/test/mpileup.3.samples /build/reproducible-path/bcftools-1.11/test/mpileup.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.11/bcftools call --no-version -mv -S /build/reproducible-path/bcftools-1.11/test/mpileup.4.samples /build/reproducible-path/bcftools-1.11/test/mpileup.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.11/bcftools call -Ob -mv -S /build/reproducible-path/bcftools-1.11/test/mpileup.4.samples /build/reproducible-path/bcftools-1.11/test/mpileup.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.11/bcftools call --no-version -mv -S /build/reproducible-path/bcftools-1.11/test/mpileup.5.samples /build/reproducible-path/bcftools-1.11/test/mpileup.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.11/bcftools call -Ob -mv -S /build/reproducible-path/bcftools-1.11/test/mpileup.5.samples /build/reproducible-path/bcftools-1.11/test/mpileup.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.11/bcftools call --no-version -mv --ploidy-file /build/reproducible-path/bcftools-1.11/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.11/test/mpileup.samples /build/reproducible-path/bcftools-1.11/test/mpileup.X.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.11/bcftools call -Ob -mv --ploidy-file /build/reproducible-path/bcftools-1.11/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.11/test/mpileup.samples /build/reproducible-path/bcftools-1.11/test/mpileup.X.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.11/bcftools call --no-version -mv --ploidy-file /build/reproducible-path/bcftools-1.11/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.11/test/mpileup.ped /build/reproducible-path/bcftools-1.11/test/mpileup.X.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.11/bcftools call -Ob -mv --ploidy-file /build/reproducible-path/bcftools-1.11/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.11/test/mpileup.ped /build/reproducible-path/bcftools-1.11/test/mpileup.X.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.11/bcftools call --no-version -mv --ploidy-file /build/reproducible-path/bcftools-1.11/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.11/test/mpileup.2.samples /build/reproducible-path/bcftools-1.11/test/mpileup.X.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.11/bcftools call -Ob -mv --ploidy-file /build/reproducible-path/bcftools-1.11/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.11/test/mpileup.2.samples /build/reproducible-path/bcftools-1.11/test/mpileup.X.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.11/bcftools call --no-version -mv /build/reproducible-path/bcftools-1.11/test/mpileup.NA19213.NA19129.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.11/bcftools call -Ob -mv /build/reproducible-path/bcftools-1.11/test/mpileup.NA19213.NA19129.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.11/bcftools call --no-version -mv -G - /build/reproducible-path/bcftools-1.11/test/mpileup.NA19213.NA19129.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.11/bcftools call -Ob -mv -G - /build/reproducible-path/bcftools-1.11/test/mpileup.NA19213.NA19129.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.11/bcftools call --no-version -mv /build/reproducible-path/bcftools-1.11/test/mpileup.hwe.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.11/bcftools call -Ob -mv /build/reproducible-path/bcftools-1.11/test/mpileup.hwe.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.11/bcftools call --no-version -mv -G - /build/reproducible-path/bcftools-1.11/test/mpileup.hwe.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.11/bcftools call -Ob -mv -G - /build/reproducible-path/bcftools-1.11/test/mpileup.hwe.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.11/bcftools call --no-version -mv -G /build/reproducible-path/bcftools-1.11/test/mpileup.hwe.samples /build/reproducible-path/bcftools-1.11/test/mpileup.hwe.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.11/bcftools call -Ob -mv -G /build/reproducible-path/bcftools-1.11/test/mpileup.hwe.samples /build/reproducible-path/bcftools-1.11/test/mpileup.hwe.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.11/bcftools call --no-version -mA -C alleles -T /tmp/vQp5weZwFe/mpileup.tab.gz /build/reproducible-path/bcftools-1.11/test/mpileup.vcf .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.11/bcftools call -Ob -mA -C alleles -T /tmp/vQp5weZwFe/mpileup.tab.gz /build/reproducible-path/bcftools-1.11/test/mpileup.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.11/bcftools call --no-version -mA -C alleles -T /tmp/vQp5weZwFe/mpileup.2.tab.gz /build/reproducible-path/bcftools-1.11/test/mpileup.2.vcf .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.11/bcftools call -Ob -mA -C alleles -T /tmp/vQp5weZwFe/mpileup.2.tab.gz /build/reproducible-path/bcftools-1.11/test/mpileup.2.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.11/bcftools call --no-version -mA -C alleles -T /tmp/vQp5weZwFe/mpileup.3.tab.gz -i /build/reproducible-path/bcftools-1.11/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.11/bcftools call -Ob -mA -C alleles -T /tmp/vQp5weZwFe/mpileup.3.tab.gz -i /build/reproducible-path/bcftools-1.11/test/mpileup.3.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.11/bcftools call --no-version -mA -C alleles -T /tmp/vQp5weZwFe/mpileup.4.tab.gz -i /build/reproducible-path/bcftools-1.11/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.11/bcftools call -Ob -mA -C alleles -T /tmp/vQp5weZwFe/mpileup.4.tab.gz -i /build/reproducible-path/bcftools-1.11/test/mpileup.3.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.11/bcftools call --no-version -mA -C alleles -T /tmp/vQp5weZwFe/mpileup.5.tab.gz -i /build/reproducible-path/bcftools-1.11/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.11/bcftools call -Ob -mA -C alleles -T /tmp/vQp5weZwFe/mpileup.5.tab.gz -i /build/reproducible-path/bcftools-1.11/test/mpileup.3.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.11/bcftools call --no-version -mA -C alleles -T /tmp/vQp5weZwFe/mpileup.6.tab.gz -i /build/reproducible-path/bcftools-1.11/test/mpileup.4.vcf .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.11/bcftools call -Ob -mA -C alleles -T /tmp/vQp5weZwFe/mpileup.6.tab.gz -i /build/reproducible-path/bcftools-1.11/test/mpileup.4.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.11/bcftools call --no-version -mA -C alleles -T /tmp/vQp5weZwFe/mpileup.7.tab.gz -i /build/reproducible-path/bcftools-1.11/test/mpileup.5.vcf .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.11/bcftools call -Ob -mA -C alleles -T /tmp/vQp5weZwFe/mpileup.7.tab.gz -i /build/reproducible-path/bcftools-1.11/test/mpileup.5.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.11/bcftools call --no-version -mA -C alleles -T /tmp/vQp5weZwFe/mpileup.cals.1.tab.gz /build/reproducible-path/bcftools-1.11/test/mpileup.cals.1.vcf .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.11/bcftools call -Ob -mA -C alleles -T /tmp/vQp5weZwFe/mpileup.cals.1.tab.gz /build/reproducible-path/bcftools-1.11/test/mpileup.cals.1.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.11/bcftools call --no-version -mA -C alleles -T /tmp/vQp5weZwFe/mpileup.cals.2.tab.gz /build/reproducible-path/bcftools-1.11/test/mpileup.cals.2.vcf .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.11/bcftools call -Ob -mA -C alleles -T /tmp/vQp5weZwFe/mpileup.cals.2.tab.gz /build/reproducible-path/bcftools-1.11/test/mpileup.cals.2.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.11/bcftools call --no-version -cv /build/reproducible-path/bcftools-1.11/test/mpileup.c.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.11/bcftools call -Ob -cv /build/reproducible-path/bcftools-1.11/test/mpileup.c.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.11/bcftools call --no-version -cv --ploidy-file /build/reproducible-path/bcftools-1.11/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.11/test/mpileup.samples /build/reproducible-path/bcftools-1.11/test/mpileup.c.X.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.11/bcftools call -Ob -cv --ploidy-file /build/reproducible-path/bcftools-1.11/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.11/test/mpileup.samples /build/reproducible-path/bcftools-1.11/test/mpileup.c.X.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.11/bcftools call --no-version -cv --ploidy-file /build/reproducible-path/bcftools-1.11/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.11/test/mpileup.ped /build/reproducible-path/bcftools-1.11/test/mpileup.c.X.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.11/bcftools call -Ob -cv --ploidy-file /build/reproducible-path/bcftools-1.11/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.11/test/mpileup.ped /build/reproducible-path/bcftools-1.11/test/mpileup.c.X.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.11/bcftools call --no-version -cv --ploidy-file /build/reproducible-path/bcftools-1.11/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.11/test/mpileup.2.samples /build/reproducible-path/bcftools-1.11/test/mpileup.c.X.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.11/bcftools call -Ob -cv --ploidy-file /build/reproducible-path/bcftools-1.11/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.11/test/mpileup.2.samples /build/reproducible-path/bcftools-1.11/test/mpileup.c.X.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -S. -e'TXT0="text"' /build/reproducible-path/bcftools-1.11/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -S. -e'TXT0="text"' /build/reproducible-path/bcftools-1.11/test/view.filter.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -S. -e'FMT/FRS[*:1]="BB"' /build/reproducible-path/bcftools-1.11/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -S. -e'FMT/FRS[*:1]="BB"' /build/reproducible-path/bcftools-1.11/test/view.filter.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -S. -e'FMT/FGS[*:0]="AAAAAA"' /build/reproducible-path/bcftools-1.11/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -S. -e'FMT/FGS[*:0]="AAAAAA"' /build/reproducible-path/bcftools-1.11/test/view.filter.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -S. -e'FMT/FGS[*:1]="BBB"' /build/reproducible-path/bcftools-1.11/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -S. -e'FMT/FGS[*:1]="BBB"' /build/reproducible-path/bcftools-1.11/test/view.filter.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -S. -e'FMT/FGS[*:4]="EE"' /build/reproducible-path/bcftools-1.11/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -S. -e'FMT/FGS[*:4]="EE"' /build/reproducible-path/bcftools-1.11/test/view.filter.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -S. -e'FMT/STR="XX"' /build/reproducible-path/bcftools-1.11/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -S. -e'FMT/STR="XX"' /build/reproducible-path/bcftools-1.11/test/view.filter.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -S. -e'FMT/FILTER="aaa"' /build/reproducible-path/bcftools-1.11/test/view.filter.2.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -S. -e'FMT/FILTER="aaa"' /build/reproducible-path/bcftools-1.11/test/view.filter.2.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -mx -g2 -G2 /build/reproducible-path/bcftools-1.11/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -mx -g2 -G2 /build/reproducible-path/bcftools-1.11/test/filter.1.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /build/reproducible-path/bcftools-1.11/test/filter.2.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /build/reproducible-path/bcftools-1.11/test/filter.2.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -e'INFO/DP=19' /build/reproducible-path/bcftools-1.11/test/filter.3.vcf | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -e'INFO/DP=19' /build/reproducible-path/bcftools-1.11/test/filter.3.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -e'INFO/DP=19' -s XX /build/reproducible-path/bcftools-1.11/test/filter.3.vcf | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -e'INFO/DP=19' -s XX /build/reproducible-path/bcftools-1.11/test/filter.3.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -e'INFO/DP=19' -s XX -m+ /build/reproducible-path/bcftools-1.11/test/filter.3.vcf | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+ /build/reproducible-path/bcftools-1.11/test/filter.3.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -e'INFO/DP=19' -s XX -mx /build/reproducible-path/bcftools-1.11/test/filter.3.vcf | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -e'INFO/DP=19' -s XX -mx /build/reproducible-path/bcftools-1.11/test/filter.3.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -e'INFO/DP=19' -s XX -m+x /build/reproducible-path/bcftools-1.11/test/filter.3.vcf | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+x /build/reproducible-path/bcftools-1.11/test/filter.3.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -e'FMT/GT="0/2"' /build/reproducible-path/bcftools-1.11/test/filter.3.vcf | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -e'FMT/GT="0/2"' /build/reproducible-path/bcftools-1.11/test/filter.3.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -e'FMT/GT="0/2"' -s XX /build/reproducible-path/bcftools-1.11/test/filter.3.vcf | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX /build/reproducible-path/bcftools-1.11/test/filter.3.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -e'FMT/GT="0/2"' -s XX -m+ /build/reproducible-path/bcftools-1.11/test/filter.3.vcf | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+ /build/reproducible-path/bcftools-1.11/test/filter.3.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -e'FMT/GT="0/2"' -s XX -mx /build/reproducible-path/bcftools-1.11/test/filter.3.vcf | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -mx /build/reproducible-path/bcftools-1.11/test/filter.3.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -e'FMT/GT="0/2"' -s XX -m+x /build/reproducible-path/bcftools-1.11/test/filter.3.vcf | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+x /build/reproducible-path/bcftools-1.11/test/filter.3.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -i'FMT/GT="0/0" && AC[*]=2' /build/reproducible-path/bcftools-1.11/test/filter.2.vcf | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -i'FMT/GT="0/0" && AC[*]=2' /build/reproducible-path/bcftools-1.11/test/filter.2.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -i'AC[*]=2 && FMT/GT="0/0"' /build/reproducible-path/bcftools-1.11/test/filter.2.vcf | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -i'AC[*]=2 && FMT/GT="0/0"' /build/reproducible-path/bcftools-1.11/test/filter.2.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -i'ALT="."' /build/reproducible-path/bcftools-1.11/test/filter.2.vcf | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -i'ALT="."' /build/reproducible-path/bcftools-1.11/test/filter.2.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -S . -i 'FORMAT/TEST3<25' /build/reproducible-path/bcftools-1.11/test/filter.4.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -S . -i 'FORMAT/TEST3<25' /build/reproducible-path/bcftools-1.11/test/filter.4.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -S . -i 'FORMAT/TEST4<25' /build/reproducible-path/bcftools-1.11/test/filter.4.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -S . -i 'FORMAT/TEST4<25' /build/reproducible-path/bcftools-1.11/test/filter.4.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -i'GT="A"' /build/reproducible-path/bcftools-1.11/test/filter.2.vcf | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -i'GT="A"' /build/reproducible-path/bcftools-1.11/test/filter.2.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -i'GT="RR"' /build/reproducible-path/bcftools-1.11/test/filter.2.vcf | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -i'GT="RR"' /build/reproducible-path/bcftools-1.11/test/filter.2.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -i'GT="RA"' /build/reproducible-path/bcftools-1.11/test/filter.2.vcf | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -i'GT="RA"' /build/reproducible-path/bcftools-1.11/test/filter.2.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -i'GT="AR"' /build/reproducible-path/bcftools-1.11/test/filter.2.vcf | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -i'GT="AR"' /build/reproducible-path/bcftools-1.11/test/filter.2.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -i'GT="AA"' /build/reproducible-path/bcftools-1.11/test/filter.2.vcf | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -i'GT="AA"' /build/reproducible-path/bcftools-1.11/test/filter.2.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -i'GT="aA"' /build/reproducible-path/bcftools-1.11/test/filter.2.vcf | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -i'GT="aA"' /build/reproducible-path/bcftools-1.11/test/filter.2.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -i'GT="Aa"' /build/reproducible-path/bcftools-1.11/test/filter.2.vcf | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -i'GT="Aa"' /build/reproducible-path/bcftools-1.11/test/filter.2.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -i'GT="HOM"' /build/reproducible-path/bcftools-1.11/test/filter.2.vcf | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -i'GT="HOM"' /build/reproducible-path/bcftools-1.11/test/filter.2.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -i'GT="HET"' /build/reproducible-path/bcftools-1.11/test/filter.2.vcf | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -i'GT="HET"' /build/reproducible-path/bcftools-1.11/test/filter.2.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -i'GT="HAP"' /build/reproducible-path/bcftools-1.11/test/filter.2.vcf | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -i'GT="HAP"' /build/reproducible-path/bcftools-1.11/test/filter.2.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -i'AD[:1]=11' /build/reproducible-path/bcftools-1.11/test/filter.5.vcf | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -i'AD[:1]=11' /build/reproducible-path/bcftools-1.11/test/filter.5.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -i'AD[1:]=11' /build/reproducible-path/bcftools-1.11/test/filter.5.vcf | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -i'AD[1:]=11' /build/reproducible-path/bcftools-1.11/test/filter.5.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -i'FR[0:1]=11' /build/reproducible-path/bcftools-1.11/test/filter.5.vcf | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS[\t%FR]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -i'FR[0:1]=11' /build/reproducible-path/bcftools-1.11/test/filter.5.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS[\t%FR]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -i'AD[*]="."' /build/reproducible-path/bcftools-1.11/test/filter.5.vcf | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -i'AD[*]="."' /build/reproducible-path/bcftools-1.11/test/filter.5.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -i'AD[0:0]=="."' /build/reproducible-path/bcftools-1.11/test/filter.5.vcf | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -i'AD[0:0]=="."' /build/reproducible-path/bcftools-1.11/test/filter.5.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -i'AD[0:0]!="."' /build/reproducible-path/bcftools-1.11/test/filter.5.vcf | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -i'AD[0:0]!="."' /build/reproducible-path/bcftools-1.11/test/filter.5.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -i'QUAL=="."' /build/reproducible-path/bcftools-1.11/test/filter.5.vcf | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS\t%QUAL\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -i'QUAL=="."' /build/reproducible-path/bcftools-1.11/test/filter.5.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS\t%QUAL\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -i'N_PASS(DP>32)=1' /build/reproducible-path/bcftools-1.11/test/filter.2.vcf | /build/reproducible-path/bcftools-1.11/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -i'N_PASS(DP>32)=1' /build/reproducible-path/bcftools-1.11/test/filter.2.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | /build/reproducible-path/bcftools-1.11/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -i'F_PASS(DP>32)=0.5' /build/reproducible-path/bcftools-1.11/test/filter.2.vcf | /build/reproducible-path/bcftools-1.11/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -i'F_PASS(DP>32)=0.5' /build/reproducible-path/bcftools-1.11/test/filter.2.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | /build/reproducible-path/bcftools-1.11/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -i'F_MISSING>=1/5' /build/reproducible-path/bcftools-1.11/test/filter.6.vcf | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -i'F_MISSING>=1/5' /build/reproducible-path/bcftools-1.11/test/filter.6.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -i'F_MISSING>=0.2' /build/reproducible-path/bcftools-1.11/test/filter.6.vcf | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -i'F_MISSING>=0.2' /build/reproducible-path/bcftools-1.11/test/filter.6.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -i'F_PASS(GT=="mis")>=1/5' /build/reproducible-path/bcftools-1.11/test/filter.6.vcf | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -i'F_PASS(GT=="mis")>=1/5' /build/reproducible-path/bcftools-1.11/test/filter.6.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -i'F_PASS(GT=="mis")>=0.2' /build/reproducible-path/bcftools-1.11/test/filter.6.vcf | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -i'F_PASS(GT=="mis")>=0.2' /build/reproducible-path/bcftools-1.11/test/filter.6.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | /build/reproducible-path/bcftools-1.11/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -mx -s + -g2:mnp,indel,other /build/reproducible-path/bcftools-1.11/test/filter.7.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -mx -s + -g2:mnp,indel,other /build/reproducible-path/bcftools-1.11/test/filter.7.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -S . -e 'FORMAT/AO==4' /build/reproducible-path/bcftools-1.11/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -S . -e 'FORMAT/AO==4' /build/reproducible-path/bcftools-1.11/test/filter.8.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -S . -e 'MAX(FORMAT/AO[0:])==4' /build/reproducible-path/bcftools-1.11/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -S . -e 'MAX(FORMAT/AO[0:])==4' /build/reproducible-path/bcftools-1.11/test/filter.8.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -S . -e 'MAX(FORMAT/AO)==4' /build/reproducible-path/bcftools-1.11/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -S . -e 'MAX(FORMAT/AO)==4' /build/reproducible-path/bcftools-1.11/test/filter.8.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -S . -e 'MIN(FORMAT/AO[0:])==3' /build/reproducible-path/bcftools-1.11/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO[0:])==3' /build/reproducible-path/bcftools-1.11/test/filter.8.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -S . -e 'MIN(FORMAT/AO)==2' /build/reproducible-path/bcftools-1.11/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO)==2' /build/reproducible-path/bcftools-1.11/test/filter.8.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -S . -e 'MIN(FORMAT/AO[0:])==3' /build/reproducible-path/bcftools-1.11/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO[0:])==3' /build/reproducible-path/bcftools-1.11/test/filter.8.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -S . -e 'AVG(FORMAT/AO[2:])==4' /build/reproducible-path/bcftools-1.11/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -S . -e 'AVG(FORMAT/AO[2:])==4' /build/reproducible-path/bcftools-1.11/test/filter.8.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -S . -e 'MEDIAN(FORMAT/AO[2:])==4' /build/reproducible-path/bcftools-1.11/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -S . -e 'MEDIAN(FORMAT/AO[2:])==4' /build/reproducible-path/bcftools-1.11/test/filter.8.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -S . -e 'STDEV(FORMAT/AO[0:])=0.5' /build/reproducible-path/bcftools-1.11/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -S . -e 'STDEV(FORMAT/AO[0:])=0.5' /build/reproducible-path/bcftools-1.11/test/filter.8.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -S . -e 'SUM(FORMAT/AO[0:])=7' /build/reproducible-path/bcftools-1.11/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -S . -e 'SUM(FORMAT/AO[0:])=7' /build/reproducible-path/bcftools-1.11/test/filter.8.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -S . -e 'SMPL_MAX(FORMAT/AO)==4' /build/reproducible-path/bcftools-1.11/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -S . -e 'SMPL_MAX(FORMAT/AO)==4' /build/reproducible-path/bcftools-1.11/test/filter.8.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -S . -e 'sMIN(FORMAT/AO)==2' /build/reproducible-path/bcftools-1.11/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -S . -e 'sMIN(FORMAT/AO)==2' /build/reproducible-path/bcftools-1.11/test/filter.8.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -S . -e 'ABS(sAVG(FORMAT/AO)-3.66666)<1e-5' /build/reproducible-path/bcftools-1.11/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -S . -e 'ABS(sAVG(FORMAT/AO)-3.66666)<1e-5' /build/reproducible-path/bcftools-1.11/test/filter.8.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -S . -e 'sMEDIAN(FORMAT/AO)==4' /build/reproducible-path/bcftools-1.11/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -S . -e 'sMEDIAN(FORMAT/AO)==4' /build/reproducible-path/bcftools-1.11/test/filter.8.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -S . -e 'ABS(sSTDEV(FORMAT/AO)-1.2472191)<1e-5' /build/reproducible-path/bcftools-1.11/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -S . -e 'ABS(sSTDEV(FORMAT/AO)-1.2472191)<1e-5' /build/reproducible-path/bcftools-1.11/test/filter.8.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -S . -e 'sSUM(FORMAT/AO)==11' /build/reproducible-path/bcftools-1.11/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -S . -e 'sSUM(FORMAT/AO)==11' /build/reproducible-path/bcftools-1.11/test/filter.8.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -i 'QUAL/FMT/AD==55' /build/reproducible-path/bcftools-1.11/test/filter.9.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -i 'QUAL/FMT/AD==55' /build/reproducible-path/bcftools-1.11/test/filter.9.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -i 'QUAL/INFO/AD==10' /build/reproducible-path/bcftools-1.11/test/filter.9.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -i 'QUAL/INFO/AD==10' /build/reproducible-path/bcftools-1.11/test/filter.9.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -S . -e 'ABS(SMPL_MAX(FORMAT/AO))=5' /build/reproducible-path/bcftools-1.11/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -S . -e 'ABS(SMPL_MAX(FORMAT/AO))=5' /build/reproducible-path/bcftools-1.11/test/filter.8.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -S . -e 'PHRED(AO[1:])>-4' /build/reproducible-path/bcftools-1.11/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -S . -e 'PHRED(AO[1:])>-4' /build/reproducible-path/bcftools-1.11/test/filter.8.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -S . -e 'ABS(AO[1:])==2' /build/reproducible-path/bcftools-1.11/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -S . -e 'ABS(AO[1:])==2' /build/reproducible-path/bcftools-1.11/test/filter.8.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -i 'sum(AD[*]) > FORMAT/DP' /build/reproducible-path/bcftools-1.11/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -i 'sum(AD[*]) > FORMAT/DP' /build/reproducible-path/bcftools-1.11/test/filter.10.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -i 'FORMAT/DP < sum(AD[*])' /build/reproducible-path/bcftools-1.11/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -i 'FORMAT/DP < sum(AD[*])' /build/reproducible-path/bcftools-1.11/test/filter.10.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -i 'sum(AD[*]) < FORMAT/DP' /build/reproducible-path/bcftools-1.11/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -i 'sum(AD[*]) < FORMAT/DP' /build/reproducible-path/bcftools-1.11/test/filter.10.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -i 'FORMAT/DP > sum(AD[*])' /build/reproducible-path/bcftools-1.11/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.11/bcftools filter -Ob -i 'FORMAT/DP > sum(AD[*])' /build/reproducible-path/bcftools-1.11/test/filter.10.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_sort: /build/reproducible-path/bcftools-1.11/bcftools sort -m 0 /build/reproducible-path/bcftools-1.11/test/sort.vcf | /build/reproducible-path/bcftools-1.11/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /build/reproducible-path/bcftools-1.11/bcftools sort -Ob -m 0 /build/reproducible-path/bcftools-1.11/test/sort.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | /build/reproducible-path/bcftools-1.11/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /build/reproducible-path/bcftools-1.11/bcftools sort -m 1000 /build/reproducible-path/bcftools-1.11/test/sort.vcf | /build/reproducible-path/bcftools-1.11/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /build/reproducible-path/bcftools-1.11/bcftools sort -Ob -m 1000 /build/reproducible-path/bcftools-1.11/test/sort.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | /build/reproducible-path/bcftools-1.11/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.11/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /build/reproducible-path/bcftools-1.11/test/regions.tab /tmp/vQp5weZwFe/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/regions.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /build/reproducible-path/bcftools-1.11/test/regions.tab .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.11/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /build/reproducible-path/bcftools-1.11/test/regions.tab /tmp/vQp5weZwFe/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.11/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/vQp5weZwFe/regions.tab.gz /tmp/vQp5weZwFe/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/regions.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/vQp5weZwFe/regions.tab.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.11/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/vQp5weZwFe/regions.tab.gz /tmp/vQp5weZwFe/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.11/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/vQp5weZwFe/regions.bed /tmp/vQp5weZwFe/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/regions.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/vQp5weZwFe/regions.bed .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.11/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/vQp5weZwFe/regions.bed /tmp/vQp5weZwFe/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.11/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/vQp5weZwFe/regions.bed.gz /tmp/vQp5weZwFe/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/regions.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/vQp5weZwFe/regions.bed.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.11/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/vQp5weZwFe/regions.bed.gz /tmp/vQp5weZwFe/regions.vcf.gz .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -a /tmp/vQp5weZwFe/annotate.tab.gz -h /build/reproducible-path/bcftools-1.11/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /build/reproducible-path/bcftools-1.11/test/annotate.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -Ob -a /tmp/vQp5weZwFe/annotate.tab.gz -h /build/reproducible-path/bcftools-1.11/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /build/reproducible-path/bcftools-1.11/test/annotate.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -a /tmp/vQp5weZwFe/annotate2.tab.gz -h /build/reproducible-path/bcftools-1.11/test/annotate.hdr -c CHROM,POS,-,T_STR /build/reproducible-path/bcftools-1.11/test/annotate.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -Ob -a /tmp/vQp5weZwFe/annotate2.tab.gz -h /build/reproducible-path/bcftools-1.11/test/annotate.hdr -c CHROM,POS,-,T_STR /build/reproducible-path/bcftools-1.11/test/annotate.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -a /tmp/vQp5weZwFe/annotate2.tab.gz -h /build/reproducible-path/bcftools-1.11/test/annotate.hdr -c CHROM,FROM,TO,T_STR /build/reproducible-path/bcftools-1.11/test/annotate.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -Ob -a /tmp/vQp5weZwFe/annotate2.tab.gz -h /build/reproducible-path/bcftools-1.11/test/annotate.hdr -c CHROM,FROM,TO,T_STR /build/reproducible-path/bcftools-1.11/test/annotate.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -a /tmp/vQp5weZwFe/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/vQp5weZwFe/annotate.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -Ob -a /tmp/vQp5weZwFe/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/vQp5weZwFe/annotate.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -a /tmp/vQp5weZwFe/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/vQp5weZwFe/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -Ob -a /tmp/vQp5weZwFe/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/vQp5weZwFe/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -a /tmp/vQp5weZwFe/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/vQp5weZwFe/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -Ob -a /tmp/vQp5weZwFe/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/vQp5weZwFe/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -a /tmp/vQp5weZwFe/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/vQp5weZwFe/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -Ob -a /tmp/vQp5weZwFe/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/vQp5weZwFe/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -a /tmp/vQp5weZwFe/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/vQp5weZwFe/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -Ob -a /tmp/vQp5weZwFe/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/vQp5weZwFe/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -a /tmp/vQp5weZwFe/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/vQp5weZwFe/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -Ob -a /tmp/vQp5weZwFe/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/vQp5weZwFe/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /build/reproducible-path/bcftools-1.11/test/annotate3.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -Ob -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /build/reproducible-path/bcftools-1.11/test/annotate3.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -x FORMAT /build/reproducible-path/bcftools-1.11/test/annotate3.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -Ob -x FORMAT /build/reproducible-path/bcftools-1.11/test/annotate3.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -a /tmp/vQp5weZwFe/annots4.vcf.gz -c +INFO /tmp/vQp5weZwFe/annotate4.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -Ob -a /tmp/vQp5weZwFe/annots4.vcf.gz -c +INFO /tmp/vQp5weZwFe/annotate4.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -a /tmp/vQp5weZwFe/annots4.tab.gz -h /build/reproducible-path/bcftools-1.11/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /build/reproducible-path/bcftools-1.11/test/annotate4.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -Ob -a /tmp/vQp5weZwFe/annots4.tab.gz -h /build/reproducible-path/bcftools-1.11/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /build/reproducible-path/bcftools-1.11/test/annotate4.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -a /tmp/vQp5weZwFe/annots10.tab.gz -h /build/reproducible-path/bcftools-1.11/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /build/reproducible-path/bcftools-1.11/test/annotate10.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -Ob -a /tmp/vQp5weZwFe/annots10.tab.gz -h /build/reproducible-path/bcftools-1.11/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /build/reproducible-path/bcftools-1.11/test/annotate10.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -a /tmp/vQp5weZwFe/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/vQp5weZwFe/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -Ob -a /tmp/vQp5weZwFe/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/vQp5weZwFe/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -a /tmp/vQp5weZwFe/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /build/reproducible-path/bcftools-1.11/test/annotate2.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -Ob -a /tmp/vQp5weZwFe/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /build/reproducible-path/bcftools-1.11/test/annotate2.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -a /tmp/vQp5weZwFe/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/vQp5weZwFe/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -Ob -a /tmp/vQp5weZwFe/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/vQp5weZwFe/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -a /tmp/vQp5weZwFe/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/vQp5weZwFe/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -Ob -a /tmp/vQp5weZwFe/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/vQp5weZwFe/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -a /tmp/vQp5weZwFe/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/vQp5weZwFe/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -Ob -a /tmp/vQp5weZwFe/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/vQp5weZwFe/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -a /tmp/vQp5weZwFe/annots11.vcf.gz -c FMT /tmp/vQp5weZwFe/annotate11.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -Ob -a /tmp/vQp5weZwFe/annots11.vcf.gz -c FMT /tmp/vQp5weZwFe/annotate11.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -a /tmp/vQp5weZwFe/annots2.vcf.gz -c FMT/newGT:=GT /tmp/vQp5weZwFe/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -Ob -a /tmp/vQp5weZwFe/annots2.vcf.gz -c FMT/newGT:=GT /tmp/vQp5weZwFe/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -a /tmp/vQp5weZwFe/annots12.vcf.gz -c FMT/GT:=newGT /tmp/vQp5weZwFe/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -Ob -a /tmp/vQp5weZwFe/annots12.vcf.gz -c FMT/GT:=newGT /tmp/vQp5weZwFe/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -a /tmp/vQp5weZwFe/annots13.tab.gz -h /build/reproducible-path/bcftools-1.11/test/annotate13.hdr -c CHROM,BEG,END,ABC /build/reproducible-path/bcftools-1.11/test/annotate13.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -Ob -a /tmp/vQp5weZwFe/annots13.tab.gz -h /build/reproducible-path/bcftools-1.11/test/annotate13.hdr -c CHROM,BEG,END,ABC /build/reproducible-path/bcftools-1.11/test/annotate13.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -a /tmp/vQp5weZwFe/annots13.tab.gz -h /build/reproducible-path/bcftools-1.11/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:append /build/reproducible-path/bcftools-1.11/test/annotate13.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -Ob -a /tmp/vQp5weZwFe/annots13.tab.gz -h /build/reproducible-path/bcftools-1.11/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:append /build/reproducible-path/bcftools-1.11/test/annotate13.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -a /tmp/vQp5weZwFe/annots13.tab.gz -h /build/reproducible-path/bcftools-1.11/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:unique /build/reproducible-path/bcftools-1.11/test/annotate13.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -Ob -a /tmp/vQp5weZwFe/annots13.tab.gz -h /build/reproducible-path/bcftools-1.11/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:unique /build/reproducible-path/bcftools-1.11/test/annotate13.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -x FILTER/XX,INFO/XX --force /build/reproducible-path/bcftools-1.11/test/annotate14.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -Ob -x FILTER/XX,INFO/XX --force /build/reproducible-path/bcftools-1.11/test/annotate14.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -a /tmp/vQp5weZwFe/annotate15.tab.gz -h /build/reproducible-path/bcftools-1.11/test/annotate15.hdr -s SAMPLE1 -c CHROM,FROM,TO,FMT/FOO,BAR /build/reproducible-path/bcftools-1.11/test/annotate15.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -Ob -a /tmp/vQp5weZwFe/annotate15.tab.gz -h /build/reproducible-path/bcftools-1.11/test/annotate15.hdr -s SAMPLE1 -c CHROM,FROM,TO,FMT/FOO,BAR /build/reproducible-path/bcftools-1.11/test/annotate15.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -a /tmp/vQp5weZwFe/annotate15.tab.gz -h /build/reproducible-path/bcftools-1.11/test/annotate15.hdr -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR /build/reproducible-path/bcftools-1.11/test/annotate15.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -Ob -a /tmp/vQp5weZwFe/annotate15.tab.gz -h /build/reproducible-path/bcftools-1.11/test/annotate15.hdr -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR /build/reproducible-path/bcftools-1.11/test/annotate15.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -x FILTER /build/reproducible-path/bcftools-1.11/test/annotate16.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -Ob -x FILTER /build/reproducible-path/bcftools-1.11/test/annotate16.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -a /tmp/vQp5weZwFe/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/reproducible-path/bcftools-1.11/test/annotate17.1.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -Ob -a /tmp/vQp5weZwFe/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/reproducible-path/bcftools-1.11/test/annotate17.1.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -a /tmp/vQp5weZwFe/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/reproducible-path/bcftools-1.11/test/annotate17.2.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -Ob -a /tmp/vQp5weZwFe/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/reproducible-path/bcftools-1.11/test/annotate17.2.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -a /tmp/vQp5weZwFe/annotate17.3.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/reproducible-path/bcftools-1.11/test/annotate17.3.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -Ob -a /tmp/vQp5weZwFe/annotate17.3.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/reproducible-path/bcftools-1.11/test/annotate17.3.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -a /tmp/vQp5weZwFe/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-1.11/test/annotate18.1.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -Ob -a /tmp/vQp5weZwFe/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-1.11/test/annotate18.1.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -a /tmp/vQp5weZwFe/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-1.11/test/annotate18.2.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -Ob -a /tmp/vQp5weZwFe/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-1.11/test/annotate18.2.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -a /tmp/vQp5weZwFe/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/vQp5weZwFe/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -Ob -a /tmp/vQp5weZwFe/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/vQp5weZwFe/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -a /tmp/vQp5weZwFe/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/vQp5weZwFe/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -Ob -a /tmp/vQp5weZwFe/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/vQp5weZwFe/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -a /tmp/vQp5weZwFe/annotate20.src.vcf.gz -c FMT/GT /tmp/vQp5weZwFe/annotate20.dst.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -Ob -a /tmp/vQp5weZwFe/annotate20.src.vcf.gz -c FMT/GT /tmp/vQp5weZwFe/annotate20.dst.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -a /tmp/vQp5weZwFe/annotate20.src.vcf.gz -c +FMT/GT /tmp/vQp5weZwFe/annotate20.dst.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -Ob -a /tmp/vQp5weZwFe/annotate20.src.vcf.gz -c +FMT/GT /tmp/vQp5weZwFe/annotate20.dst.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -a /tmp/vQp5weZwFe/annotate20.src.vcf.gz -c -FMT/GT /tmp/vQp5weZwFe/annotate20.dst.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -Ob -a /tmp/vQp5weZwFe/annotate20.src.vcf.gz -c -FMT/GT /tmp/vQp5weZwFe/annotate20.dst.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -a /tmp/vQp5weZwFe/annotate.multi.tab.gz -c CHROM,POS,REF,ALT,ANN -l ANN:append /build/reproducible-path/bcftools-1.11/test/annotate.multi.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -Ob -a /tmp/vQp5weZwFe/annotate.multi.tab.gz -c CHROM,POS,REF,ALT,ANN -l ANN:append /build/reproducible-path/bcftools-1.11/test/annotate.multi.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -a /tmp/vQp5weZwFe/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /build/reproducible-path/bcftools-1.11/test/annotate9.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.11/bcftools annotate -Ob -a /tmp/vQp5weZwFe/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /build/reproducible-path/bcftools-1.11/test/annotate9.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.11/bcftools concat --no-version /tmp/vQp5weZwFe/concat.1.a.vcf.gz /tmp/vQp5weZwFe/concat.1.b.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.11/bcftools concat -Ob /tmp/vQp5weZwFe/concat.1.a.vcf.gz /tmp/vQp5weZwFe/concat.1.b.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.11/bcftools concat --no-version /tmp/vQp5weZwFe/concat.1.a.bcf /tmp/vQp5weZwFe/concat.1.b.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.11/bcftools concat -Ob /tmp/vQp5weZwFe/concat.1.a.bcf /tmp/vQp5weZwFe/concat.1.b.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.11/bcftools concat --no-version -a /tmp/vQp5weZwFe/concat.2.a.vcf.gz /tmp/vQp5weZwFe/concat.2.b.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.11/bcftools concat -Ob -a /tmp/vQp5weZwFe/concat.2.a.vcf.gz /tmp/vQp5weZwFe/concat.2.b.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.11/bcftools concat --no-version -a /tmp/vQp5weZwFe/concat.2.a.bcf /tmp/vQp5weZwFe/concat.2.b.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.11/bcftools concat -Ob -a /tmp/vQp5weZwFe/concat.2.a.bcf /tmp/vQp5weZwFe/concat.2.b.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.11/bcftools concat --no-version -aD /tmp/vQp5weZwFe/concat.2.a.vcf.gz /tmp/vQp5weZwFe/concat.2.b.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.11/bcftools concat -Ob -aD /tmp/vQp5weZwFe/concat.2.a.vcf.gz /tmp/vQp5weZwFe/concat.2.b.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.11/bcftools concat --no-version -aD /tmp/vQp5weZwFe/concat.2.a.bcf /tmp/vQp5weZwFe/concat.2.b.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.11/bcftools concat -Ob -aD /tmp/vQp5weZwFe/concat.2.a.bcf /tmp/vQp5weZwFe/concat.2.b.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.11/bcftools concat --no-version -l /tmp/vQp5weZwFe/concat.3.a.vcf.gz /tmp/vQp5weZwFe/concat.3.b.vcf.gz /tmp/vQp5weZwFe/concat.3.0.vcf.gz /tmp/vQp5weZwFe/concat.3.c.vcf.gz /tmp/vQp5weZwFe/concat.3.d.vcf.gz /tmp/vQp5weZwFe/concat.3.e.vcf.gz /tmp/vQp5weZwFe/concat.3.f.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.11/bcftools concat -Ob -l /tmp/vQp5weZwFe/concat.3.a.vcf.gz /tmp/vQp5weZwFe/concat.3.b.vcf.gz /tmp/vQp5weZwFe/concat.3.0.vcf.gz /tmp/vQp5weZwFe/concat.3.c.vcf.gz /tmp/vQp5weZwFe/concat.3.d.vcf.gz /tmp/vQp5weZwFe/concat.3.e.vcf.gz /tmp/vQp5weZwFe/concat.3.f.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.11/bcftools concat --no-version -l /tmp/vQp5weZwFe/concat.3.a.bcf /tmp/vQp5weZwFe/concat.3.b.bcf /tmp/vQp5weZwFe/concat.3.0.bcf /tmp/vQp5weZwFe/concat.3.c.bcf /tmp/vQp5weZwFe/concat.3.d.bcf /tmp/vQp5weZwFe/concat.3.e.bcf /tmp/vQp5weZwFe/concat.3.f.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.11/bcftools concat -Ob -l /tmp/vQp5weZwFe/concat.3.a.bcf /tmp/vQp5weZwFe/concat.3.b.bcf /tmp/vQp5weZwFe/concat.3.0.bcf /tmp/vQp5weZwFe/concat.3.c.bcf /tmp/vQp5weZwFe/concat.3.d.bcf /tmp/vQp5weZwFe/concat.3.e.bcf /tmp/vQp5weZwFe/concat.3.f.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ Random seed for test_naive_concat: 1440944215 .. ok test_naive_concat: /build/reproducible-path/bcftools-1.11/bcftools concat --naive-force /tmp/vQp5weZwFe/naive_concat.0.bcf /tmp/vQp5weZwFe/naive_concat.1.bcf /tmp/vQp5weZwFe/naive_concat.2.bcf /tmp/vQp5weZwFe/naive_concat.3.bcf /tmp/vQp5weZwFe/naive_concat.4.bcf /tmp/vQp5weZwFe/naive_concat.5.bcf /tmp/vQp5weZwFe/naive_concat.6.bcf /tmp/vQp5weZwFe/naive_concat.7.bcf /tmp/vQp5weZwFe/naive_concat.8.bcf /tmp/vQp5weZwFe/naive_concat.9.bcf | /build/reproducible-path/bcftools-1.11/bcftools view -H .. ok test_naive_concat: /build/reproducible-path/bcftools-1.11/bcftools concat --naive /tmp/vQp5weZwFe/naive_concat.0.vcf.gz /tmp/vQp5weZwFe/naive_concat.1.vcf.gz /tmp/vQp5weZwFe/naive_concat.2.vcf.gz /tmp/vQp5weZwFe/naive_concat.3.vcf.gz /tmp/vQp5weZwFe/naive_concat.4.vcf.gz /tmp/vQp5weZwFe/naive_concat.5.vcf.gz /tmp/vQp5weZwFe/naive_concat.6.vcf.gz /tmp/vQp5weZwFe/naive_concat.7.vcf.gz /tmp/vQp5weZwFe/naive_concat.8.vcf.gz /tmp/vQp5weZwFe/naive_concat.9.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view -H .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.11/bcftools reheader -h /build/reproducible-path/bcftools-1.11/test/reheader.hdr /build/reproducible-path/bcftools-1.11/test/reheader.vcf | /build/reproducible-path/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /build/reproducible-path/bcftools-1.11/test/reheader.vcf | /build/reproducible-path/bcftools-1.11/bcftools reheader -h /build/reproducible-path/bcftools-1.11/test/reheader.hdr | /build/reproducible-path/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.11/bcftools reheader -h /build/reproducible-path/bcftools-1.11/test/reheader.hdr /tmp/vQp5weZwFe/reheader.bcf | /build/reproducible-path/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/vQp5weZwFe/reheader.bcf | /build/reproducible-path/bcftools-1.11/bcftools reheader -h /build/reproducible-path/bcftools-1.11/test/reheader.hdr | /build/reproducible-path/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.11/bcftools reheader -h /build/reproducible-path/bcftools-1.11/test/reheader.hdr /tmp/vQp5weZwFe/reheader.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/vQp5weZwFe/reheader.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools reheader -h /build/reproducible-path/bcftools-1.11/test/reheader.hdr | /build/reproducible-path/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.11/bcftools reheader -s /build/reproducible-path/bcftools-1.11/test/reheader.samples /build/reproducible-path/bcftools-1.11/test/reheader.vcf | /build/reproducible-path/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /build/reproducible-path/bcftools-1.11/test/reheader.vcf | /build/reproducible-path/bcftools-1.11/bcftools reheader -s /build/reproducible-path/bcftools-1.11/test/reheader.samples | /build/reproducible-path/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.11/bcftools reheader -s /build/reproducible-path/bcftools-1.11/test/reheader.samples /tmp/vQp5weZwFe/reheader.bcf | /build/reproducible-path/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/vQp5weZwFe/reheader.bcf | /build/reproducible-path/bcftools-1.11/bcftools reheader -s /build/reproducible-path/bcftools-1.11/test/reheader.samples | /build/reproducible-path/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.11/bcftools reheader -s /build/reproducible-path/bcftools-1.11/test/reheader.samples /tmp/vQp5weZwFe/reheader.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/vQp5weZwFe/reheader.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools reheader -s /build/reproducible-path/bcftools-1.11/test/reheader.samples | /build/reproducible-path/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.11/bcftools reheader -s /build/reproducible-path/bcftools-1.11/test/reheader.samples2 /build/reproducible-path/bcftools-1.11/test/reheader.vcf | /build/reproducible-path/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /build/reproducible-path/bcftools-1.11/test/reheader.vcf | /build/reproducible-path/bcftools-1.11/bcftools reheader -s /build/reproducible-path/bcftools-1.11/test/reheader.samples2 | /build/reproducible-path/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.11/bcftools reheader -s /build/reproducible-path/bcftools-1.11/test/reheader.samples2 /tmp/vQp5weZwFe/reheader.bcf | /build/reproducible-path/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/vQp5weZwFe/reheader.bcf | /build/reproducible-path/bcftools-1.11/bcftools reheader -s /build/reproducible-path/bcftools-1.11/test/reheader.samples2 | /build/reproducible-path/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.11/bcftools reheader -s /build/reproducible-path/bcftools-1.11/test/reheader.samples2 /tmp/vQp5weZwFe/reheader.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/vQp5weZwFe/reheader.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools reheader -s /build/reproducible-path/bcftools-1.11/test/reheader.samples2 | /build/reproducible-path/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.11/bcftools reheader -s /build/reproducible-path/bcftools-1.11/test/reheader.samples3 /build/reproducible-path/bcftools-1.11/test/reheader.vcf | /build/reproducible-path/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /build/reproducible-path/bcftools-1.11/test/reheader.vcf | /build/reproducible-path/bcftools-1.11/bcftools reheader -s /build/reproducible-path/bcftools-1.11/test/reheader.samples3 | /build/reproducible-path/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.11/bcftools reheader -s /build/reproducible-path/bcftools-1.11/test/reheader.samples3 /tmp/vQp5weZwFe/reheader.bcf | /build/reproducible-path/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/vQp5weZwFe/reheader.bcf | /build/reproducible-path/bcftools-1.11/bcftools reheader -s /build/reproducible-path/bcftools-1.11/test/reheader.samples3 | /build/reproducible-path/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.11/bcftools reheader -s /build/reproducible-path/bcftools-1.11/test/reheader.samples3 /tmp/vQp5weZwFe/reheader.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/vQp5weZwFe/reheader.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools reheader -s /build/reproducible-path/bcftools-1.11/test/reheader.samples3 | /build/reproducible-path/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.11/bcftools reheader -s /build/reproducible-path/bcftools-1.11/test/reheader.samples4 /build/reproducible-path/bcftools-1.11/test/reheader.vcf | /build/reproducible-path/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /build/reproducible-path/bcftools-1.11/test/reheader.vcf | /build/reproducible-path/bcftools-1.11/bcftools reheader -s /build/reproducible-path/bcftools-1.11/test/reheader.samples4 | /build/reproducible-path/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.11/bcftools reheader -s /build/reproducible-path/bcftools-1.11/test/reheader.samples4 /tmp/vQp5weZwFe/reheader.bcf | /build/reproducible-path/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/vQp5weZwFe/reheader.bcf | /build/reproducible-path/bcftools-1.11/bcftools reheader -s /build/reproducible-path/bcftools-1.11/test/reheader.samples4 | /build/reproducible-path/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.11/bcftools reheader -s /build/reproducible-path/bcftools-1.11/test/reheader.samples4 /tmp/vQp5weZwFe/reheader.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/vQp5weZwFe/reheader.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools reheader -s /build/reproducible-path/bcftools-1.11/test/reheader.samples4 | /build/reproducible-path/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.11/bcftools reheader -h /build/reproducible-path/bcftools-1.11/test/reheader.empty.hdr /build/reproducible-path/bcftools-1.11/test/empty.vcf | /build/reproducible-path/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /build/reproducible-path/bcftools-1.11/test/empty.vcf | /build/reproducible-path/bcftools-1.11/bcftools reheader -h /build/reproducible-path/bcftools-1.11/test/reheader.empty.hdr | /build/reproducible-path/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.11/bcftools reheader -h /build/reproducible-path/bcftools-1.11/test/reheader.empty.hdr /tmp/vQp5weZwFe/empty.bcf | /build/reproducible-path/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/vQp5weZwFe/empty.bcf | /build/reproducible-path/bcftools-1.11/bcftools reheader -h /build/reproducible-path/bcftools-1.11/test/reheader.empty.hdr | /build/reproducible-path/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.11/bcftools reheader -h /build/reproducible-path/bcftools-1.11/test/reheader.empty.hdr /tmp/vQp5weZwFe/empty.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/vQp5weZwFe/empty.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools reheader -h /build/reproducible-path/bcftools-1.11/test/reheader.empty.hdr | /build/reproducible-path/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.11/bcftools reheader -f /build/reproducible-path/bcftools-1.11/test/reheader.fai /build/reproducible-path/bcftools-1.11/test/reheader.2.vcf | /build/reproducible-path/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.11/bcftools reheader -f /build/reproducible-path/bcftools-1.11/test/reheader.fai /tmp/vQp5weZwFe/reheader.2.bcf | /build/reproducible-path/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.11/bcftools reheader -f /build/reproducible-path/bcftools-1.11/test/reheader.fai /tmp/vQp5weZwFe/reheader.2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.11/bcftools reheader -h /build/reproducible-path/bcftools-1.11/test/reheader.2.hdr -f /build/reproducible-path/bcftools-1.11/test/reheader.fai /build/reproducible-path/bcftools-1.11/test/reheader.2.vcf | /build/reproducible-path/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.11/bcftools reheader -h /build/reproducible-path/bcftools-1.11/test/reheader.2.hdr -f /build/reproducible-path/bcftools-1.11/test/reheader.fai /tmp/vQp5weZwFe/reheader.2.bcf | /build/reproducible-path/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.11/bcftools reheader -h /build/reproducible-path/bcftools-1.11/test/reheader.2.hdr -f /build/reproducible-path/bcftools-1.11/test/reheader.fai /tmp/vQp5weZwFe/reheader.2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view --no-version .. ok test_rename_chrs: /build/reproducible-path/bcftools-1.11/bcftools annotate --rename-chrs /tmp/vQp5weZwFe/rename.map -Ov /tmp/vQp5weZwFe/annotate.bcf | /build/reproducible-path/bcftools-1.11/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /build/reproducible-path/bcftools-1.11/bcftools annotate --rename-chrs /tmp/vQp5weZwFe/rename.map -Ob /tmp/vQp5weZwFe/annotate.bcf | /build/reproducible-path/bcftools-1.11/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /build/reproducible-path/bcftools-1.11/bcftools annotate --rename-chrs /tmp/vQp5weZwFe/rename.map -Ov /build/reproducible-path/bcftools-1.11/test/annotate.vcf | /build/reproducible-path/bcftools-1.11/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /build/reproducible-path/bcftools-1.11/bcftools annotate --rename-chrs /tmp/vQp5weZwFe/rename.map -Ob /build/reproducible-path/bcftools-1.11/test/annotate.vcf | /build/reproducible-path/bcftools-1.11/bcftools query -f'%CHROM\t%POS\n' .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.11/bcftools convert -g -,. /tmp/vQp5weZwFe/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/convert.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools convert -g -,. .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.11/bcftools convert -g .,- /tmp/vQp5weZwFe/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/convert.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools convert -g .,- .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.11/bcftools convert -g -,. --tag PL /tmp/vQp5weZwFe/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/convert.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools convert -g -,. --tag PL .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.11/bcftools convert -g .,- --tag PL /tmp/vQp5weZwFe/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/convert.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools convert -g .,- --tag PL .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.11/bcftools convert -g -,. --vcf-ids /tmp/vQp5weZwFe/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/check.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools convert -g -,. --vcf-ids .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.11/bcftools convert -g .,- --vcf-ids /tmp/vQp5weZwFe/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/check.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools convert -g .,- --vcf-ids .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.11/bcftools convert -g -,. --chrom /tmp/vQp5weZwFe/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/check.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools convert -g -,. --chrom .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.11/bcftools convert -g .,- --chrom /tmp/vQp5weZwFe/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/check.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools convert -g .,- --chrom .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.11/bcftools convert -g -,. --chrom --vcf-ids /tmp/vQp5weZwFe/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/check.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools convert -g -,. --chrom --vcf-ids .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.11/bcftools convert -g .,- --chrom --vcf-ids /tmp/vQp5weZwFe/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/check.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools convert -g .,- --chrom --vcf-ids .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.11/bcftools convert -h -,.,. /tmp/vQp5weZwFe/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/convert.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools convert -h -,.,. .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.11/bcftools convert -h .,-,. /tmp/vQp5weZwFe/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/convert.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools convert -h .,-,. .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.11/bcftools convert -h .,.,- /tmp/vQp5weZwFe/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/convert.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools convert -h .,.,- .. ok test_vcf_convert_hls2vcf: /build/reproducible-path/bcftools-1.11/bcftools convert -H /build/reproducible-path/bcftools-1.11/test/convert.hls.gt.hap,/build/reproducible-path/bcftools-1.11/test/convert.hls.gt.legend,/build/reproducible-path/bcftools-1.11/test/convert.hls.gt.samples | grep -v ^## .. ok test_vcf_convert_hls2vcf: /build/reproducible-path/bcftools-1.11/bcftools convert -H /build/reproducible-path/bcftools-1.11/test/convert.hls.gt.hap,/build/reproducible-path/bcftools-1.11/test/convert.hls.gt.legend,/build/reproducible-path/bcftools-1.11/test/convert.hls.gt.samples -Ou | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^## .. ok test_vcf_convert_hls2vcf: /build/reproducible-path/bcftools-1.11/bcftools convert --vcf-ids -H /build/reproducible-path/bcftools-1.11/test/convert.hls.gt.hap,/build/reproducible-path/bcftools-1.11/test/convert.hls.gt.legend,/build/reproducible-path/bcftools-1.11/test/convert.hls.gt.samples | grep -v ^## .. ok test_vcf_convert_hls2vcf: /build/reproducible-path/bcftools-1.11/bcftools convert --vcf-ids -H /build/reproducible-path/bcftools-1.11/test/convert.hls.gt.hap,/build/reproducible-path/bcftools-1.11/test/convert.hls.gt.legend,/build/reproducible-path/bcftools-1.11/test/convert.hls.gt.samples -Ou | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.11/bcftools convert --hapsample2vcf /build/reproducible-path/bcftools-1.11/test/convert.hs.gt.hap,/build/reproducible-path/bcftools-1.11/test/convert.hs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.11/bcftools convert --hapsample2vcf /build/reproducible-path/bcftools-1.11/test/convert.hs.gt.hap,/build/reproducible-path/bcftools-1.11/test/convert.hs.gt.samples -Ou | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.11/bcftools convert --vcf-ids --hapsample2vcf /build/reproducible-path/bcftools-1.11/test/convert.hs.gt.hap,/build/reproducible-path/bcftools-1.11/test/convert.hs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.11/bcftools convert --vcf-ids --hapsample2vcf /build/reproducible-path/bcftools-1.11/test/convert.hs.gt.hap,/build/reproducible-path/bcftools-1.11/test/convert.hs.gt.samples -Ou | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^## .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.11/bcftools convert --hapsample -,. /tmp/vQp5weZwFe/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/convert.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools convert --hapsample -,. .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.11/bcftools convert --hapsample .,- /tmp/vQp5weZwFe/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/convert.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools convert --hapsample .,- .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.11/bcftools convert --haplegendsample -,.,. /tmp/vQp5weZwFe/convert.hap-missing.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/convert.hap-missing.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools convert --haplegendsample -,.,. .. ok test_vcf_convert_gvcf: /build/reproducible-path/bcftools-1.11/bcftools convert --no-version --gvcf2vcf -i'FILTER="PASS"' -f /build/reproducible-path/bcftools-1.11/test/gvcf.fa /tmp/vQp5weZwFe/convert.gvcf.vcf.gz .. ok test_vcf_convert_gvcf: /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/vQp5weZwFe/convert.gvcf.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools convert --gvcf2vcf -i'FILTER="PASS"' -f /build/reproducible-path/bcftools-1.11/test/gvcf.fa | grep -v ^##bcftools .. ok test_vcf_convert_tsv2vcf: /build/reproducible-path/bcftools-1.11/bcftools convert --no-version -c ID,CHROM,POS,AA -s SAMPLE1 -f /build/reproducible-path/bcftools-1.11/test/23andme.fa --tsv2vcf /build/reproducible-path/bcftools-1.11/test/convert.23andme .. ok test_vcf_convert_tsv2vcf: /build/reproducible-path/bcftools-1.11/bcftools convert -Ou -c ID,CHROM,POS,AA -s SAMPLE1 -f /build/reproducible-path/bcftools-1.11/test/23andme.fa --tsv2vcf /build/reproducible-path/bcftools-1.11/test/convert.23andme | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.11/bcftools consensus /tmp/vQp5weZwFe/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.11/test/consensus.fa -m /build/reproducible-path/bcftools-1.11/test/consensus.tab .. ok test_vcf_consensus_chain: /build/reproducible-path/bcftools-1.11/bcftools consensus /tmp/vQp5weZwFe/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.11/test/consensus.fa -m /build/reproducible-path/bcftools-1.11/test/consensus.tab -c /tmp/vQp5weZwFe/consensus.1.chain.new >/dev/null; cat /tmp/vQp5weZwFe/consensus.1.chain.new .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.11/bcftools consensus /tmp/vQp5weZwFe/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.11/test/consensus.fa -H 1 -m /build/reproducible-path/bcftools-1.11/test/consensus.tab .. ok test_vcf_consensus_chain: /build/reproducible-path/bcftools-1.11/bcftools consensus /tmp/vQp5weZwFe/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.11/test/consensus.fa -H 1 -m /build/reproducible-path/bcftools-1.11/test/consensus.tab -c /tmp/vQp5weZwFe/consensus.2.chain.new >/dev/null; cat /tmp/vQp5weZwFe/consensus.2.chain.new .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.11/bcftools consensus /tmp/vQp5weZwFe/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.11/test/consensus.fa -I -m /build/reproducible-path/bcftools-1.11/test/consensus.tab .. ok test_vcf_consensus_chain: /build/reproducible-path/bcftools-1.11/bcftools consensus /tmp/vQp5weZwFe/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.11/test/consensus.fa -I -m /build/reproducible-path/bcftools-1.11/test/consensus.tab -c /tmp/vQp5weZwFe/consensus.3.chain.new >/dev/null; cat /tmp/vQp5weZwFe/consensus.3.chain.new .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.11/bcftools consensus /tmp/vQp5weZwFe/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.11/test/consensus.fa -H 1 .. ok test_vcf_consensus_chain: /build/reproducible-path/bcftools-1.11/bcftools consensus /tmp/vQp5weZwFe/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.11/test/consensus.fa -H 1 -c /tmp/vQp5weZwFe/consensus.4.chain.new >/dev/null; cat /tmp/vQp5weZwFe/consensus.4.chain.new .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.11/bcftools consensus /tmp/vQp5weZwFe/consensus2.vcf.gz -f /build/reproducible-path/bcftools-1.11/test/consensus2.fa -H 1 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.11/bcftools consensus /tmp/vQp5weZwFe/consensus2.vcf.gz -f /build/reproducible-path/bcftools-1.11/test/consensus2.fa -H 2 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.11/bcftools consensus /tmp/vQp5weZwFe/empty.vcf.gz -f /build/reproducible-path/bcftools-1.11/test/consensus.fa .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.11/bcftools consensus /tmp/vQp5weZwFe/consensus3.vcf.gz -f /build/reproducible-path/bcftools-1.11/test/consensus2.fa -H 2 -M "?" .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.11/bcftools consensus /tmp/vQp5weZwFe/consensus3.vcf.gz -f /build/reproducible-path/bcftools-1.11/test/consensus2.fa -H 2 -M "?" -p xx_ .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.11/bcftools consensus /tmp/vQp5weZwFe/consensus4.vcf.gz -f /build/reproducible-path/bcftools-1.11/test/consensus2.fa .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.11/bcftools consensus /tmp/vQp5weZwFe/consensus5.vcf.gz -f /build/reproducible-path/bcftools-1.11/test/consensus5.fa --haplotype LA .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.11/bcftools consensus /tmp/vQp5weZwFe/consensus6.vcf.gz -f /build/reproducible-path/bcftools-1.11/test/consensus6.fa .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.11/bcftools consensus /tmp/vQp5weZwFe/consensus7.vcf.gz -f /build/reproducible-path/bcftools-1.11/test/consensus7.fa -H 2 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.11/bcftools consensus /tmp/vQp5weZwFe/consensus7.vcf.gz -f /build/reproducible-path/bcftools-1.11/test/consensus7.fa -H 2pIu .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.11/bcftools consensus /tmp/vQp5weZwFe/consensus7.vcf.gz -f /build/reproducible-path/bcftools-1.11/test/consensus7.fa -H 1 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.11/bcftools consensus /tmp/vQp5weZwFe/consensus7.vcf.gz -f /build/reproducible-path/bcftools-1.11/test/consensus7.fa -H 1pIu .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.11/bcftools consensus /tmp/vQp5weZwFe/consensus8.vcf.gz -f /build/reproducible-path/bcftools-1.11/test/consensus.fa .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.11/bcftools consensus /tmp/vQp5weZwFe/consensus8.vcf.gz -f /build/reproducible-path/bcftools-1.11/test/consensus.fa -a . .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.11/bcftools consensus /tmp/vQp5weZwFe/consensus8.vcf.gz -f /build/reproducible-path/bcftools-1.11/test/consensus.fa -a . -i 'type="snp" || type="ref"' .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.11/bcftools consensus /tmp/vQp5weZwFe/consensus8.vcf.gz -f /build/reproducible-path/bcftools-1.11/test/consensus.fa -a . -i 'ALT!=""' .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.11/bcftools consensus /tmp/vQp5weZwFe/consensus8.vcf.gz -f /build/reproducible-path/bcftools-1.11/test/consensus.fa -a . -e 'MinDP>15' .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.11/bcftools consensus /tmp/vQp5weZwFe/consensus8.vcf.gz -f /build/reproducible-path/bcftools-1.11/test/consensus.fa -a . -e 'MinDP<15' .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.11/bcftools consensus /tmp/vQp5weZwFe/consensus.9.vcf.gz -f /build/reproducible-path/bcftools-1.11/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.11/bcftools consensus /tmp/vQp5weZwFe/consensus.9.vcf.gz -f /build/reproducible-path/bcftools-1.11/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.11/bcftools consensus /tmp/vQp5weZwFe/consensus.10.vcf.gz -f /build/reproducible-path/bcftools-1.11/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.11/bcftools consensus /tmp/vQp5weZwFe/consensus.10.vcf.gz -f /build/reproducible-path/bcftools-1.11/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.11/bcftools consensus /tmp/vQp5weZwFe/consensus.11.vcf.gz -f /build/reproducible-path/bcftools-1.11/test/consensus.11.fa -s smpl .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.11/bcftools consensus /tmp/vQp5weZwFe/consensus.11.vcf.gz -f /build/reproducible-path/bcftools-1.11/test/consensus.11.fa -s smpl -a N .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.11/bcftools consensus /tmp/vQp5weZwFe/consensus.12.vcf.gz -f /build/reproducible-path/bcftools-1.11/test/consensus.12.fa .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.11/bcftools consensus /tmp/vQp5weZwFe/consensus.13.vcf.gz -f /build/reproducible-path/bcftools-1.11/test/consensus.13.fa .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -r17:100-150 -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -r17:100-150 -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -r17:100-150 -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa -b /tmp/vQp5weZwFe/mpileup.bam.list --no-version | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -r17:100-150 -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob -b /tmp/vQp5weZwFe/mpileup.bam.urllist | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -r17:100-150 -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -r17:100-150 -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -r17:100-150 -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa -b /tmp/vQp5weZwFe/mpileup.cram.list --no-version | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -r17:100-150 -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob -b /tmp/vQp5weZwFe/mpileup.cram.urllist | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -a DP,DV -r17:100-600 -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -a DP,DV -r17:100-600 -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -a DP,DV -r17:100-600 -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -a DP,DV -r17:100-600 -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.1.bam | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.1.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.1.cram | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -r17:100-150 -S /build/reproducible-path/bcftools-1.11/test/mplp.samples -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -r17:100-150 -S /build/reproducible-path/bcftools-1.11/test/mplp.samples -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -r17:100-150 -S /build/reproducible-path/bcftools-1.11/test/mplp.samples -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -r17:100-150 -S /build/reproducible-path/bcftools-1.11/test/mplp.samples -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -r17:100-150 -S ^/build/reproducible-path/bcftools-1.11/test/mplp.samples -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -r17:100-150 -S ^/build/reproducible-path/bcftools-1.11/test/mplp.samples -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -r17:100-150 -S ^/build/reproducible-path/bcftools-1.11/test/mplp.samples -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -r17:100-150 -S ^/build/reproducible-path/bcftools-1.11/test/mplp.samples -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -t17:100-150 -S /build/reproducible-path/bcftools-1.11/test/mplp.9.samples -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -t17:100-150 -S /build/reproducible-path/bcftools-1.11/test/mplp.9.samples -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -t17:100-150 -S /build/reproducible-path/bcftools-1.11/test/mplp.9.samples -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -t17:100-150 -S /build/reproducible-path/bcftools-1.11/test/mplp.9.samples -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -t17:100-150 -G /build/reproducible-path/bcftools-1.11/test/mplp.10.samples -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -t17:100-150 -G /build/reproducible-path/bcftools-1.11/test/mplp.10.samples -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -t17:100-150 -G /build/reproducible-path/bcftools-1.11/test/mplp.10.samples -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -t17:100-150 -G /build/reproducible-path/bcftools-1.11/test/mplp.10.samples -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -s HG00102 -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.bam /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -s HG00102 -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.bam /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.4.bam | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -s HG00102 -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.cram /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -s HG00102 -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.cram /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.4.cram | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -s ^HG99999 -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.bam /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -s ^HG99999 -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.bam /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.4.bam | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -s ^HG99999 -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.cram /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -s ^HG99999 -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.cram /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.4.cram | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -G /build/reproducible-path/bcftools-1.11/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.bam /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -G /build/reproducible-path/bcftools-1.11/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.bam /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.4.bam | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -G /build/reproducible-path/bcftools-1.11/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.cram /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -G /build/reproducible-path/bcftools-1.11/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.cram /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.4.cram | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -G /build/reproducible-path/bcftools-1.11/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.bam /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -G /build/reproducible-path/bcftools-1.11/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.bam /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.4.bam | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -G /build/reproducible-path/bcftools-1.11/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.cram /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -G /build/reproducible-path/bcftools-1.11/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.3.cram /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup.4.cram | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -a AD -f /build/reproducible-path/bcftools-1.11/test/mpileup/indel-AD.1.fa /build/reproducible-path/bcftools-1.11/test/mpileup/indel-AD.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -a AD -f /build/reproducible-path/bcftools-1.11/test/mpileup/indel-AD.1.fa -Ob /build/reproducible-path/bcftools-1.11/test/mpileup/indel-AD.1.bam | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -a AD -f /build/reproducible-path/bcftools-1.11/test/mpileup/indel-AD.1.fa /build/reproducible-path/bcftools-1.11/test/mpileup/indel-AD.1.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -a AD -f /build/reproducible-path/bcftools-1.11/test/mpileup/indel-AD.1.fa -Ob /build/reproducible-path/bcftools-1.11/test/mpileup/indel-AD.1.cram | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -a INFO/SCR,FMT/SCR -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup-SCR.fa /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup-SCR.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -a INFO/SCR,FMT/SCR -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup-SCR.fa -Ob /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup-SCR.bam | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -a INFO/SCR,FMT/SCR -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup-SCR.fa /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup-SCR.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.11/bcftools mpileup -a INFO/SCR,FMT/SCR -f /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup-SCR.fa -Ob /build/reproducible-path/bcftools-1.11/test/mpileup/mpileup-SCR.cram | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_csq: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq.fa -g /build/reproducible-path/bcftools-1.11/test/csq.gff3 /build/reproducible-path/bcftools-1.11/test/csq.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000329454/ENST00000329454.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000329454/ENST00000329454.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000329454/boundary-deletion.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -l -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000329454/ENST00000329454.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000329454/ENST00000329454.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000329454/boundary-deletion.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000357367/ENST00000357367.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000357367/ENST00000357367.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000357367/stop-retained.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000545279/ENST00000545279.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000545279/ENST00000545279.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000545279/splice-region-insert.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000448695/ENST00000448695.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000448695/ENST00000448695.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000448695/syn-and-splice-reg.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000543077/ENST00000543077.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000543077/ENST00000543077.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000543077/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -l -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000543077/ENST00000543077.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000543077/ENST00000543077.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000543077/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000368801.2/ENST00000368801.2.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000368801.2/ENST00000368801.2.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000368801.2/start-lost.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000528237/ENST00000528237.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000528237/ENST00000528237.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000528237/retained-stop-incomplete-cds.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000519442/ENST00000519442.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000519442/ENST00000519442.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000519442/synon-splice-region-del.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000378322/ENST00000378322.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000378322/ENST00000378322.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000378322/end-overlap-tscript.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -l -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000378322/ENST00000378322.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000378322/ENST00000378322.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000378322/end-overlap-tscript.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000294661/ENST00000294661.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000294661/ENST00000294661.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000294661/non-coding-boundary.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -l -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000294661/ENST00000294661.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000294661/ENST00000294661.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000294661/non-coding-boundary.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000227471/ENST00000227471.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000227471/ENST00000227471.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000227471/insert-splice-vs-frameshift.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/ENSG00000173376/ENSG00000173376.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENSG00000173376/ENSG00000173376.gff /build/reproducible-path/bcftools-1.11/test/csq/ENSG00000173376/synon.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000390520/ENST00000390520.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000390520/ENST00000390520.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000390520/deletion-overlap.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000518414-ENST00000521270/valgrind.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000295641/ENST00000295641.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000295641/ENST00000295641.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000295641/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -l -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000295641/ENST00000295641.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000295641/ENST00000295641.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000295641/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/EDUMMY0002/EDUMMY0002.fa -g /build/reproducible-path/bcftools-1.11/test/csq/EDUMMY0002/EDUMMY0002.gff /build/reproducible-path/bcftools-1.11/test/csq/EDUMMY0002/boundaries.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000409523/ENST00000409523.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000409523/ENST00000409523.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000409523/long-overlapping-del.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000271583/ENST00000271583.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000271583/ENST00000271583.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000271583/splice-acceptor.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000373833/ENST00000373833.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000373833/ENST00000373833.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000373833/boundary-insertion.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -l -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000373833/ENST00000373833.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000373833/ENST00000373833.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000373833/boundary-insertion.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/EDUMMY0001/EDUMMY0001.fa -g /build/reproducible-path/bcftools-1.11/test/csq/EDUMMY0001/EDUMMY0001.gff /build/reproducible-path/bcftools-1.11/test/csq/EDUMMY0001/starts-with-1.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -l -f /build/reproducible-path/bcftools-1.11/test/csq/EDUMMY0001/EDUMMY0001.fa -g /build/reproducible-path/bcftools-1.11/test/csq/EDUMMY0001/EDUMMY0001.gff /build/reproducible-path/bcftools-1.11/test/csq/EDUMMY0001/starts-with-1.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000479739/ENST00000479739.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000479739/ENST00000479739.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000479739/short-cds-start-lost.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -l -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000479739/ENST00000479739.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000479739/ENST00000479739.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000479739/short-cds-start-lost.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -l -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -l -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -l -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -l -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -l -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -l -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/frame3.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -l -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/frame3.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/frame2.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -l -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/frame2.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -l -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -l -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -l -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -l -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/frame1.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -l -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000341065/frame1.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000420190/ENST00000420190.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000420190/ENST00000420190.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000420190/abort-in-csq-push.vcf | /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000218032/ENST00000218032.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000218032/ENST00000218032.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000218032/start-lost.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -l -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000218032/ENST00000218032.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000218032/ENST00000218032.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000218032/start-lost.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000218032/ENST00000218032.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000218032/ENST00000218032.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000218032/start-lost-del.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000573314/ENST00000573314.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000573314/ENST00000573314.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -l -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000573314/ENST00000573314.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000573314/ENST00000573314.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000230048/ENST00000230048.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000230048/ENST00000230048.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000230048/start-del.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000557788/ENST00000557788.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000557788/ENST00000557788.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000557788/long-overlap-del.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000256452/ENST00000256452.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000256452/ENST00000256452.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000256452/intron.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000301246/ENST00000301246.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000301246/ENST00000301246.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000301246/15bp-insert.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000520795/ENST00000520795.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000520795/ENST00000520795.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000520795/long-inside-del.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -l -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000520795/ENST00000520795.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000520795/ENST00000520795.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000520795/long-inside-del.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000520868/ENST00000520868.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000520868/ENST00000520868.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000520868/long-deletion.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000624631/ENST00000624631.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000624631/ENST00000624631.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000624631/ambiguous.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000375992/ENST00000375992.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000375992/ENST00000375992.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000375992/incorrect-synon-del-not-start-lost.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000400151/ENST00000400151.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000400151/ENST00000400151.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000400151/long-del.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000382647/ENST00000382647.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000382647/ENST00000382647.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000382647/synon-splice-region-insert.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000368801/ENST00000368801.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000368801/ENST00000368801.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000368801/compound-lost.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000536784/ENST00000536784.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000536784/ENST00000536784.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000536784/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -l -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000536784/ENST00000536784.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000536784/ENST00000536784.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000536784/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000423372/ENST00000423372.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000423372/ENST00000423372.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000423372/insert3.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -l -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000423372/ENST00000423372.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000423372/ENST00000423372.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000423372/insert3.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000423372/ENST00000423372.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000423372/ENST00000423372.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000423372/snps.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -l -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000423372/ENST00000423372.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000423372/ENST00000423372.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000423372/snps.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000542803/ENST00000542803.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000542803/ENST00000542803.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000542803/splice-region.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -l -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000542803/ENST00000542803.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000542803/ENST00000542803.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000542803/splice-region.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000436063/ENST00000436063.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000436063/ENST00000436063.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000436063/insert-before-utr.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000318249.2/ENST00000318249.2.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000318249.2/ENST00000318249.2.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000318249.2/synonymous-start-lost.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/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-1.11/test/csq/ENST00000410009 && /build/reproducible-path/bcftools-1.11/bcftools csq -b -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000410009/ENST00000410009.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000410009/ENST00000410009.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000410009/frameshift.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/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-1.11/test/csq/ENST00000410009 && /build/reproducible-path/bcftools-1.11/bcftools csq -lb -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000413103/ENST00000413103.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000413103/ENST00000413103.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000413103/long-deletion.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/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-1.11/test/csq/ENSMUST00000121418 && /build/reproducible-path/bcftools-1.11/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25496' --phase m | ../sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.11/test/csq/ENSMUST00000121418 && /build/reproducible-path/bcftools-1.11/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25105' --phase m | ../sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.11/test/csq/ENSMUST00000121418 && /build/reproducible-path/bcftools-1.11/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25500' --phase m | ../sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000263103-INS/ENST00000263103-INS.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000263103-INS/ENST00000263103-INS.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000263103-INS/insertions.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000381157/ENST00000381157.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000381157/ENST00000381157.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000381157/haploid-diploid.vcf | /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000303039/ENST00000303039.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000303039/ENST00000303039.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000303039/not-a-stop.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -l -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000303039/ENST00000303039.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000303039/ENST00000303039.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000303039/not-a-stop.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000593942/ENST00000593942.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000593942/ENST00000593942.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000593942/last-codon-deletion.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000518414/ENST00000518414.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000518414/ENST00000518414.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000518414/incorrect-inframe-del.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/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-1.11/test/csq/ENSMUST00000133836 && /build/reproducible-path/bcftools-1.11/bcftools csq -f ENSMUST00000133836.fa -g ENSMUST00000133836.gff filter-problem.vcf -i 'FILTER="PASS"' --phase m | ../sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000420670/ENST00000420670.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000420670/ENST00000420670.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000420670/start-stop-lost.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000420670/ENST00000420670.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000420670/ENST00000420670.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000420670/segfault.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/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-1.11/test/csq/EMN908947 && /build/reproducible-path/bcftools-1.11/bcftools csq -f EMN908947.fa -g simple.gff simple.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.11/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-1.11/test/csq/EMN908947 && /build/reproducible-path/bcftools-1.11/bcftools csq -f EMN908947.fa -g ribosomal-slippage.gff ribosomal-slippage.vcf --force | ../sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/EDUMMY0003/EDUMMY0003.fa -g /build/reproducible-path/bcftools-1.11/test/csq/EDUMMY0003/EDUMMY0003.gff /build/reproducible-path/bcftools-1.11/test/csq/EDUMMY0003/long-del.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000318249/ENST00000318249.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000318249/ENST00000318249.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000318249/start-lost.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.11/bcftools csq -l -f /build/reproducible-path/bcftools-1.11/test/csq/ENST00000318249/ENST00000318249.fa -g /build/reproducible-path/bcftools-1.11/test/csq/ENST00000318249/ENST00000318249.gff /build/reproducible-path/bcftools-1.11/test/csq/ENST00000318249/start-lost.vcf | /build/reproducible-path/bcftools-1.11/test/csq/sort-csq | /build/reproducible-path/bcftools-1.11/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-1.11/bcftools roh /build/reproducible-path/bcftools-1.11/test/roh.1.vcf.gz -Or -G30 --AF-dflt 0.4| grep -v ^# .. ok test_roh: /build/reproducible-path/bcftools-1.11/bcftools roh /build/reproducible-path/bcftools-1.11/test/roh.1.vcf.gz -Or -G30 --AF-file /build/reproducible-path/bcftools-1.11/test/roh.1.tab.gz| grep -v ^# .. ok test_roh: /build/reproducible-path/bcftools-1.11/bcftools roh /build/reproducible-path/bcftools-1.11/test/roh.1.vcf.gz -Or -G30 --AF-file /build/reproducible-path/bcftools-1.11/test/roh.1.tab.gz --ignore-homref| grep -v ^# .. ok test_roh: /build/reproducible-path/bcftools-1.11/bcftools roh /build/reproducible-path/bcftools-1.11/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245| grep -v ^# .. ok test_roh: /build/reproducible-path/bcftools-1.11/bcftools roh /build/reproducible-path/bcftools-1.11/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-1.11/bcftools roh /build/reproducible-path/bcftools-1.11/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-1.11/bcftools roh /build/reproducible-path/bcftools-1.11/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-1.11/bcftools gtcheck -e 0 /tmp/vQp5weZwFe/gtcheck.1.vcf.gz -g /tmp/vQp5weZwFe/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.11/bcftools gtcheck -e 0 -u GT,GT /tmp/vQp5weZwFe/gtcheck.1.vcf.gz -g /tmp/vQp5weZwFe/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.11/bcftools gtcheck -e 0 -u GT,PL /tmp/vQp5weZwFe/gtcheck.1.vcf.gz -g /tmp/vQp5weZwFe/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.11/bcftools gtcheck -e 0 -u PL,GT /tmp/vQp5weZwFe/gtcheck.1.vcf.gz -g /tmp/vQp5weZwFe/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.11/bcftools gtcheck -e 0 -u PL,PL /tmp/vQp5weZwFe/gtcheck.1.vcf.gz -g /tmp/vQp5weZwFe/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.11/bcftools gtcheck -e 0 -p s1,s1 /tmp/vQp5weZwFe/gtcheck.1.vcf.gz -g /tmp/vQp5weZwFe/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.11/bcftools gtcheck -e 0 /tmp/vQp5weZwFe/gtcheck.2.vcf.gz -g /tmp/vQp5weZwFe/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.11/bcftools gtcheck -e 0 /tmp/vQp5weZwFe/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.11/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/vQp5weZwFe/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.11/bcftools gtcheck -e 0 -P /build/reproducible-path/bcftools-1.11/test/gtcheck.3.pairs /tmp/vQp5weZwFe/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.11/bcftools gtcheck -e 0 -u PL /tmp/vQp5weZwFe/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.11/bcftools gtcheck -e 0 --n-matches 4 /tmp/vQp5weZwFe/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO | sort .. ok test_gtcheck: /build/reproducible-path/bcftools-1.11/bcftools gtcheck -e 0 -s qry:E,D,C /tmp/vQp5weZwFe/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.11/bcftools gtcheck -e 0 -s qry:E,D,C -u PL /tmp/vQp5weZwFe/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.11/bcftools gtcheck -e 0 -s qry:B -s gt:D /tmp/vQp5weZwFe/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.11/bcftools gtcheck -e 0 -s qry:B -s gt:D -u PL /tmp/vQp5weZwFe/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.11/bcftools gtcheck -e 0 -s qry:B -s gt:D,C /tmp/vQp5weZwFe/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.11/bcftools gtcheck -e 0 -p B,C,B,D /tmp/vQp5weZwFe/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.11/bcftools gtcheck -e 0 -u GT,GT -H /tmp/vQp5weZwFe/gtcheck.1.vcf.gz -g /tmp/vQp5weZwFe/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.11/bcftools gtcheck -e 0 -u GT,PL -H /tmp/vQp5weZwFe/gtcheck.1.vcf.gz -g /tmp/vQp5weZwFe/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.11/bcftools gtcheck -e 0 -u PL,GT -H /tmp/vQp5weZwFe/gtcheck.1.vcf.gz -g /tmp/vQp5weZwFe/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.11/bcftools gtcheck -e 0 -u PL,PL -H /tmp/vQp5weZwFe/gtcheck.1.vcf.gz -g /tmp/vQp5weZwFe/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.11/bcftools gtcheck -e 0 -P /build/reproducible-path/bcftools-1.11/test/gtcheck.4.pairs --distinctive-sites 3 /tmp/vQp5weZwFe/gtcheck.4.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.11/bcftools gtcheck -e 0 -P /build/reproducible-path/bcftools-1.11/test/gtcheck.4.pairs --distinctive-sites 3,1 /tmp/vQp5weZwFe/gtcheck.4.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.11/bcftools gtcheck -u GT -e 30 /tmp/vQp5weZwFe/gtcheck.1.vcf.gz -g /tmp/vQp5weZwFe/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.11/bcftools gtcheck -u GT -e 30 -p s1,s1 /tmp/vQp5weZwFe/gtcheck.1.vcf.gz -g /tmp/vQp5weZwFe/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.11/bcftools gtcheck -u GT -e 300 /tmp/vQp5weZwFe/gtcheck.1.vcf.gz -g /tmp/vQp5weZwFe/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.11/bcftools gtcheck -u PL -e 30 /tmp/vQp5weZwFe/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok Number of tests: total .. 1210 passed .. 1209 failed .. 1 make[2]: *** [Makefile:297: test-no-plugins] Error 1 make[2]: Leaving directory '/build/reproducible-path/bcftools-1.11' make[1]: *** [debian/rules:47: override_dh_auto_test] Error 2 make[1]: Leaving directory '/build/reproducible-path/bcftools-1.11' make: *** [debian/rules:11: binary] Error 2 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration E: Failed autobuilding of package I: user script /srv/workspace/pbuilder/4959/tmp/hooks/C01_cleanup starting debug output: disk usage on i-capture-the-hostname at Tue Jan 9 22:20:25 UTC 2024 Filesystem Size Used Avail Use% Mounted on tmpfs 4.0G 0 4.0G 0% /dev/shm I: user script /srv/workspace/pbuilder/4959/tmp/hooks/C01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/4959 and its subdirectories