Diff of the two buildlogs: -- --- b1/build.log 2024-01-09 22:18:34.180378154 +0000 +++ b2/build.log 2024-01-09 22:20:26.875919184 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Feb 10 16:40:17 -12 2025 -I: pbuilder-time-stamp: 1739248817 +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 @@ -18,7 +18,7 @@ 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.utNO8xZy/trustedkeys.kbx': General error +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" @@ -33,51 +33,82 @@ dpkg-source: info: applying 2to3.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/42398/tmp/hooks/D02_print_environment starting +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 - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=16 ' - DISTRIBUTION='bullseye' - HOME='/root' - HOST_ARCH='i386' + 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='50fa94921f524ddcbf8b0c555cc293c7' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='42398' - PS1='# ' - PS2='> ' + 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' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.Zw39VFPA/pbuilderrc_ifYS --distribution bullseye --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Zw39VFPA/b1 --logfile b1/build.log bcftools_1.11-1.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://85.184.249.68:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.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 ionos16-i386 6.1.0-17-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.69-1 (2023-12-30) x86_64 GNU/Linux + 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 @@ -137,7 +168,7 @@ -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 4 Feb 8 15:47 sh -> dash + 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 @@ -163,7 +194,7 @@ -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/42398/tmp/hooks/D02_print_environment finished +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 @@ -266,7 +297,7 @@ 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 2s (13.0 MB/s) +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.) @@ -494,7 +525,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/bcftools-1.11/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../bcftools_1.11-1_source.changes +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 @@ -505,7 +540,7 @@ rm -f config.mk && touch config.mk dh clean dh_auto_clean - make -j16 distclean + 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 @@ -576,7 +611,7 @@ config.status: creating config.h make[1]: Leaving directory '/build/reproducible-path/bcftools-1.11' dh_auto_build - make -j16 + 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 @@ -779,755 +814,763 @@ .. ok test_tabix: - tabix /tmp/8HYPz_snt9/merge.a.vcf.gz 2:3199812-3199812 + tabix /tmp/vQp5weZwFe/merge.a.vcf.gz 2:3199812-3199812 .. ok test_tabix: - /build/reproducible-path/bcftools-1.11/bcftools view -H /tmp/8HYPz_snt9/merge.a.bcf 2:3199812-3199812 + /build/reproducible-path/bcftools-1.11/bcftools view -H /tmp/vQp5weZwFe/merge.a.bcf 2:3199812-3199812 .. ok test_tabix: - tabix /tmp/8HYPz_snt9/merge.a.vcf.gz 1:3000151-3000151 + tabix /tmp/vQp5weZwFe/merge.a.vcf.gz 1:3000151-3000151 .. ok test_tabix: - /build/reproducible-path/bcftools-1.11/bcftools view -H /tmp/8HYPz_snt9/merge.a.bcf 1:3000151-3000151 + /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/8HYPz_snt9/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 + /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/8HYPz_snt9/large_chrom_csi_limit.bcf chr20:1-2147483647 + /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/8HYPz_snt9/large_chrom_csi_limit.bcf chr20:1-2147483647 + /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/8HYPz_snt9/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 + /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/8HYPz_snt9/large_chrom_csi_limit.bcf chr20:1-2147483647 + /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/8HYPz_snt9/large_chrom_csi_limit.vcf.gz chr20 + /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/8HYPz_snt9/large_chrom_csi_limit.bcf chr20 + /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/8HYPz_snt9/large_chrom_csi_limit.bcf chr20 + /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/8HYPz_snt9/large_chrom_csi_limit.vcf.gz chr20 + /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/8HYPz_snt9/large_chrom_csi_limit.bcf chr20 + /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/8HYPz_snt9/idx.vcf.gz + /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/8HYPz_snt9/idx.vcf.gz + /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/8HYPz_snt9/idx.bcf + /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/8HYPz_snt9/idx.vcf.gz + /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/8HYPz_snt9/idx.vcf.gz + /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/8HYPz_snt9/idx.bcf + /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/8HYPz_snt9/empty.vcf.gz + /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/8HYPz_snt9/empty.vcf.gz + /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/8HYPz_snt9/empty.bcf + /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/8HYPz_snt9/empty.vcf.gz + /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/8HYPz_snt9/empty.vcf.gz + /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/8HYPz_snt9/empty.bcf + /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/8HYPz_snt9/check.vcf.gz | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' + /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/8HYPz_snt9/check.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools stats -s - | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' + /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/8HYPz_snt9/check.1.chk /tmp/8HYPz_snt9/check.2.chk /tmp/8HYPz_snt9/check.3.chk /tmp/8HYPz_snt9/check.4.chk | grep -v 'plot-vcfstats' | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' + /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/8HYPz_snt9/stats.a.vcf.gz /tmp/8HYPz_snt9/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' + /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/8HYPz_snt9/stats.a.vcf.gz /tmp/8HYPz_snt9/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' + /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/8HYPz_snt9/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' + /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/8HYPz_snt9/isec.a.vcf.gz /tmp/8HYPz_snt9/isec.b.vcf.gz + /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/8HYPz_snt9/isec.a.vcf.gz /tmp/8HYPz_snt9/isec.b.vcf.gz + /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/8HYPz_snt9/isec.a.vcf.gz /tmp/8HYPz_snt9/isec.b.vcf.gz + /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/8HYPz_snt9/isec.a.vcf.gz /tmp/8HYPz_snt9/isec.b.vcf.gz + /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/8HYPz_snt9/isec.a.vcf.gz /tmp/8HYPz_snt9/isec.b.vcf.gz + /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/8HYPz_snt9/isec.a.vcf.gz /tmp/8HYPz_snt9/isec.b.vcf.gz + /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/8HYPz_snt9/isec.a.vcf.gz /tmp/8HYPz_snt9/isec.b.vcf.gz + /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/8HYPz_snt9/isec.a.vcf.gz /tmp/8HYPz_snt9/isec.b.vcf.gz + /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/8HYPz_snt9/isec.a.vcf.gz /tmp/8HYPz_snt9/isec.b.vcf.gz + /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/8HYPz_snt9/isec.a.vcf.gz /tmp/8HYPz_snt9/isec.b.vcf.gz + /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/8HYPz_snt9/isec.tab.gz /tmp/8HYPz_snt9/isec.a.vcf.gz + /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/8HYPz_snt9/isec.tab.gz /tmp/8HYPz_snt9/isec.a.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/isec-miss.1.1.vcf.gz /tmp/8HYPz_snt9/isec-miss.1.2.vcf.gz /tmp/8HYPz_snt9/isec-miss.1.3.vcf.gz + /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/8HYPz_snt9/isec-miss.1.1.vcf.gz /tmp/8HYPz_snt9/isec-miss.1.2.vcf.gz /tmp/8HYPz_snt9/isec-miss.1.3.vcf.gz + /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/8HYPz_snt9/isec-miss.1.1.vcf.gz /tmp/8HYPz_snt9/isec-miss.1.2.vcf.gz /tmp/8HYPz_snt9/isec-miss.1.3.vcf.gz + /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/8HYPz_snt9/isec-miss.1.1.vcf.gz /tmp/8HYPz_snt9/isec-miss.1.2.vcf.gz /tmp/8HYPz_snt9/isec-miss.1.3.vcf.gz + /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/8HYPz_snt9/isec-miss.2.1.vcf.gz /tmp/8HYPz_snt9/isec-miss.2.2.vcf.gz /tmp/8HYPz_snt9/isec-miss.2.3.vcf.gz + /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/8HYPz_snt9/isec-miss.2.1.vcf.gz /tmp/8HYPz_snt9/isec-miss.2.2.vcf.gz /tmp/8HYPz_snt9/isec-miss.2.3.vcf.gz + /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/8HYPz_snt9/isec-miss.2.1.vcf.gz /tmp/8HYPz_snt9/isec-miss.2.2.vcf.gz /tmp/8HYPz_snt9/isec-miss.2.3.vcf.gz + /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/8HYPz_snt9/isec-miss.2.1.vcf.gz /tmp/8HYPz_snt9/isec-miss.2.2.vcf.gz /tmp/8HYPz_snt9/isec-miss.2.3.vcf.gz + /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/8HYPz_snt9/merge.join.a.vcf.gz /tmp/8HYPz_snt9/merge.join.b.vcf.gz + /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/8HYPz_snt9/merge.join.a.vcf.gz /tmp/8HYPz_snt9/merge.join.b.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/merge.join.a.bcf /tmp/8HYPz_snt9/merge.join.b.bcf + /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/8HYPz_snt9/merge.join.a.bcf /tmp/8HYPz_snt9/merge.join.b.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/merge.LPL.a.vcf.gz /tmp/8HYPz_snt9/merge.LPL.b.vcf.gz /tmp/8HYPz_snt9/merge.LPL.c.vcf.gz + /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/8HYPz_snt9/merge.LPL.a.vcf.gz /tmp/8HYPz_snt9/merge.LPL.b.vcf.gz /tmp/8HYPz_snt9/merge.LPL.c.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/merge.LPL.a.bcf /tmp/8HYPz_snt9/merge.LPL.b.bcf /tmp/8HYPz_snt9/merge.LPL.c.bcf + /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/8HYPz_snt9/merge.LPL.a.bcf /tmp/8HYPz_snt9/merge.LPL.b.bcf /tmp/8HYPz_snt9/merge.LPL.c.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/merge.LPL.a.vcf.gz /tmp/8HYPz_snt9/merge.LPL.b.vcf.gz /tmp/8HYPz_snt9/merge.LPL.c.vcf.gz + /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/8HYPz_snt9/merge.LPL.a.vcf.gz /tmp/8HYPz_snt9/merge.LPL.b.vcf.gz /tmp/8HYPz_snt9/merge.LPL.c.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/merge.LPL.a.bcf /tmp/8HYPz_snt9/merge.LPL.b.bcf /tmp/8HYPz_snt9/merge.LPL.c.bcf + /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/8HYPz_snt9/merge.LPL.a.bcf /tmp/8HYPz_snt9/merge.LPL.b.bcf /tmp/8HYPz_snt9/merge.LPL.c.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/merge.LPL.a.vcf.gz /tmp/8HYPz_snt9/merge.LPL.b.vcf.gz /tmp/8HYPz_snt9/merge.LPL.c.vcf.gz + /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/8HYPz_snt9/merge.LPL.a.vcf.gz /tmp/8HYPz_snt9/merge.LPL.b.vcf.gz /tmp/8HYPz_snt9/merge.LPL.c.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/merge.LPL.a.bcf /tmp/8HYPz_snt9/merge.LPL.b.bcf /tmp/8HYPz_snt9/merge.LPL.c.bcf + /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/8HYPz_snt9/merge.LPL.a.bcf /tmp/8HYPz_snt9/merge.LPL.b.bcf /tmp/8HYPz_snt9/merge.LPL.c.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/merge.LPL.a.vcf.gz /tmp/8HYPz_snt9/merge.LPL.b.vcf.gz /tmp/8HYPz_snt9/merge.LPL.c.vcf.gz + /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/8HYPz_snt9/merge.LPL.a.vcf.gz /tmp/8HYPz_snt9/merge.LPL.b.vcf.gz /tmp/8HYPz_snt9/merge.LPL.c.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/merge.LPL.a.bcf /tmp/8HYPz_snt9/merge.LPL.b.bcf /tmp/8HYPz_snt9/merge.LPL.c.bcf -.. ok + /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/8HYPz_snt9/merge.LPL.a.bcf /tmp/8HYPz_snt9/merge.LPL.b.bcf /tmp/8HYPz_snt9/merge.LPL.c.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/merge.LPL.a.vcf.gz /tmp/8HYPz_snt9/merge.LPL.b.vcf.gz /tmp/8HYPz_snt9/merge.LPL.c.vcf.gz + /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/8HYPz_snt9/merge.LPL.a.vcf.gz /tmp/8HYPz_snt9/merge.LPL.b.vcf.gz /tmp/8HYPz_snt9/merge.LPL.c.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/merge.LPL.a.bcf /tmp/8HYPz_snt9/merge.LPL.b.bcf /tmp/8HYPz_snt9/merge.LPL.c.bcf + /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/8HYPz_snt9/merge.LPL.a.bcf /tmp/8HYPz_snt9/merge.LPL.b.bcf /tmp/8HYPz_snt9/merge.LPL.c.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/merge.LPL.a.vcf.gz /tmp/8HYPz_snt9/merge.LPL.b.vcf.gz /tmp/8HYPz_snt9/merge.LPL.c.vcf.gz + /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/8HYPz_snt9/merge.LPL.a.vcf.gz /tmp/8HYPz_snt9/merge.LPL.b.vcf.gz /tmp/8HYPz_snt9/merge.LPL.c.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/merge.LPL.a.bcf /tmp/8HYPz_snt9/merge.LPL.b.bcf /tmp/8HYPz_snt9/merge.LPL.c.bcf + /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/8HYPz_snt9/merge.LPL.a.bcf /tmp/8HYPz_snt9/merge.LPL.b.bcf /tmp/8HYPz_snt9/merge.LPL.c.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/merge.a.vcf.gz /tmp/8HYPz_snt9/merge.b.vcf.gz /tmp/8HYPz_snt9/merge.c.vcf.gz + /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/8HYPz_snt9/merge.a.vcf.gz /tmp/8HYPz_snt9/merge.b.vcf.gz /tmp/8HYPz_snt9/merge.c.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/merge.a.bcf /tmp/8HYPz_snt9/merge.b.bcf /tmp/8HYPz_snt9/merge.c.bcf + /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/8HYPz_snt9/merge.a.bcf /tmp/8HYPz_snt9/merge.b.bcf /tmp/8HYPz_snt9/merge.c.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/merge.a.vcf.gz /tmp/8HYPz_snt9/merge.b.vcf.gz /tmp/8HYPz_snt9/merge.c.vcf.gz + /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/8HYPz_snt9/merge.a.vcf.gz /tmp/8HYPz_snt9/merge.b.vcf.gz /tmp/8HYPz_snt9/merge.c.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/merge.a.bcf /tmp/8HYPz_snt9/merge.b.bcf /tmp/8HYPz_snt9/merge.c.bcf + /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/8HYPz_snt9/merge.a.bcf /tmp/8HYPz_snt9/merge.b.bcf /tmp/8HYPz_snt9/merge.c.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/merge.a.vcf.gz /tmp/8HYPz_snt9/merge.b.vcf.gz /tmp/8HYPz_snt9/merge.c.vcf.gz + /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/8HYPz_snt9/merge.a.vcf.gz /tmp/8HYPz_snt9/merge.b.vcf.gz /tmp/8HYPz_snt9/merge.c.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/merge.a.bcf /tmp/8HYPz_snt9/merge.b.bcf /tmp/8HYPz_snt9/merge.c.bcf + /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/8HYPz_snt9/merge.a.bcf /tmp/8HYPz_snt9/merge.b.bcf /tmp/8HYPz_snt9/merge.c.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/merge.2.a.vcf.gz /tmp/8HYPz_snt9/merge.2.b.vcf.gz + /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/8HYPz_snt9/merge.2.a.vcf.gz /tmp/8HYPz_snt9/merge.2.b.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/merge.2.a.bcf /tmp/8HYPz_snt9/merge.2.b.bcf + /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/8HYPz_snt9/merge.2.a.bcf /tmp/8HYPz_snt9/merge.2.b.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/merge.2.a.vcf.gz /tmp/8HYPz_snt9/merge.2.b.vcf.gz + /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/8HYPz_snt9/merge.2.a.vcf.gz /tmp/8HYPz_snt9/merge.2.b.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/merge.2.a.bcf /tmp/8HYPz_snt9/merge.2.b.bcf + /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/8HYPz_snt9/merge.2.a.bcf /tmp/8HYPz_snt9/merge.2.b.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/merge.2.a.vcf.gz /tmp/8HYPz_snt9/merge.2.b.vcf.gz + /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/8HYPz_snt9/merge.2.a.vcf.gz /tmp/8HYPz_snt9/merge.2.b.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/merge.2.a.bcf /tmp/8HYPz_snt9/merge.2.b.bcf + /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/8HYPz_snt9/merge.2.a.bcf /tmp/8HYPz_snt9/merge.2.b.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/merge.3.a.vcf.gz /tmp/8HYPz_snt9/merge.3.b.vcf.gz + /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/8HYPz_snt9/merge.3.a.vcf.gz /tmp/8HYPz_snt9/merge.3.b.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/merge.3.a.bcf /tmp/8HYPz_snt9/merge.3.b.bcf + /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/8HYPz_snt9/merge.3.a.bcf /tmp/8HYPz_snt9/merge.3.b.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/merge.4.a.vcf.gz /tmp/8HYPz_snt9/merge.4.b.vcf.gz + /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/8HYPz_snt9/merge.4.a.vcf.gz /tmp/8HYPz_snt9/merge.4.b.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/merge.4.a.bcf /tmp/8HYPz_snt9/merge.4.b.bcf + /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/8HYPz_snt9/merge.4.a.bcf /tmp/8HYPz_snt9/merge.4.b.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/gvcf.merge.1.vcf.gz /tmp/8HYPz_snt9/gvcf.merge.2.vcf.gz /tmp/8HYPz_snt9/gvcf.merge.3.vcf.gz + /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/8HYPz_snt9/gvcf.merge.1.vcf.gz /tmp/8HYPz_snt9/gvcf.merge.2.vcf.gz /tmp/8HYPz_snt9/gvcf.merge.3.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/gvcf.merge.1.bcf /tmp/8HYPz_snt9/gvcf.merge.2.bcf /tmp/8HYPz_snt9/gvcf.merge.3.bcf + /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/8HYPz_snt9/gvcf.merge.1.bcf /tmp/8HYPz_snt9/gvcf.merge.2.bcf /tmp/8HYPz_snt9/gvcf.merge.3.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/merge.gvcf.2.a.vcf.gz /tmp/8HYPz_snt9/merge.gvcf.2.b.vcf.gz /tmp/8HYPz_snt9/merge.gvcf.2.c.vcf.gz + /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/8HYPz_snt9/merge.gvcf.2.a.vcf.gz /tmp/8HYPz_snt9/merge.gvcf.2.b.vcf.gz /tmp/8HYPz_snt9/merge.gvcf.2.c.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/merge.gvcf.3.a.vcf.gz /tmp/8HYPz_snt9/merge.gvcf.3.b.vcf.gz + /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/8HYPz_snt9/merge.gvcf.3.a.vcf.gz /tmp/8HYPz_snt9/merge.gvcf.3.b.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/merge.gvcf.4.a.vcf.gz /tmp/8HYPz_snt9/merge.gvcf.4.b.vcf.gz + /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/8HYPz_snt9/merge.gvcf.4.a.vcf.gz /tmp/8HYPz_snt9/merge.gvcf.4.b.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/merge.gvcf.4.a.bcf /tmp/8HYPz_snt9/merge.gvcf.4.b.bcf + /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/8HYPz_snt9/merge.gvcf.4.a.bcf /tmp/8HYPz_snt9/merge.gvcf.4.b.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/merge.5.a.vcf.gz /tmp/8HYPz_snt9/merge.5.b.vcf.gz + /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/8HYPz_snt9/merge.5.a.vcf.gz /tmp/8HYPz_snt9/merge.5.b.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/merge.5.a.bcf /tmp/8HYPz_snt9/merge.5.b.bcf + /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/8HYPz_snt9/merge.5.a.bcf /tmp/8HYPz_snt9/merge.5.b.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/merge.6.a.vcf.gz /tmp/8HYPz_snt9/merge.6.b.vcf.gz + /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/8HYPz_snt9/merge.6.a.vcf.gz /tmp/8HYPz_snt9/merge.6.b.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/merge.6.a.bcf /tmp/8HYPz_snt9/merge.6.b.bcf + /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/8HYPz_snt9/merge.6.a.bcf /tmp/8HYPz_snt9/merge.6.b.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/merge.gvcf.7.a.vcf.gz /tmp/8HYPz_snt9/merge.gvcf.7.b.vcf.gz + /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/8HYPz_snt9/merge.gvcf.7.a.vcf.gz /tmp/8HYPz_snt9/merge.gvcf.7.b.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/merge.gvcf.7.a.bcf /tmp/8HYPz_snt9/merge.gvcf.7.b.bcf + /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/8HYPz_snt9/merge.gvcf.7.a.bcf /tmp/8HYPz_snt9/merge.gvcf.7.b.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/merge.gvcf.8.a.vcf.gz /tmp/8HYPz_snt9/merge.gvcf.8.b.vcf.gz + /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/8HYPz_snt9/merge.gvcf.8.a.vcf.gz /tmp/8HYPz_snt9/merge.gvcf.8.b.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/merge.gvcf.8.a.bcf /tmp/8HYPz_snt9/merge.gvcf.8.b.bcf + /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/8HYPz_snt9/merge.gvcf.8.a.bcf /tmp/8HYPz_snt9/merge.gvcf.8.b.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/merge.7.a.vcf.gz /tmp/8HYPz_snt9/merge.7.b.vcf.gz + /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/8HYPz_snt9/merge.7.a.vcf.gz /tmp/8HYPz_snt9/merge.7.b.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/merge.7.a.bcf /tmp/8HYPz_snt9/merge.7.b.bcf + /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/8HYPz_snt9/merge.7.a.bcf /tmp/8HYPz_snt9/merge.7.b.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/merge.gvcf.9a.vcf.gz /tmp/8HYPz_snt9/merge.gvcf.9b.vcf.gz /tmp/8HYPz_snt9/merge.gvcf.9c.vcf.gz /tmp/8HYPz_snt9/merge.gvcf.9d.vcf.gz + /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/8HYPz_snt9/merge.gvcf.9a.vcf.gz /tmp/8HYPz_snt9/merge.gvcf.9b.vcf.gz /tmp/8HYPz_snt9/merge.gvcf.9c.vcf.gz /tmp/8HYPz_snt9/merge.gvcf.9d.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/merge.gvcf.9a.bcf /tmp/8HYPz_snt9/merge.gvcf.9b.bcf /tmp/8HYPz_snt9/merge.gvcf.9c.bcf /tmp/8HYPz_snt9/merge.gvcf.9d.bcf + /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/8HYPz_snt9/merge.gvcf.9a.bcf /tmp/8HYPz_snt9/merge.gvcf.9b.bcf /tmp/8HYPz_snt9/merge.gvcf.9c.bcf /tmp/8HYPz_snt9/merge.gvcf.9d.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/merge.gvcf.9a.vcf.gz /tmp/8HYPz_snt9/merge.gvcf.9b.vcf.gz /tmp/8HYPz_snt9/merge.gvcf.9c.vcf.gz /tmp/8HYPz_snt9/merge.gvcf.9d.vcf.gz + /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/8HYPz_snt9/merge.gvcf.9a.vcf.gz /tmp/8HYPz_snt9/merge.gvcf.9b.vcf.gz /tmp/8HYPz_snt9/merge.gvcf.9c.vcf.gz /tmp/8HYPz_snt9/merge.gvcf.9d.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/merge.gvcf.9a.bcf /tmp/8HYPz_snt9/merge.gvcf.9b.bcf /tmp/8HYPz_snt9/merge.gvcf.9c.bcf /tmp/8HYPz_snt9/merge.gvcf.9d.bcf + /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/8HYPz_snt9/merge.gvcf.9a.bcf /tmp/8HYPz_snt9/merge.gvcf.9b.bcf /tmp/8HYPz_snt9/merge.gvcf.9c.bcf /tmp/8HYPz_snt9/merge.gvcf.9d.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/merge.gvcf.9a.vcf.gz /tmp/8HYPz_snt9/merge.gvcf.9b.vcf.gz /tmp/8HYPz_snt9/merge.gvcf.9c.vcf.gz /tmp/8HYPz_snt9/merge.gvcf.9d.vcf.gz /tmp/8HYPz_snt9/merge.gvcf.9e.vcf.gz + /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/8HYPz_snt9/merge.gvcf.9a.vcf.gz /tmp/8HYPz_snt9/merge.gvcf.9b.vcf.gz /tmp/8HYPz_snt9/merge.gvcf.9c.vcf.gz /tmp/8HYPz_snt9/merge.gvcf.9d.vcf.gz /tmp/8HYPz_snt9/merge.gvcf.9e.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/merge.gvcf.9a.bcf /tmp/8HYPz_snt9/merge.gvcf.9b.bcf /tmp/8HYPz_snt9/merge.gvcf.9c.bcf /tmp/8HYPz_snt9/merge.gvcf.9d.bcf /tmp/8HYPz_snt9/merge.gvcf.9e.bcf + /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/8HYPz_snt9/merge.gvcf.9a.bcf /tmp/8HYPz_snt9/merge.gvcf.9b.bcf /tmp/8HYPz_snt9/merge.gvcf.9c.bcf /tmp/8HYPz_snt9/merge.gvcf.9d.bcf /tmp/8HYPz_snt9/merge.gvcf.9e.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/merge.gvcf.9a.vcf.gz /tmp/8HYPz_snt9/merge.gvcf.9b.vcf.gz /tmp/8HYPz_snt9/merge.gvcf.9c.vcf.gz /tmp/8HYPz_snt9/merge.gvcf.9d.vcf.gz /tmp/8HYPz_snt9/merge.gvcf.9e.vcf.gz + /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/8HYPz_snt9/merge.gvcf.9a.vcf.gz /tmp/8HYPz_snt9/merge.gvcf.9b.vcf.gz /tmp/8HYPz_snt9/merge.gvcf.9c.vcf.gz /tmp/8HYPz_snt9/merge.gvcf.9d.vcf.gz /tmp/8HYPz_snt9/merge.gvcf.9e.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/merge.gvcf.9a.bcf /tmp/8HYPz_snt9/merge.gvcf.9b.bcf /tmp/8HYPz_snt9/merge.gvcf.9c.bcf /tmp/8HYPz_snt9/merge.gvcf.9d.bcf /tmp/8HYPz_snt9/merge.gvcf.9e.bcf + /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/8HYPz_snt9/merge.gvcf.9a.bcf /tmp/8HYPz_snt9/merge.gvcf.9b.bcf /tmp/8HYPz_snt9/merge.gvcf.9c.bcf /tmp/8HYPz_snt9/merge.gvcf.9d.bcf /tmp/8HYPz_snt9/merge.gvcf.9e.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/merge.gvcf.10.a.vcf.gz /tmp/8HYPz_snt9/merge.gvcf.10.b.vcf.gz + /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/8HYPz_snt9/merge.gvcf.10.a.vcf.gz /tmp/8HYPz_snt9/merge.gvcf.10.b.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/merge.gvcf.10.a.bcf /tmp/8HYPz_snt9/merge.gvcf.10.b.bcf + /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/8HYPz_snt9/merge.gvcf.10.a.bcf /tmp/8HYPz_snt9/merge.gvcf.10.b.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/merge.gvcf.10.a.vcf.gz /tmp/8HYPz_snt9/merge.gvcf.10.b.vcf.gz + /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/8HYPz_snt9/merge.gvcf.10.a.vcf.gz /tmp/8HYPz_snt9/merge.gvcf.10.b.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/merge.gvcf.10.a.bcf /tmp/8HYPz_snt9/merge.gvcf.10.b.bcf + /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/8HYPz_snt9/merge.gvcf.10.a.bcf /tmp/8HYPz_snt9/merge.gvcf.10.b.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/merge.gvcf.10.a.vcf.gz /tmp/8HYPz_snt9/merge.gvcf.10.b.vcf.gz + /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/8HYPz_snt9/merge.gvcf.10.a.vcf.gz /tmp/8HYPz_snt9/merge.gvcf.10.b.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/merge.gvcf.10.a.bcf /tmp/8HYPz_snt9/merge.gvcf.10.b.bcf + /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/8HYPz_snt9/merge.gvcf.10.a.bcf /tmp/8HYPz_snt9/merge.gvcf.10.b.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/merge.gvcf.10.a.vcf.gz /tmp/8HYPz_snt9/merge.gvcf.10.b.vcf.gz + /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/8HYPz_snt9/merge.gvcf.10.a.vcf.gz /tmp/8HYPz_snt9/merge.gvcf.10.b.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/merge.gvcf.10.a.bcf /tmp/8HYPz_snt9/merge.gvcf.10.b.bcf + /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/8HYPz_snt9/merge.gvcf.10.a.bcf /tmp/8HYPz_snt9/merge.gvcf.10.b.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/merge.gvcf.10.b.vcf.gz /tmp/8HYPz_snt9/merge.gvcf.10.a.vcf.gz + /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/8HYPz_snt9/merge.gvcf.10.b.vcf.gz /tmp/8HYPz_snt9/merge.gvcf.10.a.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/merge.gvcf.10.b.bcf /tmp/8HYPz_snt9/merge.gvcf.10.a.bcf + /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/8HYPz_snt9/merge.gvcf.10.b.bcf /tmp/8HYPz_snt9/merge.gvcf.10.a.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/merge.gvcf.10.b.vcf.gz /tmp/8HYPz_snt9/merge.gvcf.10.a.vcf.gz + /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/8HYPz_snt9/merge.gvcf.10.b.vcf.gz /tmp/8HYPz_snt9/merge.gvcf.10.a.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/merge.gvcf.10.b.bcf /tmp/8HYPz_snt9/merge.gvcf.10.a.bcf + /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/8HYPz_snt9/merge.gvcf.10.b.bcf /tmp/8HYPz_snt9/merge.gvcf.10.a.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/merge.noidx.a.vcf.gz /tmp/8HYPz_snt9/merge.noidx.b.vcf.gz /tmp/8HYPz_snt9/merge.noidx.c.vcf.gz + /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/8HYPz_snt9/merge.noidx.a.vcf.gz /tmp/8HYPz_snt9/merge.noidx.b.vcf.gz /tmp/8HYPz_snt9/merge.noidx.c.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/merge.noidx.a.bcf /tmp/8HYPz_snt9/merge.noidx.b.bcf /tmp/8HYPz_snt9/merge.noidx.c.bcf + /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/8HYPz_snt9/merge.noidx.a.bcf /tmp/8HYPz_snt9/merge.noidx.b.bcf /tmp/8HYPz_snt9/merge.noidx.c.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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: @@ -1539,1267 +1582,1267 @@ .. ok test_vcf_merge: - /build/reproducible-path/bcftools-1.11/bcftools merge --no-version --no-index /tmp/8HYPz_snt9/merge.noidx.a.bcf /tmp/8HYPz_snt9/merge.noidx.b.bcf /tmp/8HYPz_snt9/merge.noidx.c.bcf + /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/8HYPz_snt9/merge.noidx.a.bcf /tmp/8HYPz_snt9/merge.noidx.b.bcf /tmp/8HYPz_snt9/merge.noidx.c.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/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"' /tmp/vQp5weZwFe/query.string.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/8HYPz_snt9/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"' + /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/8HYPz_snt9/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"' /tmp/vQp5weZwFe/query.string.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/8HYPz_snt9/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"' + /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/8HYPz_snt9/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"' /tmp/vQp5weZwFe/query.string.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/8HYPz_snt9/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"' + /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/8HYPz_snt9/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' /tmp/vQp5weZwFe/query.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/8HYPz_snt9/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' + /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/8HYPz_snt9/query.variantkey.vcf.gz + /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/8HYPz_snt9/query.variantkey.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f '%RSX\t%VKX\n' + /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/8HYPz_snt9/view.filter.vcf.gz + /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/8HYPz_snt9/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%XRI\n' -i'XRI[*]>1111' + /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/8HYPz_snt9/view.filter.vcf.gz + /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/8HYPz_snt9/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' + /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/8HYPz_snt9/view.filter.vcf.gz + /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/8HYPz_snt9/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' + /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/8HYPz_snt9/view.filter.vcf.gz + /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/8HYPz_snt9/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' + /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/8HYPz_snt9/view.filter.vcf.gz + /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/8HYPz_snt9/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' + /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/8HYPz_snt9/view.filter.vcf.gz + /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/8HYPz_snt9/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' + /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/8HYPz_snt9/view.filter.vcf.gz + /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/8HYPz_snt9/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' + /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/8HYPz_snt9/query.vcf.gz + /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/8HYPz_snt9/query.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' + /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/8HYPz_snt9/query.vcf.gz + /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/8HYPz_snt9/query.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' + /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/8HYPz_snt9/query.vcf.gz + /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/8HYPz_snt9/query.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' + /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/8HYPz_snt9/query.vcf.gz + /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/8HYPz_snt9/query.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' + /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/8HYPz_snt9/view.filter.vcf.gz + /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/8HYPz_snt9/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' + /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/8HYPz_snt9/query.vcf.gz + /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/8HYPz_snt9/query.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' + /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/8HYPz_snt9/query.vcf.gz + /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/8HYPz_snt9/query.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' + /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/8HYPz_snt9/query.vcf.gz + /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/8HYPz_snt9/query.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' + /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/8HYPz_snt9/query.vcf.gz + /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/8HYPz_snt9/query.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' + /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/8HYPz_snt9/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' /tmp/vQp5weZwFe/view.vectors.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/8HYPz_snt9/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' + /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/8HYPz_snt9/query.filter.vcf.gz + /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/8HYPz_snt9/query.filter.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' + /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/8HYPz_snt9/query.filter.vcf.gz + /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/8HYPz_snt9/query.filter.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' + /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/8HYPz_snt9/query.filter.vcf.gz + /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/8HYPz_snt9/query.filter.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' + /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/8HYPz_snt9/query.filter.vcf.gz + /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/8HYPz_snt9/query.filter.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' + /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/8HYPz_snt9/query.2.vcf.gz + /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/8HYPz_snt9/query.2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' + /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/8HYPz_snt9/missing.vcf.gz + /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/8HYPz_snt9/missing.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -i'IINT="."' -f'%POS %IINT\n' + /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/8HYPz_snt9/missing.vcf.gz + /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/8HYPz_snt9/missing.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -i'IINT!="."' -f'%POS %IINT\n' + /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/8HYPz_snt9/missing.vcf.gz + /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/8HYPz_snt9/missing.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -e'IINT!="."' -f'%POS %IINT\n' + /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/8HYPz_snt9/missing.vcf.gz + /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/8HYPz_snt9/missing.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -e'IINT="."' -f'%POS %IINT\n' + /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/8HYPz_snt9/missing.vcf.gz + /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/8HYPz_snt9/missing.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' + /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/8HYPz_snt9/missing.vcf.gz + /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/8HYPz_snt9/missing.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' + /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/8HYPz_snt9/missing.vcf.gz + /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/8HYPz_snt9/missing.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' + /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/8HYPz_snt9/missing.vcf.gz + /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/8HYPz_snt9/missing.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' + /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/8HYPz_snt9/missing.vcf.gz + /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/8HYPz_snt9/missing.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' + /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/8HYPz_snt9/missing.vcf.gz + /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/8HYPz_snt9/missing.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' + /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/8HYPz_snt9/missing.vcf.gz + /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/8HYPz_snt9/missing.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' + /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/8HYPz_snt9/missing.vcf.gz + /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/8HYPz_snt9/missing.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' + /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/8HYPz_snt9/missing.vcf.gz + /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/8HYPz_snt9/missing.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' + /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/8HYPz_snt9/filter.11.vcf.gz + /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/8HYPz_snt9/filter.11.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -i'FILTER="A"' -f'%POS %FILTER\n' + /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/8HYPz_snt9/filter.11.vcf.gz + /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/8HYPz_snt9/filter.11.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -i'FILTER!="A"' -f'%POS %FILTER\n' + /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/8HYPz_snt9/filter.11.vcf.gz + /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/8HYPz_snt9/filter.11.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -i'FILTER~"A"' -f'%POS %FILTER\n' + /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/8HYPz_snt9/filter.11.vcf.gz + /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/8HYPz_snt9/filter.11.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n' + /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/8HYPz_snt9/query.vcf.gz + /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/8HYPz_snt9/query.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%LINE' + /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/8HYPz_snt9/query.filter-type.vcf.gz + /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/8HYPz_snt9/query.filter-type.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' + /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/8HYPz_snt9/query.filter-type.vcf.gz + /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/8HYPz_snt9/query.filter-type.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' + /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/8HYPz_snt9/query.filter-type.vcf.gz + /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/8HYPz_snt9/query.filter-type.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' + /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/8HYPz_snt9/query.filter-type.vcf.gz + /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/8HYPz_snt9/query.filter-type.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' + /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/8HYPz_snt9/query.filter-type.vcf.gz + /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/8HYPz_snt9/query.filter-type.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\n' -i'INFO/TYPE="xxx"' + /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/8HYPz_snt9/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' /tmp/vQp5weZwFe/filter-missing-floats.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/8HYPz_snt9/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' + /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/8HYPz_snt9/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' /tmp/vQp5weZwFe/filter-missing-floats.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/8HYPz_snt9/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' + /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/8HYPz_snt9/missing.vcf.gz + /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/8HYPz_snt9/missing.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' + /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/8HYPz_snt9/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"' /tmp/vQp5weZwFe/query.filter.2.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/8HYPz_snt9/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"' + /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/8HYPz_snt9/view.filter.vcf.gz + /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/8HYPz_snt9/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' + /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/8HYPz_snt9/view.filter.vcf.gz + /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/8HYPz_snt9/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' + /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/8HYPz_snt9/view.filter.vcf.gz + /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/8HYPz_snt9/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' + /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/8HYPz_snt9/view.filter.vcf.gz + /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/8HYPz_snt9/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' + /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/8HYPz_snt9/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' /tmp/vQp5weZwFe/view.filter.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/8HYPz_snt9/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' + /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/8HYPz_snt9/view.filter.vcf.gz + /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/8HYPz_snt9/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' + /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/8HYPz_snt9/view.filter.vcf.gz + /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/8HYPz_snt9/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' + /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/8HYPz_snt9/view.filter.vcf.gz + /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/8HYPz_snt9/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' + /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/8HYPz_snt9/view.filter.vcf.gz + /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/8HYPz_snt9/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' + /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/8HYPz_snt9/view.filter.vcf.gz + /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/8HYPz_snt9/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' + /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/8HYPz_snt9/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' /tmp/vQp5weZwFe/filter.5.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/8HYPz_snt9/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' + /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/8HYPz_snt9/filter.5.vcf.gz + /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/8HYPz_snt9/filter.5.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' + /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/8HYPz_snt9/view.filter.vcf.gz + /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/8HYPz_snt9/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' + /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/8HYPz_snt9/view.filter.vcf.gz + /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/8HYPz_snt9/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' + /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/8HYPz_snt9/view.filter.vcf.gz + /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/8HYPz_snt9/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' + /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/8HYPz_snt9/view.filter.vcf.gz + /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/8HYPz_snt9/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' + /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/8HYPz_snt9/view.filter.vcf.gz + /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/8HYPz_snt9/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' + /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/8HYPz_snt9/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' /tmp/vQp5weZwFe/view.filter.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/8HYPz_snt9/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' + /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/8HYPz_snt9/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' /tmp/vQp5weZwFe/view.filter.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/8HYPz_snt9/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' + /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/8HYPz_snt9/query.filter.3.vcf.gz + /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/8HYPz_snt9/query.filter.3.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' + /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/8HYPz_snt9/query.filter.3.vcf.gz + /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/8HYPz_snt9/query.filter.3.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"' + /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/8HYPz_snt9/query.filter.3.vcf.gz + /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/8HYPz_snt9/query.filter.3.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' + /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/8HYPz_snt9/filter.5.vcf.gz + /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/8HYPz_snt9/filter.5.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %AD\n]\n' -i'AD[:0]+AD[:1] > 12' + /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/8HYPz_snt9/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="*"' /tmp/vQp5weZwFe/query.filter.4.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/8HYPz_snt9/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="*"' + /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/8HYPz_snt9/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' /tmp/vQp5weZwFe/view.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/8HYPz_snt9/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' + /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/8HYPz_snt9/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' /tmp/vQp5weZwFe/query.filter.5.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/8HYPz_snt9/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' + /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/8HYPz_snt9/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' /tmp/vQp5weZwFe/query.filter.5.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/8HYPz_snt9/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' + /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/8HYPz_snt9/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' /tmp/vQp5weZwFe/query.filter.5.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/8HYPz_snt9/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' + /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/8HYPz_snt9/query.vcf.gz + /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/8HYPz_snt9/query.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%CHROM %POS\n' -i'CHROM="4"' + /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/8HYPz_snt9/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)' /tmp/vQp5weZwFe/query.negative.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/8HYPz_snt9/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)' + /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/8HYPz_snt9/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)' /tmp/vQp5weZwFe/query.negative.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/8HYPz_snt9/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)' + /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/8HYPz_snt9/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)' /tmp/vQp5weZwFe/query.negative.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/8HYPz_snt9/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)' + /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/8HYPz_snt9/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)' /tmp/vQp5weZwFe/query.negative.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/8HYPz_snt9/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)' + /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/8HYPz_snt9/query.vcf.gz + /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/8HYPz_snt9/query.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'[%POS\t%SAMPLE\t%GQ\n]' -i'N_PASS(GQ<20)==1' + /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/8HYPz_snt9/query.vcf.gz + /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/8HYPz_snt9/query.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%CHROM\t%POS\t%INFO\t%FORMAT\n' -s D,C + /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/8HYPz_snt9/query.filter.6.vcf.gz + /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/8HYPz_snt9/query.filter.6.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\n' -i'POS==16777217 || POS==33554432 || POS=118673904' + /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/8HYPz_snt9/query.filter.7.vcf.gz + /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/8HYPz_snt9/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(II)==6' + /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/8HYPz_snt9/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' /tmp/vQp5weZwFe/query.filter.7.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/8HYPz_snt9/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' + /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/8HYPz_snt9/query.filter.7.vcf.gz + /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/8HYPz_snt9/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(II)==2' + /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/8HYPz_snt9/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' /tmp/vQp5weZwFe/query.filter.7.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/8HYPz_snt9/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' + /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/8HYPz_snt9/query.filter.7.vcf.gz + /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/8HYPz_snt9/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(II)==2' + /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/8HYPz_snt9/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' /tmp/vQp5weZwFe/query.filter.7.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/8HYPz_snt9/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' + /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/8HYPz_snt9/query.filter.7.vcf.gz + /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/8HYPz_snt9/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(II)==2' + /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/8HYPz_snt9/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' /tmp/vQp5weZwFe/query.filter.7.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/8HYPz_snt9/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' + /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/8HYPz_snt9/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' /tmp/vQp5weZwFe/query.filter.8.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/8HYPz_snt9/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' + /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/8HYPz_snt9/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' /tmp/vQp5weZwFe/query.filter.8.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/8HYPz_snt9/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' + /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/8HYPz_snt9/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]' /tmp/vQp5weZwFe/query.filter.9.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/8HYPz_snt9/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]' + /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/8HYPz_snt9/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]' /tmp/vQp5weZwFe/query.filter.9.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/8HYPz_snt9/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]' + /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/8HYPz_snt9/query.filter.10.vcf.gz + /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/8HYPz_snt9/query.filter.10.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS %NUM_TAG\n' -i'COUNT(INFO/NUM_TAG)=2' + /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/8HYPz_snt9/query.filter.10.vcf.gz + /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/8HYPz_snt9/query.filter.10.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%POS %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2' + /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/8HYPz_snt9/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' /tmp/vQp5weZwFe/query.vcf.gz .. ok test_vcf_query: - /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/8HYPz_snt9/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' + /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/8HYPz_snt9/norm.vcf.gz + /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/8HYPz_snt9/norm.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/norm.split.vcf.gz + /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/8HYPz_snt9/norm.split.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/norm.split.2.vcf.gz + /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/8HYPz_snt9/norm.split.2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/norm.split.3.vcf.gz + /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/8HYPz_snt9/norm.split.3.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/norm.split.4.vcf.gz + /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/8HYPz_snt9/norm.split.4.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/norm.split.4.vcf.gz + /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/8HYPz_snt9/norm.split.4.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/norm.split.vcf.gz + /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/8HYPz_snt9/norm.split.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/norm.merge.vcf.gz + /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/8HYPz_snt9/norm.merge.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/norm.merge.2.vcf.gz + /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/8HYPz_snt9/norm.merge.2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/norm.merge.3.vcf.gz + /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/8HYPz_snt9/norm.merge.3.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/norm.merge.vcf.gz + /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/8HYPz_snt9/norm.merge.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/norm.setref.vcf.gz + /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/8HYPz_snt9/norm.setref.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/norm.telomere.vcf.gz + /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/8HYPz_snt9/norm.telomere.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/norm.rmdup.vcf.gz + /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/8HYPz_snt9/norm.rmdup.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/norm.rmdup.vcf.gz + /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/8HYPz_snt9/norm.rmdup.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/norm.rmdup.vcf.gz + /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/8HYPz_snt9/norm.rmdup.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/norm.rmdup.vcf.gz + /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/8HYPz_snt9/norm.rmdup.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/norm.rmdup.vcf.gz + /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/8HYPz_snt9/norm.rmdup.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/norm.rmdup.vcf.gz + /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/8HYPz_snt9/norm.rmdup.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/norm.rmdup.2.vcf.gz + /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/8HYPz_snt9/norm.rmdup.2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/norm.rmdup.2.vcf.gz + /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/8HYPz_snt9/norm.rmdup.2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/norm.rmdup.2.vcf.gz + /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/8HYPz_snt9/norm.rmdup.2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/norm.rmdup.2.vcf.gz + /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/8HYPz_snt9/norm.rmdup.2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/norm.rmdup.2.vcf.gz + /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/8HYPz_snt9/norm.rmdup.2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/norm.rmdup.2.vcf.gz + /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/8HYPz_snt9/norm.rmdup.2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/norm.2.vcf.gz + /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/8HYPz_snt9/norm.2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/norm.iupac.vcf.gz + /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/8HYPz_snt9/norm.iupac.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/norm.3.vcf.gz + /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/8HYPz_snt9/norm.3.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/view.vcf.gz + /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/8HYPz_snt9/view.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/view.vcf.gz -r20,Y + /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/8HYPz_snt9/view.vcf.gz -r20,Y | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/view.vcf.gz + /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/8HYPz_snt9/view.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/view.vcf.gz + /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/8HYPz_snt9/view.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/view.vcf.gz + /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/8HYPz_snt9/view.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/view.vcf.gz + /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/8HYPz_snt9/view.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/view.vcf.gz + /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/8HYPz_snt9/view.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/view.vcf.gz + /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/8HYPz_snt9/view.vcf.gz + /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/8HYPz_snt9/view.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/view.vcf.gz + /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/8HYPz_snt9/view.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/view.vcf.gz + /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/8HYPz_snt9/view.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/view.omitgenotypes.vcf.gz + /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/8HYPz_snt9/view.omitgenotypes.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/view.omitgenotypes.vcf.gz + /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/8HYPz_snt9/view.omitgenotypes.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/view.omitgenotypes.vcf.gz + /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/8HYPz_snt9/many.alleles.vcf.gz + /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/8HYPz_snt9/many.alleles.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/view.vectors.vcf.gz + /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/8HYPz_snt9/view.vectors.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/view.vectors.vcf.gz + /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/8HYPz_snt9/view.vectors.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/view.vectors.2.vcf.gz + /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/8HYPz_snt9/view.vectors.2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/view.filter.vcf.gz + /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/8HYPz_snt9/view.filter.vcf.gz + /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/8HYPz_snt9/view.filter.vcf.gz + /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/8HYPz_snt9/view.filter.vcf.gz + /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/8HYPz_snt9/view.filter.vcf.gz + /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/8HYPz_snt9/view.chrs.vcf.gz + /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/8HYPz_snt9/view.chrs.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/filter.2.vcf.gz 1:3062917-3157410 + /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/8HYPz_snt9/filter.2.vcf.gz 1:3062917-3157410 | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/idx.1.vcf.gz + /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/8HYPz_snt9/idx.2.vcf.gz + /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/8HYPz_snt9/idx.2.vcf.gz + /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/8HYPz_snt9/idx.3.vcf.gz + /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/8HYPz_snt9/idx.4.vcf.gz + /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: @@ -2859,27 +2902,27 @@ .. ok test_vcf_view: - /build/reproducible-path/bcftools-1.11/bcftools view --no-version -H -C5:nonmajor /tmp/8HYPz_snt9/view.minmaxac.vcf.gz + /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/8HYPz_snt9/view.minmaxac.vcf.gz + /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/8HYPz_snt9/view.minmaxac.vcf.gz + /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/8HYPz_snt9/view.filter.annovar.vcf.gz + /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/8HYPz_snt9/view.filter.annovar.vcf.gz + /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/8HYPz_snt9/view.filter.annovar.vcf.gz + /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: @@ -2987,75 +3030,75 @@ .. ok test_vcf_call_cAls: - /build/reproducible-path/bcftools-1.11/bcftools call --no-version -mA -C alleles -T /tmp/8HYPz_snt9/mpileup.tab.gz /build/reproducible-path/bcftools-1.11/test/mpileup.vcf + /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/8HYPz_snt9/mpileup.tab.gz /build/reproducible-path/bcftools-1.11/test/mpileup.vcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/mpileup.2.tab.gz /build/reproducible-path/bcftools-1.11/test/mpileup.2.vcf + /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/8HYPz_snt9/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_ + /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/8HYPz_snt9/mpileup.3.tab.gz -i /build/reproducible-path/bcftools-1.11/test/mpileup.3.vcf + /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/8HYPz_snt9/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_ + /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/8HYPz_snt9/mpileup.4.tab.gz -i /build/reproducible-path/bcftools-1.11/test/mpileup.3.vcf + /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/8HYPz_snt9/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_ + /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/8HYPz_snt9/mpileup.5.tab.gz -i /build/reproducible-path/bcftools-1.11/test/mpileup.3.vcf + /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/8HYPz_snt9/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_ + /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/8HYPz_snt9/mpileup.6.tab.gz -i /build/reproducible-path/bcftools-1.11/test/mpileup.4.vcf + /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/8HYPz_snt9/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_ + /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/8HYPz_snt9/mpileup.7.tab.gz -i /build/reproducible-path/bcftools-1.11/test/mpileup.5.vcf + /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/8HYPz_snt9/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_ + /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/8HYPz_snt9/mpileup.cals.1.tab.gz /build/reproducible-path/bcftools-1.11/test/mpileup.cals.1.vcf + /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/8HYPz_snt9/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_ + /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/8HYPz_snt9/mpileup.cals.2.tab.gz /build/reproducible-path/bcftools-1.11/test/mpileup.cals.2.vcf + /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/8HYPz_snt9/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_ + /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: @@ -3691,123 +3734,123 @@ .. 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/8HYPz_snt9/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 /tmp/vQp5weZwFe/regions.vcf.gz .. ok test_vcf_regions: - /build/reproducible-path/bcftools-1.11/bcftools view -Ob /tmp/8HYPz_snt9/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 + /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/8HYPz_snt9/regions.vcf.gz + /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/8HYPz_snt9/regions.tab.gz /tmp/8HYPz_snt9/regions.vcf.gz + /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/8HYPz_snt9/regions.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/8HYPz_snt9/regions.tab.gz + /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/8HYPz_snt9/regions.tab.gz /tmp/8HYPz_snt9/regions.vcf.gz + /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/8HYPz_snt9/regions.bed /tmp/8HYPz_snt9/regions.vcf.gz + /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/8HYPz_snt9/regions.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/8HYPz_snt9/regions.bed + /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/8HYPz_snt9/regions.bed /tmp/8HYPz_snt9/regions.vcf.gz + /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/8HYPz_snt9/regions.bed.gz /tmp/8HYPz_snt9/regions.vcf.gz + /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/8HYPz_snt9/regions.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/8HYPz_snt9/regions.bed.gz + /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/8HYPz_snt9/regions.bed.gz /tmp/8HYPz_snt9/regions.vcf.gz + /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/8HYPz_snt9/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_ + /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/8HYPz_snt9/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_ + /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/8HYPz_snt9/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_ + /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/8HYPz_snt9/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_ + /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/8HYPz_snt9/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_ + /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/8HYPz_snt9/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_ + /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/8HYPz_snt9/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/8HYPz_snt9/annotate.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/8HYPz_snt9/annotate.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/8HYPz_snt9/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/8HYPz_snt9/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/8HYPz_snt9/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/8HYPz_snt9/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/8HYPz_snt9/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/8HYPz_snt9/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/8HYPz_snt9/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/8HYPz_snt9/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/8HYPz_snt9/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/8HYPz_snt9/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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: @@ -3827,115 +3870,115 @@ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.11/bcftools annotate -a /tmp/8HYPz_snt9/annots4.vcf.gz -c +INFO /tmp/8HYPz_snt9/annotate4.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/annots4.vcf.gz -c +INFO /tmp/8HYPz_snt9/annotate4.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/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_ + /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/8HYPz_snt9/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_ + /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/8HYPz_snt9/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_ + /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/8HYPz_snt9/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_ + /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/8HYPz_snt9/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/8HYPz_snt9/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/8HYPz_snt9/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/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_ + /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/8HYPz_snt9/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_ + /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/8HYPz_snt9/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/8HYPz_snt9/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/8HYPz_snt9/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/8HYPz_snt9/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/8HYPz_snt9/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/8HYPz_snt9/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/8HYPz_snt9/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/annots11.vcf.gz -c FMT /tmp/8HYPz_snt9/annotate11.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/annots11.vcf.gz -c FMT /tmp/8HYPz_snt9/annotate11.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/annots2.vcf.gz -c FMT/newGT:=GT /tmp/8HYPz_snt9/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/annots2.vcf.gz -c FMT/newGT:=GT /tmp/8HYPz_snt9/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/annots12.vcf.gz -c FMT/GT:=newGT /tmp/8HYPz_snt9/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/annots12.vcf.gz -c FMT/GT:=newGT /tmp/8HYPz_snt9/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/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_ + /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/8HYPz_snt9/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_ + /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/8HYPz_snt9/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_ + /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/8HYPz_snt9/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_ + /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/8HYPz_snt9/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_ + /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/8HYPz_snt9/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_ + /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: @@ -3947,19 +3990,19 @@ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.11/bcftools annotate -a /tmp/8HYPz_snt9/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_ + /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/8HYPz_snt9/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_ + /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/8HYPz_snt9/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_ + /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/8HYPz_snt9/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_ + /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: @@ -3971,172 +4014,172 @@ .. ok test_vcf_annotate: - /build/reproducible-path/bcftools-1.11/bcftools annotate -a /tmp/8HYPz_snt9/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_ + /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/8HYPz_snt9/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_ + /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/8HYPz_snt9/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_ + /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/8HYPz_snt9/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_ + /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/8HYPz_snt9/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_ + /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/8HYPz_snt9/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_ + /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/8HYPz_snt9/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_ + /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/8HYPz_snt9/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_ + /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/8HYPz_snt9/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_ + /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/8HYPz_snt9/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_ + /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/8HYPz_snt9/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/8HYPz_snt9/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/8HYPz_snt9/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/8HYPz_snt9/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/8HYPz_snt9/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/annotate20.src.vcf.gz -c FMT/GT /tmp/8HYPz_snt9/annotate20.dst.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/annotate20.src.vcf.gz -c FMT/GT /tmp/8HYPz_snt9/annotate20.dst.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/annotate20.src.vcf.gz -c +FMT/GT /tmp/8HYPz_snt9/annotate20.dst.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/annotate20.src.vcf.gz -c +FMT/GT /tmp/8HYPz_snt9/annotate20.dst.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/annotate20.src.vcf.gz -c -FMT/GT /tmp/8HYPz_snt9/annotate20.dst.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/annotate20.src.vcf.gz -c -FMT/GT /tmp/8HYPz_snt9/annotate20.dst.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/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_ + /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/8HYPz_snt9/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_ + /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/8HYPz_snt9/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_ + /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/8HYPz_snt9/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_ + /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/8HYPz_snt9/concat.1.a.vcf.gz /tmp/8HYPz_snt9/concat.1.b.vcf.gz + /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/8HYPz_snt9/concat.1.a.vcf.gz /tmp/8HYPz_snt9/concat.1.b.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/concat.1.a.bcf /tmp/8HYPz_snt9/concat.1.b.bcf + /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/8HYPz_snt9/concat.1.a.bcf /tmp/8HYPz_snt9/concat.1.b.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/concat.2.a.vcf.gz /tmp/8HYPz_snt9/concat.2.b.vcf.gz + /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/8HYPz_snt9/concat.2.a.vcf.gz /tmp/8HYPz_snt9/concat.2.b.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/concat.2.a.bcf /tmp/8HYPz_snt9/concat.2.b.bcf + /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/8HYPz_snt9/concat.2.a.bcf /tmp/8HYPz_snt9/concat.2.b.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/concat.2.a.vcf.gz /tmp/8HYPz_snt9/concat.2.b.vcf.gz + /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/8HYPz_snt9/concat.2.a.vcf.gz /tmp/8HYPz_snt9/concat.2.b.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/concat.2.a.bcf /tmp/8HYPz_snt9/concat.2.b.bcf + /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/8HYPz_snt9/concat.2.a.bcf /tmp/8HYPz_snt9/concat.2.b.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/concat.3.a.vcf.gz /tmp/8HYPz_snt9/concat.3.b.vcf.gz /tmp/8HYPz_snt9/concat.3.0.vcf.gz /tmp/8HYPz_snt9/concat.3.c.vcf.gz /tmp/8HYPz_snt9/concat.3.d.vcf.gz /tmp/8HYPz_snt9/concat.3.e.vcf.gz /tmp/8HYPz_snt9/concat.3.f.vcf.gz + /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/8HYPz_snt9/concat.3.a.vcf.gz /tmp/8HYPz_snt9/concat.3.b.vcf.gz /tmp/8HYPz_snt9/concat.3.0.vcf.gz /tmp/8HYPz_snt9/concat.3.c.vcf.gz /tmp/8HYPz_snt9/concat.3.d.vcf.gz /tmp/8HYPz_snt9/concat.3.e.vcf.gz /tmp/8HYPz_snt9/concat.3.f.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ + /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/8HYPz_snt9/concat.3.a.bcf /tmp/8HYPz_snt9/concat.3.b.bcf /tmp/8HYPz_snt9/concat.3.0.bcf /tmp/8HYPz_snt9/concat.3.c.bcf /tmp/8HYPz_snt9/concat.3.d.bcf /tmp/8HYPz_snt9/concat.3.e.bcf /tmp/8HYPz_snt9/concat.3.f.bcf + /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/8HYPz_snt9/concat.3.a.bcf /tmp/8HYPz_snt9/concat.3.b.bcf /tmp/8HYPz_snt9/concat.3.0.bcf /tmp/8HYPz_snt9/concat.3.c.bcf /tmp/8HYPz_snt9/concat.3.d.bcf /tmp/8HYPz_snt9/concat.3.e.bcf /tmp/8HYPz_snt9/concat.3.f.bcf | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools_ -Random seed for test_naive_concat: 4038008752 + /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/8HYPz_snt9/naive_concat.0.bcf /tmp/8HYPz_snt9/naive_concat.1.bcf /tmp/8HYPz_snt9/naive_concat.2.bcf /tmp/8HYPz_snt9/naive_concat.3.bcf /tmp/8HYPz_snt9/naive_concat.4.bcf /tmp/8HYPz_snt9/naive_concat.5.bcf /tmp/8HYPz_snt9/naive_concat.6.bcf /tmp/8HYPz_snt9/naive_concat.7.bcf /tmp/8HYPz_snt9/naive_concat.8.bcf /tmp/8HYPz_snt9/naive_concat.9.bcf | /build/reproducible-path/bcftools-1.11/bcftools view -H + /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/8HYPz_snt9/naive_concat.0.vcf.gz /tmp/8HYPz_snt9/naive_concat.1.vcf.gz /tmp/8HYPz_snt9/naive_concat.2.vcf.gz /tmp/8HYPz_snt9/naive_concat.3.vcf.gz /tmp/8HYPz_snt9/naive_concat.4.vcf.gz /tmp/8HYPz_snt9/naive_concat.5.vcf.gz /tmp/8HYPz_snt9/naive_concat.6.vcf.gz /tmp/8HYPz_snt9/naive_concat.7.vcf.gz /tmp/8HYPz_snt9/naive_concat.8.vcf.gz /tmp/8HYPz_snt9/naive_concat.9.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view -H + /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: @@ -4148,19 +4191,19 @@ .. ok test_vcf_reheader: - /build/reproducible-path/bcftools-1.11/bcftools reheader -h /build/reproducible-path/bcftools-1.11/test/reheader.hdr /tmp/8HYPz_snt9/reheader.bcf | /build/reproducible-path/bcftools-1.11/bcftools view --no-version + /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/8HYPz_snt9/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 + 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/8HYPz_snt9/reheader.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view --no-version + /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/8HYPz_snt9/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 + 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: @@ -4172,19 +4215,19 @@ .. ok test_vcf_reheader: - /build/reproducible-path/bcftools-1.11/bcftools reheader -s /build/reproducible-path/bcftools-1.11/test/reheader.samples /tmp/8HYPz_snt9/reheader.bcf | /build/reproducible-path/bcftools-1.11/bcftools view --no-version + /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/8HYPz_snt9/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 + 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/8HYPz_snt9/reheader.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view --no-version + /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/8HYPz_snt9/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 + 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: @@ -4196,19 +4239,19 @@ .. ok test_vcf_reheader: - /build/reproducible-path/bcftools-1.11/bcftools reheader -s /build/reproducible-path/bcftools-1.11/test/reheader.samples2 /tmp/8HYPz_snt9/reheader.bcf | /build/reproducible-path/bcftools-1.11/bcftools view --no-version + /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/8HYPz_snt9/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 + 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/8HYPz_snt9/reheader.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view --no-version + /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/8HYPz_snt9/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 + 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: @@ -4220,19 +4263,19 @@ .. ok test_vcf_reheader: - /build/reproducible-path/bcftools-1.11/bcftools reheader -s /build/reproducible-path/bcftools-1.11/test/reheader.samples3 /tmp/8HYPz_snt9/reheader.bcf | /build/reproducible-path/bcftools-1.11/bcftools view --no-version + /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/8HYPz_snt9/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 + 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/8HYPz_snt9/reheader.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view --no-version + /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/8HYPz_snt9/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 + 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: @@ -4244,19 +4287,19 @@ .. ok test_vcf_reheader: - /build/reproducible-path/bcftools-1.11/bcftools reheader -s /build/reproducible-path/bcftools-1.11/test/reheader.samples4 /tmp/8HYPz_snt9/reheader.bcf | /build/reproducible-path/bcftools-1.11/bcftools view --no-version + /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/8HYPz_snt9/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 + 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/8HYPz_snt9/reheader.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view --no-version + /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/8HYPz_snt9/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 + 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: @@ -4268,19 +4311,19 @@ .. ok test_vcf_reheader: - /build/reproducible-path/bcftools-1.11/bcftools reheader -h /build/reproducible-path/bcftools-1.11/test/reheader.empty.hdr /tmp/8HYPz_snt9/empty.bcf | /build/reproducible-path/bcftools-1.11/bcftools view --no-version + /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/8HYPz_snt9/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 + 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/8HYPz_snt9/empty.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view --no-version + /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/8HYPz_snt9/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 + 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: @@ -4288,11 +4331,11 @@ .. ok test_vcf_reheader: - /build/reproducible-path/bcftools-1.11/bcftools reheader -f /build/reproducible-path/bcftools-1.11/test/reheader.fai /tmp/8HYPz_snt9/reheader.2.bcf | /build/reproducible-path/bcftools-1.11/bcftools view --no-version + /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/8HYPz_snt9/reheader.2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view --no-version + /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: @@ -4300,131 +4343,131 @@ .. 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/8HYPz_snt9/reheader.2.bcf | /build/reproducible-path/bcftools-1.11/bcftools view --no-version + /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/8HYPz_snt9/reheader.2.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools view --no-version + /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/8HYPz_snt9/rename.map -Ov /tmp/8HYPz_snt9/annotate.bcf | /build/reproducible-path/bcftools-1.11/bcftools query -f'%CHROM\t%POS\n' + /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/8HYPz_snt9/rename.map -Ob /tmp/8HYPz_snt9/annotate.bcf | /build/reproducible-path/bcftools-1.11/bcftools query -f'%CHROM\t%POS\n' + /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/8HYPz_snt9/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' + /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/8HYPz_snt9/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' + /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/8HYPz_snt9/convert.vcf.gz + /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/8HYPz_snt9/convert.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools convert -g -,. + /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/8HYPz_snt9/convert.vcf.gz + /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/8HYPz_snt9/convert.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools convert -g .,- + /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/8HYPz_snt9/convert.vcf.gz + /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/8HYPz_snt9/convert.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools convert -g -,. --tag PL + /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/8HYPz_snt9/convert.vcf.gz + /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/8HYPz_snt9/convert.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools convert -g .,- --tag PL + /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/8HYPz_snt9/check.vcf.gz + /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/8HYPz_snt9/check.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools convert -g -,. --vcf-ids + /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/8HYPz_snt9/check.vcf.gz + /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/8HYPz_snt9/check.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools convert -g .,- --vcf-ids + /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/8HYPz_snt9/check.vcf.gz + /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/8HYPz_snt9/check.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools convert -g -,. --chrom + /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/8HYPz_snt9/check.vcf.gz + /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/8HYPz_snt9/check.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools convert -g .,- --chrom + /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/8HYPz_snt9/check.vcf.gz + /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/8HYPz_snt9/check.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools convert -g -,. --chrom --vcf-ids + /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/8HYPz_snt9/check.vcf.gz + /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/8HYPz_snt9/check.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools convert -g .,- --chrom --vcf-ids + /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/8HYPz_snt9/convert.vcf.gz + /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/8HYPz_snt9/convert.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools convert -h -,.,. + /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/8HYPz_snt9/convert.vcf.gz + /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/8HYPz_snt9/convert.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools convert -h .,-,. + /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/8HYPz_snt9/convert.vcf.gz + /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/8HYPz_snt9/convert.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools convert -h .,.,- + /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: @@ -4460,35 +4503,35 @@ .. ok test_vcf_convert: - /build/reproducible-path/bcftools-1.11/bcftools convert --hapsample -,. /tmp/8HYPz_snt9/convert.vcf.gz + /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/8HYPz_snt9/convert.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools convert --hapsample -,. + /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/8HYPz_snt9/convert.vcf.gz + /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/8HYPz_snt9/convert.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools convert --hapsample .,- + /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/8HYPz_snt9/convert.hap-missing.vcf.gz + /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/8HYPz_snt9/convert.hap-missing.vcf.gz | /build/reproducible-path/bcftools-1.11/bcftools convert --haplegendsample -,.,. + /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/8HYPz_snt9/convert.gvcf.vcf.gz + /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/8HYPz_snt9/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 + /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: @@ -4500,139 +4543,139 @@ .. ok test_vcf_consensus: - /build/reproducible-path/bcftools-1.11/bcftools consensus /tmp/8HYPz_snt9/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.11/test/consensus.fa -m /build/reproducible-path/bcftools-1.11/test/consensus.tab + /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/8HYPz_snt9/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/8HYPz_snt9/consensus.1.chain.new >/dev/null; cat /tmp/8HYPz_snt9/consensus.1.chain.new + /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/8HYPz_snt9/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 + /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/8HYPz_snt9/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/8HYPz_snt9/consensus.2.chain.new >/dev/null; cat /tmp/8HYPz_snt9/consensus.2.chain.new + /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/8HYPz_snt9/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.11/test/consensus.fa -I -m /build/reproducible-path/bcftools-1.11/test/consensus.tab + /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/8HYPz_snt9/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/8HYPz_snt9/consensus.3.chain.new >/dev/null; cat /tmp/8HYPz_snt9/consensus.3.chain.new + /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/8HYPz_snt9/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.11/test/consensus.fa -H 1 + /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/8HYPz_snt9/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.11/test/consensus.fa -H 1 -c /tmp/8HYPz_snt9/consensus.4.chain.new >/dev/null; cat /tmp/8HYPz_snt9/consensus.4.chain.new + /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/8HYPz_snt9/consensus2.vcf.gz -f /build/reproducible-path/bcftools-1.11/test/consensus2.fa -H 1 + /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/8HYPz_snt9/consensus2.vcf.gz -f /build/reproducible-path/bcftools-1.11/test/consensus2.fa -H 2 + /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/8HYPz_snt9/empty.vcf.gz -f /build/reproducible-path/bcftools-1.11/test/consensus.fa + /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/8HYPz_snt9/consensus3.vcf.gz -f /build/reproducible-path/bcftools-1.11/test/consensus2.fa -H 2 -M "?" + /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/8HYPz_snt9/consensus3.vcf.gz -f /build/reproducible-path/bcftools-1.11/test/consensus2.fa -H 2 -M "?" -p xx_ + /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/8HYPz_snt9/consensus4.vcf.gz -f /build/reproducible-path/bcftools-1.11/test/consensus2.fa + /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/8HYPz_snt9/consensus5.vcf.gz -f /build/reproducible-path/bcftools-1.11/test/consensus5.fa --haplotype LA + /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/8HYPz_snt9/consensus6.vcf.gz -f /build/reproducible-path/bcftools-1.11/test/consensus6.fa + /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/8HYPz_snt9/consensus7.vcf.gz -f /build/reproducible-path/bcftools-1.11/test/consensus7.fa -H 2 + /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/8HYPz_snt9/consensus7.vcf.gz -f /build/reproducible-path/bcftools-1.11/test/consensus7.fa -H 2pIu + /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/8HYPz_snt9/consensus7.vcf.gz -f /build/reproducible-path/bcftools-1.11/test/consensus7.fa -H 1 + /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/8HYPz_snt9/consensus7.vcf.gz -f /build/reproducible-path/bcftools-1.11/test/consensus7.fa -H 1pIu + /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/8HYPz_snt9/consensus8.vcf.gz -f /build/reproducible-path/bcftools-1.11/test/consensus.fa + /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/8HYPz_snt9/consensus8.vcf.gz -f /build/reproducible-path/bcftools-1.11/test/consensus.fa -a . + /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/8HYPz_snt9/consensus8.vcf.gz -f /build/reproducible-path/bcftools-1.11/test/consensus.fa -a . -i 'type="snp" || type="ref"' + /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/8HYPz_snt9/consensus8.vcf.gz -f /build/reproducible-path/bcftools-1.11/test/consensus.fa -a . -i 'ALT!=""' + /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/8HYPz_snt9/consensus8.vcf.gz -f /build/reproducible-path/bcftools-1.11/test/consensus.fa -a . -e 'MinDP>15' + /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/8HYPz_snt9/consensus8.vcf.gz -f /build/reproducible-path/bcftools-1.11/test/consensus.fa -a . -e 'MinDP<15' + /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/8HYPz_snt9/consensus.9.vcf.gz -f /build/reproducible-path/bcftools-1.11/test/consensus.9.1.fa -H A + /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/8HYPz_snt9/consensus.9.vcf.gz -f /build/reproducible-path/bcftools-1.11/test/consensus.9.2.fa -H A + /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/8HYPz_snt9/consensus.10.vcf.gz -f /build/reproducible-path/bcftools-1.11/test/consensus.9.1.fa -H A + /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/8HYPz_snt9/consensus.10.vcf.gz -f /build/reproducible-path/bcftools-1.11/test/consensus.9.2.fa -H A + /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/8HYPz_snt9/consensus.11.vcf.gz -f /build/reproducible-path/bcftools-1.11/test/consensus.11.fa -s smpl + /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/8HYPz_snt9/consensus.11.vcf.gz -f /build/reproducible-path/bcftools-1.11/test/consensus.11.fa -s smpl -a N + /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/8HYPz_snt9/consensus.12.vcf.gz -f /build/reproducible-path/bcftools-1.11/test/consensus.12.fa + /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/8HYPz_snt9/consensus.13.vcf.gz -f /build/reproducible-path/bcftools-1.11/test/consensus.13.fa + /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: @@ -4644,11 +4687,11 @@ .. 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/8HYPz_snt9/mpileup.bam.list --no-version | grep -v ^##reference + /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/8HYPz_snt9/mpileup.bam.urllist | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference + /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: @@ -4660,11 +4703,11 @@ .. 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/8HYPz_snt9/mpileup.cram.list --no-version | grep -v ^##reference + /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/8HYPz_snt9/mpileup.cram.urllist | /build/reproducible-path/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference + /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: @@ -4976,115 +5019,103 @@ .. 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/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/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/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' + /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 -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' + /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 -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' + /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/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' + /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/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' + /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 -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' + /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: - 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' + /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: - 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' + /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: - 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' + /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/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' + /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/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' + /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 -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' + /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/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' + /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 -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' + /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 -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' + /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/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' + /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: - 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' + /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: - 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' + /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: - 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' + /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 -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' + /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/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' + /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: - 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' + /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: - 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' + /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/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' + /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/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' + /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: @@ -5096,75 +5127,75 @@ .. 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' + /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/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' + /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/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' + /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 -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' + /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/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' + /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 -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' + /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 -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' + /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 -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' + /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 -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' + /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 -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' + /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 -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' + /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 -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' + /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/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' + /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/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' + /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/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' + /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/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' + /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/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' + /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/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' + /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: @@ -5200,175 +5231,179 @@ .. 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' + /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/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' + /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/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' + /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 -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' + /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 -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' + /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 -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' + /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/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' + /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/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' + /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/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' + /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 -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' + /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/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' + /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 -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' + /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/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' + /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/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' + /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/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' + /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/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' + /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/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' + /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 -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' + /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/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' + /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/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' + /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/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' + /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 -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' + /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 -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' + /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 -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' + /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 -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' + /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 -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' + /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/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' + /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 -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' + /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/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' + /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/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' + /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: - /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' + 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/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' + /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: - /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' + 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/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' + /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: - /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' + 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: - /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' + 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: - /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' + 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 -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' + /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/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' + /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/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' + /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 -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' + /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 -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' + /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/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' + /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: @@ -5380,15 +5415,23 @@ .. 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' + 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: - /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' + 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/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' + /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: @@ -5420,181 +5463,141 @@ .. ok test_gtcheck: - /build/reproducible-path/bcftools-1.11/bcftools gtcheck -e 0 /tmp/8HYPz_snt9/gtcheck.1.vcf.gz -g /tmp/8HYPz_snt9/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO + /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/8HYPz_snt9/gtcheck.1.vcf.gz -g /tmp/8HYPz_snt9/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO + /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/8HYPz_snt9/gtcheck.1.vcf.gz -g /tmp/8HYPz_snt9/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO + /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/8HYPz_snt9/gtcheck.1.vcf.gz -g /tmp/8HYPz_snt9/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO + /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/8HYPz_snt9/gtcheck.1.vcf.gz -g /tmp/8HYPz_snt9/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO + /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/8HYPz_snt9/gtcheck.1.vcf.gz -g /tmp/8HYPz_snt9/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO + /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/8HYPz_snt9/gtcheck.2.vcf.gz -g /tmp/8HYPz_snt9/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO + /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/8HYPz_snt9/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO + /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/8HYPz_snt9/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO + /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/8HYPz_snt9/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO + /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/8HYPz_snt9/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO + /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/8HYPz_snt9/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO | sort + /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/8HYPz_snt9/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO + /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/8HYPz_snt9/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO + /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/8HYPz_snt9/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO + /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/8HYPz_snt9/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO + /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/8HYPz_snt9/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO + /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/8HYPz_snt9/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO + /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/8HYPz_snt9/gtcheck.1.vcf.gz -g /tmp/8HYPz_snt9/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO + /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/8HYPz_snt9/gtcheck.1.vcf.gz -g /tmp/8HYPz_snt9/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO + /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/8HYPz_snt9/gtcheck.1.vcf.gz -g /tmp/8HYPz_snt9/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO + /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/8HYPz_snt9/gtcheck.1.vcf.gz -g /tmp/8HYPz_snt9/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO + /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/8HYPz_snt9/gtcheck.4.vcf.gz | grep -v ^# | grep -v ^INFO + /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/8HYPz_snt9/gtcheck.4.vcf.gz | grep -v ^# | grep -v ^INFO + /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/8HYPz_snt9/gtcheck.1.vcf.gz -g /tmp/8HYPz_snt9/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO + /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/8HYPz_snt9/gtcheck.1.vcf.gz -g /tmp/8HYPz_snt9/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO + /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/8HYPz_snt9/gtcheck.1.vcf.gz -g /tmp/8HYPz_snt9/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO + /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/8HYPz_snt9/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO + /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 .. 1210 - failed .. 0 + 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' - create-stamp debian/debhelper-build-stamp - dh_prep - dh_auto_install - make -j16 install DESTDIR=/build/reproducible-path/bcftools-1.11/debian/bcftools AM_UPDATE_INFO_DIR=no -make[1]: Entering directory '/build/reproducible-path/bcftools-1.11' -mkdir -p -m 755 /build/reproducible-path/bcftools-1.11/debian/bcftools/usr/bin /build/reproducible-path/bcftools-1.11/debian/bcftools/usr/share/man/man1 /build/reproducible-path/bcftools-1.11/debian/bcftools/usr/lib/i386-linux-gnu/bcftools -install -p bcftools /build/reproducible-path/bcftools-1.11/debian/bcftools/usr/bin -install -p misc/color-chrs.pl misc/gff2gff.py misc/guess-ploidy.py misc/plot-vcfstats misc/plot-roh.py misc/run-roh.pl misc/vcfutils.pl /build/reproducible-path/bcftools-1.11/debian/bcftools/usr/bin -install -p -m 644 doc/bcftools.1 /build/reproducible-path/bcftools-1.11/debian/bcftools/usr/share/man/man1 -install -p plugins/*.so /build/reproducible-path/bcftools-1.11/debian/bcftools/usr/lib/i386-linux-gnu/bcftools -make[1]: Leaving directory '/build/reproducible-path/bcftools-1.11' - debian/rules override_dh_install -make[1]: Entering directory '/build/reproducible-path/bcftools-1.11' -dh_install -# Fix Perl interpreter PATH -for pscript in `grep -Rl '#!/usr/bin/env \+perl' debian/*` ; do \ - sed -i '1s?#!/usr/bin/env \+perl?#!/usr/bin/perl?' ${pscript} ; \ -done -make[1]: Leaving directory '/build/reproducible-path/bcftools-1.11' - dh_installdocs - dh_installchangelogs - debian/rules override_dh_installman -make[1]: Entering directory '/build/reproducible-path/bcftools-1.11' -dh_installman --language=C -make[1]: Leaving directory '/build/reproducible-path/bcftools-1.11' - dh_perl - dh_link - dh_strip_nondeterminism - dh_compress - dh_fixperms - dh_missing - dh_dwz -a - dh_strip -a - dh_makeshlibs -a - dh_shlibdeps -a - dh_installdeb - dh_gencontrol -dpkg-gencontrol: warning: package bcftools: substitution variable ${perl:Depends} unused, but is defined -dpkg-gencontrol: warning: package bcftools: substitution variable ${perl:Depends} unused, but is defined - dh_md5sums - dh_builddeb -dpkg-deb: building package 'bcftools' in '../bcftools_1.11-1_i386.deb'. -dpkg-deb: building package 'bcftools-dbgsym' in '../bcftools-dbgsym_1.11-1_i386.deb'. - dpkg-genbuildinfo --build=binary - dpkg-genchanges --build=binary >../bcftools_1.11-1_i386.changes -dpkg-genchanges: info: binary-only upload (no source code included) - dpkg-source --after-build . -dpkg-buildpackage: info: binary-only upload (no source included) -dpkg-genchanges: info: including full source code in upload +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/42398 and its subdirectories -I: Current time: Mon Feb 10 16:41:29 -12 2025 -I: pbuilder-time-stamp: 1739248889 +I: removing directory /srv/workspace/pbuilder/4959 and its subdirectories