I: pbuilder: network access will be disabled during build I: Current time: Tue Jan 20 22:31:22 +14 2026 I: pbuilder-time-stamp: 1768897882 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [bcftools_1.20-2.dsc] I: copying [./bcftools_1.20.orig.tar.gz] I: copying [./bcftools_1.20-2.debian.tar.xz] I: Extracting source gpgv: Signature made Mon Jun 24 23:36:49 2024 gpgv: using RSA key 73471499CC60ED9EEE805946C5BD6C8F2295D502 gpgv: issuer "plessy@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./bcftools_1.20-2.dsc: no acceptable signature found dpkg-source: info: extracting bcftools in bcftools-1.20 dpkg-source: info: unpacking bcftools_1.20.orig.tar.gz dpkg-source: info: unpacking bcftools_1.20-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying tests-pluginpath.patch dpkg-source: info: applying skip_new_test_failing_on_32bit.patch dpkg-source: info: applying 2to3.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1897391/tmp/hooks/D01_modify_environment starting debug: Running on ionos5-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Jan 20 08:31 /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/1897391/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/1897391/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.37(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=6d3ead2cbce641e19f634723fa61b2d0 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=1897391 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.ithNmtje/pbuilderrc_fg3b --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ithNmtje/b2 --logfile b2/build.log bcftools_1.20-2.dsc' SUDO_GID=110 SUDO_UID=105 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://213.165.73.152:3128 I: uname -a Linux i-capture-the-hostname 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1897391/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), zlib1g-dev, libbz2-dev, liblzma-dev, libhts-dev (>= 1.14), libgsl-dev, tabix, libio-pty-perl dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19959 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. pbuilder-satisfydepends-dummy depends on liblzma-dev; however: Package liblzma-dev is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev (>= 1.14); however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on libgsl-dev; however: Package libgsl-dev is not installed. pbuilder-satisfydepends-dummy depends on tabix; however: Package tabix is not installed. pbuilder-satisfydepends-dummy depends on libio-pty-perl; however: Package libio-pty-perl is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} comerr-dev{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} krb5-multidev{a} libarchive-zip-perl{a} libbrotli-dev{a} libbrotli1{a} libbz2-dev{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1t64{a} libevent-2.1-7t64{a} libfile-stripnondeterminism-perl{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgsl-dev{a} libgsl28{a} libgslcblas0{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libidn2-dev{a} libio-pty-perl{a} libk5crypto3{a} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} libldap-2.5-0{a} libldap-dev{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp2-dev{a} libnghttp3-9{a} libnghttp3-dev{a} libngtcp2-16{a} libngtcp2-crypto-gnutls-dev{a} libngtcp2-crypto-gnutls8{a} libngtcp2-dev{a} libp11-kit-dev{a} libpipeline1{a} libpkgconf3{a} libpsl-dev{a} libpsl5t64{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libtasn1-6-dev{a} libtool{a} libuchardet0{a} libunbound8{a} libxml2{a} libzstd-dev{a} m4{a} man-db{a} nettle-dev{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} sensible-utils{a} tabix{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc ca-certificates curl krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules libtasn1-doc lynx publicsuffix wget 0 packages upgraded, 93 newly installed, 0 to remove and 0 not upgraded. Need to get 39.9 MB of archives. After unpacking 149 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-6 [1184 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.2-12 [92.0 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.2~rc1-2 [23.8 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 comerr-dev amd64 2.1-1.47.2~rc1-2 [55.4 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-8 [517 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 24 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.20 [915 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 35 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 libgssrpc4t64 amd64 1.21.3-3 [59.5 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 libkadm5clnt-mit12 amd64 1.21.3-3 [41.7 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libkdb5-10t64 amd64 1.21.3-3 [42.0 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libkadm5srv-mit12 amd64 1.21.3-3 [53.5 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 krb5-multidev amd64 1.21.3-3 [126 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libbrotli-dev amd64 1.1.0-2+b6 [316 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8 [19.6 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8 [57.3 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 libldap-2.5-0 amd64 2.5.18+dfsg-3+b1 [188 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 libnghttp3-9 amd64 1.6.0-2 [64.8 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 libngtcp2-16 amd64 1.9.1-1 [119 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 libngtcp2-crypto-gnutls8 amd64 1.9.1-1 [18.5 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 libcurl3t64-gnutls amd64 8.11.1-1 [360 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 libunbound8 amd64 1.22.0-1 [598 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 libgnutls-dane0t64 amd64 3.8.8-2 [449 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 libgnutls-openssl27t64 amd64 3.8.8-2 [449 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 libidn2-dev amd64 2.3.7-2+b1 [123 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 libp11-kit-dev amd64 0.25.5-2+b1 [208 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 libtasn1-6-dev amd64 4.19.0-3+b3 [98.9 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-3 [329 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-3 [642 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 nettle-dev amd64 3.10-1+b1 [1317 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 libgnutls28-dev amd64 3.8.8-2 [1391 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 libkrb5-dev amd64 1.21.3-3 [15.7 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 libldap-dev amd64 2.5.18+dfsg-3+b1 [303 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 libnghttp2-dev amd64 1.64.0-1 [115 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 libnghttp3-dev amd64 1.6.0-2 [88.5 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.9.1-1 [23.1 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 libngtcp2-dev amd64 1.9.1-1 [167 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 libpsl-dev amd64 0.21.2-1.1+b1 [77.6 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-2+b5 [68.0 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 libssl-dev amd64 3.3.2-2 [2742 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 libssh2-1-dev amd64 1.11.1-1 [393 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 libzstd-dev amd64 1.5.6+dfsg-1+b1 [365 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 libcurl4-gnutls-dev amd64 8.11.1-1 [474 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.22-1 [47.3 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 libdeflate-dev amd64 1.22-1 [55.8 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 libgslcblas0 amd64 2.8+dfsg-5 [116 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 libgsl28 amd64 2.8+dfsg-5 [994 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 libgsl-dev amd64 2.8+dfsg-5 [1222 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 libhtscodecs2 amd64 1.6.1-1 [95.6 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 libhts3t64 amd64 1.20+ds-2 [455 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 liblzma-dev amd64 5.6.3-1+b1 [316 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 libhts-dev amd64 1.20+ds-2 [1701 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 libio-pty-perl amd64 1:1.20-1+b2 [34.3 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 tabix amd64 1.20+ds-2 [486 kB] Fetched 39.9 MB in 1s (41.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19959 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3+b1_amd64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.22.5-2_amd64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-6_amd64.deb ... Unpacking groff-base (1.23.0-6) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.2-12_amd64.deb ... Unpacking bsdextrautils (2.40.2-12) ... Selecting previously unselected package libpipeline1:amd64. 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Setting up libicu72:amd64 (72.1-5+b1) ... Setting up libzstd-dev:amd64 (1.5.6+dfsg-1+b1) ... Setting up bsdextrautils (2.40.2-12) ... Setting up libgslcblas0:amd64 (2.8+dfsg-5) ... Setting up libio-pty-perl (1:1.20-1+b2) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.20) ... Setting up libbrotli1:amd64 (1.1.0-2+b6) ... Setting up libmagic1t64:amd64 (1:5.45-3+b1) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up libnghttp2-14:amd64 (1.64.0-1) ... Setting up libdeflate0:amd64 (1.22-1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libevent-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up libcom-err2:amd64 (1.47.2~rc1-2) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up libpsl-dev:amd64 (0.21.2-1.1+b1) ... Setting up libkrb5support0:amd64 (1.21.3-3) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-8) ... Setting up autotools-dev (20220109.1) ... Setting up libunbound8:amd64 (1.22.0-1) ... Setting up libpkgconf3:amd64 (1.8.1-4) ... Setting up libgmpxx4ldbl:amd64 (2:6.3.0+dfsg-3) ... Setting up libgnutls-dane0t64:amd64 (3.8.8-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up comerr-dev:amd64 (2.1-1.47.2~rc1-2) ... Setting up libssl-dev:amd64 (3.3.2-2) ... Setting up autopoint (0.22.5-2) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libk5crypto3:amd64 (1.21.3-3) ... Setting up libidn2-dev:amd64 (2.3.7-2+b1) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-8) ... Setting up autoconf (2.72-3) ... Setting up libnghttp3-9:amd64 (1.6.0-2) ... Setting up libnghttp3-dev:amd64 (1.6.0-2) ... Setting up liblzma-dev:amd64 (5.6.3-1+b1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up libngtcp2-16:amd64 (1.9.1-1) ... Setting up libkrb5-3:amd64 (1.21.3-3) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up libgsl28:amd64 (2.8+dfsg-5) ... Setting up libtasn1-6-dev:amd64 (4.19.0-3+b3) ... Setting up libdeflate-dev:amd64 (1.22-1) ... Setting up tabix (1.20+ds-2) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up libbrotli-dev:amd64 (1.1.0-2+b6) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.9.1-1) ... Setting up libp11-kit-dev:amd64 (0.25.5-2+b1) ... Setting up libbz2-dev:amd64 (1.0.8-6) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up gettext (0.22.5-2) ... Setting up libgsl-dev (2.8+dfsg-5) ... Setting up libgmp-dev:amd64 (2:6.3.0+dfsg-3) ... Setting up nettle-dev:amd64 (3.10-1+b1) ... Setting up libtool (2.4.7-8) ... Setting up libngtcp2-crypto-gnutls-dev:amd64 (1.9.1-1) ... 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Setting up debhelper (13.20) ... Setting up libkadm5srv-mit12:amd64 (1.21.3-3) ... Setting up krb5-multidev:amd64 (1.21.3-3) ... Setting up libkrb5-dev:amd64 (1.21.3-3) ... Setting up libcurl4-gnutls-dev:amd64 (8.11.1-1) ... Setting up libhts-dev:amd64 (1.20+ds-2) ... Processing triggers for libc-bin (2.40-4) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/1897391/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/1897391/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/bcftools-1.20/ && 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_1.20-2_source.changes dpkg-buildpackage: info: source package bcftools dpkg-buildpackage: info: source version 1.20-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Charles Plessy dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean rm -f config.mk && touch config.mk dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/bcftools-1.20' dh_auto_clean make -j42 distclean make[2]: Entering directory '/build/reproducible-path/bcftools-1.20' rm -f test/*.o test/*.fa.fai test/*~ test/test-rbuf test/test-regidx rm -f plugins/*.so plugins/*.P rm -rf plugins/*.dSYM rm -f test/*.unsorted.hex test/*.unsorted.tsv rm -f gmon.out *.o *.a *~ bcftools version.h rm -rf *.dSYM test/*.dSYM rm -f config.cache config.h config.log config.mk config.status rm -rf autom4te.cache rm -f TAGS make[2]: Leaving directory '/build/reproducible-path/bcftools-1.20' rm -f test/mpileup/indel-AD.1.out.new test/view-t.1.out.new test/view-t.2.out.new make[1]: Leaving directory '/build/reproducible-path/bcftools-1.20' dh_clean debian/rules binary dh binary dh_update_autotools_config debian/rules override_dh_autoreconf make[1]: Entering directory '/build/reproducible-path/bcftools-1.20' rm -f config.mk && touch config.mk export MAKEFLAGS="-s"; dh_autoreconf configure.ac:94: warning: _AC_CONFIG_SUBDIRS: you should use literals ./lib/autoconf/status.m4:1096: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:94: the top level make[1]: Leaving directory '/build/reproducible-path/bcftools-1.20' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/bcftools-1.20' dh_auto_configure -- \ --with-htslib=system \ --enable-gsl \ --with-cblas=gslcblas \ --with-bcf-plugin-dir=/usr/lib/x86_64-linux-gnu/bcftools ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system --enable-gsl --with-cblas=gslcblas --with-bcf-plugin-dir=/usr/lib/x86_64-linux-gnu/bcftools checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking for gcc option to enable large file support... none needed checking for htslib/sam.h... yes checking for hts_version in -lhts... yes checking shared library type... plain .so checking for library containing dlopen... none required checking if the compiler accepts -rdynamic... yes checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing regcomp... none required configure: creating ./config.status config.status: creating config.mk config.status: creating config.h make[1]: Leaving directory '/build/reproducible-path/bcftools-1.20' dh_auto_build make -j42 make[1]: Entering directory '/build/reproducible-path/bcftools-1.20' echo '#define BCFTOOLS_VERSION "1.20"' > version.h gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfindex.o vcfindex.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tabix.o tabix.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfstats.o vcfstats.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfisec.o vcfisec.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfmerge.o vcfmerge.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfquery.o vcfquery.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcffilter.o vcffilter.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o filter.o filter.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfsom.o vcfsom.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfnorm.o vcfnorm.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfgtcheck.o vcfgtcheck.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfview.o vcfview.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfannotate.o vcfannotate.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfroh.o vcfroh.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfconcat.o vcfconcat.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcall.o vcfcall.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mcall.o mcall.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcmp.o vcmp.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gvcf.o gvcf.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o reheader.o reheader.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o convert.o convert.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfconvert.o vcfconvert.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tsv2vcf.o tsv2vcf.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcnv.o vcfcnv.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfhead.o vcfhead.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o HMM.o HMM.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o consensus.o consensus.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ploidy.o ploidy.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bin.o bin.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hclust.o hclust.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o version.o version.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o regidx.o regidx.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o smpl_ilist.o smpl_ilist.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o csq.o csq.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfbuf.o vcfbuf.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mpileup.o mpileup.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_iaux.o bam2bcf_iaux.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_edlib.o bam2bcf_edlib.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o read_consensus.o read_consensus.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sample.o bam_sample.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfsort.o vcfsort.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cols.o cols.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o extsort.o extsort.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dist.o dist.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o abuf.o abuf.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ccall.o ccall.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o em.o em.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o prob1.o prob1.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kmin.o kmin.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o str_finder.o str_finder.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gff.o gff.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o edlib.o edlib.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DPLUGINPATH='"/usr/lib/x86_64-linux-gnu/bcftools"' -c -o vcfplugin.o vcfplugin.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-rbuf.o test/test-rbuf.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-regidx.o test/test-regidx.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/GTisec.so version.c plugins/GTisec.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/GTsubset.so version.c plugins/GTsubset.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/ad-bias.so convert.c version.c plugins/ad-bias.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/add-variantkey.so version.c plugins/add-variantkey.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/af-dist.so bin.c version.c plugins/af-dist.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/allele-length.so version.c plugins/allele-length.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/check-ploidy.so version.c plugins/check-ploidy.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/check-sparsity.so version.c plugins/check-sparsity.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/color-chrs.so HMM.c version.c plugins/color-chrs.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/contrast.so version.c plugins/contrast.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/counts.so version.c plugins/counts.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/dosage.so version.c plugins/dosage.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fill-AN-AC.so version.c plugins/fill-AN-AC.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fill-from-fasta.so filter.c version.c plugins/fill-from-fasta.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fill-tags.so version.c plugins/fill-tags.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fixploidy.so ploidy.c regidx.c version.c plugins/fixploidy.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fixref.so version.c plugins/fixref.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/frameshifts.so version.c plugins/frameshifts.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/guess-ploidy.so version.c plugins/guess-ploidy.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/gvcfz.so version.c plugins/gvcfz.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/impute-info.so version.c plugins/impute-info.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/indel-stats.so version.c plugins/indel-stats.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/isecGT.so smpl_ilist.c version.c plugins/isecGT.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/mendelian2.so version.c plugins/mendelian2.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/missing2ref.so version.c plugins/missing2ref.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/parental-origin.so version.c plugins/parental-origin.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/prune.so version.c plugins/prune.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/remove-overlaps.so version.c plugins/remove-overlaps.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/scatter.so version.c plugins/scatter.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/setGT.so version.c plugins/setGT.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/smpl-stats.so version.c plugins/smpl-stats.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/split-vep.so version.c plugins/split-vep.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/split.so version.c plugins/split.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/tag2tag.so version.c plugins/tag2tag.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/trio-dnm2.so version.c plugins/trio-dnm2.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/trio-stats.so version.c plugins/trio-stats.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/trio-switch-rate.so version.c plugins/trio-switch-rate.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/variant-distance.so version.c plugins/variant-distance.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/variantkey-hex.so version.c plugins/variantkey-hex.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o main.o main.c gcc -Wl,-z,relro -o test/test-rbuf test/test-rbuf.o -lz gcc -Wl,-z,relro -o test/test-regidx test/test-regidx.o regidx.o -lhts -lpthread -lz gcc -rdynamic -Wl,-z,relro -o bcftools main.o vcfindex.o tabix.o vcfstats.o vcfisec.o vcfmerge.o vcfquery.o vcffilter.o filter.o vcfsom.o vcfnorm.o vcfgtcheck.o vcfview.o vcfannotate.o vcfroh.o vcfconcat.o vcfcall.o mcall.o vcmp.o gvcf.o reheader.o convert.o vcfconvert.o tsv2vcf.o vcfcnv.o vcfhead.o HMM.o consensus.o ploidy.o bin.o hclust.o version.o regidx.o smpl_ilist.o csq.o vcfbuf.o mpileup.o bam2bcf.o bam2bcf_indel.o bam2bcf_iaux.o bam2bcf_edlib.o read_consensus.o bam_sample.o vcfsort.o cols.o extsort.o dist.o abuf.o ccall.o em.o prob1.o kmin.o str_finder.o gff.o edlib.o vcfplugin.o -lhts -lm -lz -lpthread make[1]: Leaving directory '/build/reproducible-path/bcftools-1.20' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/bcftools-1.20' make test-no-plugins VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/bcftools-1.20' ./test/test-rbuf Inserted 1-9 starting at offset 5: 5 6 7 8 9 0 1 2 3 1 2 3 4 5 6 7 8 9 4th is 4 Deleting 1-2: 7 8 9 0 1 2 3 3 4 5 6 7 8 9 Prepending 0-8: 8 9 0 1 2 3 4 5 6 7 8 7 6 5 4 3 2 1 0 3 Expanding: 8 9 10 11 12 13 14 15 16 17 8 7 6 5 4 3 2 1 0 3 ./test/test-regidx REF_PATH=: ./test/test.pl --exec bgzip= --exec tabix= --htsdir= ${TEST_OPTS:-} test_usage: bcftools .. ok test_usage_subcommand: bcftools index .. ok test_usage_subcommand: bcftools annotate .. ok test_usage_subcommand: bcftools concat .. ok test_usage_subcommand: bcftools convert .. ok test_usage_subcommand: bcftools head .. ok test_usage_subcommand: bcftools isec .. ok test_usage_subcommand: bcftools merge .. ok test_usage_subcommand: bcftools norm .. ok test_usage_subcommand: bcftools plugin .. ok test_usage_subcommand: bcftools query .. ok test_usage_subcommand: bcftools reheader .. ok test_usage_subcommand: bcftools sort .. ok test_usage_subcommand: bcftools view .. ok test_usage_subcommand: bcftools call .. ok test_usage_subcommand: bcftools consensus .. ok test_usage_subcommand: bcftools cnv .. ok test_usage_subcommand: bcftools csq .. ok test_usage_subcommand: bcftools filter .. ok test_usage_subcommand: bcftools gtcheck .. ok test_usage_subcommand: bcftools mpileup .. ok test_usage_subcommand: bcftools roh .. ok test_usage_subcommand: bcftools stats .. ok test_tabix: tabix /tmp/MWm45bogYL/merge.a.vcf.gz 2:3199812-3199812 .. ok test_tabix: /build/reproducible-path/bcftools-1.20/bcftools view -H /tmp/MWm45bogYL/merge.a.bcf 2:3199812-3199812 .. ok test_tabix: tabix /tmp/MWm45bogYL/merge.a.vcf.gz 1:3000151-3000151 .. ok test_tabix: /build/reproducible-path/bcftools-1.20/bcftools view -H /tmp/MWm45bogYL/merge.a.bcf 1:3000151-3000151 .. ok test_index: /build/reproducible-path/bcftools-1.20/bcftools view -H /tmp/MWm45bogYL/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /build/reproducible-path/bcftools-1.20/bcftools view -H /tmp/MWm45bogYL/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/reproducible-path/bcftools-1.20/bcftools view -H /tmp/MWm45bogYL/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/reproducible-path/bcftools-1.20/bcftools view -H /tmp/MWm45bogYL/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /build/reproducible-path/bcftools-1.20/bcftools view -H /tmp/MWm45bogYL/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/reproducible-path/bcftools-1.20/bcftools view -H /tmp/MWm45bogYL/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /build/reproducible-path/bcftools-1.20/bcftools view -H /tmp/MWm45bogYL/large_chrom_csi_limit.bcf chr20 .. ok test_index: /build/reproducible-path/bcftools-1.20/bcftools view -H /tmp/MWm45bogYL/large_chrom_csi_limit.bcf chr20 .. ok test_index: /build/reproducible-path/bcftools-1.20/bcftools view -H /tmp/MWm45bogYL/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /build/reproducible-path/bcftools-1.20/bcftools view -H /tmp/MWm45bogYL/large_chrom_csi_limit.bcf chr20 .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.20/bcftools index -s /tmp/MWm45bogYL/idx.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.20/bcftools index -s /tmp/MWm45bogYL/idx.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.20/bcftools index -s /tmp/MWm45bogYL/idx.bcf .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.20/bcftools index -n /tmp/MWm45bogYL/idx.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.20/bcftools index -n /tmp/MWm45bogYL/idx.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.20/bcftools index -n /tmp/MWm45bogYL/idx.vcf.gz.csi .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.20/bcftools index -n /tmp/MWm45bogYL/idx.bcf .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.20/bcftools index -n /tmp/MWm45bogYL/idx.bcf.csi .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.20/bcftools index -s /tmp/MWm45bogYL/empty.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.20/bcftools index -s /tmp/MWm45bogYL/empty.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.20/bcftools index -s /tmp/MWm45bogYL/empty.bcf .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.20/bcftools index -n /tmp/MWm45bogYL/empty.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.20/bcftools index -n /tmp/MWm45bogYL/empty.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.20/bcftools index -n /tmp/MWm45bogYL/empty.vcf.gz.csi .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.20/bcftools index -n /tmp/MWm45bogYL/empty.bcf .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.20/bcftools index -n /tmp/MWm45bogYL/empty.bcf.csi .. ok test_vcf_check: /build/reproducible-path/bcftools-1.20/bcftools stats -s - /tmp/MWm45bogYL/check.vcf.gz | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/check.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools stats -s - | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check_merge: /build/reproducible-path/bcftools-1.20/misc/plot-vcfstats -m /tmp/MWm45bogYL/check.1.chk /tmp/MWm45bogYL/check.2.chk /tmp/MWm45bogYL/check.3.chk /tmp/MWm45bogYL/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-1.20/bcftools stats -s - /tmp/MWm45bogYL/stats.a.vcf.gz /tmp/MWm45bogYL/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/reproducible-path/bcftools-1.20/bcftools stats -s B /tmp/MWm45bogYL/stats.a.vcf.gz /tmp/MWm45bogYL/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/reproducible-path/bcftools-1.20/bcftools stats -s - /tmp/MWm45bogYL/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/reproducible-path/bcftools-1.20/bcftools stats -s - -i 'type="snp"' /tmp/MWm45bogYL/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/reproducible-path/bcftools-1.20/bcftools stats -s - /tmp/MWm45bogYL/stats.vaf.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.20/bcftools isec -n =2 /tmp/MWm45bogYL/isec.a.vcf.gz /tmp/MWm45bogYL/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.20/bcftools isec -Ob -n =2 /tmp/MWm45bogYL/isec.a.vcf.gz /tmp/MWm45bogYL/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.20/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/MWm45bogYL/isec.a.vcf.gz /tmp/MWm45bogYL/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.20/bcftools isec -Ob -n =2 -i"STRLEN(REF)==2" /tmp/MWm45bogYL/isec.a.vcf.gz /tmp/MWm45bogYL/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.20/bcftools isec -n =2 -c both /tmp/MWm45bogYL/isec.a.vcf.gz /tmp/MWm45bogYL/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.20/bcftools isec -Ob -n =2 -c both /tmp/MWm45bogYL/isec.a.vcf.gz /tmp/MWm45bogYL/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.20/bcftools isec -n =2 -c any /tmp/MWm45bogYL/isec.a.vcf.gz /tmp/MWm45bogYL/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.20/bcftools isec -Ob -n =2 -c any /tmp/MWm45bogYL/isec.a.vcf.gz /tmp/MWm45bogYL/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.20/bcftools isec -C -c any /tmp/MWm45bogYL/isec.a.vcf.gz /tmp/MWm45bogYL/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.20/bcftools isec -Ob -C -c any /tmp/MWm45bogYL/isec.a.vcf.gz /tmp/MWm45bogYL/isec.b.vcf.gz .. ok test_vcf_isec2: /build/reproducible-path/bcftools-1.20/bcftools isec --no-version -T /tmp/MWm45bogYL/isec.tab.gz /tmp/MWm45bogYL/isec.a.vcf.gz .. ok test_vcf_isec2: /build/reproducible-path/bcftools-1.20/bcftools isec -Ob -T /tmp/MWm45bogYL/isec.tab.gz /tmp/MWm45bogYL/isec.a.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.20/bcftools isec -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/MWm45bogYL/isec-miss.1.1.vcf.gz /tmp/MWm45bogYL/isec-miss.1.2.vcf.gz /tmp/MWm45bogYL/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.20/bcftools isec -Ob -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/MWm45bogYL/isec-miss.1.1.vcf.gz /tmp/MWm45bogYL/isec-miss.1.2.vcf.gz /tmp/MWm45bogYL/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.20/bcftools isec -R /build/reproducible-path/bcftools-1.20/test/isec-miss.1.regs.txt -n +1 /tmp/MWm45bogYL/isec-miss.1.1.vcf.gz /tmp/MWm45bogYL/isec-miss.1.2.vcf.gz /tmp/MWm45bogYL/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.20/bcftools isec -Ob -R /build/reproducible-path/bcftools-1.20/test/isec-miss.1.regs.txt -n +1 /tmp/MWm45bogYL/isec-miss.1.1.vcf.gz /tmp/MWm45bogYL/isec-miss.1.2.vcf.gz /tmp/MWm45bogYL/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.20/bcftools isec -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/MWm45bogYL/isec-miss.2.1.vcf.gz /tmp/MWm45bogYL/isec-miss.2.2.vcf.gz /tmp/MWm45bogYL/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.20/bcftools isec -Ob -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/MWm45bogYL/isec-miss.2.1.vcf.gz /tmp/MWm45bogYL/isec-miss.2.2.vcf.gz /tmp/MWm45bogYL/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.20/bcftools isec -R /build/reproducible-path/bcftools-1.20/test/isec-miss.1.regs.txt -n +1 /tmp/MWm45bogYL/isec-miss.2.1.vcf.gz /tmp/MWm45bogYL/isec-miss.2.2.vcf.gz /tmp/MWm45bogYL/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.20/bcftools isec -Ob -R /build/reproducible-path/bcftools-1.20/test/isec-miss.1.regs.txt -n +1 /tmp/MWm45bogYL/isec-miss.2.1.vcf.gz /tmp/MWm45bogYL/isec-miss.2.2.vcf.gz /tmp/MWm45bogYL/isec-miss.2.3.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -i AF:join /tmp/MWm45bogYL/merge.join.a.vcf.gz /tmp/MWm45bogYL/merge.join.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob -i AF:join /tmp/MWm45bogYL/merge.join.a.vcf.gz /tmp/MWm45bogYL/merge.join.b.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -i AF:join /tmp/MWm45bogYL/merge.join.a.bcf /tmp/MWm45bogYL/merge.join.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob -i AF:join /tmp/MWm45bogYL/merge.join.a.bcf /tmp/MWm45bogYL/merge.join.b.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version --force-single /tmp/MWm45bogYL/merge.LPL.a.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-single /tmp/MWm45bogYL/merge.LPL.a.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version --force-single /tmp/MWm45bogYL/merge.LPL.a.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-single /tmp/MWm45bogYL/merge.LPL.a.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version --force-samples /tmp/MWm45bogYL/merge.LPL.a.vcf.gz /tmp/MWm45bogYL/merge.LPL.b.vcf.gz /tmp/MWm45bogYL/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples /tmp/MWm45bogYL/merge.LPL.a.vcf.gz /tmp/MWm45bogYL/merge.LPL.b.vcf.gz /tmp/MWm45bogYL/merge.LPL.c.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version --force-samples /tmp/MWm45bogYL/merge.LPL.a.bcf /tmp/MWm45bogYL/merge.LPL.b.bcf /tmp/MWm45bogYL/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples /tmp/MWm45bogYL/merge.LPL.a.bcf /tmp/MWm45bogYL/merge.LPL.b.bcf /tmp/MWm45bogYL/merge.LPL.c.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version --force-samples -L 1 /tmp/MWm45bogYL/merge.LPL.a.vcf.gz /tmp/MWm45bogYL/merge.LPL.b.vcf.gz /tmp/MWm45bogYL/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -L 1 /tmp/MWm45bogYL/merge.LPL.a.vcf.gz /tmp/MWm45bogYL/merge.LPL.b.vcf.gz /tmp/MWm45bogYL/merge.LPL.c.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version --force-samples -L 1 /tmp/MWm45bogYL/merge.LPL.a.bcf /tmp/MWm45bogYL/merge.LPL.b.bcf /tmp/MWm45bogYL/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -L 1 /tmp/MWm45bogYL/merge.LPL.a.bcf /tmp/MWm45bogYL/merge.LPL.b.bcf /tmp/MWm45bogYL/merge.LPL.c.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version --force-samples -L 2 /tmp/MWm45bogYL/merge.LPL.a.vcf.gz /tmp/MWm45bogYL/merge.LPL.b.vcf.gz /tmp/MWm45bogYL/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -L 2 /tmp/MWm45bogYL/merge.LPL.a.vcf.gz /tmp/MWm45bogYL/merge.LPL.b.vcf.gz /tmp/MWm45bogYL/merge.LPL.c.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version --force-samples -L 2 /tmp/MWm45bogYL/merge.LPL.a.bcf /tmp/MWm45bogYL/merge.LPL.b.bcf /tmp/MWm45bogYL/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -L 2 /tmp/MWm45bogYL/merge.LPL.a.bcf /tmp/MWm45bogYL/merge.LPL.b.bcf /tmp/MWm45bogYL/merge.LPL.c.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version --force-samples -L 3 /tmp/MWm45bogYL/merge.LPL.a.vcf.gz /tmp/MWm45bogYL/merge.LPL.b.vcf.gz /tmp/MWm45bogYL/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -L 3 /tmp/MWm45bogYL/merge.LPL.a.vcf.gz /tmp/MWm45bogYL/merge.LPL.b.vcf.gz /tmp/MWm45bogYL/merge.LPL.c.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version --force-samples -L 3 /tmp/MWm45bogYL/merge.LPL.a.bcf /tmp/MWm45bogYL/merge.LPL.b.bcf /tmp/MWm45bogYL/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -L 3 /tmp/MWm45bogYL/merge.LPL.a.bcf /tmp/MWm45bogYL/merge.LPL.b.bcf /tmp/MWm45bogYL/merge.LPL.c.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version --force-samples -L 4 /tmp/MWm45bogYL/merge.LPL.a.vcf.gz /tmp/MWm45bogYL/merge.LPL.b.vcf.gz /tmp/MWm45bogYL/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -L 4 /tmp/MWm45bogYL/merge.LPL.a.vcf.gz /tmp/MWm45bogYL/merge.LPL.b.vcf.gz /tmp/MWm45bogYL/merge.LPL.c.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version --force-samples -L 4 /tmp/MWm45bogYL/merge.LPL.a.bcf /tmp/MWm45bogYL/merge.LPL.b.bcf /tmp/MWm45bogYL/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -L 4 /tmp/MWm45bogYL/merge.LPL.a.bcf /tmp/MWm45bogYL/merge.LPL.b.bcf /tmp/MWm45bogYL/merge.LPL.c.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version --force-samples -L 5 /tmp/MWm45bogYL/merge.LPL.a.vcf.gz /tmp/MWm45bogYL/merge.LPL.b.vcf.gz /tmp/MWm45bogYL/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -L 5 /tmp/MWm45bogYL/merge.LPL.a.vcf.gz /tmp/MWm45bogYL/merge.LPL.b.vcf.gz /tmp/MWm45bogYL/merge.LPL.c.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version --force-samples -L 5 /tmp/MWm45bogYL/merge.LPL.a.bcf /tmp/MWm45bogYL/merge.LPL.b.bcf /tmp/MWm45bogYL/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -L 5 /tmp/MWm45bogYL/merge.LPL.a.bcf /tmp/MWm45bogYL/merge.LPL.b.bcf /tmp/MWm45bogYL/merge.LPL.c.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version --force-samples /tmp/MWm45bogYL/merge.a.vcf.gz /tmp/MWm45bogYL/merge.b.vcf.gz /tmp/MWm45bogYL/merge.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples /tmp/MWm45bogYL/merge.a.vcf.gz /tmp/MWm45bogYL/merge.b.vcf.gz /tmp/MWm45bogYL/merge.c.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version --force-samples /tmp/MWm45bogYL/merge.a.bcf /tmp/MWm45bogYL/merge.b.bcf /tmp/MWm45bogYL/merge.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples /tmp/MWm45bogYL/merge.a.bcf /tmp/MWm45bogYL/merge.b.bcf /tmp/MWm45bogYL/merge.c.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version --force-samples -Fx /tmp/MWm45bogYL/merge.a.vcf.gz /tmp/MWm45bogYL/merge.b.vcf.gz /tmp/MWm45bogYL/merge.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -Fx /tmp/MWm45bogYL/merge.a.vcf.gz /tmp/MWm45bogYL/merge.b.vcf.gz /tmp/MWm45bogYL/merge.c.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version --force-samples -Fx /tmp/MWm45bogYL/merge.a.bcf /tmp/MWm45bogYL/merge.b.bcf /tmp/MWm45bogYL/merge.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -Fx /tmp/MWm45bogYL/merge.a.bcf /tmp/MWm45bogYL/merge.b.bcf /tmp/MWm45bogYL/merge.c.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version --force-samples -0 /tmp/MWm45bogYL/merge.a.vcf.gz /tmp/MWm45bogYL/merge.b.vcf.gz /tmp/MWm45bogYL/merge.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -0 /tmp/MWm45bogYL/merge.a.vcf.gz /tmp/MWm45bogYL/merge.b.vcf.gz /tmp/MWm45bogYL/merge.c.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version --force-samples -0 /tmp/MWm45bogYL/merge.a.bcf /tmp/MWm45bogYL/merge.b.bcf /tmp/MWm45bogYL/merge.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -0 /tmp/MWm45bogYL/merge.a.bcf /tmp/MWm45bogYL/merge.b.bcf /tmp/MWm45bogYL/merge.c.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version --force-samples -m none /tmp/MWm45bogYL/merge.2.a.vcf.gz /tmp/MWm45bogYL/merge.2.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -m none /tmp/MWm45bogYL/merge.2.a.vcf.gz /tmp/MWm45bogYL/merge.2.b.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version --force-samples -m none /tmp/MWm45bogYL/merge.2.a.bcf /tmp/MWm45bogYL/merge.2.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -m none /tmp/MWm45bogYL/merge.2.a.bcf /tmp/MWm45bogYL/merge.2.b.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version --force-samples -m both /tmp/MWm45bogYL/merge.2.a.vcf.gz /tmp/MWm45bogYL/merge.2.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -m both /tmp/MWm45bogYL/merge.2.a.vcf.gz /tmp/MWm45bogYL/merge.2.b.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version --force-samples -m both /tmp/MWm45bogYL/merge.2.a.bcf /tmp/MWm45bogYL/merge.2.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -m both /tmp/MWm45bogYL/merge.2.a.bcf /tmp/MWm45bogYL/merge.2.b.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version --force-samples -m all /tmp/MWm45bogYL/merge.2.a.vcf.gz /tmp/MWm45bogYL/merge.2.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -m all /tmp/MWm45bogYL/merge.2.a.vcf.gz /tmp/MWm45bogYL/merge.2.b.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version --force-samples -m all /tmp/MWm45bogYL/merge.2.a.bcf /tmp/MWm45bogYL/merge.2.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -m all /tmp/MWm45bogYL/merge.2.a.bcf /tmp/MWm45bogYL/merge.2.b.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/MWm45bogYL/merge.3.a.vcf.gz /tmp/MWm45bogYL/merge.3.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/MWm45bogYL/merge.3.a.vcf.gz /tmp/MWm45bogYL/merge.3.b.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/MWm45bogYL/merge.3.a.bcf /tmp/MWm45bogYL/merge.3.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/MWm45bogYL/merge.3.a.bcf /tmp/MWm45bogYL/merge.3.b.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version --force-samples -m id /tmp/MWm45bogYL/merge.4.a.vcf.gz /tmp/MWm45bogYL/merge.4.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -m id /tmp/MWm45bogYL/merge.4.a.vcf.gz /tmp/MWm45bogYL/merge.4.b.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version --force-samples -m id /tmp/MWm45bogYL/merge.4.a.bcf /tmp/MWm45bogYL/merge.4.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -m id /tmp/MWm45bogYL/merge.4.a.bcf /tmp/MWm45bogYL/merge.4.b.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version --gvcf - /tmp/MWm45bogYL/gvcf.merge.1.vcf.gz /tmp/MWm45bogYL/gvcf.merge.2.vcf.gz /tmp/MWm45bogYL/gvcf.merge.3.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/MWm45bogYL/gvcf.merge.1.vcf.gz /tmp/MWm45bogYL/gvcf.merge.2.vcf.gz /tmp/MWm45bogYL/gvcf.merge.3.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version --gvcf - /tmp/MWm45bogYL/gvcf.merge.1.bcf /tmp/MWm45bogYL/gvcf.merge.2.bcf /tmp/MWm45bogYL/gvcf.merge.3.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/MWm45bogYL/gvcf.merge.1.bcf /tmp/MWm45bogYL/gvcf.merge.2.bcf /tmp/MWm45bogYL/gvcf.merge.3.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version --gvcf - /tmp/MWm45bogYL/merge.gvcf.2.a.vcf.gz /tmp/MWm45bogYL/merge.gvcf.2.b.vcf.gz /tmp/MWm45bogYL/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/MWm45bogYL/merge.gvcf.2.a.vcf.gz /tmp/MWm45bogYL/merge.gvcf.2.b.vcf.gz /tmp/MWm45bogYL/merge.gvcf.2.c.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version --gvcf - -m both,* /tmp/MWm45bogYL/merge.gvcf.2.a.vcf.gz /tmp/MWm45bogYL/merge.gvcf.2.b.vcf.gz /tmp/MWm45bogYL/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - -m both,* /tmp/MWm45bogYL/merge.gvcf.2.a.vcf.gz /tmp/MWm45bogYL/merge.gvcf.2.b.vcf.gz /tmp/MWm45bogYL/merge.gvcf.2.c.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version --gvcf - -m both,** /tmp/MWm45bogYL/merge.gvcf.2.a.vcf.gz /tmp/MWm45bogYL/merge.gvcf.2.b.vcf.gz /tmp/MWm45bogYL/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - -m both,** /tmp/MWm45bogYL/merge.gvcf.2.a.vcf.gz /tmp/MWm45bogYL/merge.gvcf.2.b.vcf.gz /tmp/MWm45bogYL/merge.gvcf.2.c.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version --gvcf - -i SRC:join /tmp/MWm45bogYL/merge.gvcf.3.a.vcf.gz /tmp/MWm45bogYL/merge.gvcf.3.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - -i SRC:join /tmp/MWm45bogYL/merge.gvcf.3.a.vcf.gz /tmp/MWm45bogYL/merge.gvcf.3.b.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version --gvcf - /tmp/MWm45bogYL/merge.gvcf.4.a.vcf.gz /tmp/MWm45bogYL/merge.gvcf.4.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/MWm45bogYL/merge.gvcf.4.a.vcf.gz /tmp/MWm45bogYL/merge.gvcf.4.b.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version --gvcf - /tmp/MWm45bogYL/merge.gvcf.4.a.bcf /tmp/MWm45bogYL/merge.gvcf.4.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/MWm45bogYL/merge.gvcf.4.a.bcf /tmp/MWm45bogYL/merge.gvcf.4.b.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version /tmp/MWm45bogYL/merge.5.a.vcf.gz /tmp/MWm45bogYL/merge.5.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob /tmp/MWm45bogYL/merge.5.a.vcf.gz /tmp/MWm45bogYL/merge.5.b.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version /tmp/MWm45bogYL/merge.5.a.bcf /tmp/MWm45bogYL/merge.5.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob /tmp/MWm45bogYL/merge.5.a.bcf /tmp/MWm45bogYL/merge.5.b.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version /tmp/MWm45bogYL/merge.6.a.vcf.gz /tmp/MWm45bogYL/merge.6.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob /tmp/MWm45bogYL/merge.6.a.vcf.gz /tmp/MWm45bogYL/merge.6.b.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version /tmp/MWm45bogYL/merge.6.a.bcf /tmp/MWm45bogYL/merge.6.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob /tmp/MWm45bogYL/merge.6.a.bcf /tmp/MWm45bogYL/merge.6.b.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version --gvcf - /tmp/MWm45bogYL/merge.gvcf.7.a.vcf.gz /tmp/MWm45bogYL/merge.gvcf.7.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/MWm45bogYL/merge.gvcf.7.a.vcf.gz /tmp/MWm45bogYL/merge.gvcf.7.b.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version --gvcf - /tmp/MWm45bogYL/merge.gvcf.7.a.bcf /tmp/MWm45bogYL/merge.gvcf.7.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/MWm45bogYL/merge.gvcf.7.a.bcf /tmp/MWm45bogYL/merge.gvcf.7.b.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version --gvcf - /tmp/MWm45bogYL/merge.gvcf.8.a.vcf.gz /tmp/MWm45bogYL/merge.gvcf.8.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/MWm45bogYL/merge.gvcf.8.a.vcf.gz /tmp/MWm45bogYL/merge.gvcf.8.b.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version --gvcf - /tmp/MWm45bogYL/merge.gvcf.8.a.bcf /tmp/MWm45bogYL/merge.gvcf.8.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/MWm45bogYL/merge.gvcf.8.a.bcf /tmp/MWm45bogYL/merge.gvcf.8.b.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version --force-samples /tmp/MWm45bogYL/merge.7.a.vcf.gz /tmp/MWm45bogYL/merge.7.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples /tmp/MWm45bogYL/merge.7.a.vcf.gz /tmp/MWm45bogYL/merge.7.b.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version --force-samples /tmp/MWm45bogYL/merge.7.a.bcf /tmp/MWm45bogYL/merge.7.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples /tmp/MWm45bogYL/merge.7.a.bcf /tmp/MWm45bogYL/merge.7.b.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version --gvcf /build/reproducible-path/bcftools-1.20/test/gvcf.fa /tmp/MWm45bogYL/merge.gvcf.9a.vcf.gz /tmp/MWm45bogYL/merge.gvcf.9b.vcf.gz /tmp/MWm45bogYL/merge.gvcf.9c.vcf.gz /tmp/MWm45bogYL/merge.gvcf.9d.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf /build/reproducible-path/bcftools-1.20/test/gvcf.fa /tmp/MWm45bogYL/merge.gvcf.9a.vcf.gz /tmp/MWm45bogYL/merge.gvcf.9b.vcf.gz /tmp/MWm45bogYL/merge.gvcf.9c.vcf.gz /tmp/MWm45bogYL/merge.gvcf.9d.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version --gvcf /build/reproducible-path/bcftools-1.20/test/gvcf.fa /tmp/MWm45bogYL/merge.gvcf.9a.bcf /tmp/MWm45bogYL/merge.gvcf.9b.bcf /tmp/MWm45bogYL/merge.gvcf.9c.bcf /tmp/MWm45bogYL/merge.gvcf.9d.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf /build/reproducible-path/bcftools-1.20/test/gvcf.fa /tmp/MWm45bogYL/merge.gvcf.9a.bcf /tmp/MWm45bogYL/merge.gvcf.9b.bcf /tmp/MWm45bogYL/merge.gvcf.9c.bcf /tmp/MWm45bogYL/merge.gvcf.9d.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version --gvcf /build/reproducible-path/bcftools-1.20/test/gvcf.fa -r 22:21-23 /tmp/MWm45bogYL/merge.gvcf.9a.vcf.gz /tmp/MWm45bogYL/merge.gvcf.9b.vcf.gz /tmp/MWm45bogYL/merge.gvcf.9c.vcf.gz /tmp/MWm45bogYL/merge.gvcf.9d.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf /build/reproducible-path/bcftools-1.20/test/gvcf.fa -r 22:21-23 /tmp/MWm45bogYL/merge.gvcf.9a.vcf.gz /tmp/MWm45bogYL/merge.gvcf.9b.vcf.gz /tmp/MWm45bogYL/merge.gvcf.9c.vcf.gz /tmp/MWm45bogYL/merge.gvcf.9d.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version --gvcf /build/reproducible-path/bcftools-1.20/test/gvcf.fa -r 22:21-23 /tmp/MWm45bogYL/merge.gvcf.9a.bcf /tmp/MWm45bogYL/merge.gvcf.9b.bcf /tmp/MWm45bogYL/merge.gvcf.9c.bcf /tmp/MWm45bogYL/merge.gvcf.9d.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf /build/reproducible-path/bcftools-1.20/test/gvcf.fa -r 22:21-23 /tmp/MWm45bogYL/merge.gvcf.9a.bcf /tmp/MWm45bogYL/merge.gvcf.9b.bcf /tmp/MWm45bogYL/merge.gvcf.9c.bcf /tmp/MWm45bogYL/merge.gvcf.9d.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version --gvcf /build/reproducible-path/bcftools-1.20/test/gvcf.fa /tmp/MWm45bogYL/merge.gvcf.9a.vcf.gz /tmp/MWm45bogYL/merge.gvcf.9b.vcf.gz /tmp/MWm45bogYL/merge.gvcf.9c.vcf.gz /tmp/MWm45bogYL/merge.gvcf.9d.vcf.gz /tmp/MWm45bogYL/merge.gvcf.9e.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf /build/reproducible-path/bcftools-1.20/test/gvcf.fa /tmp/MWm45bogYL/merge.gvcf.9a.vcf.gz /tmp/MWm45bogYL/merge.gvcf.9b.vcf.gz /tmp/MWm45bogYL/merge.gvcf.9c.vcf.gz /tmp/MWm45bogYL/merge.gvcf.9d.vcf.gz /tmp/MWm45bogYL/merge.gvcf.9e.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version --gvcf /build/reproducible-path/bcftools-1.20/test/gvcf.fa /tmp/MWm45bogYL/merge.gvcf.9a.bcf /tmp/MWm45bogYL/merge.gvcf.9b.bcf /tmp/MWm45bogYL/merge.gvcf.9c.bcf /tmp/MWm45bogYL/merge.gvcf.9d.bcf /tmp/MWm45bogYL/merge.gvcf.9e.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf /build/reproducible-path/bcftools-1.20/test/gvcf.fa /tmp/MWm45bogYL/merge.gvcf.9a.bcf /tmp/MWm45bogYL/merge.gvcf.9b.bcf /tmp/MWm45bogYL/merge.gvcf.9c.bcf /tmp/MWm45bogYL/merge.gvcf.9d.bcf /tmp/MWm45bogYL/merge.gvcf.9e.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version --gvcf /build/reproducible-path/bcftools-1.20/test/gvcf.fa -r 22:21-23 /tmp/MWm45bogYL/merge.gvcf.9a.vcf.gz /tmp/MWm45bogYL/merge.gvcf.9b.vcf.gz /tmp/MWm45bogYL/merge.gvcf.9c.vcf.gz /tmp/MWm45bogYL/merge.gvcf.9d.vcf.gz /tmp/MWm45bogYL/merge.gvcf.9e.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf /build/reproducible-path/bcftools-1.20/test/gvcf.fa -r 22:21-23 /tmp/MWm45bogYL/merge.gvcf.9a.vcf.gz /tmp/MWm45bogYL/merge.gvcf.9b.vcf.gz /tmp/MWm45bogYL/merge.gvcf.9c.vcf.gz /tmp/MWm45bogYL/merge.gvcf.9d.vcf.gz /tmp/MWm45bogYL/merge.gvcf.9e.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version --gvcf /build/reproducible-path/bcftools-1.20/test/gvcf.fa -r 22:21-23 /tmp/MWm45bogYL/merge.gvcf.9a.bcf /tmp/MWm45bogYL/merge.gvcf.9b.bcf /tmp/MWm45bogYL/merge.gvcf.9c.bcf /tmp/MWm45bogYL/merge.gvcf.9d.bcf /tmp/MWm45bogYL/merge.gvcf.9e.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf /build/reproducible-path/bcftools-1.20/test/gvcf.fa -r 22:21-23 /tmp/MWm45bogYL/merge.gvcf.9a.bcf /tmp/MWm45bogYL/merge.gvcf.9b.bcf /tmp/MWm45bogYL/merge.gvcf.9c.bcf /tmp/MWm45bogYL/merge.gvcf.9d.bcf /tmp/MWm45bogYL/merge.gvcf.9e.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version /tmp/MWm45bogYL/merge.gvcf.10.a.vcf.gz /tmp/MWm45bogYL/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob /tmp/MWm45bogYL/merge.gvcf.10.a.vcf.gz /tmp/MWm45bogYL/merge.gvcf.10.b.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version /tmp/MWm45bogYL/merge.gvcf.10.a.bcf /tmp/MWm45bogYL/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob /tmp/MWm45bogYL/merge.gvcf.10.a.bcf /tmp/MWm45bogYL/merge.gvcf.10.b.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -m none /tmp/MWm45bogYL/merge.gvcf.10.a.vcf.gz /tmp/MWm45bogYL/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob -m none /tmp/MWm45bogYL/merge.gvcf.10.a.vcf.gz /tmp/MWm45bogYL/merge.gvcf.10.b.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -m none /tmp/MWm45bogYL/merge.gvcf.10.a.bcf /tmp/MWm45bogYL/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob -m none /tmp/MWm45bogYL/merge.gvcf.10.a.bcf /tmp/MWm45bogYL/merge.gvcf.10.b.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -g /build/reproducible-path/bcftools-1.20/test/merge.gvcf.10.fa /tmp/MWm45bogYL/merge.gvcf.10.a.vcf.gz /tmp/MWm45bogYL/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob -g /build/reproducible-path/bcftools-1.20/test/merge.gvcf.10.fa /tmp/MWm45bogYL/merge.gvcf.10.a.vcf.gz /tmp/MWm45bogYL/merge.gvcf.10.b.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -g /build/reproducible-path/bcftools-1.20/test/merge.gvcf.10.fa /tmp/MWm45bogYL/merge.gvcf.10.a.bcf /tmp/MWm45bogYL/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob -g /build/reproducible-path/bcftools-1.20/test/merge.gvcf.10.fa /tmp/MWm45bogYL/merge.gvcf.10.a.bcf /tmp/MWm45bogYL/merge.gvcf.10.b.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -g /build/reproducible-path/bcftools-1.20/test/merge.gvcf.10.fa -m none /tmp/MWm45bogYL/merge.gvcf.10.a.vcf.gz /tmp/MWm45bogYL/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob -g /build/reproducible-path/bcftools-1.20/test/merge.gvcf.10.fa -m none /tmp/MWm45bogYL/merge.gvcf.10.a.vcf.gz /tmp/MWm45bogYL/merge.gvcf.10.b.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -g /build/reproducible-path/bcftools-1.20/test/merge.gvcf.10.fa -m none /tmp/MWm45bogYL/merge.gvcf.10.a.bcf /tmp/MWm45bogYL/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob -g /build/reproducible-path/bcftools-1.20/test/merge.gvcf.10.fa -m none /tmp/MWm45bogYL/merge.gvcf.10.a.bcf /tmp/MWm45bogYL/merge.gvcf.10.b.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version /tmp/MWm45bogYL/merge.noidx.a.vcf.gz /tmp/MWm45bogYL/merge.noidx.b.vcf.gz /tmp/MWm45bogYL/merge.noidx.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob /tmp/MWm45bogYL/merge.noidx.a.vcf.gz /tmp/MWm45bogYL/merge.noidx.b.vcf.gz /tmp/MWm45bogYL/merge.noidx.c.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version /tmp/MWm45bogYL/merge.noidx.a.bcf /tmp/MWm45bogYL/merge.noidx.b.bcf /tmp/MWm45bogYL/merge.noidx.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob /tmp/MWm45bogYL/merge.noidx.a.bcf /tmp/MWm45bogYL/merge.noidx.b.bcf /tmp/MWm45bogYL/merge.noidx.c.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version --no-index /build/reproducible-path/bcftools-1.20/test/merge.noidx.a.vcf /build/reproducible-path/bcftools-1.20/test/merge.noidx.b.vcf /build/reproducible-path/bcftools-1.20/test/merge.noidx.c.vcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --no-index /build/reproducible-path/bcftools-1.20/test/merge.noidx.a.vcf /build/reproducible-path/bcftools-1.20/test/merge.noidx.b.vcf /build/reproducible-path/bcftools-1.20/test/merge.noidx.c.vcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version --no-index /tmp/MWm45bogYL/merge.noidx.a.bcf /tmp/MWm45bogYL/merge.noidx.b.bcf /tmp/MWm45bogYL/merge.noidx.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --no-index /tmp/MWm45bogYL/merge.noidx.a.bcf /tmp/MWm45bogYL/merge.noidx.b.bcf /tmp/MWm45bogYL/merge.noidx.c.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version /tmp/MWm45bogYL/merge.8.a.vcf.gz /tmp/MWm45bogYL/merge.8.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob /tmp/MWm45bogYL/merge.8.a.vcf.gz /tmp/MWm45bogYL/merge.8.b.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version /tmp/MWm45bogYL/merge.8.a.bcf /tmp/MWm45bogYL/merge.8.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob /tmp/MWm45bogYL/merge.8.a.bcf /tmp/MWm45bogYL/merge.8.b.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -i AN:sum,AC:sum /tmp/MWm45bogYL/merge.8.a.vcf.gz /tmp/MWm45bogYL/merge.8.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/MWm45bogYL/merge.8.a.vcf.gz /tmp/MWm45bogYL/merge.8.b.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -i AN:sum,AC:sum /tmp/MWm45bogYL/merge.8.a.bcf /tmp/MWm45bogYL/merge.8.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/MWm45bogYL/merge.8.a.bcf /tmp/MWm45bogYL/merge.8.b.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version /tmp/MWm45bogYL/merge.9.a.vcf.gz /tmp/MWm45bogYL/merge.9.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob /tmp/MWm45bogYL/merge.9.a.vcf.gz /tmp/MWm45bogYL/merge.9.b.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version /tmp/MWm45bogYL/merge.9.a.bcf /tmp/MWm45bogYL/merge.9.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob /tmp/MWm45bogYL/merge.9.a.bcf /tmp/MWm45bogYL/merge.9.b.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -i AN:sum,AC:sum /tmp/MWm45bogYL/merge.9.a.vcf.gz /tmp/MWm45bogYL/merge.9.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/MWm45bogYL/merge.9.a.vcf.gz /tmp/MWm45bogYL/merge.9.b.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -i AN:sum,AC:sum /tmp/MWm45bogYL/merge.9.a.bcf /tmp/MWm45bogYL/merge.9.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/MWm45bogYL/merge.9.a.bcf /tmp/MWm45bogYL/merge.9.b.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -m none /tmp/MWm45bogYL/merge.10.a.vcf.gz /tmp/MWm45bogYL/merge.10.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob -m none /tmp/MWm45bogYL/merge.10.a.vcf.gz /tmp/MWm45bogYL/merge.10.b.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -m none /tmp/MWm45bogYL/merge.10.a.bcf /tmp/MWm45bogYL/merge.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob -m none /tmp/MWm45bogYL/merge.10.a.bcf /tmp/MWm45bogYL/merge.10.b.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -m both /tmp/MWm45bogYL/merge.10.a.vcf.gz /tmp/MWm45bogYL/merge.10.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob -m both /tmp/MWm45bogYL/merge.10.a.vcf.gz /tmp/MWm45bogYL/merge.10.b.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -m both /tmp/MWm45bogYL/merge.10.a.bcf /tmp/MWm45bogYL/merge.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob -m both /tmp/MWm45bogYL/merge.10.a.bcf /tmp/MWm45bogYL/merge.10.b.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -m snp-ins-del /tmp/MWm45bogYL/merge.10.a.vcf.gz /tmp/MWm45bogYL/merge.10.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob -m snp-ins-del /tmp/MWm45bogYL/merge.10.a.vcf.gz /tmp/MWm45bogYL/merge.10.b.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -m snp-ins-del /tmp/MWm45bogYL/merge.10.a.bcf /tmp/MWm45bogYL/merge.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob -m snp-ins-del /tmp/MWm45bogYL/merge.10.a.bcf /tmp/MWm45bogYL/merge.10.b.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version --gvcf - /tmp/MWm45bogYL/merge.mrules.1.a.vcf.gz /tmp/MWm45bogYL/merge.mrules.1.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/MWm45bogYL/merge.mrules.1.a.vcf.gz /tmp/MWm45bogYL/merge.mrules.1.b.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version --gvcf - /tmp/MWm45bogYL/merge.mrules.1.a.bcf /tmp/MWm45bogYL/merge.mrules.1.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/MWm45bogYL/merge.mrules.1.a.bcf /tmp/MWm45bogYL/merge.mrules.1.b.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version --gvcf - -M AD:.,PL:. /tmp/MWm45bogYL/merge.mrules.1.a.vcf.gz /tmp/MWm45bogYL/merge.mrules.1.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - -M AD:.,PL:. /tmp/MWm45bogYL/merge.mrules.1.a.vcf.gz /tmp/MWm45bogYL/merge.mrules.1.b.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version --gvcf - -M AD:.,PL:. /tmp/MWm45bogYL/merge.mrules.1.a.bcf /tmp/MWm45bogYL/merge.mrules.1.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - -M AD:.,PL:. /tmp/MWm45bogYL/merge.mrules.1.a.bcf /tmp/MWm45bogYL/merge.mrules.1.b.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version --gvcf - /tmp/MWm45bogYL/merge.gvcf.5.a.vcf.gz /tmp/MWm45bogYL/merge.gvcf.5.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/MWm45bogYL/merge.gvcf.5.a.vcf.gz /tmp/MWm45bogYL/merge.gvcf.5.b.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version --gvcf - /tmp/MWm45bogYL/merge.gvcf.5.a.bcf /tmp/MWm45bogYL/merge.gvcf.5.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/MWm45bogYL/merge.gvcf.5.a.bcf /tmp/MWm45bogYL/merge.gvcf.5.b.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version --gvcf - --merge none /tmp/MWm45bogYL/merge.gvcf.5.a.vcf.gz /tmp/MWm45bogYL/merge.gvcf.5.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - --merge none /tmp/MWm45bogYL/merge.gvcf.5.a.vcf.gz /tmp/MWm45bogYL/merge.gvcf.5.b.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version --gvcf - --merge none /tmp/MWm45bogYL/merge.gvcf.5.a.bcf /tmp/MWm45bogYL/merge.gvcf.5.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - --merge none /tmp/MWm45bogYL/merge.gvcf.5.a.bcf /tmp/MWm45bogYL/merge.gvcf.5.b.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version --gvcf - /tmp/MWm45bogYL/merge.gvcf.11.a.vcf.gz /tmp/MWm45bogYL/merge.gvcf.11.b.vcf.gz /tmp/MWm45bogYL/merge.gvcf.11.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/MWm45bogYL/merge.gvcf.11.a.vcf.gz /tmp/MWm45bogYL/merge.gvcf.11.b.vcf.gz /tmp/MWm45bogYL/merge.gvcf.11.c.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version --gvcf - /tmp/MWm45bogYL/merge.gvcf.11.a.bcf /tmp/MWm45bogYL/merge.gvcf.11.b.bcf /tmp/MWm45bogYL/merge.gvcf.11.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/MWm45bogYL/merge.gvcf.11.a.bcf /tmp/MWm45bogYL/merge.gvcf.11.b.bcf /tmp/MWm45bogYL/merge.gvcf.11.c.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided,_conflicting_interpretations"' /tmp/MWm45bogYL/query.string.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.string.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided,_conflicting_interpretations"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" || CLNREVSTAT="_conflicting_interpretations"' /tmp/MWm45bogYL/query.string.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.string.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" || CLNREVSTAT="_conflicting_interpretations"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" && CLNREVSTAT="_conflicting_interpretations"' /tmp/MWm45bogYL/query.string.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.string.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" && CLNREVSTAT="_conflicting_interpretations"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f '%CHROM\t%POS\t%INFO/STR\n' -i'INFO/STR=@/build/reproducible-path/bcftools-1.20/test/query.string.2.1.txt' /tmp/MWm45bogYL/query.string.2.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.string.2.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f '%CHROM\t%POS\t%INFO/STR\n' -i'INFO/STR=@/build/reproducible-path/bcftools-1.20/test/query.string.2.1.txt' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f '%CHROM\t%POS[\t%STR]\n' -i'FMT/STR=@/build/reproducible-path/bcftools-1.20/test/query.string.2.2.txt' /tmp/MWm45bogYL/query.string.2.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.string.2.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f '%CHROM\t%POS[\t%STR]\n' -i'FMT/STR=@/build/reproducible-path/bcftools-1.20/test/query.string.2.2.txt' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' /tmp/MWm45bogYL/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.vcf.gz | /build/reproducible-path/bcftools-1.20/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-1.20/bcftools query -f '%RSX\t%VKX\n' /tmp/MWm45bogYL/query.variantkey.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.variantkey.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f '%RSX\t%VKX\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'%XRI\n' -i'XRI[*]>1111' /tmp/MWm45bogYL/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'%XRI\n' -i'XRI[*]>1111' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' /tmp/MWm45bogYL/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' /tmp/MWm45bogYL/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' /tmp/MWm45bogYL/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' /tmp/MWm45bogYL/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' /tmp/MWm45bogYL/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' /tmp/MWm45bogYL/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' /tmp/MWm45bogYL/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' /tmp/MWm45bogYL/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' /tmp/MWm45bogYL/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' /tmp/MWm45bogYL/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' /tmp/MWm45bogYL/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' /tmp/MWm45bogYL/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' /tmp/MWm45bogYL/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' /tmp/MWm45bogYL/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' /tmp/MWm45bogYL/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/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/MWm45bogYL/view.vectors.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/view.vectors.vcf.gz | /build/reproducible-path/bcftools-1.20/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-1.20/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' /tmp/MWm45bogYL/query.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.filter.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' /tmp/MWm45bogYL/query.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.filter.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' /tmp/MWm45bogYL/query.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.filter.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' /tmp/MWm45bogYL/query.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.filter.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' /tmp/MWm45bogYL/query.2.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.2.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -i'IINT="."' -f'%POS %IINT\n' /tmp/MWm45bogYL/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/missing.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -i'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -i'IINT!="."' -f'%POS %IINT\n' /tmp/MWm45bogYL/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/missing.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -i'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -e'IINT!="."' -f'%POS %IINT\n' /tmp/MWm45bogYL/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/missing.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -e'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -e'IINT="."' -f'%POS %IINT\n' /tmp/MWm45bogYL/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/missing.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -e'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' /tmp/MWm45bogYL/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/missing.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' /tmp/MWm45bogYL/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/missing.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' /tmp/MWm45bogYL/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/missing.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' /tmp/MWm45bogYL/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/missing.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' /tmp/MWm45bogYL/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/missing.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' /tmp/MWm45bogYL/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/missing.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' /tmp/MWm45bogYL/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/missing.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' /tmp/MWm45bogYL/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/missing.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' /tmp/MWm45bogYL/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/missing.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -i'FILTER="A"' -f'%POS %FILTER\n' /tmp/MWm45bogYL/filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/filter.11.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -i'FILTER="A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -i'FILTER!="A"' -f'%POS %FILTER\n' /tmp/MWm45bogYL/filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/filter.11.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -i'FILTER!="A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -i'FILTER~"A"' -f'%POS %FILTER\n' /tmp/MWm45bogYL/filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/filter.11.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -i'FILTER~"A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n' /tmp/MWm45bogYL/filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/filter.11.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'%LINE' /tmp/MWm45bogYL/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'%LINE' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' /tmp/MWm45bogYL/query.filter-type.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.filter-type.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' /tmp/MWm45bogYL/query.filter-type.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.filter-type.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' /tmp/MWm45bogYL/query.filter-type.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.filter-type.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' /tmp/MWm45bogYL/query.filter-type.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.filter-type.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\n' -i'INFO/TYPE="xxx"' /tmp/MWm45bogYL/query.filter-type.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.filter-type.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\n' -i'INFO/TYPE="xxx"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/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/MWm45bogYL/filter-missing-floats.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/filter-missing-floats.vcf.gz | /build/reproducible-path/bcftools-1.20/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-1.20/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/MWm45bogYL/filter-missing-floats.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/filter-missing-floats.vcf.gz | /build/reproducible-path/bcftools-1.20/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-1.20/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' /tmp/MWm45bogYL/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/missing.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' /tmp/MWm45bogYL/query.filter.2.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.filter.2.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' /tmp/MWm45bogYL/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' /tmp/MWm45bogYL/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' /tmp/MWm45bogYL/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' /tmp/MWm45bogYL/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' /tmp/MWm45bogYL/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' /tmp/MWm45bogYL/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' /tmp/MWm45bogYL/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' /tmp/MWm45bogYL/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' /tmp/MWm45bogYL/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' /tmp/MWm45bogYL/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' /tmp/MWm45bogYL/filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/filter.5.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' /tmp/MWm45bogYL/filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/filter.5.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' /tmp/MWm45bogYL/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' /tmp/MWm45bogYL/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' /tmp/MWm45bogYL/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' /tmp/MWm45bogYL/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' /tmp/MWm45bogYL/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 & FMT/GQ=589' /tmp/MWm45bogYL/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 & FMT/GQ=589' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' /tmp/MWm45bogYL/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' /tmp/MWm45bogYL/query.filter.3.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.filter.3.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"' /tmp/MWm45bogYL/query.filter.3.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.filter.3.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' /tmp/MWm45bogYL/query.filter.3.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.filter.3.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %AD\n]\n' -i'AD[:0]+AD[:1] > 12' /tmp/MWm45bogYL/filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/filter.5.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %AD\n]\n' -i'AD[:0]+AD[:1] > 12' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' /tmp/MWm45bogYL/query.filter.4.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.filter.4.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'%ID\n' -i 'ID=@/build/reproducible-path/bcftools-1.20/test/query.56.out' /tmp/MWm45bogYL/view.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/view.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'%ID\n' -i 'ID=@/build/reproducible-path/bcftools-1.20/test/query.56.out' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD)>0.01' /tmp/MWm45bogYL/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.filter.5.vcf.gz | /build/reproducible-path/bcftools-1.20/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-1.20/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD[:0],FMT/AD[:1])>0.01' /tmp/MWm45bogYL/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.filter.5.vcf.gz | /build/reproducible-path/bcftools-1.20/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-1.20/bcftools query -f'%POS\t%AD\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01' /tmp/MWm45bogYL/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.filter.5.vcf.gz | /build/reproducible-path/bcftools-1.20/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-1.20/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[GT]==10' /tmp/MWm45bogYL/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.filter.5.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[GT]==10' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'sSUM(FMT/AD[GT])==210' /tmp/MWm45bogYL/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.filter.5.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'sSUM(FMT/AD[GT])==210' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[0:GT]==30' /tmp/MWm45bogYL/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.filter.5.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[0:GT]==30' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TF[:GT]==1 && FMT/TF[:GT]==2' /tmp/MWm45bogYL/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.gtidx.1.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TF[:GT]==1 && FMT/TF[:GT]==2' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TI[:GT]==1 && FMT/TF[:GT]==2' /tmp/MWm45bogYL/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.gtidx.1.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TI[:GT]==1 && FMT/TF[:GT]==2' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TS[:GT]=="BB" && FMT/TS[:GT]=="CC"' /tmp/MWm45bogYL/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.gtidx.1.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TS[:GT]=="BB" && FMT/TS[:GT]=="CC"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TC[:GT]=="B" && FMT/TC[:GT]=="C"' /tmp/MWm45bogYL/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.gtidx.1.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TC[:GT]=="B" && FMT/TC[:GT]=="C"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'[%GT %TI\n]' -i'FMT/TI[:GT]=="."' /tmp/MWm45bogYL/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.gtidx.1.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%GT %TI\n]' -i'FMT/TI[:GT]=="."' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'%CHROM %POS\n' -i'CHROM="4"' /tmp/MWm45bogYL/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'%CHROM %POS\n' -i'CHROM="4"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%TAG1\n' -i'(TAG1>=-129 && TAG1<=-120) || (TAG1>=-32769 && TAG1<=-32760)' /tmp/MWm45bogYL/query.negative.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.negative.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%TAG1\n' -i'(TAG1>=-129 && TAG1<=-120) || (TAG1>=-32769 && TAG1<=-32760)' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%TAGV1\n' -i'(TAGV1>=-129 && TAGV1<=-120) || (TAGV1>=-32769 && TAGV1<=-32760)' /tmp/MWm45bogYL/query.negative.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.negative.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%TAGV1\n' -i'(TAGV1>=-129 && TAGV1<=-120) || (TAGV1>=-32769 && TAGV1<=-32760)' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%TAG2\n' -i'(TAG2>=-129 && TAG2<=-120) || (TAG2>=-32769 && TAG2<=-32760)' /tmp/MWm45bogYL/query.negative.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.negative.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%TAG2\n' -i'(TAG2>=-129 && TAG2<=-120) || (TAG2>=-32769 && TAG2<=-32760)' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%TAGV2\n' -i'(TAGV2>=-129 && TAGV2<=-120) || (TAGV2>=-32769 && TAGV2<=-32760)' /tmp/MWm45bogYL/query.negative.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.negative.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%TAGV2\n' -i'(TAGV2>=-129 && TAGV2<=-120) || (TAGV2>=-32769 && TAGV2<=-32760)' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS\t%SAMPLE\t%GQ\n]' -i'N_PASS(GQ<20)==1' /tmp/MWm45bogYL/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS\t%SAMPLE\t%GQ\n]' -i'N_PASS(GQ<20)==1' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")==1' /tmp/MWm45bogYL/query.filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.filter.11.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")==1' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")!=1' /tmp/MWm45bogYL/query.filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.filter.11.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")!=1' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")==1' /tmp/MWm45bogYL/query.filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.filter.11.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")==1' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")!=1' /tmp/MWm45bogYL/query.filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.filter.11.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")!=1' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'%CHROM\t%POS\t%INFO\t%FORMAT\n' -s D,C /tmp/MWm45bogYL/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'%CHROM\t%POS\t%INFO\t%FORMAT\n' -s D,C .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\n' -i'POS==16777217 || POS==33554432 || POS=118673904' /tmp/MWm45bogYL/query.filter.6.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.filter.6.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\n' -i'POS==16777217 || POS==33554432 || POS=118673904' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(II)==6' /tmp/MWm45bogYL/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(II)==6' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(FORMAT/FI)==7' /tmp/MWm45bogYL/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(FORMAT/FI)==7' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(II)==2' /tmp/MWm45bogYL/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(II)==2' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(FORMAT/FI)==1.75' /tmp/MWm45bogYL/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(FORMAT/FI)==1.75' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(II)==2' /tmp/MWm45bogYL/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(II)==2' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(FORMAT/FI)==1.75' /tmp/MWm45bogYL/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(FORMAT/FI)==1.75' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(II)==2' /tmp/MWm45bogYL/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(II)==2' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(FORMAT/FI)==1.5' /tmp/MWm45bogYL/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(FORMAT/FI)==1.5' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'%ILEN==1' /tmp/MWm45bogYL/query.filter.8.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.filter.8.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'%ILEN==1' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'ILEN==1' /tmp/MWm45bogYL/query.filter.8.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.filter.8.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'ILEN==1' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] < FMT/AD[:1]' /tmp/MWm45bogYL/query.filter.9.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.filter.9.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] < FMT/AD[:1]' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] > FMT/AD[:1]' /tmp/MWm45bogYL/query.filter.9.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.filter.9.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] > FMT/AD[:1]' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'[ %AD\n]' -i'AD[:1] / sum(AD[*]) > 0.5' /tmp/MWm45bogYL/query.filter.13.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.filter.13.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'[ %AD\n]' -i'AD[:1] / sum(AD[*]) > 0.5' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS %NUM_TAG\n' -i'COUNT(INFO/NUM_TAG)=2' /tmp/MWm45bogYL/query.filter.10.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.filter.10.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS %NUM_TAG\n' -i'COUNT(INFO/NUM_TAG)=2' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2' /tmp/MWm45bogYL/query.filter.10.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.filter.10.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f '%CHROM:%POS\t%N_PASS(GT="alt" & GQ>110)\t[\t%GT]\t[\t%GQ]\n' /tmp/MWm45bogYL/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f '%CHROM:%POS\t%N_PASS(GT="alt" & GQ>110)\t[\t%GT]\t[\t%GQ]\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 1,3,0 /tmp/MWm45bogYL/query.filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.filter.12.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 1,3,0 .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 0,1,3 /tmp/MWm45bogYL/query.filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.filter.12.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 0,1,3 .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f "[%SAMPLE %GT\n]" -S /build/reproducible-path/bcftools-1.20/test/query.smpl.11.txt /tmp/MWm45bogYL/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.smpl.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f "[%SAMPLE %GT\n]" -S /build/reproducible-path/bcftools-1.20/test/query.smpl.11.txt .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -l -S /build/reproducible-path/bcftools-1.20/test/query.smpl.11.txt /tmp/MWm45bogYL/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.smpl.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -l -S /build/reproducible-path/bcftools-1.20/test/query.smpl.11.txt .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f "[%SAMPLE %GT\n]" -S ^/build/reproducible-path/bcftools-1.20/test/query.smpl.11.txt /tmp/MWm45bogYL/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.smpl.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f "[%SAMPLE %GT\n]" -S ^/build/reproducible-path/bcftools-1.20/test/query.smpl.11.txt .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -l -S ^/build/reproducible-path/bcftools-1.20/test/query.smpl.11.txt /tmp/MWm45bogYL/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.smpl.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -l -S ^/build/reproducible-path/bcftools-1.20/test/query.smpl.11.txt .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f "[%SAMPLE %GT\n]" -S /build/reproducible-path/bcftools-1.20/test/query.smpl.txt /tmp/MWm45bogYL/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.smpl.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f "[%SAMPLE %GT\n]" -S /build/reproducible-path/bcftools-1.20/test/query.smpl.txt .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -l -S /build/reproducible-path/bcftools-1.20/test/query.smpl.txt /tmp/MWm45bogYL/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.smpl.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -l -S /build/reproducible-path/bcftools-1.20/test/query.smpl.txt .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'%ID\n' -i'ID~"s12"' /tmp/MWm45bogYL/query.filter.id.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.filter.id.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'%ID\n' -i'ID~"s12"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'%ID\n' -i'ID="rs123"' /tmp/MWm45bogYL/query.filter.id.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.filter.id.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'%ID\n' -i'ID="rs123"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -i'FILTER="A"' -f'%FILTER\n' /tmp/MWm45bogYL/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/filter.12.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -i'FILTER="A"' -f'%FILTER\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -i'FILTER~"A"' -f'%FILTER\n' /tmp/MWm45bogYL/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/filter.12.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -i'FILTER~"A"' -f'%FILTER\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -i'FILTER="A;B"' -f'%FILTER\n' /tmp/MWm45bogYL/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/filter.12.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -i'FILTER="A;B"' -f'%FILTER\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -i'FILTER!="A;B"' -f'%FILTER\n' /tmp/MWm45bogYL/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/filter.12.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -i'FILTER!="A;B"' -f'%FILTER\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -i'FILTER~"A;B"' -f'%FILTER\n' /tmp/MWm45bogYL/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/filter.12.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -i'FILTER~"A;B"' -f'%FILTER\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -i'FILTER!~"A;B"' -f'%FILTER\n' /tmp/MWm45bogYL/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/filter.12.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -i'FILTER!~"A;B"' -f'%FILTER\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -i'DP%10==2' -f'[ %DP]\n' /tmp/MWm45bogYL/filter.10.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/filter.10.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -i'DP%10==2' -f'[ %DP]\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -i'REF="N"' -f'%CHROM %POS %REF %ALT %QUAL\n' /tmp/MWm45bogYL/filter.13.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/filter.13.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -i'REF="N"' -f'%CHROM %POS %REF %ALT %QUAL\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -H -f'[%CHROM %POS %SAMPLE %DP %GT\n]' /tmp/MWm45bogYL/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.header.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -H -f'[%CHROM %POS %SAMPLE %DP %GT\n]' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -H -f'[%CHROM %POS %SAMPLE %DP %GT\t]\n' /tmp/MWm45bogYL/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.header.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -H -f'[%CHROM %POS %SAMPLE %DP %GT\t]\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]\n' /tmp/MWm45bogYL/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.header.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]' /tmp/MWm45bogYL/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.header.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]\n' /tmp/MWm45bogYL/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.header.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]' /tmp/MWm45bogYL/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.header.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'[%SAMPLE %DP\n]' -i'DP=1 || DP=2' /tmp/MWm45bogYL/query.filter-or.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.filter-or.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%SAMPLE %DP\n]' -i'DP=1 || DP=2' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools query -f'[%SAMPLE %DP\n]' -i'DP=1 | DP=2' /tmp/MWm45bogYL/query.filter-or.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/query.filter-or.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%SAMPLE %DP\n]' -i'DP=1 | DP=2' .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -cx /tmp/MWm45bogYL/norm.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/norm.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -cx /tmp/MWm45bogYL/norm.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/norm.fa -Ou | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m- /tmp/MWm45bogYL/norm.split.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m- /tmp/MWm45bogYL/norm.split.vcf.gz -Ou | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m- /tmp/MWm45bogYL/norm.split.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m- /tmp/MWm45bogYL/norm.split.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m- --force /tmp/MWm45bogYL/norm.split.3.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m- --force /tmp/MWm45bogYL/norm.split.3.vcf.gz -Ou | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m- /tmp/MWm45bogYL/norm.split.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m- /tmp/MWm45bogYL/norm.split.4.vcf.gz -Ou | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m- --keep-sum AD /tmp/MWm45bogYL/norm.split.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m- --keep-sum AD /tmp/MWm45bogYL/norm.split.4.vcf.gz -Ou | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m- /tmp/MWm45bogYL/norm.split.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/norm.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m- /tmp/MWm45bogYL/norm.split.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/norm.fa -Ou | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m+ /tmp/MWm45bogYL/norm.merge.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m+ /tmp/MWm45bogYL/norm.merge.vcf.gz -Ou | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m+ /tmp/MWm45bogYL/norm.merge.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m+ /tmp/MWm45bogYL/norm.merge.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m+ /tmp/MWm45bogYL/norm.merge.3.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m+ /tmp/MWm45bogYL/norm.merge.3.vcf.gz -Ou | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m+ -s /tmp/MWm45bogYL/norm.merge.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m+ -s /tmp/MWm45bogYL/norm.merge.vcf.gz -Ou | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -Nc s /tmp/MWm45bogYL/norm.setref.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/norm.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -Nc s /tmp/MWm45bogYL/norm.setref.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/norm.fa -Ou | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version /tmp/MWm45bogYL/norm.telomere.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/norm.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version /tmp/MWm45bogYL/norm.telomere.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/norm.fa -Ou | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -d snps /tmp/MWm45bogYL/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -d snps /tmp/MWm45bogYL/norm.rmdup.vcf.gz -Ou | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -d indels /tmp/MWm45bogYL/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -d indels /tmp/MWm45bogYL/norm.rmdup.vcf.gz -Ou | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -d both /tmp/MWm45bogYL/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -d both /tmp/MWm45bogYL/norm.rmdup.vcf.gz -Ou | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -d all /tmp/MWm45bogYL/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -d all /tmp/MWm45bogYL/norm.rmdup.vcf.gz -Ou | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -d none /tmp/MWm45bogYL/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -d none /tmp/MWm45bogYL/norm.rmdup.vcf.gz -Ou | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -d exact /tmp/MWm45bogYL/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -d exact /tmp/MWm45bogYL/norm.rmdup.vcf.gz -Ou | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -d none /tmp/MWm45bogYL/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -d none /tmp/MWm45bogYL/norm.rmdup.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -d exact /tmp/MWm45bogYL/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -d exact /tmp/MWm45bogYL/norm.rmdup.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -d indels /tmp/MWm45bogYL/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -d indels /tmp/MWm45bogYL/norm.rmdup.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -d any /tmp/MWm45bogYL/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -d any /tmp/MWm45bogYL/norm.rmdup.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -d both /tmp/MWm45bogYL/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -d both /tmp/MWm45bogYL/norm.rmdup.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -d snps /tmp/MWm45bogYL/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -d snps /tmp/MWm45bogYL/norm.rmdup.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -c s -a /tmp/MWm45bogYL/norm.2.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/norm.2.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -c s -a /tmp/MWm45bogYL/norm.2.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/norm.2.fa -Ou | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -c s /tmp/MWm45bogYL/norm.iupac.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/norm.iupac.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -c s /tmp/MWm45bogYL/norm.iupac.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/norm.iupac.fa -Ou | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -c s /tmp/MWm45bogYL/norm.3.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/norm.3.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -c s /tmp/MWm45bogYL/norm.3.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/norm.3.fa -Ou | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -a --old-rec-tag OLD_REC /tmp/MWm45bogYL/atomize.split.1.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m -any --force .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -a --old-rec-tag OLD_REC /tmp/MWm45bogYL/atomize.split.1.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m -any --force -Ou | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m -any --old-rec-tag OLD_REC --force /tmp/MWm45bogYL/atomize.split.1.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -a .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m -any --old-rec-tag OLD_REC --force /tmp/MWm45bogYL/atomize.split.1.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -a -Ou | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m -any --old-rec-tag OLD_REC --force -a /tmp/MWm45bogYL/atomize.split.1.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m -any --old-rec-tag OLD_REC --force -a /tmp/MWm45bogYL/atomize.split.1.vcf.gz -Ou | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/MWm45bogYL/atomize.split.1.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/MWm45bogYL/atomize.split.1.vcf.gz -Ou | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/MWm45bogYL/atomize.split.1.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/MWm45bogYL/atomize.split.1.vcf.gz -Ou | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/MWm45bogYL/atomize.split.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/MWm45bogYL/atomize.split.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/MWm45bogYL/atomize.split.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/MWm45bogYL/atomize.split.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version --atomize --atom-overlaps . /tmp/MWm45bogYL/atomize.split.3.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version --atomize --atom-overlaps . /tmp/MWm45bogYL/atomize.split.3.vcf.gz -Ou | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/MWm45bogYL/atomize.split.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/MWm45bogYL/atomize.split.4.vcf.gz -Ou | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m +both /tmp/MWm45bogYL/norm.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m +both /tmp/MWm45bogYL/norm.4.vcf.gz -Ou | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m +any /tmp/MWm45bogYL/norm.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m +any /tmp/MWm45bogYL/norm.4.vcf.gz -Ou | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m - --multi-overlaps 0 /tmp/MWm45bogYL/norm.5.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m - --multi-overlaps 0 /tmp/MWm45bogYL/norm.5.vcf.gz -Ou | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m - --multi-overlaps . /tmp/MWm45bogYL/norm.5.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m - --multi-overlaps . /tmp/MWm45bogYL/norm.5.vcf.gz -Ou | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m -any /tmp/MWm45bogYL/norm.m-any.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m -any /tmp/MWm45bogYL/norm.m-any.vcf.gz -Ou | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m -any /tmp/MWm45bogYL/norm.phased-split.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m -any /tmp/MWm45bogYL/norm.phased-split.vcf.gz -Ou | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m +any /tmp/MWm45bogYL/norm.phased-join.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m +any /tmp/MWm45bogYL/norm.phased-join.vcf.gz -Ou | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version --old-rec-tag ORI /tmp/MWm45bogYL/norm.symbolic.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/norm.symbolic.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version --old-rec-tag ORI /tmp/MWm45bogYL/norm.symbolic.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/norm.symbolic.fa -Ou | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version --old-rec-tag ORI /tmp/MWm45bogYL/norm.symbolic.2.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/norm.symbolic.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version --old-rec-tag ORI /tmp/MWm45bogYL/norm.symbolic.2.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/norm.symbolic.fa -Ou | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version --old-rec-tag ORI /tmp/MWm45bogYL/norm.right-align.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/norm.right-align.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version --old-rec-tag ORI /tmp/MWm45bogYL/norm.right-align.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/norm.right-align.fa -Ou | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version --old-rec-tag ORI -g /build/reproducible-path/bcftools-1.20/test/norm.right-align.gff /tmp/MWm45bogYL/norm.right-align.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/norm.right-align.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version --old-rec-tag ORI -g /build/reproducible-path/bcftools-1.20/test/norm.right-align.gff /tmp/MWm45bogYL/norm.right-align.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/norm.right-align.fa -Ou | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version --old-rec-tag ORI -a -m -any /tmp/MWm45bogYL/norm.atom-split-norm.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/norm.atom-split-norm.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version --old-rec-tag ORI -a -m -any /tmp/MWm45bogYL/norm.atom-split-norm.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/norm.atom-split-norm.fa -Ou | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m -any /tmp/MWm45bogYL/norm.string-tags.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m -any /tmp/MWm45bogYL/norm.string-tags.vcf.gz -Ou | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m - /tmp/MWm45bogYL/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m +both .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m - /tmp/MWm45bogYL/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m +both -Ou | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m - /tmp/MWm45bogYL/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m +indels .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m - /tmp/MWm45bogYL/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m +indels -Ou | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m - /tmp/MWm45bogYL/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m +snps .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m - /tmp/MWm45bogYL/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m +snps -Ou | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m - /tmp/MWm45bogYL/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m +any .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m - /tmp/MWm45bogYL/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m +any -Ou | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m +any /tmp/MWm45bogYL/norm.merge.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m +any /tmp/MWm45bogYL/norm.merge.4.vcf.gz -Ou | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m +both /tmp/MWm45bogYL/norm.merge.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m +both /tmp/MWm45bogYL/norm.merge.4.vcf.gz -Ou | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -i 'INFO/TAG=@/build/reproducible-path/bcftools-1.20/test/filter.string.1.txt' /tmp/MWm45bogYL/filter.string.1.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -i 'INFO/TAG=@/build/reproducible-path/bcftools-1.20/test/filter.string.1.txt' /tmp/MWm45bogYL/filter.string.1.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -i 'FMT/TAG=@/build/reproducible-path/bcftools-1.20/test/filter.string.1.txt' /tmp/MWm45bogYL/filter.string.1.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -i 'FMT/TAG=@/build/reproducible-path/bcftools-1.20/test/filter.string.1.txt' /tmp/MWm45bogYL/filter.string.1.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -HA /tmp/MWm45bogYL/merge.gvcf.2.a.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -HAA /tmp/MWm45bogYL/merge.gvcf.2.a.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version /tmp/MWm45bogYL/weird-chr-names.vcf.gz -r 1 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/weird-chr-names.vcf.gz -r 1 | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version /tmp/MWm45bogYL/weird-chr-names.vcf.gz -r 1:1-2 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/weird-chr-names.vcf.gz -r 1:1-2 | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version /tmp/MWm45bogYL/weird-chr-names.vcf.gz -r 1:1,1:2 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/weird-chr-names.vcf.gz -r 1:1,1:2 | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version /tmp/MWm45bogYL/weird-chr-names.vcf.gz -r 1:1-1 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/weird-chr-names.vcf.gz -r 1:1-1 | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version /tmp/MWm45bogYL/weird-chr-names.vcf.gz -r {1:1} .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/weird-chr-names.vcf.gz -r {1:1} | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version /tmp/MWm45bogYL/weird-chr-names.vcf.gz -r {1:1}:1-2 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/weird-chr-names.vcf.gz -r {1:1}:1-2 | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version /tmp/MWm45bogYL/weird-chr-names.vcf.gz -r {1:1}:1,{1:1}:2 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/weird-chr-names.vcf.gz -r {1:1}:1,{1:1}:2 | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version /tmp/MWm45bogYL/weird-chr-names.vcf.gz -r {1:1}:1-1 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/weird-chr-names.vcf.gz -r {1:1}:1-1 | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version /tmp/MWm45bogYL/weird-chr-names.vcf.gz -r {1:1-1} .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/weird-chr-names.vcf.gz -r {1:1-1} | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version /tmp/MWm45bogYL/weird-chr-names.vcf.gz -r {1:1-1}:1-2 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/weird-chr-names.vcf.gz -r {1:1-1}:1-2 | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version /tmp/MWm45bogYL/weird-chr-names.vcf.gz -r {1:1-1}:1,{1:1-1}:2 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/weird-chr-names.vcf.gz -r {1:1-1}:1,{1:1-1}:2 | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version /tmp/MWm45bogYL/weird-chr-names.vcf.gz -r {1:1-1}:1-1 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/weird-chr-names.vcf.gz -r {1:1-1}:1-1 | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version /tmp/MWm45bogYL/weird-chr-names.vcf.gz -r {1:1-1}-2 .. ok, expected non-zero status test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/weird-chr-names.vcf.gz -r {1:1-1}-2 | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok, expected non-zero status test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -aUc1 -C1 -s NA00002 -v snps /tmp/MWm45bogYL/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/MWm45bogYL/view.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -f PASS -Xks NA00003 /tmp/MWm45bogYL/view.vcf.gz -r20,Y .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -f PASS -Xks NA00003 /tmp/MWm45bogYL/view.vcf.gz -r20,Y | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -xs NA00003 /tmp/MWm45bogYL/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -xs NA00003 /tmp/MWm45bogYL/view.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/MWm45bogYL/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/MWm45bogYL/view.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -p /tmp/MWm45bogYL/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -p /tmp/MWm45bogYL/view.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -P /tmp/MWm45bogYL/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -P /tmp/MWm45bogYL/view.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -hm2 -M2 -q0.3 -Q0.7 /tmp/MWm45bogYL/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/MWm45bogYL/view.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -Hu /tmp/MWm45bogYL/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -GVsnps /tmp/MWm45bogYL/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -GVsnps /tmp/MWm45bogYL/view.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -ne 'INDEL=1 || PV4[0]<0.006' /tmp/MWm45bogYL/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/MWm45bogYL/view.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -s ^NA00003 /tmp/MWm45bogYL/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -s ^NA00003 /tmp/MWm45bogYL/view.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version /tmp/MWm45bogYL/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/view.omitgenotypes.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -G /tmp/MWm45bogYL/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -G /tmp/MWm45bogYL/view.omitgenotypes.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -HG /tmp/MWm45bogYL/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -a /tmp/MWm45bogYL/many.alleles.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -a /tmp/MWm45bogYL/many.alleles.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -asA /tmp/MWm45bogYL/view.vectors.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -asA /tmp/MWm45bogYL/view.vectors.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -asB /tmp/MWm45bogYL/view.vectors.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -asB /tmp/MWm45bogYL/view.vectors.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -asA /tmp/MWm45bogYL/view.vectors.2.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -asA /tmp/MWm45bogYL/view.vectors.2.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -H -i'FMT/FGS[*:0]="AAAAAA"' /tmp/MWm45bogYL/view.filter.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -H -i'FMT/FGS[*:2]="C"' /tmp/MWm45bogYL/view.filter.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -H -i'FMT/FGS[*:4]="EE"' /tmp/MWm45bogYL/view.filter.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -H -i'FMT/FRS[*:1]="BB"' /tmp/MWm45bogYL/view.filter.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -H -i'TXT0="text"' /tmp/MWm45bogYL/view.filter.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -T /build/reproducible-path/bcftools-1.20/test/view.chrs.tab /tmp/MWm45bogYL/view.chrs.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -T /build/reproducible-path/bcftools-1.20/test/view.chrs.tab /tmp/MWm45bogYL/view.chrs.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -i 'POS>=3062917' /tmp/MWm45bogYL/filter.2.vcf.gz 1:3062917-3157410 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -i 'POS>=3062917' /tmp/MWm45bogYL/filter.2.vcf.gz 1:3062917-3157410 | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -H -r 1:10,1:12,1:10 /tmp/MWm45bogYL/idx.1.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -H -r 1:1172777-1172804,1:1172806-1172808 /tmp/MWm45bogYL/idx.2.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -H -R /build/reproducible-path/bcftools-1.20/test/idx.2.bed /tmp/MWm45bogYL/idx.2.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -H -R /build/reproducible-path/bcftools-1.20/test/idx.3.bed /tmp/MWm45bogYL/idx.3.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -H -R /build/reproducible-path/bcftools-1.20/test/idx.4.bed /tmp/MWm45bogYL/idx.4.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -Ht 2 /tmp/MWm45bogYL/view-t.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -Ht 3 /tmp/MWm45bogYL/view-t.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 0 /tmp/MWm45bogYL/overlap.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 1 /tmp/MWm45bogYL/overlap.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 2 /tmp/MWm45bogYL/overlap.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 0 /tmp/MWm45bogYL/overlap.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 1 /tmp/MWm45bogYL/overlap.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 2 /tmp/MWm45bogYL/overlap.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 0 /tmp/MWm45bogYL/overlap.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 1 /tmp/MWm45bogYL/overlap.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 2 /tmp/MWm45bogYL/overlap.vcf.gz .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.20/bcftools view /build/reproducible-path/bcftools-1.20/test/view64bit.1.vcf -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.20/bcftools view /build/reproducible-path/bcftools-1.20/test/view64bit.1.vcf | /build/reproducible-path/bcftools-1.20/bcftools view -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.20/bcftools view /build/reproducible-path/bcftools-1.20/test/view64bit.1.vcf -Ou | /build/reproducible-path/bcftools-1.20/bcftools view -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.20/bcftools view /build/reproducible-path/bcftools-1.20/test/view64bit.2.vcf -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.20/bcftools view /build/reproducible-path/bcftools-1.20/test/view64bit.2.vcf | /build/reproducible-path/bcftools-1.20/bcftools view -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.20/bcftools view /build/reproducible-path/bcftools-1.20/test/view64bit.2.vcf -Ou | /build/reproducible-path/bcftools-1.20/bcftools view -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.20/bcftools view /build/reproducible-path/bcftools-1.20/test/view64bit.3.vcf -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.20/bcftools view /build/reproducible-path/bcftools-1.20/test/view64bit.3.vcf | /build/reproducible-path/bcftools-1.20/bcftools view -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.20/bcftools view /build/reproducible-path/bcftools-1.20/test/view64bit.4.vcf -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.20/bcftools view /build/reproducible-path/bcftools-1.20/test/view64bit.4.vcf | /build/reproducible-path/bcftools-1.20/bcftools view -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.20/bcftools view /build/reproducible-path/bcftools-1.20/test/view64bit.4.vcf -Ou | /build/reproducible-path/bcftools-1.20/bcftools view -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.20/bcftools view /build/reproducible-path/bcftools-1.20/test/view64bit.5.vcf -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.20/bcftools view /build/reproducible-path/bcftools-1.20/test/view64bit.5.vcf | /build/reproducible-path/bcftools-1.20/bcftools view -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.20/bcftools view /build/reproducible-path/bcftools-1.20/test/view64bit.5.vcf -Ou | /build/reproducible-path/bcftools-1.20/bcftools view -H .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -H -C5:nonmajor /tmp/MWm45bogYL/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -H -c6:nonmajor /tmp/MWm45bogYL/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -H -q0.3:major /tmp/MWm45bogYL/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/MWm45bogYL/view.filter.annovar.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -H -i 'Gene.refGene~"NOD"' /tmp/MWm45bogYL/view.filter.annovar.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -H -i 'LJB2_MutationTaster=="0.291000"' /tmp/MWm45bogYL/view.filter.annovar.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -H -a /tmp/MWm45bogYL/view-a.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -T /build/reproducible-path/bcftools-1.20/test/view.sites.txt /tmp/MWm45bogYL/view.sites.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -T /build/reproducible-path/bcftools-1.20/test/view.sites.txt /tmp/MWm45bogYL/view.sites.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -T /build/reproducible-path/bcftools-1.20/test/view.sites.txt.gz /tmp/MWm45bogYL/view.sites.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -T /build/reproducible-path/bcftools-1.20/test/view.sites.txt.gz /tmp/MWm45bogYL/view.sites.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_head: /build/reproducible-path/bcftools-1.20/bcftools head /build/reproducible-path/bcftools-1.20/test/mpileup.2.vcf .. ok test_vcf_head: /build/reproducible-path/bcftools-1.20/bcftools head -h 0 /build/reproducible-path/bcftools-1.20/test/mpileup.2.vcf .. ok test_vcf_head: /build/reproducible-path/bcftools-1.20/bcftools head -h 1 /build/reproducible-path/bcftools-1.20/test/mpileup.2.vcf .. ok test_vcf_head: /build/reproducible-path/bcftools-1.20/bcftools head -h 5 /build/reproducible-path/bcftools-1.20/test/mpileup.2.vcf .. ok test_vcf_head: /build/reproducible-path/bcftools-1.20/bcftools head -h 22 /build/reproducible-path/bcftools-1.20/test/mpileup.2.vcf .. ok test_vcf_head: /build/reproducible-path/bcftools-1.20/bcftools head -h 23 /build/reproducible-path/bcftools-1.20/test/mpileup.2.vcf .. ok test_vcf_head: /build/reproducible-path/bcftools-1.20/bcftools head -n 0 /build/reproducible-path/bcftools-1.20/test/mpileup.2.vcf .. ok test_vcf_head: /build/reproducible-path/bcftools-1.20/bcftools head -n 1 /build/reproducible-path/bcftools-1.20/test/mpileup.2.vcf .. ok test_vcf_head: /build/reproducible-path/bcftools-1.20/bcftools head -n 5 /build/reproducible-path/bcftools-1.20/test/mpileup.2.vcf .. ok test_vcf_head: /build/reproducible-path/bcftools-1.20/bcftools head -h 5 -n 5 < /build/reproducible-path/bcftools-1.20/test/mpileup.2.vcf .. ok test_vcf_head2: /build/reproducible-path/bcftools-1.20/bcftools head -s0 /tmp/MWm45bogYL/mpileup.2.vcf.gz .. ok test_vcf_head2: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -Ob /tmp/MWm45bogYL/mpileup.2.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools head -s0 .. ok test_vcf_head2: /build/reproducible-path/bcftools-1.20/bcftools head -s1 /tmp/MWm45bogYL/mpileup.2.vcf.gz .. ok test_vcf_head2: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -Ob /tmp/MWm45bogYL/mpileup.2.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools head -s1 .. ok test_vcf_head2: /build/reproducible-path/bcftools-1.20/bcftools head -s2 -h2 /tmp/MWm45bogYL/mpileup.2.vcf.gz .. ok test_vcf_head2: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -Ob /tmp/MWm45bogYL/mpileup.2.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools head -s2 -h2 .. ok test_vcf_call: /build/reproducible-path/bcftools-1.20/bcftools call --no-version -mv /build/reproducible-path/bcftools-1.20/test/mpileup.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.20/bcftools call -Ob -mv /build/reproducible-path/bcftools-1.20/test/mpileup.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.20/bcftools call --no-version -mg0 /build/reproducible-path/bcftools-1.20/test/mpileup.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.20/bcftools call -Ob -mg0 /build/reproducible-path/bcftools-1.20/test/mpileup.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.20/bcftools call --no-version -mv -S /build/reproducible-path/bcftools-1.20/test/mpileup.3.samples /build/reproducible-path/bcftools-1.20/test/mpileup.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.20/bcftools call -Ob -mv -S /build/reproducible-path/bcftools-1.20/test/mpileup.3.samples /build/reproducible-path/bcftools-1.20/test/mpileup.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.20/bcftools call --no-version -mv -S /build/reproducible-path/bcftools-1.20/test/mpileup.4.samples /build/reproducible-path/bcftools-1.20/test/mpileup.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.20/bcftools call -Ob -mv -S /build/reproducible-path/bcftools-1.20/test/mpileup.4.samples /build/reproducible-path/bcftools-1.20/test/mpileup.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.20/bcftools call --no-version -mv -S /build/reproducible-path/bcftools-1.20/test/mpileup.5.samples /build/reproducible-path/bcftools-1.20/test/mpileup.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.20/bcftools call -Ob -mv -S /build/reproducible-path/bcftools-1.20/test/mpileup.5.samples /build/reproducible-path/bcftools-1.20/test/mpileup.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.20/bcftools call --no-version -mv --ploidy-file /build/reproducible-path/bcftools-1.20/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.20/test/mpileup.samples /build/reproducible-path/bcftools-1.20/test/mpileup.X.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.20/bcftools call -Ob -mv --ploidy-file /build/reproducible-path/bcftools-1.20/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.20/test/mpileup.samples /build/reproducible-path/bcftools-1.20/test/mpileup.X.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.20/bcftools call --no-version -mv --ploidy-file /build/reproducible-path/bcftools-1.20/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.20/test/mpileup.ped /build/reproducible-path/bcftools-1.20/test/mpileup.X.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.20/bcftools call -Ob -mv --ploidy-file /build/reproducible-path/bcftools-1.20/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.20/test/mpileup.ped /build/reproducible-path/bcftools-1.20/test/mpileup.X.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.20/bcftools call --no-version -mv --ploidy-file /build/reproducible-path/bcftools-1.20/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.20/test/mpileup.2.samples /build/reproducible-path/bcftools-1.20/test/mpileup.X.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.20/bcftools call -Ob -mv --ploidy-file /build/reproducible-path/bcftools-1.20/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.20/test/mpileup.2.samples /build/reproducible-path/bcftools-1.20/test/mpileup.X.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.20/bcftools call --no-version -mv /build/reproducible-path/bcftools-1.20/test/mpileup.NA19213.NA19129.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.20/bcftools call -Ob -mv /build/reproducible-path/bcftools-1.20/test/mpileup.NA19213.NA19129.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.20/bcftools call --no-version -mv -G - --group-samples-tag AD /build/reproducible-path/bcftools-1.20/test/mpileup.NA19213.NA19129.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.20/bcftools call -Ob -mv -G - --group-samples-tag AD /build/reproducible-path/bcftools-1.20/test/mpileup.NA19213.NA19129.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.20/bcftools call --no-version -mv /build/reproducible-path/bcftools-1.20/test/mpileup.hwe.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.20/bcftools call -Ob -mv /build/reproducible-path/bcftools-1.20/test/mpileup.hwe.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.20/bcftools call --no-version -mv -G - --group-samples-tag AD /build/reproducible-path/bcftools-1.20/test/mpileup.hwe.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.20/bcftools call -Ob -mv -G - --group-samples-tag AD /build/reproducible-path/bcftools-1.20/test/mpileup.hwe.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.20/bcftools call --no-version -mv -G /build/reproducible-path/bcftools-1.20/test/mpileup.hwe.samples --group-samples-tag AD /build/reproducible-path/bcftools-1.20/test/mpileup.hwe.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.20/bcftools call -Ob -mv -G /build/reproducible-path/bcftools-1.20/test/mpileup.hwe.samples --group-samples-tag AD /build/reproducible-path/bcftools-1.20/test/mpileup.hwe.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.20/bcftools call --no-version -mA -C alleles -T /tmp/MWm45bogYL/mpileup.tab.gz /build/reproducible-path/bcftools-1.20/test/mpileup.vcf .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.20/bcftools call -Ob -mA -C alleles -T /tmp/MWm45bogYL/mpileup.tab.gz /build/reproducible-path/bcftools-1.20/test/mpileup.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.20/bcftools call --no-version -mA -C alleles -T /tmp/MWm45bogYL/mpileup.2.tab.gz /build/reproducible-path/bcftools-1.20/test/mpileup.2.vcf .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.20/bcftools call -Ob -mA -C alleles -T /tmp/MWm45bogYL/mpileup.2.tab.gz /build/reproducible-path/bcftools-1.20/test/mpileup.2.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.20/bcftools call --no-version -mA -C alleles -T /tmp/MWm45bogYL/mpileup.3.tab.gz -i /build/reproducible-path/bcftools-1.20/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.20/bcftools call -Ob -mA -C alleles -T /tmp/MWm45bogYL/mpileup.3.tab.gz -i /build/reproducible-path/bcftools-1.20/test/mpileup.3.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.20/bcftools call --no-version -mA -C alleles -T /tmp/MWm45bogYL/mpileup.4.tab.gz -i /build/reproducible-path/bcftools-1.20/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.20/bcftools call -Ob -mA -C alleles -T /tmp/MWm45bogYL/mpileup.4.tab.gz -i /build/reproducible-path/bcftools-1.20/test/mpileup.3.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.20/bcftools call --no-version -mA -C alleles -T /tmp/MWm45bogYL/mpileup.5.tab.gz -i /build/reproducible-path/bcftools-1.20/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.20/bcftools call -Ob -mA -C alleles -T /tmp/MWm45bogYL/mpileup.5.tab.gz -i /build/reproducible-path/bcftools-1.20/test/mpileup.3.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.20/bcftools call --no-version -mA -C alleles -T /tmp/MWm45bogYL/mpileup.6.tab.gz -i /build/reproducible-path/bcftools-1.20/test/mpileup.4.vcf .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.20/bcftools call -Ob -mA -C alleles -T /tmp/MWm45bogYL/mpileup.6.tab.gz -i /build/reproducible-path/bcftools-1.20/test/mpileup.4.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.20/bcftools call --no-version -mA -C alleles -T /tmp/MWm45bogYL/mpileup.7.tab.gz -i /build/reproducible-path/bcftools-1.20/test/mpileup.5.vcf .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.20/bcftools call -Ob -mA -C alleles -T /tmp/MWm45bogYL/mpileup.7.tab.gz -i /build/reproducible-path/bcftools-1.20/test/mpileup.5.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.20/bcftools call --no-version -mA -C alleles -T /tmp/MWm45bogYL/mpileup.cals.1.tab.gz /build/reproducible-path/bcftools-1.20/test/mpileup.cals.1.vcf .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.20/bcftools call -Ob -mA -C alleles -T /tmp/MWm45bogYL/mpileup.cals.1.tab.gz /build/reproducible-path/bcftools-1.20/test/mpileup.cals.1.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.20/bcftools call --no-version -mA -C alleles -T /tmp/MWm45bogYL/mpileup.cals.2.tab.gz /build/reproducible-path/bcftools-1.20/test/mpileup.cals.2.vcf .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.20/bcftools call -Ob -mA -C alleles -T /tmp/MWm45bogYL/mpileup.cals.2.tab.gz /build/reproducible-path/bcftools-1.20/test/mpileup.cals.2.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.20/bcftools call --no-version -cv /build/reproducible-path/bcftools-1.20/test/mpileup.c.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.20/bcftools call -Ob -cv /build/reproducible-path/bcftools-1.20/test/mpileup.c.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.20/bcftools call --no-version -cv --ploidy-file /build/reproducible-path/bcftools-1.20/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.20/test/mpileup.samples /build/reproducible-path/bcftools-1.20/test/mpileup.c.X.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.20/bcftools call -Ob -cv --ploidy-file /build/reproducible-path/bcftools-1.20/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.20/test/mpileup.samples /build/reproducible-path/bcftools-1.20/test/mpileup.c.X.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.20/bcftools call --no-version -cv --ploidy-file /build/reproducible-path/bcftools-1.20/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.20/test/mpileup.ped /build/reproducible-path/bcftools-1.20/test/mpileup.c.X.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.20/bcftools call -Ob -cv --ploidy-file /build/reproducible-path/bcftools-1.20/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.20/test/mpileup.ped /build/reproducible-path/bcftools-1.20/test/mpileup.c.X.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.20/bcftools call --no-version -cv --ploidy-file /build/reproducible-path/bcftools-1.20/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.20/test/mpileup.2.samples /build/reproducible-path/bcftools-1.20/test/mpileup.c.X.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.20/bcftools call -Ob -cv --ploidy-file /build/reproducible-path/bcftools-1.20/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.20/test/mpileup.2.samples /build/reproducible-path/bcftools-1.20/test/mpileup.c.X.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.20/bcftools call --no-version -mv /build/reproducible-path/bcftools-1.20/test/call-G.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.20/bcftools call -Ob -mv /build/reproducible-path/bcftools-1.20/test/call-G.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.20/bcftools call --no-version -mv -G - --group-samples-tag AD /build/reproducible-path/bcftools-1.20/test/call-G.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.20/bcftools call -Ob -mv -G - --group-samples-tag AD /build/reproducible-path/bcftools-1.20/test/call-G.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.20/bcftools call --no-version -mv -F AN_POP,AC_POP /build/reproducible-path/bcftools-1.20/test/call-G.2.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.20/bcftools call -Ob -mv -F AN_POP,AC_POP /build/reproducible-path/bcftools-1.20/test/call-G.2.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.20/bcftools call --no-version -m /build/reproducible-path/bcftools-1.20/test/call.af-fixation.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.20/bcftools call -Ob -m /build/reproducible-path/bcftools-1.20/test/call.af-fixation.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.20/bcftools call --no-version -m -G /build/reproducible-path/bcftools-1.20/test/call.af-fixation.txt /build/reproducible-path/bcftools-1.20/test/call.af-fixation.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.20/bcftools call -Ob -m -G /build/reproducible-path/bcftools-1.20/test/call.af-fixation.txt /build/reproducible-path/bcftools-1.20/test/call.af-fixation.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.20/bcftools call --no-version -m -G /build/reproducible-path/bcftools-1.20/test/call.af-fixation.txt -a GP,GQ /build/reproducible-path/bcftools-1.20/test/call.af-fixation.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.20/bcftools call -Ob -m -G /build/reproducible-path/bcftools-1.20/test/call.af-fixation.txt -a GP,GQ /build/reproducible-path/bcftools-1.20/test/call.af-fixation.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -S. -e'TXT0="text"' /build/reproducible-path/bcftools-1.20/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -S. -e'TXT0="text"' /build/reproducible-path/bcftools-1.20/test/view.filter.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -S. -e'FMT/FRS[*:1]="BB"' /build/reproducible-path/bcftools-1.20/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -S. -e'FMT/FRS[*:1]="BB"' /build/reproducible-path/bcftools-1.20/test/view.filter.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -S. -e'FMT/FGS[*:0]="AAAAAA"' /build/reproducible-path/bcftools-1.20/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -S. -e'FMT/FGS[*:0]="AAAAAA"' /build/reproducible-path/bcftools-1.20/test/view.filter.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -S. -e'FMT/FGS[*:1]="BBB"' /build/reproducible-path/bcftools-1.20/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -S. -e'FMT/FGS[*:1]="BBB"' /build/reproducible-path/bcftools-1.20/test/view.filter.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -S. -e'FMT/FGS[*:4]="EE"' /build/reproducible-path/bcftools-1.20/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -S. -e'FMT/FGS[*:4]="EE"' /build/reproducible-path/bcftools-1.20/test/view.filter.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -S. -e'FMT/STR="XX"' /build/reproducible-path/bcftools-1.20/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -S. -e'FMT/STR="XX"' /build/reproducible-path/bcftools-1.20/test/view.filter.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -S. -e'FMT/FILTER="aaa"' /build/reproducible-path/bcftools-1.20/test/view.filter.2.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -S. -e'FMT/FILTER="aaa"' /build/reproducible-path/bcftools-1.20/test/view.filter.2.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -mx -g2 -G2 /build/reproducible-path/bcftools-1.20/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -mx -g2 -G2 /build/reproducible-path/bcftools-1.20/test/filter.1.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /build/reproducible-path/bcftools-1.20/test/filter.2.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /build/reproducible-path/bcftools-1.20/test/filter.2.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -e'INFO/DP=19' /build/reproducible-path/bcftools-1.20/test/filter.3.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -e'INFO/DP=19' /build/reproducible-path/bcftools-1.20/test/filter.3.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -e'INFO/DP=19' -s XX /build/reproducible-path/bcftools-1.20/test/filter.3.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -e'INFO/DP=19' -s XX /build/reproducible-path/bcftools-1.20/test/filter.3.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -e'INFO/DP=19' -s XX -m+ /build/reproducible-path/bcftools-1.20/test/filter.3.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+ /build/reproducible-path/bcftools-1.20/test/filter.3.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -e'INFO/DP=19' -s XX -mx /build/reproducible-path/bcftools-1.20/test/filter.3.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -e'INFO/DP=19' -s XX -mx /build/reproducible-path/bcftools-1.20/test/filter.3.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -e'INFO/DP=19' -s XX -m+x /build/reproducible-path/bcftools-1.20/test/filter.3.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+x /build/reproducible-path/bcftools-1.20/test/filter.3.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -e'FMT/GT="0/2"' /build/reproducible-path/bcftools-1.20/test/filter.3.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -e'FMT/GT="0/2"' /build/reproducible-path/bcftools-1.20/test/filter.3.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -e'FMT/GT="0/2"' -s XX /build/reproducible-path/bcftools-1.20/test/filter.3.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX /build/reproducible-path/bcftools-1.20/test/filter.3.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -e'FMT/GT="0/2"' -s XX -m+ /build/reproducible-path/bcftools-1.20/test/filter.3.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+ /build/reproducible-path/bcftools-1.20/test/filter.3.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -e'FMT/GT="0/2"' -s XX -mx /build/reproducible-path/bcftools-1.20/test/filter.3.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -mx /build/reproducible-path/bcftools-1.20/test/filter.3.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -e'FMT/GT="0/2"' -s XX -m+x /build/reproducible-path/bcftools-1.20/test/filter.3.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+x /build/reproducible-path/bcftools-1.20/test/filter.3.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -i'FMT/GT="0/0" && AC[*]=2' /build/reproducible-path/bcftools-1.20/test/filter.2.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -i'FMT/GT="0/0" && AC[*]=2' /build/reproducible-path/bcftools-1.20/test/filter.2.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -i'AC[*]=2 && FMT/GT="0/0"' /build/reproducible-path/bcftools-1.20/test/filter.2.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -i'AC[*]=2 && FMT/GT="0/0"' /build/reproducible-path/bcftools-1.20/test/filter.2.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -i'ALT="."' /build/reproducible-path/bcftools-1.20/test/filter.2.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -i'ALT="."' /build/reproducible-path/bcftools-1.20/test/filter.2.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -S . -i 'FORMAT/TEST3<25' /build/reproducible-path/bcftools-1.20/test/filter.4.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -S . -i 'FORMAT/TEST3<25' /build/reproducible-path/bcftools-1.20/test/filter.4.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -S . -i 'FORMAT/TEST4<25' /build/reproducible-path/bcftools-1.20/test/filter.4.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -S . -i 'FORMAT/TEST4<25' /build/reproducible-path/bcftools-1.20/test/filter.4.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -i'GT="A"' /build/reproducible-path/bcftools-1.20/test/filter.2.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -i'GT="A"' /build/reproducible-path/bcftools-1.20/test/filter.2.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -i'GT="RR"' /build/reproducible-path/bcftools-1.20/test/filter.2.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -i'GT="RR"' /build/reproducible-path/bcftools-1.20/test/filter.2.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -i'GT="RA"' /build/reproducible-path/bcftools-1.20/test/filter.2.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -i'GT="RA"' /build/reproducible-path/bcftools-1.20/test/filter.2.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -i'GT="AR"' /build/reproducible-path/bcftools-1.20/test/filter.2.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -i'GT="AR"' /build/reproducible-path/bcftools-1.20/test/filter.2.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -i'GT="AA"' /build/reproducible-path/bcftools-1.20/test/filter.2.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -i'GT="AA"' /build/reproducible-path/bcftools-1.20/test/filter.2.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -i'GT="aA"' /build/reproducible-path/bcftools-1.20/test/filter.2.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -i'GT="aA"' /build/reproducible-path/bcftools-1.20/test/filter.2.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -i'GT="Aa"' /build/reproducible-path/bcftools-1.20/test/filter.2.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -i'GT="Aa"' /build/reproducible-path/bcftools-1.20/test/filter.2.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -i'GT="HOM"' /build/reproducible-path/bcftools-1.20/test/filter.2.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -i'GT="HOM"' /build/reproducible-path/bcftools-1.20/test/filter.2.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -i'GT="HET"' /build/reproducible-path/bcftools-1.20/test/filter.2.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -i'GT="HET"' /build/reproducible-path/bcftools-1.20/test/filter.2.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -i'GT="HAP"' /build/reproducible-path/bcftools-1.20/test/filter.2.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -i'GT="HAP"' /build/reproducible-path/bcftools-1.20/test/filter.2.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -i'AD[:1]=11' /build/reproducible-path/bcftools-1.20/test/filter.5.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -i'AD[:1]=11' /build/reproducible-path/bcftools-1.20/test/filter.5.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -i'AD[1:]=11' /build/reproducible-path/bcftools-1.20/test/filter.5.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -i'AD[1:]=11' /build/reproducible-path/bcftools-1.20/test/filter.5.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -i'FR[0:1]=11' /build/reproducible-path/bcftools-1.20/test/filter.5.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS[\t%FR]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -i'FR[0:1]=11' /build/reproducible-path/bcftools-1.20/test/filter.5.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS[\t%FR]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -i'AD[*]="."' /build/reproducible-path/bcftools-1.20/test/filter.5.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -i'AD[*]="."' /build/reproducible-path/bcftools-1.20/test/filter.5.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -i'AD[0:0]=="."' /build/reproducible-path/bcftools-1.20/test/filter.5.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -i'AD[0:0]=="."' /build/reproducible-path/bcftools-1.20/test/filter.5.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -i'AD[0:0]!="."' /build/reproducible-path/bcftools-1.20/test/filter.5.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -i'AD[0:0]!="."' /build/reproducible-path/bcftools-1.20/test/filter.5.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -i'QUAL=="."' /build/reproducible-path/bcftools-1.20/test/filter.5.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS\t%QUAL\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -i'QUAL=="."' /build/reproducible-path/bcftools-1.20/test/filter.5.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS\t%QUAL\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -i'N_PASS(DP>32)=1' /build/reproducible-path/bcftools-1.20/test/filter.2.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -i'N_PASS(DP>32)=1' /build/reproducible-path/bcftools-1.20/test/filter.2.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | /build/reproducible-path/bcftools-1.20/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -i'F_PASS(DP>32)=0.5' /build/reproducible-path/bcftools-1.20/test/filter.2.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -i'F_PASS(DP>32)=0.5' /build/reproducible-path/bcftools-1.20/test/filter.2.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | /build/reproducible-path/bcftools-1.20/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -i'F_MISSING>=1/5' /build/reproducible-path/bcftools-1.20/test/filter.6.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -i'F_MISSING>=1/5' /build/reproducible-path/bcftools-1.20/test/filter.6.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -i'F_MISSING>=0.2' /build/reproducible-path/bcftools-1.20/test/filter.6.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -i'F_MISSING>=0.2' /build/reproducible-path/bcftools-1.20/test/filter.6.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -i'F_PASS(GT=="mis")>=1/5' /build/reproducible-path/bcftools-1.20/test/filter.6.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -i'F_PASS(GT=="mis")>=1/5' /build/reproducible-path/bcftools-1.20/test/filter.6.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -i'F_PASS(GT=="mis")>=0.2' /build/reproducible-path/bcftools-1.20/test/filter.6.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -i'F_PASS(GT=="mis")>=0.2' /build/reproducible-path/bcftools-1.20/test/filter.6.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | /build/reproducible-path/bcftools-1.20/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -mx -s + -g2:mnp,indel,other /build/reproducible-path/bcftools-1.20/test/filter.7.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -mx -s + -g2:mnp,indel,other /build/reproducible-path/bcftools-1.20/test/filter.7.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -S . -e 'FORMAT/AO==4' /build/reproducible-path/bcftools-1.20/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -S . -e 'FORMAT/AO==4' /build/reproducible-path/bcftools-1.20/test/filter.8.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -S . -e 'MAX(FORMAT/AO[0:])==4' /build/reproducible-path/bcftools-1.20/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -S . -e 'MAX(FORMAT/AO[0:])==4' /build/reproducible-path/bcftools-1.20/test/filter.8.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -S . -e 'MAX(FORMAT/AO)==4' /build/reproducible-path/bcftools-1.20/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -S . -e 'MAX(FORMAT/AO)==4' /build/reproducible-path/bcftools-1.20/test/filter.8.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -S . -e 'MIN(FORMAT/AO[0:])==3' /build/reproducible-path/bcftools-1.20/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO[0:])==3' /build/reproducible-path/bcftools-1.20/test/filter.8.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -S . -e 'MIN(FORMAT/AO)==2' /build/reproducible-path/bcftools-1.20/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO)==2' /build/reproducible-path/bcftools-1.20/test/filter.8.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -S . -e 'MIN(FORMAT/AO[0:])==3' /build/reproducible-path/bcftools-1.20/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO[0:])==3' /build/reproducible-path/bcftools-1.20/test/filter.8.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -S . -e 'AVG(FORMAT/AO[2:])==4' /build/reproducible-path/bcftools-1.20/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -S . -e 'AVG(FORMAT/AO[2:])==4' /build/reproducible-path/bcftools-1.20/test/filter.8.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -S . -e 'MEDIAN(FORMAT/AO[2:])==4' /build/reproducible-path/bcftools-1.20/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -S . -e 'MEDIAN(FORMAT/AO[2:])==4' /build/reproducible-path/bcftools-1.20/test/filter.8.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -S . -e 'STDEV(FORMAT/AO[0:])=0.5' /build/reproducible-path/bcftools-1.20/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -S . -e 'STDEV(FORMAT/AO[0:])=0.5' /build/reproducible-path/bcftools-1.20/test/filter.8.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -S . -e 'SUM(FORMAT/AO[0:])=7' /build/reproducible-path/bcftools-1.20/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -S . -e 'SUM(FORMAT/AO[0:])=7' /build/reproducible-path/bcftools-1.20/test/filter.8.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -S . -e 'SMPL_MAX(FORMAT/AO)==4' /build/reproducible-path/bcftools-1.20/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -S . -e 'SMPL_MAX(FORMAT/AO)==4' /build/reproducible-path/bcftools-1.20/test/filter.8.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -S . -e 'sMIN(FORMAT/AO)==2' /build/reproducible-path/bcftools-1.20/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -S . -e 'sMIN(FORMAT/AO)==2' /build/reproducible-path/bcftools-1.20/test/filter.8.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -S . -e 'ABS(sAVG(FORMAT/AO)-3.66666)<1e-5' /build/reproducible-path/bcftools-1.20/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -S . -e 'ABS(sAVG(FORMAT/AO)-3.66666)<1e-5' /build/reproducible-path/bcftools-1.20/test/filter.8.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -S . -e 'sMEDIAN(FORMAT/AO)==4' /build/reproducible-path/bcftools-1.20/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -S . -e 'sMEDIAN(FORMAT/AO)==4' /build/reproducible-path/bcftools-1.20/test/filter.8.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -S . -e 'ABS(sSTDEV(FORMAT/AO)-1.2472191)<1e-5' /build/reproducible-path/bcftools-1.20/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -S . -e 'ABS(sSTDEV(FORMAT/AO)-1.2472191)<1e-5' /build/reproducible-path/bcftools-1.20/test/filter.8.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -S . -e 'sSUM(FORMAT/AO)==11' /build/reproducible-path/bcftools-1.20/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -S . -e 'sSUM(FORMAT/AO)==11' /build/reproducible-path/bcftools-1.20/test/filter.8.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -i 'QUAL/FMT/AD==55' /build/reproducible-path/bcftools-1.20/test/filter.9.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -i 'QUAL/FMT/AD==55' /build/reproducible-path/bcftools-1.20/test/filter.9.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -i 'QUAL/INFO/AD==10' /build/reproducible-path/bcftools-1.20/test/filter.9.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -i 'QUAL/INFO/AD==10' /build/reproducible-path/bcftools-1.20/test/filter.9.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -S . -e 'ABS(SMPL_MAX(FORMAT/AO))=5' /build/reproducible-path/bcftools-1.20/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -S . -e 'ABS(SMPL_MAX(FORMAT/AO))=5' /build/reproducible-path/bcftools-1.20/test/filter.8.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -S . -e 'PHRED(AO[1:])>-4' /build/reproducible-path/bcftools-1.20/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -S . -e 'PHRED(AO[1:])>-4' /build/reproducible-path/bcftools-1.20/test/filter.8.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -S . -e 'ABS(AO[1:])==2' /build/reproducible-path/bcftools-1.20/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -S . -e 'ABS(AO[1:])==2' /build/reproducible-path/bcftools-1.20/test/filter.8.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -i 'sum(AD[*]) > FORMAT/DP' /build/reproducible-path/bcftools-1.20/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -i 'sum(AD[*]) > FORMAT/DP' /build/reproducible-path/bcftools-1.20/test/filter.10.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -i 'FORMAT/DP < sum(AD[*])' /build/reproducible-path/bcftools-1.20/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -i 'FORMAT/DP < sum(AD[*])' /build/reproducible-path/bcftools-1.20/test/filter.10.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -i 'sum(AD[*]) < FORMAT/DP' /build/reproducible-path/bcftools-1.20/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -i 'sum(AD[*]) < FORMAT/DP' /build/reproducible-path/bcftools-1.20/test/filter.10.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -i 'FORMAT/DP > sum(AD[*])' /build/reproducible-path/bcftools-1.20/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob -i 'FORMAT/DP > sum(AD[*])' /build/reproducible-path/bcftools-1.20/test/filter.10.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 0 /build/reproducible-path/bcftools-1.20/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 0 /build/reproducible-path/bcftools-1.20/test/filter.1.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 1 /build/reproducible-path/bcftools-1.20/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 1 /build/reproducible-path/bcftools-1.20/test/filter.1.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 2 /build/reproducible-path/bcftools-1.20/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 2 /build/reproducible-path/bcftools-1.20/test/filter.1.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter --soft-filter xxx --mask ^2:1005-1008 /build/reproducible-path/bcftools-1.20/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.20/bcftools filter -Ob --soft-filter xxx --mask ^2:1005-1008 /build/reproducible-path/bcftools-1.20/test/filter.1.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_sort: /build/reproducible-path/bcftools-1.20/bcftools sort -m 0 /build/reproducible-path/bcftools-1.20/test/sort.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /build/reproducible-path/bcftools-1.20/bcftools sort -Ob -m 0 /build/reproducible-path/bcftools-1.20/test/sort.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | /build/reproducible-path/bcftools-1.20/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /build/reproducible-path/bcftools-1.20/bcftools sort -m 1000 /build/reproducible-path/bcftools-1.20/test/sort.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /build/reproducible-path/bcftools-1.20/bcftools sort -Ob -m 1000 /build/reproducible-path/bcftools-1.20/test/sort.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | /build/reproducible-path/bcftools-1.20/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.20/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /build/reproducible-path/bcftools-1.20/test/regions.tab /tmp/MWm45bogYL/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/regions.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /build/reproducible-path/bcftools-1.20/test/regions.tab .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.20/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /build/reproducible-path/bcftools-1.20/test/regions.tab /tmp/MWm45bogYL/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.20/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/MWm45bogYL/regions.tab.gz /tmp/MWm45bogYL/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/regions.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/MWm45bogYL/regions.tab.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.20/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/MWm45bogYL/regions.tab.gz /tmp/MWm45bogYL/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.20/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/MWm45bogYL/regions.bed /tmp/MWm45bogYL/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/regions.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/MWm45bogYL/regions.bed .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.20/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/MWm45bogYL/regions.bed /tmp/MWm45bogYL/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.20/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/MWm45bogYL/regions.bed.gz /tmp/MWm45bogYL/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/regions.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/MWm45bogYL/regions.bed.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.20/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/MWm45bogYL/regions.bed.gz /tmp/MWm45bogYL/regions.vcf.gz .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annotate.tab.gz -h /build/reproducible-path/bcftools-1.20/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /build/reproducible-path/bcftools-1.20/test/annotate.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annotate.tab.gz -h /build/reproducible-path/bcftools-1.20/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /build/reproducible-path/bcftools-1.20/test/annotate.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annotate2.tab.gz -h /build/reproducible-path/bcftools-1.20/test/annotate.hdr -c CHROM,POS,-,T_STR /build/reproducible-path/bcftools-1.20/test/annotate.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annotate2.tab.gz -h /build/reproducible-path/bcftools-1.20/test/annotate.hdr -c CHROM,POS,-,T_STR /build/reproducible-path/bcftools-1.20/test/annotate.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annotate2.tab.gz -h /build/reproducible-path/bcftools-1.20/test/annotate.hdr -c CHROM,FROM,TO,T_STR /build/reproducible-path/bcftools-1.20/test/annotate.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annotate2.tab.gz -h /build/reproducible-path/bcftools-1.20/test/annotate.hdr -c CHROM,FROM,TO,T_STR /build/reproducible-path/bcftools-1.20/test/annotate.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/MWm45bogYL/annotate.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/MWm45bogYL/annotate.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/MWm45bogYL/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/MWm45bogYL/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/MWm45bogYL/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/MWm45bogYL/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/MWm45bogYL/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/MWm45bogYL/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/MWm45bogYL/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/MWm45bogYL/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/MWm45bogYL/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/MWm45bogYL/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /build/reproducible-path/bcftools-1.20/test/annotate3.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /build/reproducible-path/bcftools-1.20/test/annotate3.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -x FORMAT /build/reproducible-path/bcftools-1.20/test/annotate3.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -x FORMAT /build/reproducible-path/bcftools-1.20/test/annotate3.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annots4.vcf.gz -c +INFO /tmp/MWm45bogYL/annotate4.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annots4.vcf.gz -c +INFO /tmp/MWm45bogYL/annotate4.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annots4.tab.gz -h /build/reproducible-path/bcftools-1.20/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /build/reproducible-path/bcftools-1.20/test/annotate4.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annots4.tab.gz -h /build/reproducible-path/bcftools-1.20/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /build/reproducible-path/bcftools-1.20/test/annotate4.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annots10.tab.gz -h /build/reproducible-path/bcftools-1.20/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /build/reproducible-path/bcftools-1.20/test/annotate10.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annots10.tab.gz -h /build/reproducible-path/bcftools-1.20/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /build/reproducible-path/bcftools-1.20/test/annotate10.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/MWm45bogYL/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/MWm45bogYL/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /build/reproducible-path/bcftools-1.20/test/annotate2.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /build/reproducible-path/bcftools-1.20/test/annotate2.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/MWm45bogYL/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/MWm45bogYL/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/MWm45bogYL/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/MWm45bogYL/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/MWm45bogYL/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/MWm45bogYL/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annots11.vcf.gz -c FMT /tmp/MWm45bogYL/annotate11.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annots11.vcf.gz -c FMT /tmp/MWm45bogYL/annotate11.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annots2.vcf.gz -c FMT/newGT:=GT /tmp/MWm45bogYL/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annots2.vcf.gz -c FMT/newGT:=GT /tmp/MWm45bogYL/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annots12.vcf.gz -c FMT/GT:=newGT /tmp/MWm45bogYL/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annots12.vcf.gz -c FMT/GT:=newGT /tmp/MWm45bogYL/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annots13.tab.gz -h /build/reproducible-path/bcftools-1.20/test/annotate13.hdr -c CHROM,BEG,END,ABC /build/reproducible-path/bcftools-1.20/test/annotate13.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annots13.tab.gz -h /build/reproducible-path/bcftools-1.20/test/annotate13.hdr -c CHROM,BEG,END,ABC /build/reproducible-path/bcftools-1.20/test/annotate13.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annots13.tab.gz -h /build/reproducible-path/bcftools-1.20/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:append /build/reproducible-path/bcftools-1.20/test/annotate13.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annots13.tab.gz -h /build/reproducible-path/bcftools-1.20/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:append /build/reproducible-path/bcftools-1.20/test/annotate13.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annots13.tab.gz -h /build/reproducible-path/bcftools-1.20/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:unique /build/reproducible-path/bcftools-1.20/test/annotate13.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annots13.tab.gz -h /build/reproducible-path/bcftools-1.20/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:unique /build/reproducible-path/bcftools-1.20/test/annotate13.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -x FILTER/XX,INFO/XX --force /build/reproducible-path/bcftools-1.20/test/annotate14.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -x FILTER/XX,INFO/XX --force /build/reproducible-path/bcftools-1.20/test/annotate14.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annotate15.tab.gz -h /build/reproducible-path/bcftools-1.20/test/annotate15.hdr -s SAMPLE1 -c CHROM,FROM,TO,FMT/FOO,BAR /build/reproducible-path/bcftools-1.20/test/annotate15.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annotate15.tab.gz -h /build/reproducible-path/bcftools-1.20/test/annotate15.hdr -s SAMPLE1 -c CHROM,FROM,TO,FMT/FOO,BAR /build/reproducible-path/bcftools-1.20/test/annotate15.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annotate15.tab.gz -h /build/reproducible-path/bcftools-1.20/test/annotate15.hdr -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR /build/reproducible-path/bcftools-1.20/test/annotate15.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annotate15.tab.gz -h /build/reproducible-path/bcftools-1.20/test/annotate15.hdr -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR /build/reproducible-path/bcftools-1.20/test/annotate15.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annotate15.tab.gz -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR -H '##FORMAT=' -H '##INFO=' /build/reproducible-path/bcftools-1.20/test/annotate15.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annotate15.tab.gz -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR -H '##FORMAT=' -H '##INFO=' /build/reproducible-path/bcftools-1.20/test/annotate15.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -x FILTER /build/reproducible-path/bcftools-1.20/test/annotate16.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -x FILTER /build/reproducible-path/bcftools-1.20/test/annotate16.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/reproducible-path/bcftools-1.20/test/annotate17.1.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/reproducible-path/bcftools-1.20/test/annotate17.1.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/reproducible-path/bcftools-1.20/test/annotate17.2.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/reproducible-path/bcftools-1.20/test/annotate17.2.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annotate17.3.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/reproducible-path/bcftools-1.20/test/annotate17.3.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annotate17.3.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/reproducible-path/bcftools-1.20/test/annotate17.3.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/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-1.20/test/annotate18.1.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/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-1.20/test/annotate18.1.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/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-1.20/test/annotate18.2.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/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-1.20/test/annotate18.2.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/MWm45bogYL/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/MWm45bogYL/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/MWm45bogYL/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/MWm45bogYL/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/MWm45bogYL/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/MWm45bogYL/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -c INFO/FILTER:=FILTER /build/reproducible-path/bcftools-1.20/test/annotate19.dst.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -c INFO/FILTER:=FILTER /build/reproducible-path/bcftools-1.20/test/annotate19.dst.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER /tmp/MWm45bogYL/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER /tmp/MWm45bogYL/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER /tmp/MWm45bogYL/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER /tmp/MWm45bogYL/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER,FILTER /tmp/MWm45bogYL/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER,FILTER /tmp/MWm45bogYL/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=./FILTER /tmp/MWm45bogYL/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=./FILTER /tmp/MWm45bogYL/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annotate20.src.vcf.gz -c FMT/GT /tmp/MWm45bogYL/annotate20.dst.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annotate20.src.vcf.gz -c FMT/GT /tmp/MWm45bogYL/annotate20.dst.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annotate20.src.vcf.gz -c +FMT/GT /tmp/MWm45bogYL/annotate20.dst.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annotate20.src.vcf.gz -c +FMT/GT /tmp/MWm45bogYL/annotate20.dst.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annotate20.src.vcf.gz -c -FMT/GT /tmp/MWm45bogYL/annotate20.dst.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annotate20.src.vcf.gz -c -FMT/GT /tmp/MWm45bogYL/annotate20.dst.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annotate.multi.tab.gz -c CHROM,POS,REF,ALT,ANN -l ANN:append /build/reproducible-path/bcftools-1.20/test/annotate.multi.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annotate.multi.tab.gz -c CHROM,POS,REF,ALT,ANN -l ANN:append /build/reproducible-path/bcftools-1.20/test/annotate.multi.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annotate.missing-append.tab.gz -c CHROM,POS,REF,ALT,STR,INT,FLT -l STR:append-missing,INT:append-missing,FLT:append-missing /build/reproducible-path/bcftools-1.20/test/annotate.missing-append.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annotate.missing-append.tab.gz -c CHROM,POS,REF,ALT,STR,INT,FLT -l STR:append-missing,INT:append-missing,FLT:append-missing /build/reproducible-path/bcftools-1.20/test/annotate.missing-append.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /build/reproducible-path/bcftools-1.20/test/annotate9.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /build/reproducible-path/bcftools-1.20/test/annotate9.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate --rename-annots /build/reproducible-path/bcftools-1.20/test/annotate21.txt /build/reproducible-path/bcftools-1.20/test/annotate21.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob --rename-annots /build/reproducible-path/bcftools-1.20/test/annotate21.txt /build/reproducible-path/bcftools-1.20/test/annotate21.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -c XX:=FORMAT/X-X,YY:=FORMAT/Y-Y,AA:=FORMAT/A-A,AA:=INFO/A-A,BB:=INFO/B-B,XX:=INFO/X-X,YY:=INFO/Y-Y,fltA:=FILTER/flt-A,fltB:=FILTER/flt-B,fltX:=FILTER/flt-X,fltY:=FILTER/flt-Y /build/reproducible-path/bcftools-1.20/test/annotate21.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -c XX:=FORMAT/X-X,YY:=FORMAT/Y-Y,AA:=FORMAT/A-A,AA:=INFO/A-A,BB:=INFO/B-B,XX:=INFO/X-X,YY:=INFO/Y-Y,fltA:=FILTER/flt-A,fltB:=FILTER/flt-B,fltX:=FILTER/flt-X,fltY:=FILTER/flt-Y /build/reproducible-path/bcftools-1.20/test/annotate21.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/MWm45bogYL/annotate22.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/MWm45bogYL/annotate22.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annotate23.tab.gz -c CHROM,POS,~ID,REF,ALT,INFO/END /build/reproducible-path/bcftools-1.20/test/annotate23.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annotate23.tab.gz -c CHROM,POS,~ID,REF,ALT,INFO/END /build/reproducible-path/bcftools-1.20/test/annotate23.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annotate24.src.vcf.gz -c XX /tmp/MWm45bogYL/annotate24.dst.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annotate24.src.vcf.gz -c XX /tmp/MWm45bogYL/annotate24.dst.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annotate25.tab.gz -c CHROM,POS,ID,REF,ALT,~INFO/END /build/reproducible-path/bcftools-1.20/test/annotate25.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annotate25.tab.gz -c CHROM,POS,ID,REF,ALT,~INFO/END /build/reproducible-path/bcftools-1.20/test/annotate25.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annotate26.tab.gz -c CHROM,POS,~POS /build/reproducible-path/bcftools-1.20/test/annotate26.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annotate26.tab.gz -c CHROM,POS,~POS /build/reproducible-path/bcftools-1.20/test/annotate26.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,TSTR,TFLT,TINT /build/reproducible-path/bcftools-1.20/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,TSTR,TFLT,TINT /build/reproducible-path/bcftools-1.20/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.TSTR,.TFLT,.TINT /build/reproducible-path/bcftools-1.20/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.TSTR,.TFLT,.TINT /build/reproducible-path/bcftools-1.20/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.+TSTR,.+TFLT,.+TINT /build/reproducible-path/bcftools-1.20/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.+TSTR,.+TFLT,.+TINT /build/reproducible-path/bcftools-1.20/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,+TSTR,+TFLT,+TINT /build/reproducible-path/bcftools-1.20/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,+TSTR,+TFLT,+TINT /build/reproducible-path/bcftools-1.20/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.=TSTR,.=TFLT,.=TINT /build/reproducible-path/bcftools-1.20/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.=TSTR,.=TFLT,.=TINT /build/reproducible-path/bcftools-1.20/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,=TSTR,=TFLT,=TINT /build/reproducible-path/bcftools-1.20/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,=TSTR,=TFLT,=TINT /build/reproducible-path/bcftools-1.20/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique /build/reproducible-path/bcftools-1.20/test/annotate.olap.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique /build/reproducible-path/bcftools-1.20/test/annotate.olap.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique --min-overlap 0.4:0.5 -m XXX /build/reproducible-path/bcftools-1.20/test/annotate.olap.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique --min-overlap 0.4:0.5 -m XXX /build/reproducible-path/bcftools-1.20/test/annotate.olap.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annots.id.vcf.gz -c ALT /tmp/MWm45bogYL/annotate.id.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annots.id.vcf.gz -c ALT /tmp/MWm45bogYL/annotate.id.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annots.id.vcf.gz -c +ALT /tmp/MWm45bogYL/annotate.id.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annots.id.vcf.gz -c +ALT /tmp/MWm45bogYL/annotate.id.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annots.id.2.vcf.gz --pair-logic some -c +ID /tmp/MWm45bogYL/annotate.id.2.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annots.id.2.vcf.gz --pair-logic some -c +ID /tmp/MWm45bogYL/annotate.id.2.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annots.id.2.vcf.gz --pair-logic any -c +ID /tmp/MWm45bogYL/annotate.id.2.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annots.id.2.vcf.gz --pair-logic any -c +ID /tmp/MWm45bogYL/annotate.id.2.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annotate27.tab.gz -c CHROM,POS,REF,ALT,EVIDENCE /build/reproducible-path/bcftools-1.20/test/annotate27.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annotate27.tab.gz -c CHROM,POS,REF,ALT,EVIDENCE /build/reproducible-path/bcftools-1.20/test/annotate27.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1,smpl2 /build/reproducible-path/bcftools-1.20/test/annotate28.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1,smpl2 /build/reproducible-path/bcftools-1.20/test/annotate28.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2,smpl1 /build/reproducible-path/bcftools-1.20/test/annotate28.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2,smpl1 /build/reproducible-path/bcftools-1.20/test/annotate28.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1 /build/reproducible-path/bcftools-1.20/test/annotate28.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1 /build/reproducible-path/bcftools-1.20/test/annotate28.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2 /build/reproducible-path/bcftools-1.20/test/annotate28.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2 /build/reproducible-path/bcftools-1.20/test/annotate28.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -m XXX /build/reproducible-path/bcftools-1.20/test/annotate.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -m XXX /build/reproducible-path/bcftools-1.20/test/annotate.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annots34.tab.gz -c CHROM,FROM,TO,INFO/END -H '##INFO=' /build/reproducible-path/bcftools-1.20/test/annotate34.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annots34.tab.gz -c CHROM,FROM,TO,INFO/END -H '##INFO=' /build/reproducible-path/bcftools-1.20/test/annotate34.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/MWm45bogYL/annots-mark.bed.gz -c CHROM,FROM,TO -m TAG /build/reproducible-path/bcftools-1.20/test/annots-mark.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -Ob -a /tmp/MWm45bogYL/annots-mark.bed.gz -c CHROM,FROM,TO -m TAG /build/reproducible-path/bcftools-1.20/test/annots-mark.vcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat --no-version /tmp/MWm45bogYL/concat.1.a.vcf.gz /tmp/MWm45bogYL/concat.1.b.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat -Ob /tmp/MWm45bogYL/concat.1.a.vcf.gz /tmp/MWm45bogYL/concat.1.b.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat --no-version /tmp/MWm45bogYL/concat.1.a.bcf /tmp/MWm45bogYL/concat.1.b.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat -Ob /tmp/MWm45bogYL/concat.1.a.bcf /tmp/MWm45bogYL/concat.1.b.bcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat --no-version -a /tmp/MWm45bogYL/concat.2.a.vcf.gz /tmp/MWm45bogYL/concat.2.b.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat -Ob -a /tmp/MWm45bogYL/concat.2.a.vcf.gz /tmp/MWm45bogYL/concat.2.b.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat --no-version -a /tmp/MWm45bogYL/concat.2.a.bcf /tmp/MWm45bogYL/concat.2.b.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat -Ob -a /tmp/MWm45bogYL/concat.2.a.bcf /tmp/MWm45bogYL/concat.2.b.bcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat --no-version -aD /tmp/MWm45bogYL/concat.2.a.vcf.gz /tmp/MWm45bogYL/concat.2.b.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat -Ob -aD /tmp/MWm45bogYL/concat.2.a.vcf.gz /tmp/MWm45bogYL/concat.2.b.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat --no-version -aD /tmp/MWm45bogYL/concat.2.a.bcf /tmp/MWm45bogYL/concat.2.b.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat -Ob -aD /tmp/MWm45bogYL/concat.2.a.bcf /tmp/MWm45bogYL/concat.2.b.bcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat --no-version -l --ligate-warn /tmp/MWm45bogYL/concat.3.a.vcf.gz /tmp/MWm45bogYL/concat.3.b.vcf.gz /tmp/MWm45bogYL/concat.3.0.vcf.gz /tmp/MWm45bogYL/concat.3.c.vcf.gz /tmp/MWm45bogYL/concat.3.d.vcf.gz /tmp/MWm45bogYL/concat.3.e.vcf.gz /tmp/MWm45bogYL/concat.3.f.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat -Ob -l --ligate-warn /tmp/MWm45bogYL/concat.3.a.vcf.gz /tmp/MWm45bogYL/concat.3.b.vcf.gz /tmp/MWm45bogYL/concat.3.0.vcf.gz /tmp/MWm45bogYL/concat.3.c.vcf.gz /tmp/MWm45bogYL/concat.3.d.vcf.gz /tmp/MWm45bogYL/concat.3.e.vcf.gz /tmp/MWm45bogYL/concat.3.f.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat --no-version -l --ligate-warn /tmp/MWm45bogYL/concat.3.a.bcf /tmp/MWm45bogYL/concat.3.b.bcf /tmp/MWm45bogYL/concat.3.0.bcf /tmp/MWm45bogYL/concat.3.c.bcf /tmp/MWm45bogYL/concat.3.d.bcf /tmp/MWm45bogYL/concat.3.e.bcf /tmp/MWm45bogYL/concat.3.f.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat -Ob -l --ligate-warn /tmp/MWm45bogYL/concat.3.a.bcf /tmp/MWm45bogYL/concat.3.b.bcf /tmp/MWm45bogYL/concat.3.0.bcf /tmp/MWm45bogYL/concat.3.c.bcf /tmp/MWm45bogYL/concat.3.d.bcf /tmp/MWm45bogYL/concat.3.e.bcf /tmp/MWm45bogYL/concat.3.f.bcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ Random seed for test_naive_concat: 3214471827 .. ok test_naive_concat: /build/reproducible-path/bcftools-1.20/bcftools concat --naive-force /tmp/MWm45bogYL/naive_concat.0.bcf /tmp/MWm45bogYL/naive_concat.1.bcf /tmp/MWm45bogYL/naive_concat.2.bcf /tmp/MWm45bogYL/naive_concat.3.bcf /tmp/MWm45bogYL/naive_concat.4.bcf /tmp/MWm45bogYL/naive_concat.5.bcf /tmp/MWm45bogYL/naive_concat.6.bcf /tmp/MWm45bogYL/naive_concat.7.bcf /tmp/MWm45bogYL/naive_concat.8.bcf /tmp/MWm45bogYL/naive_concat.9.bcf | /build/reproducible-path/bcftools-1.20/bcftools view -H .. ok test_naive_concat: /build/reproducible-path/bcftools-1.20/bcftools concat --naive /tmp/MWm45bogYL/naive_concat.0.vcf.gz /tmp/MWm45bogYL/naive_concat.1.vcf.gz /tmp/MWm45bogYL/naive_concat.2.vcf.gz /tmp/MWm45bogYL/naive_concat.3.vcf.gz /tmp/MWm45bogYL/naive_concat.4.vcf.gz /tmp/MWm45bogYL/naive_concat.5.vcf.gz /tmp/MWm45bogYL/naive_concat.6.vcf.gz /tmp/MWm45bogYL/naive_concat.7.vcf.gz /tmp/MWm45bogYL/naive_concat.8.vcf.gz /tmp/MWm45bogYL/naive_concat.9.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view -H .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat --no-version -l /tmp/MWm45bogYL/concat.4.a.vcf.gz /tmp/MWm45bogYL/concat.4.b.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat -Ob -l /tmp/MWm45bogYL/concat.4.a.vcf.gz /tmp/MWm45bogYL/concat.4.b.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat --no-version -l /tmp/MWm45bogYL/concat.4.a.bcf /tmp/MWm45bogYL/concat.4.b.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat -Ob -l /tmp/MWm45bogYL/concat.4.a.bcf /tmp/MWm45bogYL/concat.4.b.bcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat --no-version -l --ligate-warn /tmp/MWm45bogYL/concat.5.a.vcf.gz /tmp/MWm45bogYL/concat.5.b.vcf.gz /tmp/MWm45bogYL/concat.5.c.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat -Ob -l --ligate-warn /tmp/MWm45bogYL/concat.5.a.vcf.gz /tmp/MWm45bogYL/concat.5.b.vcf.gz /tmp/MWm45bogYL/concat.5.c.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat --no-version -l --ligate-warn /tmp/MWm45bogYL/concat.5.a.bcf /tmp/MWm45bogYL/concat.5.b.bcf /tmp/MWm45bogYL/concat.5.c.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat -Ob -l --ligate-warn /tmp/MWm45bogYL/concat.5.a.bcf /tmp/MWm45bogYL/concat.5.b.bcf /tmp/MWm45bogYL/concat.5.c.bcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat --no-version -l --ligate-force /tmp/MWm45bogYL/concat.5.a.bcf /tmp/MWm45bogYL/concat.5.b.bcf /tmp/MWm45bogYL/concat.5.c.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat -Ob -l --ligate-force /tmp/MWm45bogYL/concat.5.a.bcf /tmp/MWm45bogYL/concat.5.b.bcf /tmp/MWm45bogYL/concat.5.c.bcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat --no-version -G -a -D /tmp/MWm45bogYL/concat.5.a.vcf.gz /tmp/MWm45bogYL/concat.5.b.vcf.gz /tmp/MWm45bogYL/concat.5.c.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat -Ob -G -a -D /tmp/MWm45bogYL/concat.5.a.vcf.gz /tmp/MWm45bogYL/concat.5.b.vcf.gz /tmp/MWm45bogYL/concat.5.c.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat --no-version -G -a -D /tmp/MWm45bogYL/concat.5.a.bcf /tmp/MWm45bogYL/concat.5.b.bcf /tmp/MWm45bogYL/concat.5.c.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat -Ob -G -a -D /tmp/MWm45bogYL/concat.5.a.bcf /tmp/MWm45bogYL/concat.5.b.bcf /tmp/MWm45bogYL/concat.5.c.bcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.20/bcftools reheader -h /build/reproducible-path/bcftools-1.20/test/reheader.hdr /build/reproducible-path/bcftools-1.20/test/reheader.vcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: cat /build/reproducible-path/bcftools-1.20/test/reheader.vcf | /build/reproducible-path/bcftools-1.20/bcftools reheader -h /build/reproducible-path/bcftools-1.20/test/reheader.hdr | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.20/bcftools reheader -h /build/reproducible-path/bcftools-1.20/test/reheader.hdr /tmp/MWm45bogYL/reheader.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/MWm45bogYL/reheader.bcf | /build/reproducible-path/bcftools-1.20/bcftools reheader -h /build/reproducible-path/bcftools-1.20/test/reheader.hdr | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.20/bcftools reheader -h /build/reproducible-path/bcftools-1.20/test/reheader.hdr /tmp/MWm45bogYL/reheader.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/MWm45bogYL/reheader.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools reheader -h /build/reproducible-path/bcftools-1.20/test/reheader.hdr | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.20/bcftools reheader -s /build/reproducible-path/bcftools-1.20/test/reheader.samples /build/reproducible-path/bcftools-1.20/test/reheader.vcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: cat /build/reproducible-path/bcftools-1.20/test/reheader.vcf | /build/reproducible-path/bcftools-1.20/bcftools reheader -s /build/reproducible-path/bcftools-1.20/test/reheader.samples | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.20/bcftools reheader -s /build/reproducible-path/bcftools-1.20/test/reheader.samples /tmp/MWm45bogYL/reheader.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/MWm45bogYL/reheader.bcf | /build/reproducible-path/bcftools-1.20/bcftools reheader -s /build/reproducible-path/bcftools-1.20/test/reheader.samples | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.20/bcftools reheader -s /build/reproducible-path/bcftools-1.20/test/reheader.samples /tmp/MWm45bogYL/reheader.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/MWm45bogYL/reheader.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools reheader -s /build/reproducible-path/bcftools-1.20/test/reheader.samples | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.20/bcftools reheader -s /build/reproducible-path/bcftools-1.20/test/reheader.samples2 /build/reproducible-path/bcftools-1.20/test/reheader.vcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: cat /build/reproducible-path/bcftools-1.20/test/reheader.vcf | /build/reproducible-path/bcftools-1.20/bcftools reheader -s /build/reproducible-path/bcftools-1.20/test/reheader.samples2 | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.20/bcftools reheader -s /build/reproducible-path/bcftools-1.20/test/reheader.samples2 /tmp/MWm45bogYL/reheader.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/MWm45bogYL/reheader.bcf | /build/reproducible-path/bcftools-1.20/bcftools reheader -s /build/reproducible-path/bcftools-1.20/test/reheader.samples2 | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.20/bcftools reheader -s /build/reproducible-path/bcftools-1.20/test/reheader.samples2 /tmp/MWm45bogYL/reheader.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/MWm45bogYL/reheader.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools reheader -s /build/reproducible-path/bcftools-1.20/test/reheader.samples2 | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.20/bcftools reheader -s /build/reproducible-path/bcftools-1.20/test/reheader.samples3 /build/reproducible-path/bcftools-1.20/test/reheader.vcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: cat /build/reproducible-path/bcftools-1.20/test/reheader.vcf | /build/reproducible-path/bcftools-1.20/bcftools reheader -s /build/reproducible-path/bcftools-1.20/test/reheader.samples3 | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.20/bcftools reheader -s /build/reproducible-path/bcftools-1.20/test/reheader.samples3 /tmp/MWm45bogYL/reheader.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/MWm45bogYL/reheader.bcf | /build/reproducible-path/bcftools-1.20/bcftools reheader -s /build/reproducible-path/bcftools-1.20/test/reheader.samples3 | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.20/bcftools reheader -s /build/reproducible-path/bcftools-1.20/test/reheader.samples3 /tmp/MWm45bogYL/reheader.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/MWm45bogYL/reheader.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools reheader -s /build/reproducible-path/bcftools-1.20/test/reheader.samples3 | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.20/bcftools reheader -s /build/reproducible-path/bcftools-1.20/test/reheader.samples4 /build/reproducible-path/bcftools-1.20/test/reheader.vcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: cat /build/reproducible-path/bcftools-1.20/test/reheader.vcf | /build/reproducible-path/bcftools-1.20/bcftools reheader -s /build/reproducible-path/bcftools-1.20/test/reheader.samples4 | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.20/bcftools reheader -s /build/reproducible-path/bcftools-1.20/test/reheader.samples4 /tmp/MWm45bogYL/reheader.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/MWm45bogYL/reheader.bcf | /build/reproducible-path/bcftools-1.20/bcftools reheader -s /build/reproducible-path/bcftools-1.20/test/reheader.samples4 | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.20/bcftools reheader -s /build/reproducible-path/bcftools-1.20/test/reheader.samples4 /tmp/MWm45bogYL/reheader.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/MWm45bogYL/reheader.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools reheader -s /build/reproducible-path/bcftools-1.20/test/reheader.samples4 | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.20/bcftools reheader -h /build/reproducible-path/bcftools-1.20/test/reheader.empty.hdr /build/reproducible-path/bcftools-1.20/test/empty.vcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: cat /build/reproducible-path/bcftools-1.20/test/empty.vcf | /build/reproducible-path/bcftools-1.20/bcftools reheader -h /build/reproducible-path/bcftools-1.20/test/reheader.empty.hdr | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.20/bcftools reheader -h /build/reproducible-path/bcftools-1.20/test/reheader.empty.hdr /tmp/MWm45bogYL/empty.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/MWm45bogYL/empty.bcf | /build/reproducible-path/bcftools-1.20/bcftools reheader -h /build/reproducible-path/bcftools-1.20/test/reheader.empty.hdr | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.20/bcftools reheader -h /build/reproducible-path/bcftools-1.20/test/reheader.empty.hdr /tmp/MWm45bogYL/empty.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/MWm45bogYL/empty.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools reheader -h /build/reproducible-path/bcftools-1.20/test/reheader.empty.hdr | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.20/bcftools reheader -f /build/reproducible-path/bcftools-1.20/test/reheader.fai /build/reproducible-path/bcftools-1.20/test/reheader.2.vcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.20/bcftools reheader -f /build/reproducible-path/bcftools-1.20/test/reheader.fai /tmp/MWm45bogYL/reheader.2.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.20/bcftools reheader -f /build/reproducible-path/bcftools-1.20/test/reheader.fai /tmp/MWm45bogYL/reheader.2.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.20/bcftools reheader -h /build/reproducible-path/bcftools-1.20/test/reheader.2.hdr -f /build/reproducible-path/bcftools-1.20/test/reheader.fai /build/reproducible-path/bcftools-1.20/test/reheader.2.vcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.20/bcftools reheader -h /build/reproducible-path/bcftools-1.20/test/reheader.2.hdr -f /build/reproducible-path/bcftools-1.20/test/reheader.fai /tmp/MWm45bogYL/reheader.2.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.20/bcftools reheader -h /build/reproducible-path/bcftools-1.20/test/reheader.2.hdr -f /build/reproducible-path/bcftools-1.20/test/reheader.fai /tmp/MWm45bogYL/reheader.2.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.20/bcftools reheader -f /build/reproducible-path/bcftools-1.20/test/reheader.3.fai /build/reproducible-path/bcftools-1.20/test/reheader.3.vcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.20/bcftools reheader -f /build/reproducible-path/bcftools-1.20/test/reheader.3.fai /tmp/MWm45bogYL/reheader.3.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.20/bcftools reheader -f /build/reproducible-path/bcftools-1.20/test/reheader.3.fai /tmp/MWm45bogYL/reheader.3.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_rename_chrs: /build/reproducible-path/bcftools-1.20/bcftools annotate --rename-chrs /tmp/MWm45bogYL/rename.map -Ov /tmp/MWm45bogYL/annotate.bcf | /build/reproducible-path/bcftools-1.20/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /build/reproducible-path/bcftools-1.20/bcftools annotate --rename-chrs /tmp/MWm45bogYL/rename.map -Ob /tmp/MWm45bogYL/annotate.bcf | /build/reproducible-path/bcftools-1.20/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /build/reproducible-path/bcftools-1.20/bcftools annotate --rename-chrs /tmp/MWm45bogYL/rename.map -Ov /build/reproducible-path/bcftools-1.20/test/annotate.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /build/reproducible-path/bcftools-1.20/bcftools annotate --rename-chrs /tmp/MWm45bogYL/rename.map -Ob /build/reproducible-path/bcftools-1.20/test/annotate.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f'%CHROM\t%POS\n' .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools convert -g -,. /tmp/MWm45bogYL/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/convert.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools convert -g -,. .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools convert -g -,. --vcf-ids /tmp/MWm45bogYL/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/convert.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools convert -g -,. --vcf-ids .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools convert -g -,. --vcf-ids --3N6 /tmp/MWm45bogYL/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/convert.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools convert -g -,. --vcf-ids --3N6 .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools convert -g .,- /tmp/MWm45bogYL/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/convert.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools convert -g .,- .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.20/bcftools convert --vcf-ids -G /build/reproducible-path/bcftools-1.20/test/convert.gs.gt.ids.gen,/build/reproducible-path/bcftools-1.20/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.20/bcftools convert --vcf-ids -G /build/reproducible-path/bcftools-1.20/test/convert.gs.gt.ids.gen,/build/reproducible-path/bcftools-1.20/test/convert.gs.gt.samples -Ou | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.20/bcftools convert -G /build/reproducible-path/bcftools-1.20/test/convert.gs.gt.ids.gen,/build/reproducible-path/bcftools-1.20/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.20/bcftools convert -G /build/reproducible-path/bcftools-1.20/test/convert.gs.gt.ids.gen,/build/reproducible-path/bcftools-1.20/test/convert.gs.gt.samples -Ou | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.20/bcftools convert --3N6 -G /build/reproducible-path/bcftools-1.20/test/convert.gs.gt.ids.3N6.gen,/build/reproducible-path/bcftools-1.20/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.20/bcftools convert --3N6 -G /build/reproducible-path/bcftools-1.20/test/convert.gs.gt.ids.3N6.gen,/build/reproducible-path/bcftools-1.20/test/convert.gs.gt.samples -Ou | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.20/bcftools convert --vcf-ids -G /build/reproducible-path/bcftools-1.20/test/convert.gs.gt.ids.gen.rev,/build/reproducible-path/bcftools-1.20/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.20/bcftools convert --vcf-ids -G /build/reproducible-path/bcftools-1.20/test/convert.gs.gt.ids.gen.rev,/build/reproducible-path/bcftools-1.20/test/convert.gs.gt.samples -Ou | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.20/bcftools convert -G /build/reproducible-path/bcftools-1.20/test/convert.gs.gt.ids.gen.rev,/build/reproducible-path/bcftools-1.20/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.20/bcftools convert -G /build/reproducible-path/bcftools-1.20/test/convert.gs.gt.ids.gen.rev,/build/reproducible-path/bcftools-1.20/test/convert.gs.gt.samples -Ou | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^## .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools convert -g -,. --tag PL /tmp/MWm45bogYL/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/convert.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools convert -g -,. --tag PL .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools convert -g .,- --tag PL /tmp/MWm45bogYL/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/convert.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools convert -g .,- --tag PL .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools convert -g -,. --vcf-ids /tmp/MWm45bogYL/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/check.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools convert -g -,. --vcf-ids .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools convert -g .,- --vcf-ids /tmp/MWm45bogYL/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/check.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools convert -g .,- --vcf-ids .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools convert -g -,. --3N6 /tmp/MWm45bogYL/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/check.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools convert -g -,. --3N6 .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools convert -g .,- --3N6 /tmp/MWm45bogYL/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/check.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools convert -g .,- --3N6 .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools convert -g -,. --3N6 --vcf-ids /tmp/MWm45bogYL/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/check.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools convert -g -,. --3N6 --vcf-ids .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools convert -g .,- --3N6 --vcf-ids /tmp/MWm45bogYL/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/check.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools convert -g .,- --3N6 --vcf-ids .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools convert -h -,.,. /tmp/MWm45bogYL/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/convert.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools convert -h -,.,. .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools convert -h .,-,. /tmp/MWm45bogYL/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/convert.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools convert -h .,-,. .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools convert -h .,-,. --vcf-ids /tmp/MWm45bogYL/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/convert.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools convert -h .,-,. --vcf-ids .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools convert -h .,.,- /tmp/MWm45bogYL/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/convert.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools convert -h .,.,- .. ok test_vcf_convert_hls2vcf: /build/reproducible-path/bcftools-1.20/bcftools convert -H /build/reproducible-path/bcftools-1.20/test/convert.hls.gt.hap,/build/reproducible-path/bcftools-1.20/test/convert.hls.gt.legend,/build/reproducible-path/bcftools-1.20/test/convert.hls.gt.samples | grep -v ^## .. ok test_vcf_convert_hls2vcf: /build/reproducible-path/bcftools-1.20/bcftools convert -H /build/reproducible-path/bcftools-1.20/test/convert.hls.gt.hap,/build/reproducible-path/bcftools-1.20/test/convert.hls.gt.legend,/build/reproducible-path/bcftools-1.20/test/convert.hls.gt.samples -Ou | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^## .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools convert --haplegendsample -,.,. /tmp/MWm45bogYL/convert.hap-missing.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/convert.hap-missing.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools convert --haplegendsample -,.,. .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools convert --hapsample -,. /tmp/MWm45bogYL/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/convert.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools convert --hapsample -,. .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools convert --hapsample -,. --vcf-ids /tmp/MWm45bogYL/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/convert.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools convert --hapsample -,. --vcf-ids .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools convert --hapsample .,- /tmp/MWm45bogYL/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/convert.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools convert --hapsample .,- .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.20/bcftools convert --hapsample2vcf /build/reproducible-path/bcftools-1.20/test/convert.hs.gt.hap,/build/reproducible-path/bcftools-1.20/test/convert.hs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.20/bcftools convert --hapsample2vcf /build/reproducible-path/bcftools-1.20/test/convert.hs.gt.hap,/build/reproducible-path/bcftools-1.20/test/convert.hs.gt.samples -Ou | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.20/bcftools convert --vcf-ids --hapsample2vcf /build/reproducible-path/bcftools-1.20/test/convert.hs.gt.ids.hap,/build/reproducible-path/bcftools-1.20/test/convert.hs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.20/bcftools convert --vcf-ids --hapsample2vcf /build/reproducible-path/bcftools-1.20/test/convert.hs.gt.ids.hap,/build/reproducible-path/bcftools-1.20/test/convert.hs.gt.samples -Ou | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^## .. ok test_vcf_convert_gvcf: /build/reproducible-path/bcftools-1.20/bcftools convert --no-version --gvcf2vcf -i'FILTER="PASS"' -f /build/reproducible-path/bcftools-1.20/test/gvcf.fa /tmp/MWm45bogYL/convert.gvcf.vcf.gz .. ok test_vcf_convert_gvcf: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/MWm45bogYL/convert.gvcf.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools convert --gvcf2vcf -i'FILTER="PASS"' -f /build/reproducible-path/bcftools-1.20/test/gvcf.fa | grep -v ^##bcftools .. ok test_vcf_convert_tsv2vcf: /build/reproducible-path/bcftools-1.20/bcftools convert --no-version -c ID,CHROM,POS,AA -s SAMPLE1 -f /build/reproducible-path/bcftools-1.20/test/23andme.fa --tsv2vcf /build/reproducible-path/bcftools-1.20/test/convert.23andme .. ok test_vcf_convert_tsv2vcf: /build/reproducible-path/bcftools-1.20/bcftools convert -Ou -c ID,CHROM,POS,AA -s SAMPLE1 -f /build/reproducible-path/bcftools-1.20/test/23andme.fa --tsv2vcf /build/reproducible-path/bcftools-1.20/test/convert.23andme | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_convert_tsv2vcf: /build/reproducible-path/bcftools-1.20/bcftools convert --no-version -c -,CHROM,POS,REF,ALT -f /build/reproducible-path/bcftools-1.20/test/23andme.fa --tsv2vcf /build/reproducible-path/bcftools-1.20/test/convert.tsv .. ok test_vcf_convert_tsv2vcf: /build/reproducible-path/bcftools-1.20/bcftools convert -Ou -c -,CHROM,POS,REF,ALT -f /build/reproducible-path/bcftools-1.20/test/23andme.fa --tsv2vcf /build/reproducible-path/bcftools-1.20/test/convert.tsv | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/consensus.fa -s - -m /build/reproducible-path/bcftools-1.20/test/consensus.tab .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.bcf -f /build/reproducible-path/bcftools-1.20/test/consensus.fa -s - -m /build/reproducible-path/bcftools-1.20/test/consensus.tab .. ok test_vcf_consensus_chain: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/consensus.fa -s - -m /build/reproducible-path/bcftools-1.20/test/consensus.tab -c /tmp/MWm45bogYL/consensus.1.chain.new >/dev/null; cat /tmp/MWm45bogYL/consensus.1.chain.new .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/consensus.fa -H 1 -m /build/reproducible-path/bcftools-1.20/test/consensus.tab .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.bcf -f /build/reproducible-path/bcftools-1.20/test/consensus.fa -H 1 -m /build/reproducible-path/bcftools-1.20/test/consensus.tab .. ok test_vcf_consensus_chain: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/consensus.fa -H 1 -m /build/reproducible-path/bcftools-1.20/test/consensus.tab -c /tmp/MWm45bogYL/consensus.2.chain.new >/dev/null; cat /tmp/MWm45bogYL/consensus.2.chain.new .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/consensus.fa -I -s - -m /build/reproducible-path/bcftools-1.20/test/consensus.tab .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.bcf -f /build/reproducible-path/bcftools-1.20/test/consensus.fa -I -s - -m /build/reproducible-path/bcftools-1.20/test/consensus.tab .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/consensus.fa -s - -I -m /build/reproducible-path/bcftools-1.20/test/consensus.tab --mask-with X -m /build/reproducible-path/bcftools-1.20/test/consensus.tab --mask-with lc .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.bcf -f /build/reproducible-path/bcftools-1.20/test/consensus.fa -s - -I -m /build/reproducible-path/bcftools-1.20/test/consensus.tab --mask-with X -m /build/reproducible-path/bcftools-1.20/test/consensus.tab --mask-with lc .. ok test_vcf_consensus_chain: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/consensus.fa -I -m /build/reproducible-path/bcftools-1.20/test/consensus.tab -c /tmp/MWm45bogYL/consensus.3.chain.new >/dev/null; cat /tmp/MWm45bogYL/consensus.3.chain.new .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/consensus.fa -H 1 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.bcf -f /build/reproducible-path/bcftools-1.20/test/consensus.fa -H 1 .. ok test_vcf_consensus_chain: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/consensus.fa -H 1 -c /tmp/MWm45bogYL/consensus.4.chain.new >/dev/null; cat /tmp/MWm45bogYL/consensus.4.chain.new .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus2.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/consensus2.fa -H 1 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus2.bcf -f /build/reproducible-path/bcftools-1.20/test/consensus2.fa -H 1 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus2.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/consensus2.fa -H 2 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus2.bcf -f /build/reproducible-path/bcftools-1.20/test/consensus2.fa -H 2 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/empty.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/consensus.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/empty.bcf -f /build/reproducible-path/bcftools-1.20/test/consensus.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus3.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/consensus2.fa -H 2 -M "?" .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus3.bcf -f /build/reproducible-path/bcftools-1.20/test/consensus2.fa -H 2 -M "?" .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus3.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/consensus2.fa -H 2 -M "?" -p xx_ .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus3.bcf -f /build/reproducible-path/bcftools-1.20/test/consensus2.fa -H 2 -M "?" -p xx_ .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus4.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/consensus2.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus4.bcf -f /build/reproducible-path/bcftools-1.20/test/consensus2.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus5.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/consensus5.fa --haplotype LA .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus5.bcf -f /build/reproducible-path/bcftools-1.20/test/consensus5.fa --haplotype LA .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus6.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/consensus6.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus6.bcf -f /build/reproducible-path/bcftools-1.20/test/consensus6.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus7.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/consensus7.fa -H 2 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus7.bcf -f /build/reproducible-path/bcftools-1.20/test/consensus7.fa -H 2 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus7.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/consensus7.fa -H 4 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus7.bcf -f /build/reproducible-path/bcftools-1.20/test/consensus7.fa -H 4 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus7.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/consensus7.fa -H 2pIu .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus7.bcf -f /build/reproducible-path/bcftools-1.20/test/consensus7.fa -H 2pIu .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus7.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/consensus7.fa -H 4pIu .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus7.bcf -f /build/reproducible-path/bcftools-1.20/test/consensus7.fa -H 4pIu .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus7.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/consensus7.fa -H 1 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus7.bcf -f /build/reproducible-path/bcftools-1.20/test/consensus7.fa -H 1 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus7.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/consensus7.fa -H 3 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus7.bcf -f /build/reproducible-path/bcftools-1.20/test/consensus7.fa -H 3 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus7.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/consensus7.fa -H 1pIu .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus7.bcf -f /build/reproducible-path/bcftools-1.20/test/consensus7.fa -H 1pIu .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus7.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/consensus7.fa -H 3pIu .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus7.bcf -f /build/reproducible-path/bcftools-1.20/test/consensus7.fa -H 3pIu .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus8.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/consensus.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus8.bcf -f /build/reproducible-path/bcftools-1.20/test/consensus.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus8.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/consensus.fa -s - -a . .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus8.bcf -f /build/reproducible-path/bcftools-1.20/test/consensus.fa -s - -a . .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus8.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/consensus.fa -s - -a . -i 'type="snp" || type="ref"' .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus8.bcf -f /build/reproducible-path/bcftools-1.20/test/consensus.fa -s - -a . -i 'type="snp" || type="ref"' .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus8.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/consensus.fa -s - -a . -i 'ALT!=""' .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus8.bcf -f /build/reproducible-path/bcftools-1.20/test/consensus.fa -s - -a . -i 'ALT!=""' .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus8.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/consensus.fa -s - -a . -e 'MinDP>15' .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus8.bcf -f /build/reproducible-path/bcftools-1.20/test/consensus.fa -s - -a . -e 'MinDP>15' .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus8.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/consensus.fa -s - -a . -e 'MinDP<15' .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus8.bcf -f /build/reproducible-path/bcftools-1.20/test/consensus.fa -s - -a . -e 'MinDP<15' .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.9.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.9.bcf -f /build/reproducible-path/bcftools-1.20/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.9.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.9.bcf -f /build/reproducible-path/bcftools-1.20/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.10.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.10.bcf -f /build/reproducible-path/bcftools-1.20/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.10.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.10.bcf -f /build/reproducible-path/bcftools-1.20/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.11.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/consensus.11.fa -s smpl .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.11.bcf -f /build/reproducible-path/bcftools-1.20/test/consensus.11.fa -s smpl .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.11.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/consensus.11.fa -s smpl -a N .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.11.bcf -f /build/reproducible-path/bcftools-1.20/test/consensus.11.fa -s smpl -a N .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.12.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/consensus.12.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.12.bcf -f /build/reproducible-path/bcftools-1.20/test/consensus.12.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.13.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/consensus.13.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.13.bcf -f /build/reproducible-path/bcftools-1.20/test/consensus.13.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.14.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/consensus.14.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.14.bcf -f /build/reproducible-path/bcftools-1.20/test/consensus.14.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.12.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/consensus.12.fa -s - --mark-del - --mark-ins uc --mark-snv uc .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.12.bcf -f /build/reproducible-path/bcftools-1.20/test/consensus.12.fa -s - --mark-del - --mark-ins uc --mark-snv uc .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.12.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/consensus.12.fa -s - --mark-del - --mark-ins + --mark-snv : .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.12.bcf -f /build/reproducible-path/bcftools-1.20/test/consensus.12.fa -s - --mark-del - --mark-ins + --mark-snv : .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.15.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/consensus.15.fa -H I --mark-ins lc --mark-snv lc .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.15.bcf -f /build/reproducible-path/bcftools-1.20/test/consensus.15.fa -H I --mark-ins lc --mark-snv lc .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.16.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/consensus.fa -s - -I .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.16.bcf -f /build/reproducible-path/bcftools-1.20/test/consensus.fa -s - -I .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.16.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/consensus.fa -H I .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.16.bcf -f /build/reproducible-path/bcftools-1.20/test/consensus.fa -H I .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.17.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/consensus2.fa -s - -M N -m /build/reproducible-path/bcftools-1.20/test/consensus.17.bed .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.17.bcf -f /build/reproducible-path/bcftools-1.20/test/consensus2.fa -s - -M N -m /build/reproducible-path/bcftools-1.20/test/consensus.17.bed .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.18.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/consensus.18.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.18.bcf -f /build/reproducible-path/bcftools-1.20/test/consensus.18.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.19.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/consensus.19.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.19.bcf -f /build/reproducible-path/bcftools-1.20/test/consensus.19.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.20.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/consensus.20.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.20.bcf -f /build/reproducible-path/bcftools-1.20/test/consensus.20.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.20.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/consensus.20.fa .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.20.bcf -f /build/reproducible-path/bcftools-1.20/test/consensus.20.fa .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.20.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/consensus.20.fa -M . -s b .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.20.bcf -f /build/reproducible-path/bcftools-1.20/test/consensus.20.fa -M . -s b .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.20.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/consensus.20.fa -M . -s a .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.20.bcf -f /build/reproducible-path/bcftools-1.20/test/consensus.20.fa -M . -s a .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.21.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/consensus.21.fa .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.21.bcf -f /build/reproducible-path/bcftools-1.20/test/consensus.21.fa .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.22.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/consensus.22.fa --regions-overlap 0 --mark-del . .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.22.bcf -f /build/reproducible-path/bcftools-1.20/test/consensus.22.fa --regions-overlap 0 --mark-del . .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.22.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/consensus.22.fa --regions-overlap 1 --mark-del . .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.22.bcf -f /build/reproducible-path/bcftools-1.20/test/consensus.22.fa --regions-overlap 1 --mark-del . .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.22.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/consensus.22.fa --regions-overlap 2 --mark-del . .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.22.bcf -f /build/reproducible-path/bcftools-1.20/test/consensus.22.fa --regions-overlap 2 --mark-del . .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.22.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/consensus.22.fa --regions-overlap 0 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.22.bcf -f /build/reproducible-path/bcftools-1.20/test/consensus.22.fa --regions-overlap 0 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.22.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/consensus.22.fa --regions-overlap 1 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.22.bcf -f /build/reproducible-path/bcftools-1.20/test/consensus.22.fa --regions-overlap 1 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.22.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/consensus.22.fa --regions-overlap 2 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/MWm45bogYL/consensus.22.bcf -f /build/reproducible-path/bcftools-1.20/test/consensus.22.fa --regions-overlap 2 .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -r17:100-150 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -r17:100-150 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -r17:100-150 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -b /tmp/MWm45bogYL/mpileup.bam.list --no-version | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -r17:100-150 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob -b /tmp/MWm45bogYL/mpileup.bam.urllist | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -r17:100-150 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -r17:100-150 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -r17:100-150 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -b /tmp/MWm45bogYL/mpileup.cram.list --no-version | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -r17:100-150 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob -b /tmp/MWm45bogYL/mpileup.cram.urllist | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a DP,DV -r17:100-600 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a DP,DV -r17:100-600 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a DP,DV -r17:100-600 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a DP,DV -r17:100-600 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.bam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.cram | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -r17:100-150 -S /build/reproducible-path/bcftools-1.20/test/mplp.samples -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -r17:100-150 -S /build/reproducible-path/bcftools-1.20/test/mplp.samples -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -r17:100-150 -S /build/reproducible-path/bcftools-1.20/test/mplp.samples -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -r17:100-150 -S /build/reproducible-path/bcftools-1.20/test/mplp.samples -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -r17:100-150 -S ^/build/reproducible-path/bcftools-1.20/test/mplp.samples -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -r17:100-150 -S ^/build/reproducible-path/bcftools-1.20/test/mplp.samples -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -r17:100-150 -S ^/build/reproducible-path/bcftools-1.20/test/mplp.samples -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -r17:100-150 -S ^/build/reproducible-path/bcftools-1.20/test/mplp.samples -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -t17:100-150 -S /build/reproducible-path/bcftools-1.20/test/mplp.9.samples -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.sam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.sam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -t17:100-150 -S /build/reproducible-path/bcftools-1.20/test/mplp.9.samples -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.sam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.sam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.sam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -t17:100-150 -S /build/reproducible-path/bcftools-1.20/test/mplp.9.samples -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -t17:100-150 -S /build/reproducible-path/bcftools-1.20/test/mplp.9.samples -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -t17:100-150 -S /build/reproducible-path/bcftools-1.20/test/mplp.9.samples -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -t17:100-150 -S /build/reproducible-path/bcftools-1.20/test/mplp.9.samples -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -t17:100-150 -G /build/reproducible-path/bcftools-1.20/test/mplp.10.samples -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.sam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.sam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -t17:100-150 -G /build/reproducible-path/bcftools-1.20/test/mplp.10.samples -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.sam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.sam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.sam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -t17:100-150 -G /build/reproducible-path/bcftools-1.20/test/mplp.10.samples -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -t17:100-150 -G /build/reproducible-path/bcftools-1.20/test/mplp.10.samples -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -t17:100-150 -G /build/reproducible-path/bcftools-1.20/test/mplp.10.samples -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -t17:100-150 -G /build/reproducible-path/bcftools-1.20/test/mplp.10.samples -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.sam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -s HG00102 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.sam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -s HG00102 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.sam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.4.sam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -s HG00102 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -s HG00102 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.4.bam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -s HG00102 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -s HG00102 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.4.cram | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -s ^HG99999 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.sam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -s ^HG99999 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.sam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.4.sam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -s ^HG99999 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -s ^HG99999 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.4.bam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -s ^HG99999 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -s ^HG99999 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.4.cram | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -G /build/reproducible-path/bcftools-1.20/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.sam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -G /build/reproducible-path/bcftools-1.20/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.sam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.4.sam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -G /build/reproducible-path/bcftools-1.20/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -G /build/reproducible-path/bcftools-1.20/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.4.bam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -G /build/reproducible-path/bcftools-1.20/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -G /build/reproducible-path/bcftools-1.20/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.4.cram | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -G /build/reproducible-path/bcftools-1.20/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.sam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -G /build/reproducible-path/bcftools-1.20/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.sam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.4.sam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -G /build/reproducible-path/bcftools-1.20/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -G /build/reproducible-path/bcftools-1.20/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.4.bam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -G /build/reproducible-path/bcftools-1.20/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -G /build/reproducible-path/bcftools-1.20/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.4.cram | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a AD -f /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.1.fa /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.1.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a AD -f /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.1.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.1.sam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a AD -f /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.1.fa /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a AD -f /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.1.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.1.bam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a AD -f /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.1.fa /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.1.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a AD -f /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.1.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.1.cram | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a AD --indels-cns -f /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.1.fa /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.1.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a AD --indels-cns -f /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.1.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.1.sam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a AD --indels-cns -f /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.1.fa /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a AD --indels-cns -f /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.1.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.1.bam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a AD --indels-cns -f /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.1.fa /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.1.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a AD --indels-cns -f /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.1.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.1.cram | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a AD -r 11:75 -f /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.2.fa /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a AD -r 11:75 -f /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.2.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.2.bam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a AD -r 11:75 -f /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.2.fa /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a AD -r 11:75 -f /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.2.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.2.cram | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.2.fa /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.2.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.2.bam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.2.fa /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.2.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.2.cram | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.2.fa /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.2.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.2.bam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.2.fa /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.2.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.2.cram | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a INFO/SCR,FMT/SCR -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup-SCR.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup-SCR.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a INFO/SCR,FMT/SCR -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup-SCR.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup-SCR.bam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a INFO/SCR,FMT/SCR -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup-SCR.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup-SCR.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a INFO/SCR,FMT/SCR -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup-SCR.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup-SCR.cram | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -t 1:100 --skip-all-set PAIRED,PROPER_PAIR,MREVERSE -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup-SCR.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -t 1:100 --skip-all-set PAIRED,PROPER_PAIR,MREVERSE -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup-SCR.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup-filter.sam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -t 1:100 --skip-any-set READ1 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup-SCR.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -t 1:100 --skip-any-set READ1 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup-SCR.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup-filter.sam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -t 1:100 --skip-all-unset READ1 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup-SCR.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -t 1:100 --skip-all-unset READ1 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup-SCR.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup-filter.sam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -t 1:100 --skip-any-unset READ1 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup-SCR.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -t 1:100 --skip-any-unset READ1 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup-SCR.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup-filter.sam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a INFO/NMBZ -r chr19:69-99 -f /build/reproducible-path/bcftools-1.20/test/mpileup/annot-NMBZ.1.fa /build/reproducible-path/bcftools-1.20/test/mpileup/annot-NMBZ.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a INFO/NMBZ -r chr19:69-99 -f /build/reproducible-path/bcftools-1.20/test/mpileup/annot-NMBZ.1.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/annot-NMBZ.1.bam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a INFO/NMBZ -r chr6:75 -f /build/reproducible-path/bcftools-1.20/test/mpileup/annot-NMBZ.2.fa /build/reproducible-path/bcftools-1.20/test/mpileup/annot-NMBZ.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a INFO/NMBZ -r chr6:75 -f /build/reproducible-path/bcftools-1.20/test/mpileup/annot-NMBZ.2.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/annot-NMBZ.2.bam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a INFO/NMBZ -r chr16:75 -f /build/reproducible-path/bcftools-1.20/test/mpileup/annot-NMBZ.3.fa /build/reproducible-path/bcftools-1.20/test/mpileup/annot-NMBZ.3.1.bam /build/reproducible-path/bcftools-1.20/test/mpileup/annot-NMBZ.3.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a INFO/NMBZ -r chr16:75 -f /build/reproducible-path/bcftools-1.20/test/mpileup/annot-NMBZ.3.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/annot-NMBZ.3.1.bam /build/reproducible-path/bcftools-1.20/test/mpileup/annot-NMBZ.3.2.bam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_csq: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq.fa -g /build/reproducible-path/bcftools-1.20/test/csq.gff3 /build/reproducible-path/bcftools-1.20/test/csq.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq.fa -g /build/reproducible-path/bcftools-1.20/test/csq.chr.gff3 /build/reproducible-path/bcftools-1.20/test/csq.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq.fa -g /build/reproducible-path/bcftools-1.20/test/csq.2.gff /build/reproducible-path/bcftools-1.20/test/csq.2.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq.fa -g /build/reproducible-path/bcftools-1.20/test/csq.2.gff --ncsq 64 /build/reproducible-path/bcftools-1.20/test/csq.2.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq.nchr.fa -g /build/reproducible-path/bcftools-1.20/test/csq.nchr.gff /build/reproducible-path/bcftools-1.20/test/csq.nchr.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq.ychr.fa -g /build/reproducible-path/bcftools-1.20/test/csq.nchr.gff /build/reproducible-path/bcftools-1.20/test/csq.nchr.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq.nchr.fa -g /build/reproducible-path/bcftools-1.20/test/csq.ychr.gff /build/reproducible-path/bcftools-1.20/test/csq.nchr.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq.ychr.fa -g /build/reproducible-path/bcftools-1.20/test/csq.ychr.gff /build/reproducible-path/bcftools-1.20/test/csq.nchr.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq.ychr.fa -g /build/reproducible-path/bcftools-1.20/test/csq.ychr.gff /build/reproducible-path/bcftools-1.20/test/csq.ychr.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq.ychr.fa -g /build/reproducible-path/bcftools-1.20/test/csq.nchr.gff /build/reproducible-path/bcftools-1.20/test/csq.ychr.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq.nchr.fa -g /build/reproducible-path/bcftools-1.20/test/csq.ychr.gff /build/reproducible-path/bcftools-1.20/test/csq.ychr.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq.nchr.fa -g /build/reproducible-path/bcftools-1.20/test/csq.nchr.gff /build/reproducible-path/bcftools-1.20/test/csq.ychr.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000420670/ENST00000420670.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000420670/ENST00000420670.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000420670/start-stop-lost.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000420670/ENST00000420670.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000420670/ENST00000420670.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000420670/segfault.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/frame2.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -l -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/frame2.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -l -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -l -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/frame3.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -l -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/frame3.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -l -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -l -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -l -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/frame1.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -l -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/frame1.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -l -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -l -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -l -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -l -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -l -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000375992/ENST00000375992.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000375992/ENST00000375992.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000375992/incorrect-synon-del-not-start-lost.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000373833/ENST00000373833.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000373833/ENST00000373833.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000373833/boundary-insertion.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -l -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000373833/ENST00000373833.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000373833/ENST00000373833.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000373833/boundary-insertion.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000218032/ENST00000218032.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000218032/ENST00000218032.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000218032/start-lost.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -l -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000218032/ENST00000218032.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000218032/ENST00000218032.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000218032/start-lost.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000218032/ENST00000218032.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000218032/ENST00000218032.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000218032/start-lost-del.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/EDUMMY0002/EDUMMY0002.fa -g /build/reproducible-path/bcftools-1.20/test/csq/EDUMMY0002/EDUMMY0002.gff /build/reproducible-path/bcftools-1.20/test/csq/EDUMMY0002/boundaries.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000420190/ENST00000420190.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000420190/ENST00000420190.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000420190/abort-in-csq-push.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000378322/ENST00000378322.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000378322/ENST00000378322.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000378322/end-overlap-tscript.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -l -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000378322/ENST00000378322.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000378322/ENST00000378322.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000378322/end-overlap-tscript.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000230048/ENST00000230048.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000230048/ENST00000230048.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000230048/start-del.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000400151/ENST00000400151.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000400151/ENST00000400151.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000400151/long-del.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000390520/ENST00000390520.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000390520/ENST00000390520.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000390520/deletion-overlap.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000542803/ENST00000542803.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000542803/ENST00000542803.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000542803/splice-region.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -l -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000542803/ENST00000542803.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000542803/ENST00000542803.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000542803/splice-region.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/EDUMMY0003/EDUMMY0003.fa -g /build/reproducible-path/bcftools-1.20/test/csq/EDUMMY0003/EDUMMY0003.gff /build/reproducible-path/bcftools-1.20/test/csq/EDUMMY0003/long-del.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000545279/ENST00000545279.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000545279/ENST00000545279.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000545279/splice-region-insert.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/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-1.20/test/csq/ENSMUST00000121418 && /build/reproducible-path/bcftools-1.20/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25496' --phase m | ../sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.20/test/csq/ENSMUST00000121418 && /build/reproducible-path/bcftools-1.20/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25500' --phase m | ../sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.20/test/csq/ENSMUST00000121418 && /build/reproducible-path/bcftools-1.20/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25105' --phase m | ../sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000520795/ENST00000520795.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000520795/ENST00000520795.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000520795/long-inside-del.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -l -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000520795/ENST00000520795.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000520795/ENST00000520795.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000520795/long-inside-del.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000528237/ENST00000528237.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000528237/ENST00000528237.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000528237/retained-stop-incomplete-cds.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000436063/ENST00000436063.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000436063/ENST00000436063.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000436063/insert-before-utr.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000573314/ENST00000573314.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000573314/ENST00000573314.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -l -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000573314/ENST00000573314.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000573314/ENST00000573314.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000285021/ENST00000285021.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000285021/ENST00000285021.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000285021/stop-gained-inframe-indel.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000382647/ENST00000382647.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000382647/ENST00000382647.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000382647/synon-splice-region-insert.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000571540/ENST00000571540.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000571540/ENST00000571540.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000571540/nmd.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000413103/ENST00000413103.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000413103/ENST00000413103.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000413103/long-deletion.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000536784/ENST00000536784.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000536784/ENST00000536784.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000536784/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -l -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000536784/ENST00000536784.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000536784/ENST00000536784.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000536784/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000423372/ENST00000423372.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000423372/ENST00000423372.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000423372/snps.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -l -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000423372/ENST00000423372.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000423372/ENST00000423372.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000423372/snps.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000423372/ENST00000423372.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000423372/ENST00000423372.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000423372/insert3.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -l -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000423372/ENST00000423372.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000423372/ENST00000423372.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000423372/insert3.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/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-1.20/test/csq/ENSMUST00000133836 && /build/reproducible-path/bcftools-1.20/bcftools csq -f ENSMUST00000133836.fa -g ENSMUST00000133836.gff filter-problem.vcf -i 'FILTER="PASS"' --phase m | ../sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.20/test/csq/ENST00000000000 && /build/reproducible-path/bcftools-1.20/bcftools csq -p a -f ENST00000000000.fa -g ENST00000000000.gff upstream-stop.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS\t%REF\t%ALT\t%SAMPLE\t%GT\t%TBCSQ\n]' | ../sort-csq -q .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.20/test/csq/ENST00000422159 && /build/reproducible-path/bcftools-1.20/bcftools csq -f ENST00000422159.fa -g ENST00000422159.gff multiallelic.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS\t%REF\t%ALT\t%GT\t%TBCSQ\n]' | ../sort-csq -q ; echo ; /build/reproducible-path/bcftools-1.20/bcftools csq -f ENST00000422159.fa -g short.gff multiallelic.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS\t%REF\t%ALT\t%GT\t%TBCSQ\n]' | ../sort-csq -q .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000479739/ENST00000479739.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000479739/ENST00000479739.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000479739/short-cds-start-lost.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -l -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000479739/ENST00000479739.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000479739/ENST00000479739.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000479739/short-cds-start-lost.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000557788/ENST00000557788.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000557788/ENST00000557788.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000557788/long-overlap-del.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/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-1.20/test/csq/ENST00000410009 && /build/reproducible-path/bcftools-1.20/bcftools csq -B 5 -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000410009/ENST00000410009.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000410009/ENST00000410009.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000410009/frameshift.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/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-1.20/test/csq/ENST00000410009 && /build/reproducible-path/bcftools-1.20/bcftools csq -lb -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.20/test/csq/ENST00000410009 && /build/reproducible-path/bcftools-1.20/bcftools csq -b -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000269081/ENST00000269081.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000269081/ENST00000269081.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000269081/stop-gained-not-inframe-insertion.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000520868/ENST00000520868.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000520868/ENST00000520868.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000520868/long-deletion.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/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-1.20/test/csq/EMN908947 && /build/reproducible-path/bcftools-1.20/bcftools csq -f EMN908947.fa -g simple.gff simple.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.20/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-1.20/test/csq/EMN908947 && /build/reproducible-path/bcftools-1.20/bcftools csq -f EMN908947.fa -g ribosomal-slippage.gff ribosomal-slippage.vcf --force | ../sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000409523/ENST00000409523.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000409523/ENST00000409523.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000409523/long-overlapping-del.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000368801.2/ENST00000368801.2.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000368801.2/ENST00000368801.2.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000368801.2/start-lost.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000357367/ENST00000357367.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000357367/ENST00000357367.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000357367/stop-retained.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000519442/ENST00000519442.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000519442/ENST00000519442.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000519442/synon-splice-region-del.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000256452/ENST00000256452.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000256452/ENST00000256452.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000256452/intron.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000518414-ENST00000521270/valgrind.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/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-1.20/test/csq/ENST00000580206 && /build/reproducible-path/bcftools-1.20/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.ins-snv.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.20/bcftools csq -f ENST00000580206.fa -g short.gff compound.ins-snv.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.20/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff single.ins-snv.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.20/bcftools csq -f ENST00000580206.fa -g short.gff single.ins-snv.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.20/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.del-snv.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.20/bcftools csq -f ENST00000580206.fa -g short.gff compound.del-snv.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.20/bcftools csq -f ENST00000580206.fa -g short.gff single.del-snv.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.20/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.del-ins.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.20/bcftools csq -f ENST00000580206.fa -g short.gff compound.del-ins.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.20/bcftools csq -f ENST00000580206.fa -g short.gff single.del-ins.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.20/test/csq/ENST00000379416 && /build/reproducible-path/bcftools-1.20/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.del-snp.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.20/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-del.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.20/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-ins.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.20/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-snp.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.20/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff single.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000263103-INS/ENST00000263103-INS.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000263103-INS/ENST00000263103-INS.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000263103-INS/insertions.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000381157/ENST00000381157.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000381157/ENST00000381157.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000381157/haploid-diploid.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000543077/ENST00000543077.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000543077/ENST00000543077.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000543077/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -l -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000543077/ENST00000543077.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000543077/ENST00000543077.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000543077/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENSG00000173376/ENSG00000173376.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENSG00000173376/ENSG00000173376.gff /build/reproducible-path/bcftools-1.20/test/csq/ENSG00000173376/synon.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000318249.2/ENST00000318249.2.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000318249.2/ENST00000318249.2.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000318249.2/synonymous-start-lost.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000518414/ENST00000518414.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000518414/ENST00000518414.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000518414/incorrect-inframe-del.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000360372/ENST00000360372.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000360372/ENST00000360372.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000360372/mnp.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000593942/ENST00000593942.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000593942/ENST00000593942.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000593942/last-codon-deletion.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000448695/ENST00000448695.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000448695/ENST00000448695.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000448695/syn-and-splice-reg.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000227471/ENST00000227471.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000227471/ENST00000227471.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000227471/insert-splice-vs-frameshift.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000624631/ENST00000624631.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000624631/ENST00000624631.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000624631/ambiguous.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000295641/ENST00000295641.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000295641/ENST00000295641.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000295641/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -l -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000295641/ENST00000295641.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000295641/ENST00000295641.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000295641/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000294661/ENST00000294661.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000294661/ENST00000294661.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000294661/non-coding-boundary.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -l -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000294661/ENST00000294661.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000294661/ENST00000294661.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000294661/non-coding-boundary.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000303039/ENST00000303039.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000303039/ENST00000303039.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000303039/not-a-stop.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -l -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000303039/ENST00000303039.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000303039/ENST00000303039.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000303039/not-a-stop.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000318249/ENST00000318249.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000318249/ENST00000318249.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000318249/start-lost.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -l -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000318249/ENST00000318249.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000318249/ENST00000318249.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000318249/start-lost.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000368801/ENST00000368801.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000368801/ENST00000368801.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000368801/compound-lost.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000329454/ENST00000329454.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000329454/ENST00000329454.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000329454/boundary-deletion.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -l -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000329454/ENST00000329454.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000329454/ENST00000329454.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000329454/boundary-deletion.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000271583/ENST00000271583.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000271583/ENST00000271583.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000271583/splice-acceptor.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000301246/ENST00000301246.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000301246/ENST00000301246.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000301246/15bp-insert.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/EDUMMY0001/EDUMMY0001.fa -g /build/reproducible-path/bcftools-1.20/test/csq/EDUMMY0001/EDUMMY0001.gff /build/reproducible-path/bcftools-1.20/test/csq/EDUMMY0001/starts-with-1.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -l -f /build/reproducible-path/bcftools-1.20/test/csq/EDUMMY0001/EDUMMY0001.fa -g /build/reproducible-path/bcftools-1.20/test/csq/EDUMMY0001/EDUMMY0001.gff /build/reproducible-path/bcftools-1.20/test/csq/EDUMMY0001/starts-with-1.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_roh: /build/reproducible-path/bcftools-1.20/bcftools roh /build/reproducible-path/bcftools-1.20/test/roh.1.vcf.gz -Or -G30 --AF-dflt 0.4| grep -v ^# .. ok test_roh: /build/reproducible-path/bcftools-1.20/bcftools roh /build/reproducible-path/bcftools-1.20/test/roh.1.vcf.gz -Or -G30 --AF-file /build/reproducible-path/bcftools-1.20/test/roh.1.tab.gz| grep -v ^# .. ok test_roh: /build/reproducible-path/bcftools-1.20/bcftools roh /build/reproducible-path/bcftools-1.20/test/roh.1.vcf.gz -Or -G30 --AF-file /build/reproducible-path/bcftools-1.20/test/roh.1.tab.gz --ignore-homref| grep -v ^# .. ok test_roh: /build/reproducible-path/bcftools-1.20/bcftools roh /build/reproducible-path/bcftools-1.20/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245| grep -v ^# .. ok test_roh: /build/reproducible-path/bcftools-1.20/bcftools roh /build/reproducible-path/bcftools-1.20/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --ignore-homref| grep -v ^# .. ok test_roh: /build/reproducible-path/bcftools-1.20/bcftools roh /build/reproducible-path/bcftools-1.20/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --ignore-homref --include-noalt| grep -v ^# .. ok test_roh: /build/reproducible-path/bcftools-1.20/bcftools roh /build/reproducible-path/bcftools-1.20/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --include-noalt| grep -v ^# .. ok test_gtcheck: /build/reproducible-path/bcftools-1.20/bcftools gtcheck -e 0 /tmp/MWm45bogYL/gtcheck.1.vcf.gz -g /tmp/MWm45bogYL/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.20/bcftools gtcheck -e 0 -u GT,GT /tmp/MWm45bogYL/gtcheck.1.vcf.gz -g /tmp/MWm45bogYL/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.20/bcftools gtcheck -e 0 -u GT,PL /tmp/MWm45bogYL/gtcheck.1.vcf.gz -g /tmp/MWm45bogYL/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.20/bcftools gtcheck -e 0 -u PL,GT /tmp/MWm45bogYL/gtcheck.1.vcf.gz -g /tmp/MWm45bogYL/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.20/bcftools gtcheck -e 0 -u PL,PL /tmp/MWm45bogYL/gtcheck.1.vcf.gz -g /tmp/MWm45bogYL/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.20/bcftools gtcheck -e 0 -p s1,s1 /tmp/MWm45bogYL/gtcheck.1.vcf.gz -g /tmp/MWm45bogYL/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.20/bcftools gtcheck -e 0 /tmp/MWm45bogYL/gtcheck.2.vcf.gz -g /tmp/MWm45bogYL/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.20/bcftools gtcheck -e 0 /tmp/MWm45bogYL/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.20/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/MWm45bogYL/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.20/bcftools gtcheck -e 0 -P /build/reproducible-path/bcftools-1.20/test/gtcheck.3.pairs /tmp/MWm45bogYL/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.20/bcftools gtcheck -e 0 -u PL /tmp/MWm45bogYL/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.20/bcftools gtcheck -e 0 --n-matches 4 /tmp/MWm45bogYL/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO | sort .. ok test_gtcheck: /build/reproducible-path/bcftools-1.20/bcftools gtcheck -e 0 -s qry:E,D,C /tmp/MWm45bogYL/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.20/bcftools gtcheck -e 0 -s qry:E,D,C -u PL /tmp/MWm45bogYL/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.20/bcftools gtcheck -e 0 -s qry:B -s gt:D /tmp/MWm45bogYL/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.20/bcftools gtcheck -e 0 -s qry:B -s gt:D -u PL /tmp/MWm45bogYL/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.20/bcftools gtcheck -e 0 -s qry:B -s gt:D,C /tmp/MWm45bogYL/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.20/bcftools gtcheck -e 0 -p B,C,B,D /tmp/MWm45bogYL/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.20/bcftools gtcheck -e 0 -u GT,GT -H /tmp/MWm45bogYL/gtcheck.1.vcf.gz -g /tmp/MWm45bogYL/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.20/bcftools gtcheck -e 0 -u GT,PL -H /tmp/MWm45bogYL/gtcheck.1.vcf.gz -g /tmp/MWm45bogYL/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.20/bcftools gtcheck -e 0 -u PL,GT -H /tmp/MWm45bogYL/gtcheck.1.vcf.gz -g /tmp/MWm45bogYL/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.20/bcftools gtcheck -e 0 -u PL,PL -H /tmp/MWm45bogYL/gtcheck.1.vcf.gz -g /tmp/MWm45bogYL/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.20/bcftools gtcheck -e 0 -P /build/reproducible-path/bcftools-1.20/test/gtcheck.4.pairs --distinctive-sites 3 /tmp/MWm45bogYL/gtcheck.4.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.20/bcftools gtcheck -e 0 -P /build/reproducible-path/bcftools-1.20/test/gtcheck.4.pairs --distinctive-sites 3,1 /tmp/MWm45bogYL/gtcheck.4.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.20/bcftools gtcheck -u GT -e 30 /tmp/MWm45bogYL/gtcheck.1.vcf.gz -g /tmp/MWm45bogYL/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.20/bcftools gtcheck -u GT -e 30 -p s1,s1 /tmp/MWm45bogYL/gtcheck.1.vcf.gz -g /tmp/MWm45bogYL/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.20/bcftools gtcheck -u GT -e 300 /tmp/MWm45bogYL/gtcheck.1.vcf.gz -g /tmp/MWm45bogYL/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.20/bcftools gtcheck -u PL -e 30 /tmp/MWm45bogYL/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.20/bcftools gtcheck /tmp/MWm45bogYL/gtcheck.ntop.vcf.gz -g /tmp/MWm45bogYL/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.20/bcftools gtcheck --n-matches 2 /tmp/MWm45bogYL/gtcheck.ntop.vcf.gz -g /tmp/MWm45bogYL/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.20/bcftools gtcheck /tmp/MWm45bogYL/gtcheck.5.vcf.gz -g /tmp/MWm45bogYL/gtcheck.5.gts.vcf.gz | grep -v ^# | grep -v Time .. ok test_gtcheck: /build/reproducible-path/bcftools-1.20/bcftools gtcheck -p A,B,B,C /tmp/MWm45bogYL/gtcheck.6.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.20/bcftools gtcheck -t 11:33 -p A,D,A,E,D,E -u GT -e 10 /tmp/MWm45bogYL/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok Number of tests: total .. 1745 passed .. 1745 failed .. 0 make[2]: Leaving directory '/build/reproducible-path/bcftools-1.20' make[1]: Leaving directory '/build/reproducible-path/bcftools-1.20' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/bcftools/ make -j42 install DESTDIR=/build/reproducible-path/bcftools-1.20/debian/bcftools AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/bcftools-1.20' mkdir -p -m 755 /build/reproducible-path/bcftools-1.20/debian/bcftools/usr/bin /build/reproducible-path/bcftools-1.20/debian/bcftools/usr/share/man/man1 /build/reproducible-path/bcftools-1.20/debian/bcftools/usr/lib/x86_64-linux-gnu/bcftools install -p bcftools /build/reproducible-path/bcftools-1.20/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-1.20/debian/bcftools/usr/bin install -p -m 644 doc/bcftools.1 /build/reproducible-path/bcftools-1.20/debian/bcftools/usr/share/man/man1 install -p plugins/*.so /build/reproducible-path/bcftools-1.20/debian/bcftools/usr/lib/x86_64-linux-gnu/bcftools make[1]: Leaving directory '/build/reproducible-path/bcftools-1.20' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/bcftools-1.20' 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-1.20' dh_installdocs dh_installchangelogs debian/rules override_dh_installman make[1]: Entering directory '/build/reproducible-path/bcftools-1.20' dh_installman --language=C make[1]: Leaving directory '/build/reproducible-path/bcftools-1.20' dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dpkg-gencontrol: warning: package bcftools: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package bcftools: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'bcftools' in '../bcftools_1.20-2_amd64.deb'. dpkg-deb: building package 'bcftools-dbgsym' in '../bcftools-dbgsym_1.20-2_amd64.deb'. dpkg-genbuildinfo --build=binary -O../bcftools_1.20-2_amd64.buildinfo dpkg-genchanges --build=binary -O../bcftools_1.20-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/1897391/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/1897391/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1897391 and its subdirectories I: Current time: Tue Jan 20 22:33:41 +14 2026 I: pbuilder-time-stamp: 1768898021