Tue Dec 31 11:39:24 UTC 2024 I: starting to build bcftools/trixie/i386 on jenkins on '2024-12-31 11:39' Tue Dec 31 11:39:24 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_5/45547/console.log Tue Dec 31 11:39:24 UTC 2024 I: Downloading source for trixie/bcftools=1.20-2 --2024-12-31 11:39:24-- http://deb.debian.org/debian/pool/main/b/bcftools/bcftools_1.20-2.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2150 (2.1K) [text/prs.lines.tag] Saving to: ‘bcftools_1.20-2.dsc’ 0K .. 100% 234M=0s 2024-12-31 11:39:24 (234 MB/s) - ‘bcftools_1.20-2.dsc’ saved [2150/2150] Tue Dec 31 11:39:24 UTC 2024 I: bcftools_1.20-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: bcftools Binary: bcftools Architecture: any Version: 1.20-2 Maintainer: Debian Med Packaging Team Uploaders: Michael R. Crusoe , Étienne Mollier Homepage: https://samtools.github.io/bcftools/ Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/bcftools Vcs-Git: https://salsa.debian.org/med-team/bcftools.git Testsuite: autopkgtest Testsuite-Triggers: perl, tabix Build-Depends: debhelper-compat (= 13), zlib1g-dev, libbz2-dev, liblzma-dev, libhts-dev (>= 1.14), libgsl-dev, tabix , libio-pty-perl Package-List: bcftools deb science optional arch=any Checksums-Sha1: a3505e61b1e5d646a0e221abe2698b8c42e71993 3621678 bcftools_1.20.orig.tar.gz c925b1ca0077b9aec29892e70acf11022df0f057 7836 bcftools_1.20-2.debian.tar.xz Checksums-Sha256: 7f34abf9bc0ded947e1a1409b65eda4a00eb17e33b71ba92b883902709840fbc 3621678 bcftools_1.20.orig.tar.gz a1ff25568b1c641c9bf55dc5932efaa6e281c29efc6aff1c40cd2a2091585053 7836 bcftools_1.20-2.debian.tar.xz Files: c4b63687a028a08467f64f2a209c7dbd 3621678 bcftools_1.20.orig.tar.gz 321310607a83802b72a602acffcbb85e 7836 bcftools_1.20-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJGBAEBCgAwFiEEc0cUmcxg7Z7ugFlGxb1sjyKV1QIFAmZ6AxESHHBsZXNzeUBk ZWJpYW4ub3JnAAoJEMW9bI8ildUCBrUP/0k6uzsOVMPpplfMmD4pcPht+CJMphqj 6Pqnt18Ubp8RfOBn/bfXEj9kAiqLwgUZHUM05JdFlK7O+4Yv8kXli/aLJjRq6zg4 rswTDiIy8g19LZKeWcZQdaQBdoYRy4rq8QHRxruu3whFhqPKeQb8kS4ElW7Mv6oW h/Bnyu8O0Nh9aWCepAdNZMaVV/Kc/Ouq7fJ0KWOhB0Ijp9R4n/SJDkx7fsNOgNf+ bzAvaJS53wC+iSmw853NQhTNCTc0XvIO+uNsPrd3/t9BBjZBNVNIlngHgbUM4UjO SRn/MBJGiWL0tu6NOhDJB+FgCDlB6o3Ry3qSX+R2Jd1KdEZYYBx97+ldkSpG/qyu ST4nmmSEb1olNJomVERK2+bfEwHoAJqByqk7t5pImiTqqxE9rkuR3PcP+6kZTcC6 ifN82kEWHWQtkpsg469WUp+CoFi/7h8NXwhuJDQd3x63aIREqeJs9JqZvkyz0fyU bybYfMC0SVZYo5V6dO3/Zlu9LScZjFmX/hXdbrxCwDzL7OYeisE14S4n6nfZhk8R bAbZFL9zfviE8QkWuKCTGxMh+a/s6UBb3wa4CTatgRhtabKVM9HZXnk8KVVTO/5b IYB8aFd9Sa1Ui7kpxWktJyy2OzeNHtIQjUkJ1xc77pxNgQ5A5KiRT3+QpAGewanN KhKAWweySyYb =gI2+ -----END PGP SIGNATURE----- Tue Dec 31 11:39:24 UTC 2024 I: Checking whether the package is not for us Tue Dec 31 11:39:24 UTC 2024 I: Starting 1st build on remote node ionos12-i386.debian.net. Tue Dec 31 11:39:24 UTC 2024 I: Preparing to do remote build '1' on ionos12-i386.debian.net. Tue Dec 31 11:44:40 UTC 2024 I: Deleting $TMPDIR on ionos12-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Dec 30 23:39:33 -12 2024 I: pbuilder-time-stamp: 1735645173 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: using eatmydata during job 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/59287/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=11 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='10bf23f02250432bb0bacaa0b787d94c' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='59287' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.8k8lWpVN/pbuilderrc_SVYd --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.8k8lWpVN/b1 --logfile b1/build.log bcftools_1.20-2.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos12-i386 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/59287/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: i386 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), zlib1g-dev, libbz2-dev, liblzma-dev, libhts-dev (>= 1.14), 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 ... 19952 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 40.8 MB of archives. After unpacking 142 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main i386 libmagic1t64 i386 1:5.45-3+b1 [115 kB] Get: 4 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-3+b1 [43.2 kB] Get: 5 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.22.5-3 [201 kB] Get: 6 http://deb.debian.org/debian trixie/main i386 libuchardet0 i386 0.0.8-1+b2 [69.2 kB] Get: 7 http://deb.debian.org/debian trixie/main i386 groff-base i386 1.23.0-7 [1199 kB] Get: 8 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.40.2-12 [95.9 kB] Get: 9 http://deb.debian.org/debian trixie/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB] Get: 10 http://deb.debian.org/debian trixie/main i386 man-db i386 2.13.0-1 [1428 kB] Get: 11 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-4 [293 kB] Get: 12 http://deb.debian.org/debian trixie/main i386 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian trixie/main i386 autopoint all 0.22.5-3 [723 kB] Get: 16 http://deb.debian.org/debian trixie/main i386 libcom-err2 i386 1.47.2~rc1-2 [24.0 kB] Get: 17 http://deb.debian.org/debian trixie/main i386 comerr-dev i386 2.1-1.47.2~rc1-2 [55.9 kB] Get: 18 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.20 [89.7 kB] Get: 19 http://deb.debian.org/debian trixie/main i386 libtool all 2.4.7-8 [517 kB] Get: 20 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB] Get: 21 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 22 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 23 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 24 http://deb.debian.org/debian trixie/main i386 libelf1t64 i386 0.192-4 [195 kB] Get: 25 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1+b1 [116 kB] Get: 26 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-5+b1 [9583 kB] Get: 27 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.2+b1 [734 kB] Get: 28 http://deb.debian.org/debian trixie/main i386 gettext i386 0.22.5-3 [1631 kB] Get: 29 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 30 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian trixie/main i386 debhelper all 13.20 [915 kB] Get: 32 http://deb.debian.org/debian trixie/main i386 libkrb5support0 i386 1.21.3-3 [34.9 kB] Get: 33 http://deb.debian.org/debian trixie/main i386 libk5crypto3 i386 1.21.3-3 [83.6 kB] Get: 34 http://deb.debian.org/debian trixie/main i386 libkeyutils1 i386 1.6.3-4 [9600 B] Get: 35 http://deb.debian.org/debian trixie/main i386 libkrb5-3 i386 1.21.3-3 [350 kB] Get: 36 http://deb.debian.org/debian trixie/main i386 libgssapi-krb5-2 i386 1.21.3-3 [146 kB] Get: 37 http://deb.debian.org/debian trixie/main i386 libgssrpc4t64 i386 1.21.3-3 [63.1 kB] Get: 38 http://deb.debian.org/debian trixie/main i386 libkadm5clnt-mit12 i386 1.21.3-3 [43.2 kB] Get: 39 http://deb.debian.org/debian trixie/main i386 libkdb5-10t64 i386 1.21.3-3 [45.1 kB] Get: 40 http://deb.debian.org/debian trixie/main i386 libkadm5srv-mit12 i386 1.21.3-3 [57.0 kB] Get: 41 http://deb.debian.org/debian trixie/main i386 krb5-multidev i386 1.21.3-3 [126 kB] Get: 42 http://deb.debian.org/debian trixie/main i386 libbrotli1 i386 1.1.0-2+b6 [308 kB] Get: 43 http://deb.debian.org/debian trixie/main i386 libbrotli-dev i386 1.1.0-2+b6 [313 kB] Get: 44 http://deb.debian.org/debian trixie/main i386 libbz2-dev i386 1.0.8-6 [32.1 kB] Get: 45 http://deb.debian.org/debian trixie/main i386 libsasl2-modules-db i386 2.1.28+dfsg1-8 [20.6 kB] Get: 46 http://deb.debian.org/debian trixie/main i386 libsasl2-2 i386 2.1.28+dfsg1-8 [61.0 kB] Get: 47 http://deb.debian.org/debian trixie/main i386 libldap-2.5-0 i386 2.5.19+dfsg-1 [200 kB] Get: 48 http://deb.debian.org/debian trixie/main i386 libnghttp2-14 i386 1.64.0-1 [82.4 kB] Get: 49 http://deb.debian.org/debian trixie/main i386 libnghttp3-9 i386 1.6.0-2 [75.9 kB] Get: 50 http://deb.debian.org/debian trixie/main i386 libngtcp2-16 i386 1.9.1-1 [151 kB] Get: 51 http://deb.debian.org/debian trixie/main i386 libngtcp2-crypto-gnutls8 i386 1.9.1-1 [19.1 kB] Get: 52 http://deb.debian.org/debian trixie/main i386 libpsl5t64 i386 0.21.2-1.1+b1 [57.7 kB] Get: 53 http://deb.debian.org/debian trixie/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b5 [62.4 kB] Get: 54 http://deb.debian.org/debian trixie/main i386 libssh2-1t64 i386 1.11.1-1 [256 kB] Get: 55 http://deb.debian.org/debian trixie/main i386 libcurl3t64-gnutls i386 8.11.1-1 [404 kB] Get: 56 http://deb.debian.org/debian trixie/main i386 libevent-2.1-7t64 i386 2.1.12-stable-10+b1 [195 kB] Get: 57 http://deb.debian.org/debian trixie/main i386 libunbound8 i386 1.22.0-1 [632 kB] Get: 58 http://deb.debian.org/debian trixie/main i386 libgnutls-dane0t64 i386 3.8.8-2 [447 kB] Get: 59 http://deb.debian.org/debian trixie/main i386 libgnutls-openssl27t64 i386 3.8.8-2 [447 kB] Get: 60 http://deb.debian.org/debian trixie/main i386 libidn2-dev i386 2.3.7-2+b1 [126 kB] Get: 61 http://deb.debian.org/debian trixie/main i386 libp11-kit-dev i386 0.25.5-3 [208 kB] Get: 62 http://deb.debian.org/debian trixie/main i386 libtasn1-6-dev i386 4.19.0-3+b3 [102 kB] Get: 63 http://deb.debian.org/debian trixie/main i386 libgmpxx4ldbl i386 2:6.3.0+dfsg-3 [329 kB] Get: 64 http://deb.debian.org/debian trixie/main i386 libgmp-dev i386 2:6.3.0+dfsg-3 [661 kB] Get: 65 http://deb.debian.org/debian trixie/main i386 nettle-dev i386 3.10-1+b1 [1334 kB] Get: 66 http://deb.debian.org/debian trixie/main i386 libgnutls28-dev i386 3.8.8-2 [1453 kB] Get: 67 http://deb.debian.org/debian trixie/main i386 libkrb5-dev i386 1.21.3-3 [15.7 kB] Get: 68 http://deb.debian.org/debian trixie/main i386 libldap-dev i386 2.5.19+dfsg-1 [324 kB] Get: 69 http://deb.debian.org/debian trixie/main i386 libpkgconf3 i386 1.8.1-4 [38.4 kB] Get: 70 http://deb.debian.org/debian trixie/main i386 pkgconf-bin i386 1.8.1-4 [30.6 kB] Get: 71 http://deb.debian.org/debian trixie/main i386 pkgconf i386 1.8.1-4 [26.2 kB] Get: 72 http://deb.debian.org/debian trixie/main i386 libnghttp2-dev i386 1.64.0-1 [123 kB] Get: 73 http://deb.debian.org/debian trixie/main i386 libnghttp3-dev i386 1.6.0-2 [101 kB] Get: 74 http://deb.debian.org/debian trixie/main i386 libngtcp2-crypto-gnutls-dev i386 1.9.1-1 [24.0 kB] Get: 75 http://deb.debian.org/debian trixie/main i386 libngtcp2-dev i386 1.9.1-1 [202 kB] Get: 76 http://deb.debian.org/debian trixie/main i386 libpsl-dev i386 0.21.2-1.1+b1 [78.4 kB] Get: 77 http://deb.debian.org/debian trixie/main i386 zlib1g-dev i386 1:1.3.dfsg+really1.3.1-1+b1 [916 kB] Get: 78 http://deb.debian.org/debian trixie/main i386 librtmp-dev i386 2.4+20151223.gitfa8646d.1-2+b5 [72.3 kB] Get: 79 http://deb.debian.org/debian trixie/main i386 libssl-dev i386 3.3.2-2 [2790 kB] Get: 80 http://deb.debian.org/debian trixie/main i386 libssh2-1-dev i386 1.11.1-1 [407 kB] Get: 81 http://deb.debian.org/debian trixie/main i386 libzstd-dev i386 1.5.6+dfsg-1+b1 [355 kB] Get: 82 http://deb.debian.org/debian trixie/main i386 libcurl4-gnutls-dev i386 8.11.1-1 [535 kB] Get: 83 http://deb.debian.org/debian trixie/main i386 libdeflate0 i386 1.22-1 [48.1 kB] Get: 84 http://deb.debian.org/debian trixie/main i386 libdeflate-dev i386 1.22-1 [57.2 kB] Get: 85 http://deb.debian.org/debian trixie/main i386 libgslcblas0 i386 2.8+dfsg-5 [106 kB] Get: 86 http://deb.debian.org/debian trixie/main i386 libgsl28 i386 2.8+dfsg-5 [978 kB] Get: 87 http://deb.debian.org/debian trixie/main i386 libgsl-dev i386 2.8+dfsg-5 [1240 kB] Get: 88 http://deb.debian.org/debian trixie/main i386 libhtscodecs2 i386 1.6.1-1 [70.8 kB] Get: 89 http://deb.debian.org/debian trixie/main i386 libhts3t64 i386 1.20+ds-2 [500 kB] Get: 90 http://deb.debian.org/debian trixie/main i386 liblzma-dev i386 5.6.3-1+b1 [328 kB] Get: 91 http://deb.debian.org/debian trixie/main i386 libhts-dev i386 1.20+ds-2 [1693 kB] Get: 92 http://deb.debian.org/debian trixie/main i386 libio-pty-perl i386 1:1.20-1+b2 [35.8 kB] Get: 93 http://deb.debian.org/debian trixie/main i386 tabix i386 1.20+ds-2 [536 kB] Fetched 40.8 MB in 2s (26.9 MB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19952 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_i386.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:i386. 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Unpacking libpipeline1:i386 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.0-1_i386.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_i386.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.22.5-3_all.deb ... Unpacking autopoint (0.22.5-3) ... Selecting previously unselected package libcom-err2:i386. 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Preparing to unpack .../21-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../22-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:i386. Preparing to unpack .../23-libelf1t64_0.192-4_i386.deb ... Unpacking libelf1t64:i386 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../24-dwz_0.15-1+b1_i386.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:i386. Preparing to unpack .../25-libicu72_72.1-5+b1_i386.deb ... Unpacking libicu72:i386 (72.1-5+b1) ... Selecting previously unselected package libxml2:i386. Preparing to unpack .../26-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_i386.deb ... Unpacking libxml2:i386 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../27-gettext_0.22.5-3_i386.deb ... Unpacking gettext (0.22.5-3) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../28-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../29-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../30-debhelper_13.20_all.deb ... Unpacking debhelper (13.20) ... Selecting previously unselected package libkrb5support0:i386. Preparing to unpack .../31-libkrb5support0_1.21.3-3_i386.deb ... Unpacking libkrb5support0:i386 (1.21.3-3) ... Selecting previously unselected package libk5crypto3:i386. Preparing to unpack .../32-libk5crypto3_1.21.3-3_i386.deb ... Unpacking libk5crypto3:i386 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:i386. Preparing to unpack .../33-libkeyutils1_1.6.3-4_i386.deb ... Unpacking libkeyutils1:i386 (1.6.3-4) ... Selecting previously unselected package libkrb5-3:i386. Preparing to unpack .../34-libkrb5-3_1.21.3-3_i386.deb ... Unpacking libkrb5-3:i386 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:i386. Preparing to unpack .../35-libgssapi-krb5-2_1.21.3-3_i386.deb ... Unpacking libgssapi-krb5-2:i386 (1.21.3-3) ... Selecting previously unselected package libgssrpc4t64:i386. Preparing to unpack .../36-libgssrpc4t64_1.21.3-3_i386.deb ... Unpacking libgssrpc4t64:i386 (1.21.3-3) ... Selecting previously unselected package libkadm5clnt-mit12:i386. Preparing to unpack .../37-libkadm5clnt-mit12_1.21.3-3_i386.deb ... Unpacking libkadm5clnt-mit12:i386 (1.21.3-3) ... Selecting previously unselected package libkdb5-10t64:i386. Preparing to unpack .../38-libkdb5-10t64_1.21.3-3_i386.deb ... Unpacking libkdb5-10t64:i386 (1.21.3-3) ... Selecting previously unselected package libkadm5srv-mit12:i386. Preparing to unpack .../39-libkadm5srv-mit12_1.21.3-3_i386.deb ... Unpacking libkadm5srv-mit12:i386 (1.21.3-3) ... Selecting previously unselected package krb5-multidev:i386. Preparing to unpack .../40-krb5-multidev_1.21.3-3_i386.deb ... Unpacking krb5-multidev:i386 (1.21.3-3) ... Selecting previously unselected package libbrotli1:i386. Preparing to unpack .../41-libbrotli1_1.1.0-2+b6_i386.deb ... Unpacking libbrotli1:i386 (1.1.0-2+b6) ... Selecting previously unselected package libbrotli-dev:i386. Preparing to unpack .../42-libbrotli-dev_1.1.0-2+b6_i386.deb ... Unpacking libbrotli-dev:i386 (1.1.0-2+b6) ... Selecting previously unselected package libbz2-dev:i386. Preparing to unpack .../43-libbz2-dev_1.0.8-6_i386.deb ... Unpacking libbz2-dev:i386 (1.0.8-6) ... Selecting previously unselected package libsasl2-modules-db:i386. 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Selecting previously unselected package libngtcp2-crypto-gnutls8:i386. Preparing to unpack .../50-libngtcp2-crypto-gnutls8_1.9.1-1_i386.deb ... Unpacking libngtcp2-crypto-gnutls8:i386 (1.9.1-1) ... Selecting previously unselected package libpsl5t64:i386. Preparing to unpack .../51-libpsl5t64_0.21.2-1.1+b1_i386.deb ... Unpacking libpsl5t64:i386 (0.21.2-1.1+b1) ... Selecting previously unselected package librtmp1:i386. Preparing to unpack .../52-librtmp1_2.4+20151223.gitfa8646d.1-2+b5_i386.deb ... Unpacking librtmp1:i386 (2.4+20151223.gitfa8646d.1-2+b5) ... Selecting previously unselected package libssh2-1t64:i386. Preparing to unpack .../53-libssh2-1t64_1.11.1-1_i386.deb ... Unpacking libssh2-1t64:i386 (1.11.1-1) ... Selecting previously unselected package libcurl3t64-gnutls:i386. Preparing to unpack .../54-libcurl3t64-gnutls_8.11.1-1_i386.deb ... Unpacking libcurl3t64-gnutls:i386 (8.11.1-1) ... Selecting previously unselected package libevent-2.1-7t64:i386. 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Unpacking librtmp-dev:i386 (2.4+20151223.gitfa8646d.1-2+b5) ... Selecting previously unselected package libssl-dev:i386. Preparing to unpack .../78-libssl-dev_3.3.2-2_i386.deb ... Unpacking libssl-dev:i386 (3.3.2-2) ... Selecting previously unselected package libssh2-1-dev:i386. Preparing to unpack .../79-libssh2-1-dev_1.11.1-1_i386.deb ... Unpacking libssh2-1-dev:i386 (1.11.1-1) ... Selecting previously unselected package libzstd-dev:i386. Preparing to unpack .../80-libzstd-dev_1.5.6+dfsg-1+b1_i386.deb ... Unpacking libzstd-dev:i386 (1.5.6+dfsg-1+b1) ... Selecting previously unselected package libcurl4-gnutls-dev:i386. Preparing to unpack .../81-libcurl4-gnutls-dev_8.11.1-1_i386.deb ... Unpacking libcurl4-gnutls-dev:i386 (8.11.1-1) ... Selecting previously unselected package libdeflate0:i386. Preparing to unpack .../82-libdeflate0_1.22-1_i386.deb ... Unpacking libdeflate0:i386 (1.22-1) ... Selecting previously unselected package libdeflate-dev:i386. 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/bcftools-1.20/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../bcftools_1.20-2_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 i386 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 -j11 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 -f test/*.unsorted.hex test/*.unsorted.tsv rm -rf plugins/*.dSYM rm -f gmon.out *.o *.a *~ bcftools version.h rm -rf *.dSYM test/*.dSYM rm -f config.cache config.h config.log config.mk config.status rm -rf autom4te.cache rm -f TAGS make[2]: Leaving directory '/build/reproducible-path/bcftools-1.20' 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/i386-linux-gnu/bcftools ./configure --build=i686-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/i386-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system --enable-gsl --with-cblas=gslcblas --with-bcf-plugin-dir=/usr/lib/i386-linux-gnu/bcftools checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether 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... -D_FILE_OFFSET_BITS=64 checking for htslib/sam.h... yes checking for hts_version in -lhts... yes checking shared library type... plain .so checking for library containing dlopen... 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 -j11 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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time 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-Werror=format-security -mfpmath=sse -msse2 -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o smpl_ilist.o smpl_ilist.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o csq.o csq.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfbuf.o vcfbuf.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mpileup.o mpileup.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sample.o bam_sample.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfsort.o vcfsort.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cols.o cols.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o extsort.o extsort.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DPLUGINPATH='"/usr/lib/i386-linux-gnu/bcftools"' -c -o vcfplugin.o vcfplugin.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-rbuf.o test/test-rbuf.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-regidx.o test/test-regidx.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/GTisec.so version.c plugins/GTisec.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/GTsubset.so version.c plugins/GTsubset.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/ad-bias.so convert.c version.c plugins/ad-bias.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/add-variantkey.so version.c plugins/add-variantkey.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/af-dist.so bin.c version.c plugins/af-dist.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/allele-length.so version.c plugins/allele-length.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/check-ploidy.so version.c plugins/check-ploidy.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/check-sparsity.so version.c plugins/check-sparsity.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/color-chrs.so HMM.c version.c plugins/color-chrs.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/contrast.so version.c plugins/contrast.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/counts.so version.c plugins/counts.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/dosage.so version.c plugins/dosage.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fill-AN-AC.so version.c plugins/fill-AN-AC.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fill-from-fasta.so filter.c version.c plugins/fill-from-fasta.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fill-tags.so version.c plugins/fill-tags.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fixploidy.so ploidy.c regidx.c version.c plugins/fixploidy.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fixref.so version.c plugins/fixref.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/frameshifts.so version.c plugins/frameshifts.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/guess-ploidy.so version.c plugins/guess-ploidy.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/gvcfz.so version.c plugins/gvcfz.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/impute-info.so version.c plugins/impute-info.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/indel-stats.so version.c plugins/indel-stats.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/isecGT.so smpl_ilist.c version.c plugins/isecGT.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/missing2ref.so version.c plugins/missing2ref.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/parental-origin.so version.c plugins/parental-origin.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/prune.so version.c plugins/prune.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/remove-overlaps.so version.c plugins/remove-overlaps.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/scatter.so version.c plugins/scatter.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/setGT.so version.c plugins/setGT.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/smpl-stats.so version.c plugins/smpl-stats.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/split-vep.so version.c plugins/split-vep.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/split.so version.c plugins/split.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/tag2tag.so version.c plugins/tag2tag.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/trio-stats.so version.c plugins/trio-stats.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/trio-switch-rate.so version.c plugins/trio-switch-rate.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/variantkey-hex.so version.c plugins/variantkey-hex.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o main.o main.c gcc -Wl,-z,relro -o test/test-rbuf test/test-rbuf.o -lz 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/M6VbetYrDG/merge.a.vcf.gz 2:3199812-3199812 .. ok test_tabix: /build/reproducible-path/bcftools-1.20/bcftools view -H /tmp/M6VbetYrDG/merge.a.bcf 2:3199812-3199812 .. ok test_tabix: tabix /tmp/M6VbetYrDG/merge.a.vcf.gz 1:3000151-3000151 .. ok test_tabix: /build/reproducible-path/bcftools-1.20/bcftools view -H /tmp/M6VbetYrDG/merge.a.bcf 1:3000151-3000151 .. ok test_index: /build/reproducible-path/bcftools-1.20/bcftools view -H /tmp/M6VbetYrDG/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /build/reproducible-path/bcftools-1.20/bcftools view -H /tmp/M6VbetYrDG/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/reproducible-path/bcftools-1.20/bcftools view -H /tmp/M6VbetYrDG/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/reproducible-path/bcftools-1.20/bcftools view -H /tmp/M6VbetYrDG/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /build/reproducible-path/bcftools-1.20/bcftools view -H /tmp/M6VbetYrDG/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/reproducible-path/bcftools-1.20/bcftools view -H /tmp/M6VbetYrDG/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /build/reproducible-path/bcftools-1.20/bcftools view -H /tmp/M6VbetYrDG/large_chrom_csi_limit.bcf chr20 .. ok test_index: /build/reproducible-path/bcftools-1.20/bcftools view -H /tmp/M6VbetYrDG/large_chrom_csi_limit.bcf chr20 .. ok test_index: /build/reproducible-path/bcftools-1.20/bcftools view -H /tmp/M6VbetYrDG/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /build/reproducible-path/bcftools-1.20/bcftools view -H /tmp/M6VbetYrDG/large_chrom_csi_limit.bcf chr20 .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.20/bcftools index -s /tmp/M6VbetYrDG/idx.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.20/bcftools index -s /tmp/M6VbetYrDG/idx.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.20/bcftools index -s /tmp/M6VbetYrDG/idx.bcf .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.20/bcftools index -n /tmp/M6VbetYrDG/idx.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.20/bcftools index -n /tmp/M6VbetYrDG/idx.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.20/bcftools index -n /tmp/M6VbetYrDG/idx.vcf.gz.csi .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.20/bcftools index -n /tmp/M6VbetYrDG/idx.bcf .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.20/bcftools index -n /tmp/M6VbetYrDG/idx.bcf.csi .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.20/bcftools index -s /tmp/M6VbetYrDG/empty.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.20/bcftools index -s /tmp/M6VbetYrDG/empty.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.20/bcftools index -s /tmp/M6VbetYrDG/empty.bcf .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.20/bcftools index -n /tmp/M6VbetYrDG/empty.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.20/bcftools index -n /tmp/M6VbetYrDG/empty.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.20/bcftools index -n /tmp/M6VbetYrDG/empty.vcf.gz.csi .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.20/bcftools index -n /tmp/M6VbetYrDG/empty.bcf .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.20/bcftools index -n /tmp/M6VbetYrDG/empty.bcf.csi .. ok test_vcf_check: /build/reproducible-path/bcftools-1.20/bcftools stats -s - /tmp/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/check.1.chk /tmp/M6VbetYrDG/check.2.chk /tmp/M6VbetYrDG/check.3.chk /tmp/M6VbetYrDG/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/M6VbetYrDG/stats.a.vcf.gz /tmp/M6VbetYrDG/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/reproducible-path/bcftools-1.20/bcftools stats -s B /tmp/M6VbetYrDG/stats.a.vcf.gz /tmp/M6VbetYrDG/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/reproducible-path/bcftools-1.20/bcftools stats -s - /tmp/M6VbetYrDG/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/M6VbetYrDG/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/reproducible-path/bcftools-1.20/bcftools stats -s - /tmp/M6VbetYrDG/stats.vaf.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.20/bcftools isec -n =2 /tmp/M6VbetYrDG/isec.a.vcf.gz /tmp/M6VbetYrDG/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.20/bcftools isec -Ob -n =2 /tmp/M6VbetYrDG/isec.a.vcf.gz /tmp/M6VbetYrDG/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.20/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/M6VbetYrDG/isec.a.vcf.gz /tmp/M6VbetYrDG/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.20/bcftools isec -Ob -n =2 -i"STRLEN(REF)==2" /tmp/M6VbetYrDG/isec.a.vcf.gz /tmp/M6VbetYrDG/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.20/bcftools isec -n =2 -c both /tmp/M6VbetYrDG/isec.a.vcf.gz /tmp/M6VbetYrDG/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.20/bcftools isec -Ob -n =2 -c both /tmp/M6VbetYrDG/isec.a.vcf.gz /tmp/M6VbetYrDG/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.20/bcftools isec -n =2 -c any /tmp/M6VbetYrDG/isec.a.vcf.gz /tmp/M6VbetYrDG/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.20/bcftools isec -Ob -n =2 -c any /tmp/M6VbetYrDG/isec.a.vcf.gz /tmp/M6VbetYrDG/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.20/bcftools isec -C -c any /tmp/M6VbetYrDG/isec.a.vcf.gz /tmp/M6VbetYrDG/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.20/bcftools isec -Ob -C -c any /tmp/M6VbetYrDG/isec.a.vcf.gz /tmp/M6VbetYrDG/isec.b.vcf.gz .. ok test_vcf_isec2: /build/reproducible-path/bcftools-1.20/bcftools isec --no-version -T /tmp/M6VbetYrDG/isec.tab.gz /tmp/M6VbetYrDG/isec.a.vcf.gz .. ok test_vcf_isec2: /build/reproducible-path/bcftools-1.20/bcftools isec -Ob -T /tmp/M6VbetYrDG/isec.tab.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/isec-miss.1.1.vcf.gz /tmp/M6VbetYrDG/isec-miss.1.2.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/isec-miss.1.1.vcf.gz /tmp/M6VbetYrDG/isec-miss.1.2.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/isec-miss.1.1.vcf.gz /tmp/M6VbetYrDG/isec-miss.1.2.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/isec-miss.1.1.vcf.gz /tmp/M6VbetYrDG/isec-miss.1.2.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/isec-miss.2.1.vcf.gz /tmp/M6VbetYrDG/isec-miss.2.2.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/isec-miss.2.1.vcf.gz /tmp/M6VbetYrDG/isec-miss.2.2.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/isec-miss.2.1.vcf.gz /tmp/M6VbetYrDG/isec-miss.2.2.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/isec-miss.2.1.vcf.gz /tmp/M6VbetYrDG/isec-miss.2.2.vcf.gz /tmp/M6VbetYrDG/isec-miss.2.3.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -i AF:join /tmp/M6VbetYrDG/merge.join.a.vcf.gz /tmp/M6VbetYrDG/merge.join.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob -i AF:join /tmp/M6VbetYrDG/merge.join.a.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.join.a.bcf /tmp/M6VbetYrDG/merge.join.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob -i AF:join /tmp/M6VbetYrDG/merge.join.a.bcf /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.LPL.a.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-single /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.LPL.a.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-single /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.LPL.a.vcf.gz /tmp/M6VbetYrDG/merge.LPL.b.vcf.gz /tmp/M6VbetYrDG/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples /tmp/M6VbetYrDG/merge.LPL.a.vcf.gz /tmp/M6VbetYrDG/merge.LPL.b.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.LPL.a.bcf /tmp/M6VbetYrDG/merge.LPL.b.bcf /tmp/M6VbetYrDG/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples /tmp/M6VbetYrDG/merge.LPL.a.bcf /tmp/M6VbetYrDG/merge.LPL.b.bcf /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.LPL.a.vcf.gz /tmp/M6VbetYrDG/merge.LPL.b.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.LPL.a.vcf.gz /tmp/M6VbetYrDG/merge.LPL.b.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.LPL.a.bcf /tmp/M6VbetYrDG/merge.LPL.b.bcf /tmp/M6VbetYrDG/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -L 1 /tmp/M6VbetYrDG/merge.LPL.a.bcf /tmp/M6VbetYrDG/merge.LPL.b.bcf /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.LPL.a.vcf.gz /tmp/M6VbetYrDG/merge.LPL.b.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.LPL.a.vcf.gz /tmp/M6VbetYrDG/merge.LPL.b.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.LPL.a.bcf /tmp/M6VbetYrDG/merge.LPL.b.bcf /tmp/M6VbetYrDG/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -L 2 /tmp/M6VbetYrDG/merge.LPL.a.bcf /tmp/M6VbetYrDG/merge.LPL.b.bcf /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.LPL.a.vcf.gz /tmp/M6VbetYrDG/merge.LPL.b.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.LPL.a.vcf.gz /tmp/M6VbetYrDG/merge.LPL.b.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.LPL.a.bcf /tmp/M6VbetYrDG/merge.LPL.b.bcf /tmp/M6VbetYrDG/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -L 3 /tmp/M6VbetYrDG/merge.LPL.a.bcf /tmp/M6VbetYrDG/merge.LPL.b.bcf /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.LPL.a.vcf.gz /tmp/M6VbetYrDG/merge.LPL.b.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.LPL.a.vcf.gz /tmp/M6VbetYrDG/merge.LPL.b.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.LPL.a.bcf /tmp/M6VbetYrDG/merge.LPL.b.bcf /tmp/M6VbetYrDG/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -L 4 /tmp/M6VbetYrDG/merge.LPL.a.bcf /tmp/M6VbetYrDG/merge.LPL.b.bcf /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.LPL.a.vcf.gz /tmp/M6VbetYrDG/merge.LPL.b.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.LPL.a.vcf.gz /tmp/M6VbetYrDG/merge.LPL.b.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.LPL.a.bcf /tmp/M6VbetYrDG/merge.LPL.b.bcf /tmp/M6VbetYrDG/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -L 5 /tmp/M6VbetYrDG/merge.LPL.a.bcf /tmp/M6VbetYrDG/merge.LPL.b.bcf /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.a.vcf.gz /tmp/M6VbetYrDG/merge.b.vcf.gz /tmp/M6VbetYrDG/merge.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples /tmp/M6VbetYrDG/merge.a.vcf.gz /tmp/M6VbetYrDG/merge.b.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.a.bcf /tmp/M6VbetYrDG/merge.b.bcf /tmp/M6VbetYrDG/merge.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples /tmp/M6VbetYrDG/merge.a.bcf /tmp/M6VbetYrDG/merge.b.bcf /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.a.vcf.gz /tmp/M6VbetYrDG/merge.b.vcf.gz /tmp/M6VbetYrDG/merge.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -Fx /tmp/M6VbetYrDG/merge.a.vcf.gz /tmp/M6VbetYrDG/merge.b.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.a.bcf /tmp/M6VbetYrDG/merge.b.bcf /tmp/M6VbetYrDG/merge.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -Fx /tmp/M6VbetYrDG/merge.a.bcf /tmp/M6VbetYrDG/merge.b.bcf /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.a.vcf.gz /tmp/M6VbetYrDG/merge.b.vcf.gz /tmp/M6VbetYrDG/merge.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -0 /tmp/M6VbetYrDG/merge.a.vcf.gz /tmp/M6VbetYrDG/merge.b.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.a.bcf /tmp/M6VbetYrDG/merge.b.bcf /tmp/M6VbetYrDG/merge.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -0 /tmp/M6VbetYrDG/merge.a.bcf /tmp/M6VbetYrDG/merge.b.bcf /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.2.a.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.2.a.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.2.a.bcf /tmp/M6VbetYrDG/merge.2.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -m none /tmp/M6VbetYrDG/merge.2.a.bcf /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.2.a.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.2.a.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.2.a.bcf /tmp/M6VbetYrDG/merge.2.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -m both /tmp/M6VbetYrDG/merge.2.a.bcf /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.2.a.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.2.a.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.2.a.bcf /tmp/M6VbetYrDG/merge.2.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -m all /tmp/M6VbetYrDG/merge.2.a.bcf /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.3.a.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.3.a.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.3.a.bcf /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.3.a.bcf /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.4.a.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.4.a.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.4.a.bcf /tmp/M6VbetYrDG/merge.4.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -m id /tmp/M6VbetYrDG/merge.4.a.bcf /tmp/M6VbetYrDG/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/M6VbetYrDG/gvcf.merge.1.vcf.gz /tmp/M6VbetYrDG/gvcf.merge.2.vcf.gz /tmp/M6VbetYrDG/gvcf.merge.3.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/M6VbetYrDG/gvcf.merge.1.vcf.gz /tmp/M6VbetYrDG/gvcf.merge.2.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/gvcf.merge.1.bcf /tmp/M6VbetYrDG/gvcf.merge.2.bcf /tmp/M6VbetYrDG/gvcf.merge.3.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/M6VbetYrDG/gvcf.merge.1.bcf /tmp/M6VbetYrDG/gvcf.merge.2.bcf /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.gvcf.2.a.vcf.gz /tmp/M6VbetYrDG/merge.gvcf.2.b.vcf.gz /tmp/M6VbetYrDG/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/M6VbetYrDG/merge.gvcf.2.a.vcf.gz /tmp/M6VbetYrDG/merge.gvcf.2.b.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.gvcf.2.a.vcf.gz /tmp/M6VbetYrDG/merge.gvcf.2.b.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.gvcf.2.a.vcf.gz /tmp/M6VbetYrDG/merge.gvcf.2.b.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.gvcf.2.a.vcf.gz /tmp/M6VbetYrDG/merge.gvcf.2.b.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.gvcf.2.a.vcf.gz /tmp/M6VbetYrDG/merge.gvcf.2.b.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.gvcf.3.a.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.gvcf.3.a.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.gvcf.4.a.vcf.gz /tmp/M6VbetYrDG/merge.gvcf.4.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/M6VbetYrDG/merge.gvcf.4.a.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.gvcf.4.a.bcf /tmp/M6VbetYrDG/merge.gvcf.4.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/M6VbetYrDG/merge.gvcf.4.a.bcf /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.5.a.vcf.gz /tmp/M6VbetYrDG/merge.5.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob /tmp/M6VbetYrDG/merge.5.a.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.5.a.bcf /tmp/M6VbetYrDG/merge.5.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob /tmp/M6VbetYrDG/merge.5.a.bcf /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.6.a.vcf.gz /tmp/M6VbetYrDG/merge.6.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob /tmp/M6VbetYrDG/merge.6.a.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.6.a.bcf /tmp/M6VbetYrDG/merge.6.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob /tmp/M6VbetYrDG/merge.6.a.bcf /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.gvcf.7.a.vcf.gz /tmp/M6VbetYrDG/merge.gvcf.7.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/M6VbetYrDG/merge.gvcf.7.a.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.gvcf.7.a.bcf /tmp/M6VbetYrDG/merge.gvcf.7.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/M6VbetYrDG/merge.gvcf.7.a.bcf /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.gvcf.8.a.vcf.gz /tmp/M6VbetYrDG/merge.gvcf.8.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/M6VbetYrDG/merge.gvcf.8.a.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.gvcf.8.a.bcf /tmp/M6VbetYrDG/merge.gvcf.8.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/M6VbetYrDG/merge.gvcf.8.a.bcf /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.7.a.vcf.gz /tmp/M6VbetYrDG/merge.7.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples /tmp/M6VbetYrDG/merge.7.a.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.7.a.bcf /tmp/M6VbetYrDG/merge.7.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples /tmp/M6VbetYrDG/merge.7.a.bcf /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.gvcf.9a.vcf.gz /tmp/M6VbetYrDG/merge.gvcf.9b.vcf.gz /tmp/M6VbetYrDG/merge.gvcf.9c.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.gvcf.9a.vcf.gz /tmp/M6VbetYrDG/merge.gvcf.9b.vcf.gz /tmp/M6VbetYrDG/merge.gvcf.9c.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.gvcf.9a.bcf /tmp/M6VbetYrDG/merge.gvcf.9b.bcf /tmp/M6VbetYrDG/merge.gvcf.9c.bcf /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.gvcf.9a.bcf /tmp/M6VbetYrDG/merge.gvcf.9b.bcf /tmp/M6VbetYrDG/merge.gvcf.9c.bcf /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.gvcf.9a.vcf.gz /tmp/M6VbetYrDG/merge.gvcf.9b.vcf.gz /tmp/M6VbetYrDG/merge.gvcf.9c.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.gvcf.9a.vcf.gz /tmp/M6VbetYrDG/merge.gvcf.9b.vcf.gz /tmp/M6VbetYrDG/merge.gvcf.9c.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.gvcf.9a.bcf /tmp/M6VbetYrDG/merge.gvcf.9b.bcf /tmp/M6VbetYrDG/merge.gvcf.9c.bcf /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.gvcf.9a.bcf /tmp/M6VbetYrDG/merge.gvcf.9b.bcf /tmp/M6VbetYrDG/merge.gvcf.9c.bcf /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.gvcf.9a.vcf.gz /tmp/M6VbetYrDG/merge.gvcf.9b.vcf.gz /tmp/M6VbetYrDG/merge.gvcf.9c.vcf.gz /tmp/M6VbetYrDG/merge.gvcf.9d.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.gvcf.9a.vcf.gz /tmp/M6VbetYrDG/merge.gvcf.9b.vcf.gz /tmp/M6VbetYrDG/merge.gvcf.9c.vcf.gz /tmp/M6VbetYrDG/merge.gvcf.9d.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.gvcf.9a.bcf /tmp/M6VbetYrDG/merge.gvcf.9b.bcf /tmp/M6VbetYrDG/merge.gvcf.9c.bcf /tmp/M6VbetYrDG/merge.gvcf.9d.bcf /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.gvcf.9a.bcf /tmp/M6VbetYrDG/merge.gvcf.9b.bcf /tmp/M6VbetYrDG/merge.gvcf.9c.bcf /tmp/M6VbetYrDG/merge.gvcf.9d.bcf /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.gvcf.9a.vcf.gz /tmp/M6VbetYrDG/merge.gvcf.9b.vcf.gz /tmp/M6VbetYrDG/merge.gvcf.9c.vcf.gz /tmp/M6VbetYrDG/merge.gvcf.9d.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.gvcf.9a.vcf.gz /tmp/M6VbetYrDG/merge.gvcf.9b.vcf.gz /tmp/M6VbetYrDG/merge.gvcf.9c.vcf.gz /tmp/M6VbetYrDG/merge.gvcf.9d.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.gvcf.9a.bcf /tmp/M6VbetYrDG/merge.gvcf.9b.bcf /tmp/M6VbetYrDG/merge.gvcf.9c.bcf /tmp/M6VbetYrDG/merge.gvcf.9d.bcf /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.gvcf.9a.bcf /tmp/M6VbetYrDG/merge.gvcf.9b.bcf /tmp/M6VbetYrDG/merge.gvcf.9c.bcf /tmp/M6VbetYrDG/merge.gvcf.9d.bcf /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.gvcf.10.a.vcf.gz /tmp/M6VbetYrDG/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob /tmp/M6VbetYrDG/merge.gvcf.10.a.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.gvcf.10.a.bcf /tmp/M6VbetYrDG/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob /tmp/M6VbetYrDG/merge.gvcf.10.a.bcf /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.gvcf.10.a.vcf.gz /tmp/M6VbetYrDG/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob -m none /tmp/M6VbetYrDG/merge.gvcf.10.a.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.gvcf.10.a.bcf /tmp/M6VbetYrDG/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob -m none /tmp/M6VbetYrDG/merge.gvcf.10.a.bcf /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.gvcf.10.a.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.gvcf.10.a.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.gvcf.10.a.bcf /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.gvcf.10.a.bcf /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.gvcf.10.a.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.gvcf.10.a.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.gvcf.10.a.bcf /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.gvcf.10.a.bcf /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.noidx.a.vcf.gz /tmp/M6VbetYrDG/merge.noidx.b.vcf.gz /tmp/M6VbetYrDG/merge.noidx.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob /tmp/M6VbetYrDG/merge.noidx.a.vcf.gz /tmp/M6VbetYrDG/merge.noidx.b.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.noidx.a.bcf /tmp/M6VbetYrDG/merge.noidx.b.bcf /tmp/M6VbetYrDG/merge.noidx.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob /tmp/M6VbetYrDG/merge.noidx.a.bcf /tmp/M6VbetYrDG/merge.noidx.b.bcf /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.noidx.a.bcf /tmp/M6VbetYrDG/merge.noidx.b.bcf /tmp/M6VbetYrDG/merge.noidx.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --no-index /tmp/M6VbetYrDG/merge.noidx.a.bcf /tmp/M6VbetYrDG/merge.noidx.b.bcf /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.8.a.vcf.gz /tmp/M6VbetYrDG/merge.8.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob /tmp/M6VbetYrDG/merge.8.a.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.8.a.bcf /tmp/M6VbetYrDG/merge.8.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob /tmp/M6VbetYrDG/merge.8.a.bcf /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.8.a.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.8.a.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.8.a.bcf /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.8.a.bcf /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.9.a.vcf.gz /tmp/M6VbetYrDG/merge.9.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob /tmp/M6VbetYrDG/merge.9.a.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.9.a.bcf /tmp/M6VbetYrDG/merge.9.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob /tmp/M6VbetYrDG/merge.9.a.bcf /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.9.a.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.9.a.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.9.a.bcf /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.9.a.bcf /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.10.a.vcf.gz /tmp/M6VbetYrDG/merge.10.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob -m none /tmp/M6VbetYrDG/merge.10.a.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.10.a.bcf /tmp/M6VbetYrDG/merge.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob -m none /tmp/M6VbetYrDG/merge.10.a.bcf /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.10.a.vcf.gz /tmp/M6VbetYrDG/merge.10.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob -m both /tmp/M6VbetYrDG/merge.10.a.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.10.a.bcf /tmp/M6VbetYrDG/merge.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob -m both /tmp/M6VbetYrDG/merge.10.a.bcf /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.10.a.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.10.a.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.10.a.bcf /tmp/M6VbetYrDG/merge.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob -m snp-ins-del /tmp/M6VbetYrDG/merge.10.a.bcf /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.mrules.1.a.vcf.gz /tmp/M6VbetYrDG/merge.mrules.1.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/M6VbetYrDG/merge.mrules.1.a.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.mrules.1.a.bcf /tmp/M6VbetYrDG/merge.mrules.1.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/M6VbetYrDG/merge.mrules.1.a.bcf /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.mrules.1.a.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.mrules.1.a.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.mrules.1.a.bcf /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.mrules.1.a.bcf /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.gvcf.5.a.vcf.gz /tmp/M6VbetYrDG/merge.gvcf.5.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/M6VbetYrDG/merge.gvcf.5.a.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.gvcf.5.a.bcf /tmp/M6VbetYrDG/merge.gvcf.5.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/M6VbetYrDG/merge.gvcf.5.a.bcf /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.gvcf.5.a.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.gvcf.5.a.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.gvcf.5.a.bcf /tmp/M6VbetYrDG/merge.gvcf.5.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - --merge none /tmp/M6VbetYrDG/merge.gvcf.5.a.bcf /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.gvcf.11.a.vcf.gz /tmp/M6VbetYrDG/merge.gvcf.11.b.vcf.gz /tmp/M6VbetYrDG/merge.gvcf.11.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/M6VbetYrDG/merge.gvcf.11.a.vcf.gz /tmp/M6VbetYrDG/merge.gvcf.11.b.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/merge.gvcf.11.a.bcf /tmp/M6VbetYrDG/merge.gvcf.11.b.bcf /tmp/M6VbetYrDG/merge.gvcf.11.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/M6VbetYrDG/merge.gvcf.11.a.bcf /tmp/M6VbetYrDG/merge.gvcf.11.b.bcf /tmp/M6VbetYrDG/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/M6VbetYrDG/query.string.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.string.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.string.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.string.2.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.string.2.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.variantkey.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/view.vectors.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.2.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.filter-type.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.filter-type.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.filter-type.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.filter-type.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.filter-type.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/filter-missing-floats.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/filter-missing-floats.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.filter.2.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.filter.3.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.filter.3.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.filter.3.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.filter.4.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/view.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.negative.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.negative.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.negative.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.negative.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.filter.6.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.filter.8.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.filter.8.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.filter.9.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.filter.9.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.filter.13.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.filter.10.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.filter.10.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.filter.id.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.filter.id.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/filter.10.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/filter.13.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.filter-or.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/query.filter-or.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/norm.split.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m- /tmp/M6VbetYrDG/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/M6VbetYrDG/norm.split.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m- /tmp/M6VbetYrDG/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/M6VbetYrDG/norm.split.3.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m- --force /tmp/M6VbetYrDG/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/M6VbetYrDG/norm.split.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m- /tmp/M6VbetYrDG/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/M6VbetYrDG/norm.split.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m- --keep-sum AD /tmp/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/norm.merge.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m+ /tmp/M6VbetYrDG/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/M6VbetYrDG/norm.merge.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m+ /tmp/M6VbetYrDG/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/M6VbetYrDG/norm.merge.3.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m+ /tmp/M6VbetYrDG/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/M6VbetYrDG/norm.merge.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m+ -s /tmp/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -d snps /tmp/M6VbetYrDG/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/M6VbetYrDG/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -d indels /tmp/M6VbetYrDG/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/M6VbetYrDG/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -d both /tmp/M6VbetYrDG/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/M6VbetYrDG/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -d all /tmp/M6VbetYrDG/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/M6VbetYrDG/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -d none /tmp/M6VbetYrDG/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/M6VbetYrDG/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -d exact /tmp/M6VbetYrDG/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/M6VbetYrDG/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -d none /tmp/M6VbetYrDG/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/M6VbetYrDG/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -d exact /tmp/M6VbetYrDG/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/M6VbetYrDG/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -d indels /tmp/M6VbetYrDG/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/M6VbetYrDG/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -d any /tmp/M6VbetYrDG/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/M6VbetYrDG/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -d both /tmp/M6VbetYrDG/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/M6VbetYrDG/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -d snps /tmp/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/atomize.split.3.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version --atomize --atom-overlaps . /tmp/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/norm.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m +both /tmp/M6VbetYrDG/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/M6VbetYrDG/norm.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m +any /tmp/M6VbetYrDG/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/M6VbetYrDG/norm.5.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m - --multi-overlaps 0 /tmp/M6VbetYrDG/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/M6VbetYrDG/norm.5.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m - --multi-overlaps . /tmp/M6VbetYrDG/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/M6VbetYrDG/norm.m-any.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m -any /tmp/M6VbetYrDG/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/M6VbetYrDG/norm.phased-split.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m -any /tmp/M6VbetYrDG/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/M6VbetYrDG/norm.phased-join.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m +any /tmp/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/norm.string-tags.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m -any /tmp/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/norm.merge.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m +any /tmp/M6VbetYrDG/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/M6VbetYrDG/norm.merge.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m +both /tmp/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/merge.gvcf.2.a.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -HAA /tmp/M6VbetYrDG/merge.gvcf.2.a.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version /tmp/M6VbetYrDG/weird-chr-names.vcf.gz -r 1 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/weird-chr-names.vcf.gz -r 1:1-2 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/weird-chr-names.vcf.gz -r 1:1,1:2 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/weird-chr-names.vcf.gz -r 1:1-1 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/weird-chr-names.vcf.gz -r {1:1} .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/weird-chr-names.vcf.gz -r {1:1}:1-2 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/weird-chr-names.vcf.gz -r {1:1}:1-1 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/weird-chr-names.vcf.gz -r {1:1-1} .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/M6VbetYrDG/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/M6VbetYrDG/view.vcf.gz -r20,Y .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -f PASS -Xks NA00003 /tmp/M6VbetYrDG/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/M6VbetYrDG/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -xs NA00003 /tmp/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -p /tmp/M6VbetYrDG/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/M6VbetYrDG/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -P /tmp/M6VbetYrDG/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/M6VbetYrDG/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/M6VbetYrDG/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/M6VbetYrDG/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -GVsnps /tmp/M6VbetYrDG/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -GVsnps /tmp/M6VbetYrDG/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/M6VbetYrDG/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/M6VbetYrDG/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/M6VbetYrDG/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -s ^NA00003 /tmp/M6VbetYrDG/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/M6VbetYrDG/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -G /tmp/M6VbetYrDG/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/M6VbetYrDG/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -a /tmp/M6VbetYrDG/many.alleles.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -a /tmp/M6VbetYrDG/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/M6VbetYrDG/view.vectors.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -asA /tmp/M6VbetYrDG/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/M6VbetYrDG/view.vectors.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -asB /tmp/M6VbetYrDG/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/M6VbetYrDG/view.vectors.2.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -asA /tmp/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/view.filter.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -H -i'TXT0="text"' /tmp/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/filter.2.vcf.gz 1:3062917-3157410 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -i 'POS>=3062917' /tmp/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/idx.4.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -Ht 2 /tmp/M6VbetYrDG/view-t.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -Ht 3 /tmp/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -H -c6:nonmajor /tmp/M6VbetYrDG/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -H -q0.3:major /tmp/M6VbetYrDG/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/view.filter.annovar.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -H -a /tmp/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/mpileup.2.vcf.gz .. ok test_vcf_head2: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/mpileup.2.vcf.gz .. ok test_vcf_head2: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/mpileup.2.vcf.gz .. ok test_vcf_head2: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.20/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/M6VbetYrDG/regions.tab.gz /tmp/M6VbetYrDG/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/regions.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/M6VbetYrDG/regions.tab.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.20/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/M6VbetYrDG/regions.tab.gz /tmp/M6VbetYrDG/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.20/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/M6VbetYrDG/regions.bed /tmp/M6VbetYrDG/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/regions.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/M6VbetYrDG/regions.bed .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.20/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/M6VbetYrDG/regions.bed /tmp/M6VbetYrDG/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.20/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/M6VbetYrDG/regions.bed.gz /tmp/M6VbetYrDG/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/regions.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/M6VbetYrDG/regions.bed.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.20/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/M6VbetYrDG/regions.bed.gz /tmp/M6VbetYrDG/regions.vcf.gz .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/M6VbetYrDG/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/M6VbetYrDG/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/M6VbetYrDG/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/M6VbetYrDG/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/M6VbetYrDG/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/M6VbetYrDG/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/M6VbetYrDG/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/M6VbetYrDG/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/M6VbetYrDG/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/M6VbetYrDG/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/M6VbetYrDG/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/M6VbetYrDG/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/M6VbetYrDG/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/M6VbetYrDG/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/M6VbetYrDG/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/M6VbetYrDG/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/M6VbetYrDG/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/M6VbetYrDG/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/M6VbetYrDG/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/M6VbetYrDG/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/M6VbetYrDG/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/M6VbetYrDG/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/M6VbetYrDG/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/M6VbetYrDG/annots4.vcf.gz -c +INFO /tmp/M6VbetYrDG/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/M6VbetYrDG/annots4.vcf.gz -c +INFO /tmp/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/M6VbetYrDG/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/M6VbetYrDG/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/M6VbetYrDG/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/M6VbetYrDG/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/M6VbetYrDG/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/M6VbetYrDG/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/M6VbetYrDG/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/M6VbetYrDG/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/M6VbetYrDG/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/M6VbetYrDG/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/M6VbetYrDG/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/M6VbetYrDG/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/M6VbetYrDG/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/M6VbetYrDG/annots11.vcf.gz -c FMT /tmp/M6VbetYrDG/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/M6VbetYrDG/annots11.vcf.gz -c FMT /tmp/M6VbetYrDG/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/M6VbetYrDG/annots2.vcf.gz -c FMT/newGT:=GT /tmp/M6VbetYrDG/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/M6VbetYrDG/annots2.vcf.gz -c FMT/newGT:=GT /tmp/M6VbetYrDG/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/M6VbetYrDG/annots12.vcf.gz -c FMT/GT:=newGT /tmp/M6VbetYrDG/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/M6VbetYrDG/annots12.vcf.gz -c FMT/GT:=newGT /tmp/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/M6VbetYrDG/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/M6VbetYrDG/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/M6VbetYrDG/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/M6VbetYrDG/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/M6VbetYrDG/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/M6VbetYrDG/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/M6VbetYrDG/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/M6VbetYrDG/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/M6VbetYrDG/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/M6VbetYrDG/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/M6VbetYrDG/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/M6VbetYrDG/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER /tmp/M6VbetYrDG/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/M6VbetYrDG/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER /tmp/M6VbetYrDG/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/M6VbetYrDG/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER /tmp/M6VbetYrDG/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/M6VbetYrDG/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER /tmp/M6VbetYrDG/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/M6VbetYrDG/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER,FILTER /tmp/M6VbetYrDG/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/M6VbetYrDG/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER,FILTER /tmp/M6VbetYrDG/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/M6VbetYrDG/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=./FILTER /tmp/M6VbetYrDG/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/M6VbetYrDG/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=./FILTER /tmp/M6VbetYrDG/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/M6VbetYrDG/annotate20.src.vcf.gz -c FMT/GT /tmp/M6VbetYrDG/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/M6VbetYrDG/annotate20.src.vcf.gz -c FMT/GT /tmp/M6VbetYrDG/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/M6VbetYrDG/annotate20.src.vcf.gz -c +FMT/GT /tmp/M6VbetYrDG/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/M6VbetYrDG/annotate20.src.vcf.gz -c +FMT/GT /tmp/M6VbetYrDG/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/M6VbetYrDG/annotate20.src.vcf.gz -c -FMT/GT /tmp/M6VbetYrDG/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/M6VbetYrDG/annotate20.src.vcf.gz -c -FMT/GT /tmp/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/M6VbetYrDG/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/M6VbetYrDG/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/annotate24.src.vcf.gz -c XX /tmp/M6VbetYrDG/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/M6VbetYrDG/annotate24.src.vcf.gz -c XX /tmp/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/annots.id.vcf.gz -c ALT /tmp/M6VbetYrDG/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/M6VbetYrDG/annots.id.vcf.gz -c ALT /tmp/M6VbetYrDG/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/M6VbetYrDG/annots.id.vcf.gz -c +ALT /tmp/M6VbetYrDG/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/M6VbetYrDG/annots.id.vcf.gz -c +ALT /tmp/M6VbetYrDG/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/M6VbetYrDG/annots.id.2.vcf.gz --pair-logic some -c +ID /tmp/M6VbetYrDG/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/M6VbetYrDG/annots.id.2.vcf.gz --pair-logic some -c +ID /tmp/M6VbetYrDG/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/M6VbetYrDG/annots.id.2.vcf.gz --pair-logic any -c +ID /tmp/M6VbetYrDG/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/M6VbetYrDG/annots.id.2.vcf.gz --pair-logic any -c +ID /tmp/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/concat.1.a.vcf.gz /tmp/M6VbetYrDG/concat.1.b.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat -Ob /tmp/M6VbetYrDG/concat.1.a.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/concat.1.a.bcf /tmp/M6VbetYrDG/concat.1.b.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat -Ob /tmp/M6VbetYrDG/concat.1.a.bcf /tmp/M6VbetYrDG/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/M6VbetYrDG/concat.2.a.vcf.gz /tmp/M6VbetYrDG/concat.2.b.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat -Ob -a /tmp/M6VbetYrDG/concat.2.a.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/concat.2.a.bcf /tmp/M6VbetYrDG/concat.2.b.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat -Ob -a /tmp/M6VbetYrDG/concat.2.a.bcf /tmp/M6VbetYrDG/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/M6VbetYrDG/concat.2.a.vcf.gz /tmp/M6VbetYrDG/concat.2.b.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat -Ob -aD /tmp/M6VbetYrDG/concat.2.a.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/concat.2.a.bcf /tmp/M6VbetYrDG/concat.2.b.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat -Ob -aD /tmp/M6VbetYrDG/concat.2.a.bcf /tmp/M6VbetYrDG/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/M6VbetYrDG/concat.3.a.vcf.gz /tmp/M6VbetYrDG/concat.3.b.vcf.gz /tmp/M6VbetYrDG/concat.3.0.vcf.gz /tmp/M6VbetYrDG/concat.3.c.vcf.gz /tmp/M6VbetYrDG/concat.3.d.vcf.gz /tmp/M6VbetYrDG/concat.3.e.vcf.gz /tmp/M6VbetYrDG/concat.3.f.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat -Ob -l --ligate-warn /tmp/M6VbetYrDG/concat.3.a.vcf.gz /tmp/M6VbetYrDG/concat.3.b.vcf.gz /tmp/M6VbetYrDG/concat.3.0.vcf.gz /tmp/M6VbetYrDG/concat.3.c.vcf.gz /tmp/M6VbetYrDG/concat.3.d.vcf.gz /tmp/M6VbetYrDG/concat.3.e.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/concat.3.a.bcf /tmp/M6VbetYrDG/concat.3.b.bcf /tmp/M6VbetYrDG/concat.3.0.bcf /tmp/M6VbetYrDG/concat.3.c.bcf /tmp/M6VbetYrDG/concat.3.d.bcf /tmp/M6VbetYrDG/concat.3.e.bcf /tmp/M6VbetYrDG/concat.3.f.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat -Ob -l --ligate-warn /tmp/M6VbetYrDG/concat.3.a.bcf /tmp/M6VbetYrDG/concat.3.b.bcf /tmp/M6VbetYrDG/concat.3.0.bcf /tmp/M6VbetYrDG/concat.3.c.bcf /tmp/M6VbetYrDG/concat.3.d.bcf /tmp/M6VbetYrDG/concat.3.e.bcf /tmp/M6VbetYrDG/concat.3.f.bcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ Random seed for test_naive_concat: 1774241957 .. ok test_naive_concat: /build/reproducible-path/bcftools-1.20/bcftools concat --naive-force /tmp/M6VbetYrDG/naive_concat.0.bcf /tmp/M6VbetYrDG/naive_concat.1.bcf /tmp/M6VbetYrDG/naive_concat.2.bcf /tmp/M6VbetYrDG/naive_concat.3.bcf /tmp/M6VbetYrDG/naive_concat.4.bcf /tmp/M6VbetYrDG/naive_concat.5.bcf /tmp/M6VbetYrDG/naive_concat.6.bcf /tmp/M6VbetYrDG/naive_concat.7.bcf /tmp/M6VbetYrDG/naive_concat.8.bcf /tmp/M6VbetYrDG/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/M6VbetYrDG/naive_concat.0.vcf.gz /tmp/M6VbetYrDG/naive_concat.1.vcf.gz /tmp/M6VbetYrDG/naive_concat.2.vcf.gz /tmp/M6VbetYrDG/naive_concat.3.vcf.gz /tmp/M6VbetYrDG/naive_concat.4.vcf.gz /tmp/M6VbetYrDG/naive_concat.5.vcf.gz /tmp/M6VbetYrDG/naive_concat.6.vcf.gz /tmp/M6VbetYrDG/naive_concat.7.vcf.gz /tmp/M6VbetYrDG/naive_concat.8.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/concat.4.a.vcf.gz /tmp/M6VbetYrDG/concat.4.b.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat -Ob -l /tmp/M6VbetYrDG/concat.4.a.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/concat.4.a.bcf /tmp/M6VbetYrDG/concat.4.b.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat -Ob -l /tmp/M6VbetYrDG/concat.4.a.bcf /tmp/M6VbetYrDG/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/M6VbetYrDG/concat.5.a.vcf.gz /tmp/M6VbetYrDG/concat.5.b.vcf.gz /tmp/M6VbetYrDG/concat.5.c.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat -Ob -l --ligate-warn /tmp/M6VbetYrDG/concat.5.a.vcf.gz /tmp/M6VbetYrDG/concat.5.b.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/concat.5.a.bcf /tmp/M6VbetYrDG/concat.5.b.bcf /tmp/M6VbetYrDG/concat.5.c.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat -Ob -l --ligate-warn /tmp/M6VbetYrDG/concat.5.a.bcf /tmp/M6VbetYrDG/concat.5.b.bcf /tmp/M6VbetYrDG/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/M6VbetYrDG/concat.5.a.bcf /tmp/M6VbetYrDG/concat.5.b.bcf /tmp/M6VbetYrDG/concat.5.c.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat -Ob -l --ligate-force /tmp/M6VbetYrDG/concat.5.a.bcf /tmp/M6VbetYrDG/concat.5.b.bcf /tmp/M6VbetYrDG/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/M6VbetYrDG/concat.5.a.vcf.gz /tmp/M6VbetYrDG/concat.5.b.vcf.gz /tmp/M6VbetYrDG/concat.5.c.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat -Ob -G -a -D /tmp/M6VbetYrDG/concat.5.a.vcf.gz /tmp/M6VbetYrDG/concat.5.b.vcf.gz /tmp/M6VbetYrDG/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/M6VbetYrDG/concat.5.a.bcf /tmp/M6VbetYrDG/concat.5.b.bcf /tmp/M6VbetYrDG/concat.5.c.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat -Ob -G -a -D /tmp/M6VbetYrDG/concat.5.a.bcf /tmp/M6VbetYrDG/concat.5.b.bcf /tmp/M6VbetYrDG/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/M6VbetYrDG/reheader.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/M6VbetYrDG/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/M6VbetYrDG/reheader.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/M6VbetYrDG/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/M6VbetYrDG/reheader.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/M6VbetYrDG/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/M6VbetYrDG/reheader.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/M6VbetYrDG/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/M6VbetYrDG/reheader.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/M6VbetYrDG/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/M6VbetYrDG/reheader.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/M6VbetYrDG/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/M6VbetYrDG/reheader.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/M6VbetYrDG/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/M6VbetYrDG/reheader.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/M6VbetYrDG/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/M6VbetYrDG/reheader.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/M6VbetYrDG/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/M6VbetYrDG/reheader.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/M6VbetYrDG/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/M6VbetYrDG/empty.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/M6VbetYrDG/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/M6VbetYrDG/empty.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/rename.map -Ov /tmp/M6VbetYrDG/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/M6VbetYrDG/rename.map -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/convert.hap-missing.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/convert.gvcf.vcf.gz .. ok test_vcf_convert_gvcf: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/consensus.1.chain.new >/dev/null; cat /tmp/M6VbetYrDG/consensus.1.chain.new .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/consensus.2.chain.new >/dev/null; cat /tmp/M6VbetYrDG/consensus.2.chain.new .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/consensus.3.chain.new >/dev/null; cat /tmp/M6VbetYrDG/consensus.3.chain.new .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/consensus.fa -H 1 -c /tmp/M6VbetYrDG/consensus.4.chain.new >/dev/null; cat /tmp/M6VbetYrDG/consensus.4.chain.new .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/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/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/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/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: /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/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/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: 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: /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/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/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/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/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/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/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/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: /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/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: 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/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/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/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/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/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_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/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/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-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-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-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/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-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/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/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-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/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/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/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/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/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/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/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/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/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: /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/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/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/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: /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/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/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/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/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/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/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: /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/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/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/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: 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: 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/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 -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: 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: /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: 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!=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: 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: /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/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/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/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: 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: /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/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: 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/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/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_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/M6VbetYrDG/gtcheck.1.vcf.gz -g /tmp/M6VbetYrDG/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/M6VbetYrDG/gtcheck.1.vcf.gz -g /tmp/M6VbetYrDG/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/M6VbetYrDG/gtcheck.1.vcf.gz -g /tmp/M6VbetYrDG/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/M6VbetYrDG/gtcheck.1.vcf.gz -g /tmp/M6VbetYrDG/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/M6VbetYrDG/gtcheck.1.vcf.gz -g /tmp/M6VbetYrDG/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/M6VbetYrDG/gtcheck.1.vcf.gz -g /tmp/M6VbetYrDG/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.20/bcftools gtcheck -e 0 /tmp/M6VbetYrDG/gtcheck.2.vcf.gz -g /tmp/M6VbetYrDG/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.20/bcftools gtcheck -e 0 /tmp/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/gtcheck.1.vcf.gz -g /tmp/M6VbetYrDG/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/M6VbetYrDG/gtcheck.1.vcf.gz -g /tmp/M6VbetYrDG/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/M6VbetYrDG/gtcheck.1.vcf.gz -g /tmp/M6VbetYrDG/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/M6VbetYrDG/gtcheck.1.vcf.gz -g /tmp/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/gtcheck.1.vcf.gz -g /tmp/M6VbetYrDG/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/M6VbetYrDG/gtcheck.1.vcf.gz -g /tmp/M6VbetYrDG/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/M6VbetYrDG/gtcheck.1.vcf.gz -g /tmp/M6VbetYrDG/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/M6VbetYrDG/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.20/bcftools gtcheck /tmp/M6VbetYrDG/gtcheck.ntop.vcf.gz -g /tmp/M6VbetYrDG/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/M6VbetYrDG/gtcheck.ntop.vcf.gz -g /tmp/M6VbetYrDG/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.20/bcftools gtcheck /tmp/M6VbetYrDG/gtcheck.5.vcf.gz -g /tmp/M6VbetYrDG/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/M6VbetYrDG/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/M6VbetYrDG/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 -j11 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/i386-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/i386-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-dbgsym' in '../bcftools-dbgsym_1.20-2_i386.deb'. dpkg-deb: building package 'bcftools' in '../bcftools_1.20-2_i386.deb'. dpkg-genbuildinfo --build=binary -O../bcftools_1.20-2_i386.buildinfo dpkg-genchanges --build=binary -O../bcftools_1.20-2_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/59287 and its subdirectories I: Current time: Mon Dec 30 23:44:39 -12 2024 I: pbuilder-time-stamp: 1735645479 Tue Dec 31 11:44:41 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos6-i386.debian.net. Tue Dec 31 11:44:41 UTC 2024 I: Preparing to do remote build '2' on ionos6-i386.debian.net. Tue Dec 31 11:46:23 UTC 2024 I: Deleting $TMPDIR on ionos6-i386.debian.net. Tue Dec 31 11:46:24 UTC 2024 I: bcftools_1.20-2_i386.changes: Format: 1.8 Date: Tue, 25 Jun 2024 08:34:02 +0900 Source: bcftools Binary: bcftools bcftools-dbgsym Architecture: i386 Version: 1.20-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Charles Plessy Description: bcftools - genomic variant calling and manipulation of VCF/BCF files Changes: bcftools (1.20-2) unstable; urgency=medium . * Team upload * Only recommend python-matplotlib and python3-gffutils Checksums-Sha1: ee862299ba5d0f9cf5af92121f737135c9b48860 2000636 bcftools-dbgsym_1.20-2_i386.deb 4e1fdf8bde6d0959825b2e8162b15368a7bdd4db 7136 bcftools_1.20-2_i386.buildinfo 37c482b46ddaf642c1ed45fbfa0b02858d8b1c52 812608 bcftools_1.20-2_i386.deb Checksums-Sha256: 20bf377e892b71d59366c3dad58ab346c1c55fdfeb9416e40cf13fa66234fb86 2000636 bcftools-dbgsym_1.20-2_i386.deb a92a7f5fe8c544effa3e56795b6aa644ba6cb5c8deb356b4d3c6686cba57b533 7136 bcftools_1.20-2_i386.buildinfo 99114656c7dea221ca4dd116c6b3a8825b1fc8cc0fb2d435c99967c9956e2d32 812608 bcftools_1.20-2_i386.deb Files: fa518d05f516f11235de4e624329e6b7 2000636 debug optional bcftools-dbgsym_1.20-2_i386.deb 11448cbb3c1ccce3df0717969084d302 7136 science optional bcftools_1.20-2_i386.buildinfo 9f248b3fe925577391fe563cbfe33c8e 812608 science optional bcftools_1.20-2_i386.deb Tue Dec 31 11:46:25 UTC 2024 I: diffoscope 284 will be used to compare the two builds: Running as unit: rb-diffoscope-i386_5-45547.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.8k8lWpVN/bcftools_1.20-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.8k8lWpVN/bcftools_1.20-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.8k8lWpVN/bcftools_1.20-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.8k8lWpVN/b1/bcftools_1.20-2_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.8k8lWpVN/b2/bcftools_1.20-2_i386.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.356s) 0.356s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.038s) 0.038s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 659ms CPU time consumed: 659ms Tue Dec 31 11:46:26 UTC 2024 I: diffoscope 284 found no differences in the changes files, and a .buildinfo file also exists. Tue Dec 31 11:46:26 UTC 2024 I: bcftools from trixie built successfully and reproducibly on i386. Tue Dec 31 11:46:27 UTC 2024 I: Submitting .buildinfo files to external archives: Tue Dec 31 11:46:27 UTC 2024 I: Submitting 8.0K b1/bcftools_1.20-2_i386.buildinfo.asc Tue Dec 31 11:46:28 UTC 2024 I: Submitting 8.0K b2/bcftools_1.20-2_i386.buildinfo.asc Tue Dec 31 11:46:28 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Dec 31 11:46:28 UTC 2024 I: Done submitting .buildinfo files. Tue Dec 31 11:46:28 UTC 2024 I: Removing signed bcftools_1.20-2_i386.buildinfo.asc files: removed './b1/bcftools_1.20-2_i386.buildinfo.asc' removed './b2/bcftools_1.20-2_i386.buildinfo.asc'