Wed May 8 16:32:55 UTC 2024 I: starting to build bcftools/unstable/amd64 on jenkins on '2024-05-08 16:32' Wed May 8 16:32:55 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_4/20125/console.log Wed May 8 16:32:55 UTC 2024 I: Downloading source for unstable/bcftools=1.20-1 --2024-05-08 16:32:55-- http://deb.debian.org/debian/pool/main/b/bcftools/bcftools_1.20-1.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_1.20-1.dsc’ 0K .. 100% 277M=0s 2024-05-08 16:32:55 (277 MB/s) - ‘bcftools_1.20-1.dsc’ saved [2150/2150] Wed May 8 16:32:55 UTC 2024 I: bcftools_1.20-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: bcftools Binary: bcftools Architecture: any Version: 1.20-1 Maintainer: Debian Med Packaging Team Uploaders: Michael R. Crusoe , Étienne Mollier Homepage: https://samtools.github.io/bcftools/ Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/bcftools Vcs-Git: https://salsa.debian.org/med-team/bcftools.git Testsuite: autopkgtest Testsuite-Triggers: perl, tabix Build-Depends: debhelper-compat (= 13), zlib1g-dev, libbz2-dev, liblzma-dev, libhts-dev (>= 1.14), libgsl-dev, tabix , libio-pty-perl Package-List: bcftools deb science optional arch=any Checksums-Sha1: a3505e61b1e5d646a0e221abe2698b8c42e71993 3621678 bcftools_1.20.orig.tar.gz 57185d0f9f03b467c1aed4d25e2b266bfa38f6bc 7796 bcftools_1.20-1.debian.tar.xz Checksums-Sha256: 7f34abf9bc0ded947e1a1409b65eda4a00eb17e33b71ba92b883902709840fbc 3621678 bcftools_1.20.orig.tar.gz 22aa10ee052576b64dfd4cca6dde6a50fea352d222bb1518b453430448690274 7796 bcftools_1.20-1.debian.tar.xz Files: c4b63687a028a08467f64f2a209c7dbd 3621678 bcftools_1.20.orig.tar.gz 1beeb07d6acfb6e408c0d2633e68ee34 7796 bcftools_1.20-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmYhS7gRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtEcshAAhLnC16iB7XfYQO/uE5MkE2qysdE96f/j VBTMYvpnb/v98GlHkADUS8/WVrjkXQvXwBbPxY7lkNMXJPqQeQJebmUnICR1ZZei NncsZiY+OsFNlHBBqFCPvROanl8rpgr8AOY+r/WHVddGPJAvXpWBcKnUMbDJbP0f Pk4bfpEIxZxuEnNBblPKaeyFLpBSILsJB1ZCncCHbIYC+U8q0891Qr083NrEhqxH PPyMZcyEBlEx22jhXPbzCLK91M3ufdHoZjAS2Ljg/jS5ltB4mGNgtlApbwk7elHG q/lrLwmIjZi6WOhKUyU+BUv2vGbtyUlRW2a569qjsuDvm/tHgH3fIX5VrFvtUdoO YFSVy+LALdP5HLcvM8ikPoRcwnoZ3KSWZUIMYp4u2PqtOKDRrG+7d1Y6bCDJnDAj zP1ZWxncs9KJHZJmHkzrSUu3eNABZUgIwnEaB6t00v2SfVSUoGGel+89HFkslsTU zkHeYmw7MJNGWSR88242RHw5hK/OR9kFbUjuMwGOTFxxNZXPYF8yhRQxiovd1ieX xT6zideAdKltuBYJR5y3Z9iehxMAqKuNL8fZ6KkAcm+AYAY5sR2Ssw9VL4SS0EQV 3XTwxAQSfTA5tbmlyJDcKQeV0wLBuCHeA+t2xidlgc0KuYK/x6V82/126oo06VjL nuhuEvh7QMY= =YmBq -----END PGP SIGNATURE----- Wed May 8 16:32:55 UTC 2024 I: Checking whether the package is not for us Wed May 8 16:32:55 UTC 2024 I: Starting 1st build on remote node ionos15-amd64.debian.net. Wed May 8 16:32:55 UTC 2024 I: Preparing to do remote build '1' on ionos15-amd64.debian.net. Wed May 8 16:34:41 UTC 2024 I: Deleting $TMPDIR on ionos15-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Jun 10 10:55:59 -12 2025 I: pbuilder-time-stamp: 1749596159 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [bcftools_1.20-1.dsc] I: copying [./bcftools_1.20.orig.tar.gz] I: copying [./bcftools_1.20-1.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Apr 18 16:35:04 2024 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./bcftools_1.20-1.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_1.20-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying tests-pluginpath.patch dpkg-source: info: applying skip_new_test_failing_on_32bit.patch dpkg-source: info: applying 2to3.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/4183933/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='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='045de15899664a6bb664f5971a58a475' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='4183933' 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.ktNlkeuK/pbuilderrc_JQf6 --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ktNlkeuK/b1 --logfile b1/build.log bcftools_1.20-1.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos15-amd64 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Jun 10 14:05 /bin -> usr/bin I: user script /srv/workspace/pbuilder/4183933/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), zlib1g-dev, libbz2-dev, liblzma-dev, libhts-dev (>= 1.14), libgsl-dev, tabix, libio-pty-perl dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19699 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} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbrotli1{a} libbz2-dev{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libgsl-dev{a} libgsl27{a} libgslcblas0{a} libgssapi-krb5-2{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libio-pty-perl{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.5-0{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libpipeline1{a} libpsl5t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} tabix{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc ca-certificates curl krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix wget 0 packages upgraded, 59 newly installed, 0 to remove and 0 not upgraded. Need to get 27.9 MB of archives. After unpacking 105 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-4 [1180 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40-8 [92.8 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.21-14 [496 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-7 [517 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 23 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.15.3 [901 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libbz2-dev amd64 1.0.8-5.1 [31.3 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.1~rc2-1 [22.6 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.20.1-6+b1 [33.3 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.20.1-6+b1 [79.8 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get: 37 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.20.1-6+b1 [333 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.20.1-6+b1 [135 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-6 [19.5 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-6 [56.9 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 libldap-2.5-0 amd64 2.5.17+dfsg-1 [186 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.61.0-1+b1 [75.6 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.0-4.1+b2 [215 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.7.1-5 [433 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls-dev amd64 8.7.1-5 [538 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.20-1 [46.0 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libdeflate-dev amd64 1.20-1 [54.5 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libgslcblas0 amd64 2.7.1+dfsg-6+b1 [107 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 libgsl27 amd64 2.7.1+dfsg-6+b1 [934 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 libgsl-dev amd64 2.7.1+dfsg-6+b1 [1146 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.0-1+b1 [93.0 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.19+ds-1.1+b1 [448 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.6.1+really5.4.5-1 [293 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg-3.1 [918 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 libhts-dev amd64 1.19+ds-1.1+b1 [1667 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 libio-pty-perl amd64 1:1.20-1+b1 [34.4 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 tabix amd64 1.19+ds-1.1+b1 [476 kB] Fetched 27.9 MB in 0s (107 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19699 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3_amd64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-14+b1_amd64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-4_amd64.deb ... Unpacking groff-base (1.23.0-4) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40-8_amd64.deb ... Unpacking bsdextrautils (2.40-8) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.7-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.12.1-1_amd64.deb ... Unpacking man-db (2.12.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_amd64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... 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_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.15.3_all.deb ... Unpacking libdebhelper-perl (13.15.3) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../19-libsub-override-perl_0.10-1_all.deb ... Unpacking libsub-override-perl (0.10-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../22-libelf1t64_0.191-1+b1_amd64.deb ... Unpacking libelf1t64:amd64 (0.191-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../24-libicu72_72.1-4+b1_amd64.deb ... Unpacking libicu72:amd64 (72.1-4+b1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../25-libxml2_2.9.14+dfsg-1.3+b3_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.3+b3) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.21-14+b1_amd64.deb ... Unpacking gettext (0.21-14+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-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 .../28-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../29-debhelper_13.15.3_all.deb ... Unpacking debhelper (13.15.3) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../30-libbrotli1_1.1.0-2+b3_amd64.deb ... Unpacking libbrotli1:amd64 (1.1.0-2+b3) ... Selecting previously unselected package libbz2-dev:amd64. Preparing to unpack .../31-libbz2-dev_1.0.8-5.1_amd64.deb ... Unpacking libbz2-dev:amd64 (1.0.8-5.1) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../32-libcom-err2_1.47.1~rc2-1_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.1~rc2-1) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../33-libkrb5support0_1.20.1-6+b1_amd64.deb ... Unpacking libkrb5support0:amd64 (1.20.1-6+b1) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../34-libk5crypto3_1.20.1-6+b1_amd64.deb ... Unpacking libk5crypto3:amd64 (1.20.1-6+b1) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../35-libkeyutils1_1.6.3-3_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-3) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../36-libkrb5-3_1.20.1-6+b1_amd64.deb ... Unpacking libkrb5-3:amd64 (1.20.1-6+b1) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../37-libgssapi-krb5-2_1.20.1-6+b1_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.20.1-6+b1) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../38-libsasl2-modules-db_2.1.28+dfsg1-6_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg1-6) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../39-libsasl2-2_2.1.28+dfsg1-6_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg1-6) ... Selecting previously unselected package libldap-2.5-0:amd64. Preparing to unpack .../40-libldap-2.5-0_2.5.17+dfsg-1_amd64.deb ... Unpacking libldap-2.5-0:amd64 (2.5.17+dfsg-1) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../41-libnghttp2-14_1.61.0-1+b1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.61.0-1+b1) ... Selecting previously unselected package libpsl5t64:amd64. Preparing to unpack .../42-libpsl5t64_0.21.2-1.1_amd64.deb ... Unpacking libpsl5t64:amd64 (0.21.2-1.1) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../43-librtmp1_2.4+20151223.gitfa8646d.1-2+b4_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Selecting previously unselected package libssh2-1t64:amd64. Preparing to unpack .../44-libssh2-1t64_1.11.0-4.1+b2_amd64.deb ... Unpacking libssh2-1t64:amd64 (1.11.0-4.1+b2) ... Selecting previously unselected package libcurl3t64-gnutls:amd64. Preparing to unpack .../45-libcurl3t64-gnutls_8.7.1-5_amd64.deb ... Unpacking libcurl3t64-gnutls:amd64 (8.7.1-5) ... Selecting previously unselected package libcurl4-gnutls-dev:amd64. Preparing to unpack .../46-libcurl4-gnutls-dev_8.7.1-5_amd64.deb ... Unpacking libcurl4-gnutls-dev:amd64 (8.7.1-5) ... Selecting previously unselected package libdeflate0:amd64. Preparing to unpack .../47-libdeflate0_1.20-1_amd64.deb ... Unpacking libdeflate0:amd64 (1.20-1) ... Selecting previously unselected package libdeflate-dev:amd64. Preparing to unpack .../48-libdeflate-dev_1.20-1_amd64.deb ... Unpacking libdeflate-dev:amd64 (1.20-1) ... Selecting previously unselected package libgslcblas0:amd64. Preparing to unpack .../49-libgslcblas0_2.7.1+dfsg-6+b1_amd64.deb ... Unpacking libgslcblas0:amd64 (2.7.1+dfsg-6+b1) ... Selecting previously unselected package libgsl27:amd64. Preparing to unpack .../50-libgsl27_2.7.1+dfsg-6+b1_amd64.deb ... Unpacking libgsl27:amd64 (2.7.1+dfsg-6+b1) ... Selecting previously unselected package libgsl-dev. Preparing to unpack .../51-libgsl-dev_2.7.1+dfsg-6+b1_amd64.deb ... Unpacking libgsl-dev (2.7.1+dfsg-6+b1) ... Selecting previously unselected package libhtscodecs2:amd64. Preparing to unpack .../52-libhtscodecs2_1.6.0-1+b1_amd64.deb ... Unpacking libhtscodecs2:amd64 (1.6.0-1+b1) ... Selecting previously unselected package libhts3t64:amd64. Preparing to unpack .../53-libhts3t64_1.19+ds-1.1+b1_amd64.deb ... Unpacking libhts3t64:amd64 (1.19+ds-1.1+b1) ... Selecting previously unselected package liblzma-dev:amd64. Preparing to unpack .../54-liblzma-dev_5.6.1+really5.4.5-1_amd64.deb ... Unpacking liblzma-dev:amd64 (5.6.1+really5.4.5-1) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../55-zlib1g-dev_1%3a1.3.dfsg-3.1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.3.dfsg-3.1) ... Selecting previously unselected package libhts-dev:amd64. Preparing to unpack .../56-libhts-dev_1.19+ds-1.1+b1_amd64.deb ... Unpacking libhts-dev:amd64 (1.19+ds-1.1+b1) ... Selecting previously unselected package libio-pty-perl. Preparing to unpack .../57-libio-pty-perl_1%3a1.20-1+b1_amd64.deb ... Unpacking libio-pty-perl (1:1.20-1+b1) ... Selecting previously unselected package tabix. Preparing to unpack .../58-tabix_1.19+ds-1.1+b1_amd64.deb ... Unpacking tabix (1.19+ds-1.1+b1) ... Setting up libhtscodecs2:amd64 (1.6.0-1+b1) ... Setting up libpipeline1:amd64 (1.5.7-2) ... Setting up libkeyutils1:amd64 (1.6.3-3) ... Setting up libicu72:amd64 (72.1-4+b1) ... Setting up bsdextrautils (2.40-8) ... Setting up libgslcblas0:amd64 (2.7.1+dfsg-6+b1) ... Setting up libio-pty-perl (1:1.20-1+b1) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libbrotli1:amd64 (1.1.0-2+b3) ... Setting up libmagic1t64:amd64 (1:5.45-3) ... Setting up libpsl5t64:amd64 (0.21.2-1.1) ... Setting up libnghttp2-14:amd64 (1.61.0-1+b1) ... Setting up libdeflate0:amd64 (1.20-1) ... Setting up gettext-base (0.21-14+b1) ... Setting up libgsl27:amd64 (2.7.1+dfsg-6+b1) ... Setting up m4 (1.4.19-4) ... Setting up libcom-err2:amd64 (1.47.1~rc2-1) ... Setting up file (1:5.45-3) ... Setting up libelf1t64:amd64 (0.191-1+b1) ... Setting up libkrb5support0:amd64 (1.20.1-6+b1) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-6) ... Setting up autotools-dev (20220109.1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up autopoint (0.21-14) ... Setting up libk5crypto3:amd64 (1.20.1-6+b1) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-6) ... Setting up autoconf (2.71-3) ... Setting up liblzma-dev:amd64 (5.6.1+really5.4.5-1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg-3.1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up libsub-override-perl (0.10-1) ... Setting up libkrb5-3:amd64 (1.20.1-6+b1) ... Setting up libssh2-1t64:amd64 (1.11.0-4.1+b2) ... Setting up libdeflate-dev:amd64 (1.20-1) ... Setting up tabix (1.19+ds-1.1+b1) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3+b3) ... Setting up libbz2-dev:amd64 (1.0.8-5.1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up gettext (0.21-14+b1) ... Setting up libgsl-dev (2.7.1+dfsg-6+b1) ... Setting up libtool (2.4.7-7) ... Setting up libldap-2.5-0:amd64 (2.5.17+dfsg-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-6+b1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up groff-base (1.23.0-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3t64-gnutls:amd64 (8.7.1-5) ... Setting up libcurl4-gnutls-dev:amd64 (8.7.1-5) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libhts3t64:amd64 (1.19+ds-1.1+b1) ... Setting up libhts-dev:amd64 (1.19+ds-1.1+b1) ... Setting up debhelper (13.15.3) ... Processing triggers for libc-bin (2.38-8) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/bcftools-1.20/ && 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_1.20-1_source.changes dpkg-buildpackage: info: source package bcftools dpkg-buildpackage: info: source version 1.20-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean rm -f config.mk && touch config.mk dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/bcftools-1.20' dh_auto_clean make -j42 distclean make[2]: Entering directory '/build/reproducible-path/bcftools-1.20' rm -f test/*.o test/*.fa.fai test/*~ test/test-rbuf test/test-regidx rm -f plugins/*.so plugins/*.P rm -rf plugins/*.dSYM rm -f test/*.unsorted.hex test/*.unsorted.tsv rm -f gmon.out *.o *.a *~ bcftools version.h rm -rf *.dSYM test/*.dSYM rm -f config.cache config.h config.log config.mk config.status rm -rf autom4te.cache rm -f TAGS make[2]: Leaving directory '/build/reproducible-path/bcftools-1.20' rm -f test/mpileup/indel-AD.1.out.new test/view-t.1.out.new test/view-t.2.out.new make[1]: Leaving directory '/build/reproducible-path/bcftools-1.20' dh_clean debian/rules binary dh binary dh_update_autotools_config debian/rules override_dh_autoreconf make[1]: Entering directory '/build/reproducible-path/bcftools-1.20' rm -f config.mk && touch config.mk export MAKEFLAGS="-s"; dh_autoreconf configure.ac:94: warning: _AC_CONFIG_SUBDIRS: you should use literals ./lib/autoconf/status.m4:1096: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:94: the top level make[1]: Leaving directory '/build/reproducible-path/bcftools-1.20' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/bcftools-1.20' dh_auto_configure -- \ --with-htslib=system \ --enable-gsl \ --with-cblas=gslcblas \ --with-bcf-plugin-dir=/usr/lib/x86_64-linux-gnu/bcftools ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system --enable-gsl --with-cblas=gslcblas --with-bcf-plugin-dir=/usr/lib/x86_64-linux-gnu/bcftools checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for htslib/sam.h... yes checking for hts_version in -lhts... yes checking shared library type... plain .so checking for library containing dlopen... none required checking if the compiler accepts -rdynamic... yes checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing regcomp... none required configure: creating ./config.status config.status: creating config.mk config.status: creating config.h make[1]: Leaving directory '/build/reproducible-path/bcftools-1.20' dh_auto_build make -j42 make[1]: Entering directory '/build/reproducible-path/bcftools-1.20' echo '#define BCFTOOLS_VERSION "1.20"' > version.h gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfindex.o vcfindex.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tabix.o tabix.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfstats.o vcfstats.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfisec.o vcfisec.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfmerge.o vcfmerge.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfquery.o vcfquery.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcffilter.o vcffilter.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o filter.o filter.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfsom.o vcfsom.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfnorm.o vcfnorm.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfgtcheck.o vcfgtcheck.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfview.o vcfview.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfannotate.o vcfannotate.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfroh.o vcfroh.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfconcat.o vcfconcat.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcall.o vcfcall.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mcall.o mcall.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcmp.o vcmp.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gvcf.o gvcf.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o reheader.o reheader.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o convert.o convert.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfconvert.o vcfconvert.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tsv2vcf.o tsv2vcf.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcnv.o vcfcnv.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfhead.o vcfhead.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o HMM.o HMM.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o consensus.o consensus.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ploidy.o ploidy.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bin.o bin.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hclust.o hclust.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o version.o version.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o regidx.o regidx.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o smpl_ilist.o smpl_ilist.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o csq.o csq.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfbuf.o vcfbuf.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mpileup.o mpileup.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_iaux.o bam2bcf_iaux.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_edlib.o bam2bcf_edlib.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o read_consensus.o read_consensus.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sample.o bam_sample.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfsort.o vcfsort.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cols.o cols.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o extsort.o extsort.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dist.o dist.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o abuf.o abuf.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ccall.o ccall.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o em.o em.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o prob1.o prob1.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kmin.o kmin.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o str_finder.o str_finder.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gff.o gff.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o edlib.o edlib.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DPLUGINPATH='"/usr/lib/x86_64-linux-gnu/bcftools"' -c -o vcfplugin.o vcfplugin.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-rbuf.o test/test-rbuf.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-regidx.o test/test-regidx.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/GTisec.so version.c plugins/GTisec.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/GTsubset.so version.c plugins/GTsubset.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/ad-bias.so convert.c version.c plugins/ad-bias.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/add-variantkey.so version.c plugins/add-variantkey.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/af-dist.so bin.c version.c plugins/af-dist.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/allele-length.so version.c plugins/allele-length.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/check-ploidy.so version.c plugins/check-ploidy.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/check-sparsity.so version.c plugins/check-sparsity.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/color-chrs.so HMM.c version.c plugins/color-chrs.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/contrast.so version.c plugins/contrast.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/counts.so version.c plugins/counts.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/dosage.so version.c plugins/dosage.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fill-AN-AC.so version.c plugins/fill-AN-AC.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fill-from-fasta.so filter.c version.c plugins/fill-from-fasta.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fill-tags.so version.c plugins/fill-tags.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fixploidy.so ploidy.c regidx.c version.c plugins/fixploidy.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fixref.so version.c plugins/fixref.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/frameshifts.so version.c plugins/frameshifts.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/guess-ploidy.so version.c plugins/guess-ploidy.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/gvcfz.so version.c plugins/gvcfz.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/impute-info.so version.c plugins/impute-info.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/indel-stats.so version.c plugins/indel-stats.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/isecGT.so smpl_ilist.c version.c plugins/isecGT.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/mendelian2.so version.c plugins/mendelian2.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/missing2ref.so version.c plugins/missing2ref.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/parental-origin.so version.c plugins/parental-origin.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/prune.so version.c plugins/prune.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/remove-overlaps.so version.c plugins/remove-overlaps.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/scatter.so version.c plugins/scatter.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/setGT.so version.c plugins/setGT.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/smpl-stats.so version.c plugins/smpl-stats.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/split-vep.so version.c plugins/split-vep.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/split.so version.c plugins/split.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/tag2tag.so version.c plugins/tag2tag.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/trio-dnm2.so version.c plugins/trio-dnm2.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/trio-stats.so version.c plugins/trio-stats.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/trio-switch-rate.so version.c plugins/trio-switch-rate.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/variant-distance.so version.c plugins/variant-distance.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/variantkey-hex.so version.c plugins/variantkey-hex.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.20=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o main.o main.c gcc -Wl,-z,relro -o test/test-rbuf test/test-rbuf.o -lz gcc -Wl,-z,relro -o test/test-regidx test/test-regidx.o regidx.o -lhts -lpthread -lz gcc -rdynamic -Wl,-z,relro -o bcftools main.o vcfindex.o tabix.o vcfstats.o vcfisec.o vcfmerge.o vcfquery.o vcffilter.o filter.o vcfsom.o vcfnorm.o vcfgtcheck.o vcfview.o vcfannotate.o vcfroh.o vcfconcat.o vcfcall.o mcall.o vcmp.o gvcf.o reheader.o convert.o vcfconvert.o tsv2vcf.o vcfcnv.o vcfhead.o HMM.o consensus.o ploidy.o bin.o hclust.o version.o regidx.o smpl_ilist.o csq.o vcfbuf.o mpileup.o bam2bcf.o bam2bcf_indel.o bam2bcf_iaux.o bam2bcf_edlib.o read_consensus.o bam_sample.o vcfsort.o cols.o extsort.o dist.o abuf.o ccall.o em.o prob1.o kmin.o str_finder.o gff.o edlib.o vcfplugin.o -lhts -lm -lz -lpthread make[1]: Leaving directory '/build/reproducible-path/bcftools-1.20' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/bcftools-1.20' make test-no-plugins VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/bcftools-1.20' ./test/test-rbuf Inserted 1-9 starting at offset 5: 5 6 7 8 9 0 1 2 3 1 2 3 4 5 6 7 8 9 4th is 4 Deleting 1-2: 7 8 9 0 1 2 3 3 4 5 6 7 8 9 Prepending 0-8: 8 9 0 1 2 3 4 5 6 7 8 7 6 5 4 3 2 1 0 3 Expanding: 8 9 10 11 12 13 14 15 16 17 8 7 6 5 4 3 2 1 0 3 ./test/test-regidx REF_PATH=: ./test/test.pl --exec bgzip= --exec tabix= --htsdir= ${TEST_OPTS:-} test_usage: bcftools .. ok test_usage_subcommand: bcftools index .. ok test_usage_subcommand: bcftools annotate .. ok test_usage_subcommand: bcftools concat .. ok test_usage_subcommand: bcftools convert .. ok test_usage_subcommand: bcftools head .. ok test_usage_subcommand: bcftools isec .. ok test_usage_subcommand: bcftools merge .. ok test_usage_subcommand: bcftools norm .. ok test_usage_subcommand: bcftools plugin .. ok test_usage_subcommand: bcftools query .. ok test_usage_subcommand: bcftools reheader .. ok test_usage_subcommand: bcftools sort .. ok test_usage_subcommand: bcftools view .. ok test_usage_subcommand: bcftools call .. ok test_usage_subcommand: bcftools consensus .. ok test_usage_subcommand: bcftools cnv .. ok test_usage_subcommand: bcftools csq .. ok test_usage_subcommand: bcftools filter .. ok test_usage_subcommand: bcftools gtcheck .. ok test_usage_subcommand: bcftools mpileup .. ok test_usage_subcommand: bcftools roh .. ok test_usage_subcommand: bcftools stats .. ok test_tabix: tabix /tmp/4Bla9USopM/merge.a.vcf.gz 2:3199812-3199812 .. ok test_tabix: /build/reproducible-path/bcftools-1.20/bcftools view -H /tmp/4Bla9USopM/merge.a.bcf 2:3199812-3199812 .. ok test_tabix: tabix /tmp/4Bla9USopM/merge.a.vcf.gz 1:3000151-3000151 .. ok test_tabix: /build/reproducible-path/bcftools-1.20/bcftools view -H /tmp/4Bla9USopM/merge.a.bcf 1:3000151-3000151 .. ok test_index: /build/reproducible-path/bcftools-1.20/bcftools view -H /tmp/4Bla9USopM/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /build/reproducible-path/bcftools-1.20/bcftools view -H /tmp/4Bla9USopM/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/reproducible-path/bcftools-1.20/bcftools view -H /tmp/4Bla9USopM/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/reproducible-path/bcftools-1.20/bcftools view -H /tmp/4Bla9USopM/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /build/reproducible-path/bcftools-1.20/bcftools view -H /tmp/4Bla9USopM/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/reproducible-path/bcftools-1.20/bcftools view -H /tmp/4Bla9USopM/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /build/reproducible-path/bcftools-1.20/bcftools view -H /tmp/4Bla9USopM/large_chrom_csi_limit.bcf chr20 .. ok test_index: /build/reproducible-path/bcftools-1.20/bcftools view -H /tmp/4Bla9USopM/large_chrom_csi_limit.bcf chr20 .. ok test_index: /build/reproducible-path/bcftools-1.20/bcftools view -H /tmp/4Bla9USopM/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /build/reproducible-path/bcftools-1.20/bcftools view -H /tmp/4Bla9USopM/large_chrom_csi_limit.bcf chr20 .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.20/bcftools index -s /tmp/4Bla9USopM/idx.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.20/bcftools index -s /tmp/4Bla9USopM/idx.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.20/bcftools index -s /tmp/4Bla9USopM/idx.bcf .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.20/bcftools index -n /tmp/4Bla9USopM/idx.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.20/bcftools index -n /tmp/4Bla9USopM/idx.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.20/bcftools index -n /tmp/4Bla9USopM/idx.vcf.gz.csi .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.20/bcftools index -n /tmp/4Bla9USopM/idx.bcf .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.20/bcftools index -n /tmp/4Bla9USopM/idx.bcf.csi .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.20/bcftools index -s /tmp/4Bla9USopM/empty.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.20/bcftools index -s /tmp/4Bla9USopM/empty.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.20/bcftools index -s /tmp/4Bla9USopM/empty.bcf .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.20/bcftools index -n /tmp/4Bla9USopM/empty.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.20/bcftools index -n /tmp/4Bla9USopM/empty.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.20/bcftools index -n /tmp/4Bla9USopM/empty.vcf.gz.csi .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.20/bcftools index -n /tmp/4Bla9USopM/empty.bcf .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.20/bcftools index -n /tmp/4Bla9USopM/empty.bcf.csi .. ok test_vcf_check: /build/reproducible-path/bcftools-1.20/bcftools stats -s - /tmp/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/check.1.chk /tmp/4Bla9USopM/check.2.chk /tmp/4Bla9USopM/check.3.chk /tmp/4Bla9USopM/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/4Bla9USopM/stats.a.vcf.gz /tmp/4Bla9USopM/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/reproducible-path/bcftools-1.20/bcftools stats -s B /tmp/4Bla9USopM/stats.a.vcf.gz /tmp/4Bla9USopM/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/reproducible-path/bcftools-1.20/bcftools stats -s - /tmp/4Bla9USopM/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/4Bla9USopM/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/reproducible-path/bcftools-1.20/bcftools stats -s - /tmp/4Bla9USopM/stats.vaf.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.20/bcftools isec -n =2 /tmp/4Bla9USopM/isec.a.vcf.gz /tmp/4Bla9USopM/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.20/bcftools isec -Ob -n =2 /tmp/4Bla9USopM/isec.a.vcf.gz /tmp/4Bla9USopM/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.20/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/4Bla9USopM/isec.a.vcf.gz /tmp/4Bla9USopM/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.20/bcftools isec -Ob -n =2 -i"STRLEN(REF)==2" /tmp/4Bla9USopM/isec.a.vcf.gz /tmp/4Bla9USopM/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.20/bcftools isec -n =2 -c both /tmp/4Bla9USopM/isec.a.vcf.gz /tmp/4Bla9USopM/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.20/bcftools isec -Ob -n =2 -c both /tmp/4Bla9USopM/isec.a.vcf.gz /tmp/4Bla9USopM/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.20/bcftools isec -n =2 -c any /tmp/4Bla9USopM/isec.a.vcf.gz /tmp/4Bla9USopM/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.20/bcftools isec -Ob -n =2 -c any /tmp/4Bla9USopM/isec.a.vcf.gz /tmp/4Bla9USopM/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.20/bcftools isec -C -c any /tmp/4Bla9USopM/isec.a.vcf.gz /tmp/4Bla9USopM/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.20/bcftools isec -Ob -C -c any /tmp/4Bla9USopM/isec.a.vcf.gz /tmp/4Bla9USopM/isec.b.vcf.gz .. ok test_vcf_isec2: /build/reproducible-path/bcftools-1.20/bcftools isec --no-version -T /tmp/4Bla9USopM/isec.tab.gz /tmp/4Bla9USopM/isec.a.vcf.gz .. ok test_vcf_isec2: /build/reproducible-path/bcftools-1.20/bcftools isec -Ob -T /tmp/4Bla9USopM/isec.tab.gz /tmp/4Bla9USopM/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/4Bla9USopM/isec-miss.1.1.vcf.gz /tmp/4Bla9USopM/isec-miss.1.2.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/isec-miss.1.1.vcf.gz /tmp/4Bla9USopM/isec-miss.1.2.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/isec-miss.1.1.vcf.gz /tmp/4Bla9USopM/isec-miss.1.2.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/isec-miss.1.1.vcf.gz /tmp/4Bla9USopM/isec-miss.1.2.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/isec-miss.2.1.vcf.gz /tmp/4Bla9USopM/isec-miss.2.2.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/isec-miss.2.1.vcf.gz /tmp/4Bla9USopM/isec-miss.2.2.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/isec-miss.2.1.vcf.gz /tmp/4Bla9USopM/isec-miss.2.2.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/isec-miss.2.1.vcf.gz /tmp/4Bla9USopM/isec-miss.2.2.vcf.gz /tmp/4Bla9USopM/isec-miss.2.3.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -i AF:join /tmp/4Bla9USopM/merge.join.a.vcf.gz /tmp/4Bla9USopM/merge.join.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob -i AF:join /tmp/4Bla9USopM/merge.join.a.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.join.a.bcf /tmp/4Bla9USopM/merge.join.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob -i AF:join /tmp/4Bla9USopM/merge.join.a.bcf /tmp/4Bla9USopM/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/4Bla9USopM/merge.LPL.a.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-single /tmp/4Bla9USopM/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/4Bla9USopM/merge.LPL.a.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-single /tmp/4Bla9USopM/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/4Bla9USopM/merge.LPL.a.vcf.gz /tmp/4Bla9USopM/merge.LPL.b.vcf.gz /tmp/4Bla9USopM/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples /tmp/4Bla9USopM/merge.LPL.a.vcf.gz /tmp/4Bla9USopM/merge.LPL.b.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.LPL.a.bcf /tmp/4Bla9USopM/merge.LPL.b.bcf /tmp/4Bla9USopM/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples /tmp/4Bla9USopM/merge.LPL.a.bcf /tmp/4Bla9USopM/merge.LPL.b.bcf /tmp/4Bla9USopM/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/4Bla9USopM/merge.LPL.a.vcf.gz /tmp/4Bla9USopM/merge.LPL.b.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.LPL.a.vcf.gz /tmp/4Bla9USopM/merge.LPL.b.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.LPL.a.bcf /tmp/4Bla9USopM/merge.LPL.b.bcf /tmp/4Bla9USopM/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -L 1 /tmp/4Bla9USopM/merge.LPL.a.bcf /tmp/4Bla9USopM/merge.LPL.b.bcf /tmp/4Bla9USopM/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/4Bla9USopM/merge.LPL.a.vcf.gz /tmp/4Bla9USopM/merge.LPL.b.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.LPL.a.vcf.gz /tmp/4Bla9USopM/merge.LPL.b.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.LPL.a.bcf /tmp/4Bla9USopM/merge.LPL.b.bcf /tmp/4Bla9USopM/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -L 2 /tmp/4Bla9USopM/merge.LPL.a.bcf /tmp/4Bla9USopM/merge.LPL.b.bcf /tmp/4Bla9USopM/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/4Bla9USopM/merge.LPL.a.vcf.gz /tmp/4Bla9USopM/merge.LPL.b.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.LPL.a.vcf.gz /tmp/4Bla9USopM/merge.LPL.b.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.LPL.a.bcf /tmp/4Bla9USopM/merge.LPL.b.bcf /tmp/4Bla9USopM/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -L 3 /tmp/4Bla9USopM/merge.LPL.a.bcf /tmp/4Bla9USopM/merge.LPL.b.bcf /tmp/4Bla9USopM/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/4Bla9USopM/merge.LPL.a.vcf.gz /tmp/4Bla9USopM/merge.LPL.b.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.LPL.a.vcf.gz /tmp/4Bla9USopM/merge.LPL.b.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.LPL.a.bcf /tmp/4Bla9USopM/merge.LPL.b.bcf /tmp/4Bla9USopM/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -L 4 /tmp/4Bla9USopM/merge.LPL.a.bcf /tmp/4Bla9USopM/merge.LPL.b.bcf /tmp/4Bla9USopM/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/4Bla9USopM/merge.LPL.a.vcf.gz /tmp/4Bla9USopM/merge.LPL.b.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.LPL.a.vcf.gz /tmp/4Bla9USopM/merge.LPL.b.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.LPL.a.bcf /tmp/4Bla9USopM/merge.LPL.b.bcf /tmp/4Bla9USopM/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -L 5 /tmp/4Bla9USopM/merge.LPL.a.bcf /tmp/4Bla9USopM/merge.LPL.b.bcf /tmp/4Bla9USopM/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/4Bla9USopM/merge.a.vcf.gz /tmp/4Bla9USopM/merge.b.vcf.gz /tmp/4Bla9USopM/merge.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples /tmp/4Bla9USopM/merge.a.vcf.gz /tmp/4Bla9USopM/merge.b.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.a.bcf /tmp/4Bla9USopM/merge.b.bcf /tmp/4Bla9USopM/merge.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples /tmp/4Bla9USopM/merge.a.bcf /tmp/4Bla9USopM/merge.b.bcf /tmp/4Bla9USopM/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/4Bla9USopM/merge.a.vcf.gz /tmp/4Bla9USopM/merge.b.vcf.gz /tmp/4Bla9USopM/merge.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -Fx /tmp/4Bla9USopM/merge.a.vcf.gz /tmp/4Bla9USopM/merge.b.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.a.bcf /tmp/4Bla9USopM/merge.b.bcf /tmp/4Bla9USopM/merge.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -Fx /tmp/4Bla9USopM/merge.a.bcf /tmp/4Bla9USopM/merge.b.bcf /tmp/4Bla9USopM/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/4Bla9USopM/merge.a.vcf.gz /tmp/4Bla9USopM/merge.b.vcf.gz /tmp/4Bla9USopM/merge.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -0 /tmp/4Bla9USopM/merge.a.vcf.gz /tmp/4Bla9USopM/merge.b.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.a.bcf /tmp/4Bla9USopM/merge.b.bcf /tmp/4Bla9USopM/merge.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -0 /tmp/4Bla9USopM/merge.a.bcf /tmp/4Bla9USopM/merge.b.bcf /tmp/4Bla9USopM/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/4Bla9USopM/merge.2.a.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.2.a.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.2.a.bcf /tmp/4Bla9USopM/merge.2.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -m none /tmp/4Bla9USopM/merge.2.a.bcf /tmp/4Bla9USopM/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/4Bla9USopM/merge.2.a.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.2.a.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.2.a.bcf /tmp/4Bla9USopM/merge.2.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -m both /tmp/4Bla9USopM/merge.2.a.bcf /tmp/4Bla9USopM/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/4Bla9USopM/merge.2.a.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.2.a.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.2.a.bcf /tmp/4Bla9USopM/merge.2.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -m all /tmp/4Bla9USopM/merge.2.a.bcf /tmp/4Bla9USopM/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/4Bla9USopM/merge.3.a.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.3.a.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.3.a.bcf /tmp/4Bla9USopM/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/4Bla9USopM/merge.3.a.bcf /tmp/4Bla9USopM/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/4Bla9USopM/merge.4.a.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.4.a.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.4.a.bcf /tmp/4Bla9USopM/merge.4.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -m id /tmp/4Bla9USopM/merge.4.a.bcf /tmp/4Bla9USopM/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/4Bla9USopM/gvcf.merge.1.vcf.gz /tmp/4Bla9USopM/gvcf.merge.2.vcf.gz /tmp/4Bla9USopM/gvcf.merge.3.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/4Bla9USopM/gvcf.merge.1.vcf.gz /tmp/4Bla9USopM/gvcf.merge.2.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/gvcf.merge.1.bcf /tmp/4Bla9USopM/gvcf.merge.2.bcf /tmp/4Bla9USopM/gvcf.merge.3.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/4Bla9USopM/gvcf.merge.1.bcf /tmp/4Bla9USopM/gvcf.merge.2.bcf /tmp/4Bla9USopM/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/4Bla9USopM/merge.gvcf.2.a.vcf.gz /tmp/4Bla9USopM/merge.gvcf.2.b.vcf.gz /tmp/4Bla9USopM/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/4Bla9USopM/merge.gvcf.2.a.vcf.gz /tmp/4Bla9USopM/merge.gvcf.2.b.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.gvcf.2.a.vcf.gz /tmp/4Bla9USopM/merge.gvcf.2.b.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.gvcf.2.a.vcf.gz /tmp/4Bla9USopM/merge.gvcf.2.b.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.gvcf.2.a.vcf.gz /tmp/4Bla9USopM/merge.gvcf.2.b.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.gvcf.2.a.vcf.gz /tmp/4Bla9USopM/merge.gvcf.2.b.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.gvcf.3.a.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.gvcf.3.a.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.gvcf.4.a.vcf.gz /tmp/4Bla9USopM/merge.gvcf.4.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/4Bla9USopM/merge.gvcf.4.a.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.gvcf.4.a.bcf /tmp/4Bla9USopM/merge.gvcf.4.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/4Bla9USopM/merge.gvcf.4.a.bcf /tmp/4Bla9USopM/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/4Bla9USopM/merge.5.a.vcf.gz /tmp/4Bla9USopM/merge.5.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob /tmp/4Bla9USopM/merge.5.a.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.5.a.bcf /tmp/4Bla9USopM/merge.5.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob /tmp/4Bla9USopM/merge.5.a.bcf /tmp/4Bla9USopM/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/4Bla9USopM/merge.6.a.vcf.gz /tmp/4Bla9USopM/merge.6.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob /tmp/4Bla9USopM/merge.6.a.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.6.a.bcf /tmp/4Bla9USopM/merge.6.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob /tmp/4Bla9USopM/merge.6.a.bcf /tmp/4Bla9USopM/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/4Bla9USopM/merge.gvcf.7.a.vcf.gz /tmp/4Bla9USopM/merge.gvcf.7.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/4Bla9USopM/merge.gvcf.7.a.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.gvcf.7.a.bcf /tmp/4Bla9USopM/merge.gvcf.7.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/4Bla9USopM/merge.gvcf.7.a.bcf /tmp/4Bla9USopM/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/4Bla9USopM/merge.gvcf.8.a.vcf.gz /tmp/4Bla9USopM/merge.gvcf.8.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/4Bla9USopM/merge.gvcf.8.a.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.gvcf.8.a.bcf /tmp/4Bla9USopM/merge.gvcf.8.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/4Bla9USopM/merge.gvcf.8.a.bcf /tmp/4Bla9USopM/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/4Bla9USopM/merge.7.a.vcf.gz /tmp/4Bla9USopM/merge.7.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples /tmp/4Bla9USopM/merge.7.a.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.7.a.bcf /tmp/4Bla9USopM/merge.7.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples /tmp/4Bla9USopM/merge.7.a.bcf /tmp/4Bla9USopM/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/4Bla9USopM/merge.gvcf.9a.vcf.gz /tmp/4Bla9USopM/merge.gvcf.9b.vcf.gz /tmp/4Bla9USopM/merge.gvcf.9c.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.gvcf.9a.vcf.gz /tmp/4Bla9USopM/merge.gvcf.9b.vcf.gz /tmp/4Bla9USopM/merge.gvcf.9c.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.gvcf.9a.bcf /tmp/4Bla9USopM/merge.gvcf.9b.bcf /tmp/4Bla9USopM/merge.gvcf.9c.bcf /tmp/4Bla9USopM/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/4Bla9USopM/merge.gvcf.9a.bcf /tmp/4Bla9USopM/merge.gvcf.9b.bcf /tmp/4Bla9USopM/merge.gvcf.9c.bcf /tmp/4Bla9USopM/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/4Bla9USopM/merge.gvcf.9a.vcf.gz /tmp/4Bla9USopM/merge.gvcf.9b.vcf.gz /tmp/4Bla9USopM/merge.gvcf.9c.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.gvcf.9a.vcf.gz /tmp/4Bla9USopM/merge.gvcf.9b.vcf.gz /tmp/4Bla9USopM/merge.gvcf.9c.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.gvcf.9a.bcf /tmp/4Bla9USopM/merge.gvcf.9b.bcf /tmp/4Bla9USopM/merge.gvcf.9c.bcf /tmp/4Bla9USopM/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/4Bla9USopM/merge.gvcf.9a.bcf /tmp/4Bla9USopM/merge.gvcf.9b.bcf /tmp/4Bla9USopM/merge.gvcf.9c.bcf /tmp/4Bla9USopM/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/4Bla9USopM/merge.gvcf.9a.vcf.gz /tmp/4Bla9USopM/merge.gvcf.9b.vcf.gz /tmp/4Bla9USopM/merge.gvcf.9c.vcf.gz /tmp/4Bla9USopM/merge.gvcf.9d.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.gvcf.9a.vcf.gz /tmp/4Bla9USopM/merge.gvcf.9b.vcf.gz /tmp/4Bla9USopM/merge.gvcf.9c.vcf.gz /tmp/4Bla9USopM/merge.gvcf.9d.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.gvcf.9a.bcf /tmp/4Bla9USopM/merge.gvcf.9b.bcf /tmp/4Bla9USopM/merge.gvcf.9c.bcf /tmp/4Bla9USopM/merge.gvcf.9d.bcf /tmp/4Bla9USopM/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/4Bla9USopM/merge.gvcf.9a.bcf /tmp/4Bla9USopM/merge.gvcf.9b.bcf /tmp/4Bla9USopM/merge.gvcf.9c.bcf /tmp/4Bla9USopM/merge.gvcf.9d.bcf /tmp/4Bla9USopM/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/4Bla9USopM/merge.gvcf.9a.vcf.gz /tmp/4Bla9USopM/merge.gvcf.9b.vcf.gz /tmp/4Bla9USopM/merge.gvcf.9c.vcf.gz /tmp/4Bla9USopM/merge.gvcf.9d.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.gvcf.9a.vcf.gz /tmp/4Bla9USopM/merge.gvcf.9b.vcf.gz /tmp/4Bla9USopM/merge.gvcf.9c.vcf.gz /tmp/4Bla9USopM/merge.gvcf.9d.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.gvcf.9a.bcf /tmp/4Bla9USopM/merge.gvcf.9b.bcf /tmp/4Bla9USopM/merge.gvcf.9c.bcf /tmp/4Bla9USopM/merge.gvcf.9d.bcf /tmp/4Bla9USopM/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/4Bla9USopM/merge.gvcf.9a.bcf /tmp/4Bla9USopM/merge.gvcf.9b.bcf /tmp/4Bla9USopM/merge.gvcf.9c.bcf /tmp/4Bla9USopM/merge.gvcf.9d.bcf /tmp/4Bla9USopM/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/4Bla9USopM/merge.gvcf.10.a.vcf.gz /tmp/4Bla9USopM/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob /tmp/4Bla9USopM/merge.gvcf.10.a.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.gvcf.10.a.bcf /tmp/4Bla9USopM/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob /tmp/4Bla9USopM/merge.gvcf.10.a.bcf /tmp/4Bla9USopM/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/4Bla9USopM/merge.gvcf.10.a.vcf.gz /tmp/4Bla9USopM/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob -m none /tmp/4Bla9USopM/merge.gvcf.10.a.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.gvcf.10.a.bcf /tmp/4Bla9USopM/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob -m none /tmp/4Bla9USopM/merge.gvcf.10.a.bcf /tmp/4Bla9USopM/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/4Bla9USopM/merge.gvcf.10.a.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.gvcf.10.a.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.gvcf.10.a.bcf /tmp/4Bla9USopM/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/4Bla9USopM/merge.gvcf.10.a.bcf /tmp/4Bla9USopM/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/4Bla9USopM/merge.gvcf.10.a.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.gvcf.10.a.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.gvcf.10.a.bcf /tmp/4Bla9USopM/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/4Bla9USopM/merge.gvcf.10.a.bcf /tmp/4Bla9USopM/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/4Bla9USopM/merge.noidx.a.vcf.gz /tmp/4Bla9USopM/merge.noidx.b.vcf.gz /tmp/4Bla9USopM/merge.noidx.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob /tmp/4Bla9USopM/merge.noidx.a.vcf.gz /tmp/4Bla9USopM/merge.noidx.b.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.noidx.a.bcf /tmp/4Bla9USopM/merge.noidx.b.bcf /tmp/4Bla9USopM/merge.noidx.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob /tmp/4Bla9USopM/merge.noidx.a.bcf /tmp/4Bla9USopM/merge.noidx.b.bcf /tmp/4Bla9USopM/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/4Bla9USopM/merge.noidx.a.bcf /tmp/4Bla9USopM/merge.noidx.b.bcf /tmp/4Bla9USopM/merge.noidx.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --no-index /tmp/4Bla9USopM/merge.noidx.a.bcf /tmp/4Bla9USopM/merge.noidx.b.bcf /tmp/4Bla9USopM/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/4Bla9USopM/merge.8.a.vcf.gz /tmp/4Bla9USopM/merge.8.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob /tmp/4Bla9USopM/merge.8.a.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.8.a.bcf /tmp/4Bla9USopM/merge.8.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob /tmp/4Bla9USopM/merge.8.a.bcf /tmp/4Bla9USopM/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/4Bla9USopM/merge.8.a.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.8.a.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.8.a.bcf /tmp/4Bla9USopM/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/4Bla9USopM/merge.8.a.bcf /tmp/4Bla9USopM/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/4Bla9USopM/merge.9.a.vcf.gz /tmp/4Bla9USopM/merge.9.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob /tmp/4Bla9USopM/merge.9.a.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.9.a.bcf /tmp/4Bla9USopM/merge.9.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob /tmp/4Bla9USopM/merge.9.a.bcf /tmp/4Bla9USopM/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/4Bla9USopM/merge.9.a.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.9.a.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.9.a.bcf /tmp/4Bla9USopM/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/4Bla9USopM/merge.9.a.bcf /tmp/4Bla9USopM/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/4Bla9USopM/merge.10.a.vcf.gz /tmp/4Bla9USopM/merge.10.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob -m none /tmp/4Bla9USopM/merge.10.a.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.10.a.bcf /tmp/4Bla9USopM/merge.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob -m none /tmp/4Bla9USopM/merge.10.a.bcf /tmp/4Bla9USopM/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/4Bla9USopM/merge.10.a.vcf.gz /tmp/4Bla9USopM/merge.10.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob -m both /tmp/4Bla9USopM/merge.10.a.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.10.a.bcf /tmp/4Bla9USopM/merge.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob -m both /tmp/4Bla9USopM/merge.10.a.bcf /tmp/4Bla9USopM/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/4Bla9USopM/merge.10.a.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.10.a.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.10.a.bcf /tmp/4Bla9USopM/merge.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob -m snp-ins-del /tmp/4Bla9USopM/merge.10.a.bcf /tmp/4Bla9USopM/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/4Bla9USopM/merge.mrules.1.a.vcf.gz /tmp/4Bla9USopM/merge.mrules.1.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/4Bla9USopM/merge.mrules.1.a.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.mrules.1.a.bcf /tmp/4Bla9USopM/merge.mrules.1.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/4Bla9USopM/merge.mrules.1.a.bcf /tmp/4Bla9USopM/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/4Bla9USopM/merge.mrules.1.a.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.mrules.1.a.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.mrules.1.a.bcf /tmp/4Bla9USopM/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/4Bla9USopM/merge.mrules.1.a.bcf /tmp/4Bla9USopM/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/4Bla9USopM/merge.gvcf.5.a.vcf.gz /tmp/4Bla9USopM/merge.gvcf.5.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/4Bla9USopM/merge.gvcf.5.a.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.gvcf.5.a.bcf /tmp/4Bla9USopM/merge.gvcf.5.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/4Bla9USopM/merge.gvcf.5.a.bcf /tmp/4Bla9USopM/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/4Bla9USopM/merge.gvcf.5.a.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.gvcf.5.a.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.gvcf.5.a.bcf /tmp/4Bla9USopM/merge.gvcf.5.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - --merge none /tmp/4Bla9USopM/merge.gvcf.5.a.bcf /tmp/4Bla9USopM/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/4Bla9USopM/merge.gvcf.11.a.vcf.gz /tmp/4Bla9USopM/merge.gvcf.11.b.vcf.gz /tmp/4Bla9USopM/merge.gvcf.11.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/4Bla9USopM/merge.gvcf.11.a.vcf.gz /tmp/4Bla9USopM/merge.gvcf.11.b.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/merge.gvcf.11.a.bcf /tmp/4Bla9USopM/merge.gvcf.11.b.bcf /tmp/4Bla9USopM/merge.gvcf.11.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/4Bla9USopM/merge.gvcf.11.a.bcf /tmp/4Bla9USopM/merge.gvcf.11.b.bcf /tmp/4Bla9USopM/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/4Bla9USopM/query.string.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.string.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.string.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.string.2.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.string.2.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.variantkey.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/view.vectors.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.2.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.filter-type.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.filter-type.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.filter-type.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.filter-type.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.filter-type.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/filter-missing-floats.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/filter-missing-floats.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.filter.2.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.filter.3.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.filter.3.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.filter.3.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.filter.4.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/view.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.negative.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.negative.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.negative.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.negative.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.filter.6.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.filter.8.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.filter.8.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.filter.9.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.filter.9.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.filter.13.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.filter.10.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.filter.10.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.filter.id.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.filter.id.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/filter.10.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/filter.13.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.filter-or.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/query.filter-or.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/norm.split.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m- /tmp/4Bla9USopM/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/4Bla9USopM/norm.split.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m- /tmp/4Bla9USopM/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/4Bla9USopM/norm.split.3.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m- --force /tmp/4Bla9USopM/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/4Bla9USopM/norm.split.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m- /tmp/4Bla9USopM/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/4Bla9USopM/norm.split.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m- --keep-sum AD /tmp/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/norm.merge.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m+ /tmp/4Bla9USopM/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/4Bla9USopM/norm.merge.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m+ /tmp/4Bla9USopM/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/4Bla9USopM/norm.merge.3.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m+ /tmp/4Bla9USopM/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/4Bla9USopM/norm.merge.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m+ -s /tmp/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -d snps /tmp/4Bla9USopM/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/4Bla9USopM/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -d indels /tmp/4Bla9USopM/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/4Bla9USopM/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -d both /tmp/4Bla9USopM/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/4Bla9USopM/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -d all /tmp/4Bla9USopM/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/4Bla9USopM/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -d none /tmp/4Bla9USopM/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/4Bla9USopM/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -d exact /tmp/4Bla9USopM/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/4Bla9USopM/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -d none /tmp/4Bla9USopM/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/4Bla9USopM/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -d exact /tmp/4Bla9USopM/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/4Bla9USopM/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -d indels /tmp/4Bla9USopM/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/4Bla9USopM/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -d any /tmp/4Bla9USopM/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/4Bla9USopM/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -d both /tmp/4Bla9USopM/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/4Bla9USopM/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -d snps /tmp/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/atomize.split.3.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version --atomize --atom-overlaps . /tmp/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/norm.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m +both /tmp/4Bla9USopM/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/4Bla9USopM/norm.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m +any /tmp/4Bla9USopM/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/4Bla9USopM/norm.5.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m - --multi-overlaps 0 /tmp/4Bla9USopM/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/4Bla9USopM/norm.5.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m - --multi-overlaps . /tmp/4Bla9USopM/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/4Bla9USopM/norm.m-any.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m -any /tmp/4Bla9USopM/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/4Bla9USopM/norm.phased-split.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m -any /tmp/4Bla9USopM/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/4Bla9USopM/norm.phased-join.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m +any /tmp/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/norm.string-tags.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m -any /tmp/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/norm.merge.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m +any /tmp/4Bla9USopM/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/4Bla9USopM/norm.merge.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m +both /tmp/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/merge.gvcf.2.a.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -HAA /tmp/4Bla9USopM/merge.gvcf.2.a.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version /tmp/4Bla9USopM/weird-chr-names.vcf.gz -r 1 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/weird-chr-names.vcf.gz -r 1:1-2 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/weird-chr-names.vcf.gz -r 1:1,1:2 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/weird-chr-names.vcf.gz -r 1:1-1 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/weird-chr-names.vcf.gz -r {1:1} .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/weird-chr-names.vcf.gz -r {1:1}:1-2 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/weird-chr-names.vcf.gz -r {1:1}:1-1 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/weird-chr-names.vcf.gz -r {1:1-1} .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/4Bla9USopM/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/4Bla9USopM/view.vcf.gz -r20,Y .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -f PASS -Xks NA00003 /tmp/4Bla9USopM/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/4Bla9USopM/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -xs NA00003 /tmp/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -p /tmp/4Bla9USopM/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/4Bla9USopM/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -P /tmp/4Bla9USopM/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/4Bla9USopM/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/4Bla9USopM/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/4Bla9USopM/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -GVsnps /tmp/4Bla9USopM/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -GVsnps /tmp/4Bla9USopM/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/4Bla9USopM/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/4Bla9USopM/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/4Bla9USopM/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -s ^NA00003 /tmp/4Bla9USopM/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/4Bla9USopM/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -G /tmp/4Bla9USopM/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/4Bla9USopM/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -a /tmp/4Bla9USopM/many.alleles.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -a /tmp/4Bla9USopM/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/4Bla9USopM/view.vectors.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -asA /tmp/4Bla9USopM/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/4Bla9USopM/view.vectors.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -asB /tmp/4Bla9USopM/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/4Bla9USopM/view.vectors.2.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -asA /tmp/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/view.filter.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -H -i'TXT0="text"' /tmp/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/filter.2.vcf.gz 1:3062917-3157410 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -i 'POS>=3062917' /tmp/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/idx.4.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -Ht 2 /tmp/4Bla9USopM/view-t.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -Ht 3 /tmp/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -H -c6:nonmajor /tmp/4Bla9USopM/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -H -q0.3:major /tmp/4Bla9USopM/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/view.filter.annovar.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -H -a /tmp/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/mpileup.2.vcf.gz .. ok test_vcf_head2: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -Ob /tmp/4Bla9USopM/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/4Bla9USopM/mpileup.2.vcf.gz .. ok test_vcf_head2: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -Ob /tmp/4Bla9USopM/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/4Bla9USopM/mpileup.2.vcf.gz .. ok test_vcf_head2: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -Ob /tmp/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.20/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/4Bla9USopM/regions.tab.gz /tmp/4Bla9USopM/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/regions.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/4Bla9USopM/regions.tab.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.20/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/4Bla9USopM/regions.tab.gz /tmp/4Bla9USopM/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.20/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/4Bla9USopM/regions.bed /tmp/4Bla9USopM/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/regions.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/4Bla9USopM/regions.bed .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.20/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/4Bla9USopM/regions.bed /tmp/4Bla9USopM/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.20/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/4Bla9USopM/regions.bed.gz /tmp/4Bla9USopM/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/regions.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/4Bla9USopM/regions.bed.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.20/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/4Bla9USopM/regions.bed.gz /tmp/4Bla9USopM/regions.vcf.gz .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/4Bla9USopM/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/4Bla9USopM/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/4Bla9USopM/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/4Bla9USopM/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/4Bla9USopM/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/4Bla9USopM/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/4Bla9USopM/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/4Bla9USopM/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/4Bla9USopM/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/4Bla9USopM/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/4Bla9USopM/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/4Bla9USopM/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/4Bla9USopM/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/4Bla9USopM/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/4Bla9USopM/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/4Bla9USopM/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/4Bla9USopM/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/4Bla9USopM/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/4Bla9USopM/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/4Bla9USopM/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/4Bla9USopM/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/4Bla9USopM/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/4Bla9USopM/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/4Bla9USopM/annots4.vcf.gz -c +INFO /tmp/4Bla9USopM/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/4Bla9USopM/annots4.vcf.gz -c +INFO /tmp/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/4Bla9USopM/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/4Bla9USopM/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/4Bla9USopM/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/4Bla9USopM/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/4Bla9USopM/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/4Bla9USopM/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/4Bla9USopM/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/4Bla9USopM/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/4Bla9USopM/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/4Bla9USopM/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/4Bla9USopM/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/4Bla9USopM/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/4Bla9USopM/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/4Bla9USopM/annots11.vcf.gz -c FMT /tmp/4Bla9USopM/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/4Bla9USopM/annots11.vcf.gz -c FMT /tmp/4Bla9USopM/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/4Bla9USopM/annots2.vcf.gz -c FMT/newGT:=GT /tmp/4Bla9USopM/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/4Bla9USopM/annots2.vcf.gz -c FMT/newGT:=GT /tmp/4Bla9USopM/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/4Bla9USopM/annots12.vcf.gz -c FMT/GT:=newGT /tmp/4Bla9USopM/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/4Bla9USopM/annots12.vcf.gz -c FMT/GT:=newGT /tmp/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/4Bla9USopM/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/4Bla9USopM/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/4Bla9USopM/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/4Bla9USopM/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/4Bla9USopM/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/4Bla9USopM/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/4Bla9USopM/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/4Bla9USopM/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/4Bla9USopM/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/4Bla9USopM/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/4Bla9USopM/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/4Bla9USopM/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER /tmp/4Bla9USopM/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/4Bla9USopM/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER /tmp/4Bla9USopM/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/4Bla9USopM/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER /tmp/4Bla9USopM/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/4Bla9USopM/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER /tmp/4Bla9USopM/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/4Bla9USopM/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER,FILTER /tmp/4Bla9USopM/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/4Bla9USopM/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER,FILTER /tmp/4Bla9USopM/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/4Bla9USopM/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=./FILTER /tmp/4Bla9USopM/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/4Bla9USopM/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=./FILTER /tmp/4Bla9USopM/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/4Bla9USopM/annotate20.src.vcf.gz -c FMT/GT /tmp/4Bla9USopM/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/4Bla9USopM/annotate20.src.vcf.gz -c FMT/GT /tmp/4Bla9USopM/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/4Bla9USopM/annotate20.src.vcf.gz -c +FMT/GT /tmp/4Bla9USopM/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/4Bla9USopM/annotate20.src.vcf.gz -c +FMT/GT /tmp/4Bla9USopM/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/4Bla9USopM/annotate20.src.vcf.gz -c -FMT/GT /tmp/4Bla9USopM/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/4Bla9USopM/annotate20.src.vcf.gz -c -FMT/GT /tmp/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/4Bla9USopM/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/4Bla9USopM/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/annotate24.src.vcf.gz -c XX /tmp/4Bla9USopM/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/4Bla9USopM/annotate24.src.vcf.gz -c XX /tmp/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/annots.id.vcf.gz -c ALT /tmp/4Bla9USopM/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/4Bla9USopM/annots.id.vcf.gz -c ALT /tmp/4Bla9USopM/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/4Bla9USopM/annots.id.vcf.gz -c +ALT /tmp/4Bla9USopM/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/4Bla9USopM/annots.id.vcf.gz -c +ALT /tmp/4Bla9USopM/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/4Bla9USopM/annots.id.2.vcf.gz --pair-logic some -c +ID /tmp/4Bla9USopM/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/4Bla9USopM/annots.id.2.vcf.gz --pair-logic some -c +ID /tmp/4Bla9USopM/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/4Bla9USopM/annots.id.2.vcf.gz --pair-logic any -c +ID /tmp/4Bla9USopM/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/4Bla9USopM/annots.id.2.vcf.gz --pair-logic any -c +ID /tmp/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/concat.1.a.vcf.gz /tmp/4Bla9USopM/concat.1.b.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat -Ob /tmp/4Bla9USopM/concat.1.a.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/concat.1.a.bcf /tmp/4Bla9USopM/concat.1.b.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat -Ob /tmp/4Bla9USopM/concat.1.a.bcf /tmp/4Bla9USopM/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/4Bla9USopM/concat.2.a.vcf.gz /tmp/4Bla9USopM/concat.2.b.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat -Ob -a /tmp/4Bla9USopM/concat.2.a.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/concat.2.a.bcf /tmp/4Bla9USopM/concat.2.b.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat -Ob -a /tmp/4Bla9USopM/concat.2.a.bcf /tmp/4Bla9USopM/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/4Bla9USopM/concat.2.a.vcf.gz /tmp/4Bla9USopM/concat.2.b.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat -Ob -aD /tmp/4Bla9USopM/concat.2.a.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/concat.2.a.bcf /tmp/4Bla9USopM/concat.2.b.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat -Ob -aD /tmp/4Bla9USopM/concat.2.a.bcf /tmp/4Bla9USopM/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/4Bla9USopM/concat.3.a.vcf.gz /tmp/4Bla9USopM/concat.3.b.vcf.gz /tmp/4Bla9USopM/concat.3.0.vcf.gz /tmp/4Bla9USopM/concat.3.c.vcf.gz /tmp/4Bla9USopM/concat.3.d.vcf.gz /tmp/4Bla9USopM/concat.3.e.vcf.gz /tmp/4Bla9USopM/concat.3.f.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat -Ob -l --ligate-warn /tmp/4Bla9USopM/concat.3.a.vcf.gz /tmp/4Bla9USopM/concat.3.b.vcf.gz /tmp/4Bla9USopM/concat.3.0.vcf.gz /tmp/4Bla9USopM/concat.3.c.vcf.gz /tmp/4Bla9USopM/concat.3.d.vcf.gz /tmp/4Bla9USopM/concat.3.e.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/concat.3.a.bcf /tmp/4Bla9USopM/concat.3.b.bcf /tmp/4Bla9USopM/concat.3.0.bcf /tmp/4Bla9USopM/concat.3.c.bcf /tmp/4Bla9USopM/concat.3.d.bcf /tmp/4Bla9USopM/concat.3.e.bcf /tmp/4Bla9USopM/concat.3.f.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat -Ob -l --ligate-warn /tmp/4Bla9USopM/concat.3.a.bcf /tmp/4Bla9USopM/concat.3.b.bcf /tmp/4Bla9USopM/concat.3.0.bcf /tmp/4Bla9USopM/concat.3.c.bcf /tmp/4Bla9USopM/concat.3.d.bcf /tmp/4Bla9USopM/concat.3.e.bcf /tmp/4Bla9USopM/concat.3.f.bcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ Random seed for test_naive_concat: 3694548244 .. ok test_naive_concat: /build/reproducible-path/bcftools-1.20/bcftools concat --naive-force /tmp/4Bla9USopM/naive_concat.0.bcf /tmp/4Bla9USopM/naive_concat.1.bcf /tmp/4Bla9USopM/naive_concat.2.bcf /tmp/4Bla9USopM/naive_concat.3.bcf /tmp/4Bla9USopM/naive_concat.4.bcf /tmp/4Bla9USopM/naive_concat.5.bcf /tmp/4Bla9USopM/naive_concat.6.bcf /tmp/4Bla9USopM/naive_concat.7.bcf /tmp/4Bla9USopM/naive_concat.8.bcf /tmp/4Bla9USopM/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/4Bla9USopM/naive_concat.0.vcf.gz /tmp/4Bla9USopM/naive_concat.1.vcf.gz /tmp/4Bla9USopM/naive_concat.2.vcf.gz /tmp/4Bla9USopM/naive_concat.3.vcf.gz /tmp/4Bla9USopM/naive_concat.4.vcf.gz /tmp/4Bla9USopM/naive_concat.5.vcf.gz /tmp/4Bla9USopM/naive_concat.6.vcf.gz /tmp/4Bla9USopM/naive_concat.7.vcf.gz /tmp/4Bla9USopM/naive_concat.8.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/concat.4.a.vcf.gz /tmp/4Bla9USopM/concat.4.b.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat -Ob -l /tmp/4Bla9USopM/concat.4.a.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/concat.4.a.bcf /tmp/4Bla9USopM/concat.4.b.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat -Ob -l /tmp/4Bla9USopM/concat.4.a.bcf /tmp/4Bla9USopM/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/4Bla9USopM/concat.5.a.vcf.gz /tmp/4Bla9USopM/concat.5.b.vcf.gz /tmp/4Bla9USopM/concat.5.c.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat -Ob -l --ligate-warn /tmp/4Bla9USopM/concat.5.a.vcf.gz /tmp/4Bla9USopM/concat.5.b.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/concat.5.a.bcf /tmp/4Bla9USopM/concat.5.b.bcf /tmp/4Bla9USopM/concat.5.c.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat -Ob -l --ligate-warn /tmp/4Bla9USopM/concat.5.a.bcf /tmp/4Bla9USopM/concat.5.b.bcf /tmp/4Bla9USopM/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/4Bla9USopM/concat.5.a.bcf /tmp/4Bla9USopM/concat.5.b.bcf /tmp/4Bla9USopM/concat.5.c.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat -Ob -l --ligate-force /tmp/4Bla9USopM/concat.5.a.bcf /tmp/4Bla9USopM/concat.5.b.bcf /tmp/4Bla9USopM/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/4Bla9USopM/concat.5.a.vcf.gz /tmp/4Bla9USopM/concat.5.b.vcf.gz /tmp/4Bla9USopM/concat.5.c.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat -Ob -G -a -D /tmp/4Bla9USopM/concat.5.a.vcf.gz /tmp/4Bla9USopM/concat.5.b.vcf.gz /tmp/4Bla9USopM/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/4Bla9USopM/concat.5.a.bcf /tmp/4Bla9USopM/concat.5.b.bcf /tmp/4Bla9USopM/concat.5.c.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat -Ob -G -a -D /tmp/4Bla9USopM/concat.5.a.bcf /tmp/4Bla9USopM/concat.5.b.bcf /tmp/4Bla9USopM/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/4Bla9USopM/reheader.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/4Bla9USopM/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/4Bla9USopM/reheader.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/4Bla9USopM/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/4Bla9USopM/reheader.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/4Bla9USopM/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/4Bla9USopM/reheader.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/4Bla9USopM/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/4Bla9USopM/reheader.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/4Bla9USopM/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/4Bla9USopM/reheader.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/4Bla9USopM/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/4Bla9USopM/reheader.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/4Bla9USopM/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/4Bla9USopM/reheader.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/4Bla9USopM/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/4Bla9USopM/reheader.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/4Bla9USopM/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/4Bla9USopM/reheader.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/4Bla9USopM/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/4Bla9USopM/empty.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/4Bla9USopM/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/4Bla9USopM/empty.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/rename.map -Ov /tmp/4Bla9USopM/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/4Bla9USopM/rename.map -Ob /tmp/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/convert.hap-missing.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/convert.gvcf.vcf.gz .. ok test_vcf_convert_gvcf: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/consensus.1.chain.new >/dev/null; cat /tmp/4Bla9USopM/consensus.1.chain.new .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/consensus.2.chain.new >/dev/null; cat /tmp/4Bla9USopM/consensus.2.chain.new .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/consensus.3.chain.new >/dev/null; cat /tmp/4Bla9USopM/consensus.3.chain.new .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/consensus.fa -H 1 -c /tmp/4Bla9USopM/consensus.4.chain.new >/dev/null; cat /tmp/4Bla9USopM/consensus.4.chain.new .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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: cd /build/reproducible-path/bcftools-1.20/test/csq/ENST00000000000 && /build/reproducible-path/bcftools-1.20/bcftools csq -p a -f ENST00000000000.fa -g ENST00000000000.gff upstream-stop.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS\t%REF\t%ALT\t%SAMPLE\t%GT\t%TBCSQ\n]' | ../sort-csq -q .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.20/test/csq/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/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/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/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/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/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: cd /build/reproducible-path/bcftools-1.20/test/csq/ENSMUST00000121418 && /build/reproducible-path/bcftools-1.20/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25496' --phase m | ../sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.20/test/csq/ENSMUST00000121418 && /build/reproducible-path/bcftools-1.20/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25500' --phase m | ../sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.20/test/csq/ENSMUST00000121418 && /build/reproducible-path/bcftools-1.20/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25105' --phase m | ../sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/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: 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: 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: /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/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/ENST00000256452/ENST00000256452.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000256452/ENST00000256452.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000256452/intron.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000518414/ENST00000518414.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000518414/ENST00000518414.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000518414/incorrect-inframe-del.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/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/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/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/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/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/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/ENST00000368801.2/ENST00000368801.2.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000368801.2/ENST00000368801.2.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000368801.2/start-lost.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/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/ENST00000410009 && /build/reproducible-path/bcftools-1.20/bcftools csq -lb -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.20/test/csq/ENST00000410009 && /build/reproducible-path/bcftools-1.20/bcftools csq -B 5 -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000410009/ENST00000410009.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000410009/ENST00000410009.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000410009/frameshift.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.20/test/csq/ENST00000410009 && /build/reproducible-path/bcftools-1.20/bcftools csq -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/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/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/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/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/ENST00000379416 && /build/reproducible-path/bcftools-1.20/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.del-snp.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.20/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-del.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.20/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-ins.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.20/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-snp.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.20/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff single.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/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/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: 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/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/ENST00000423372/ENST00000423372.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000423372/ENST00000423372.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000423372/snps.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -l -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000423372/ENST00000423372.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000423372/ENST00000423372.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000423372/snps.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000423372/ENST00000423372.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000423372/ENST00000423372.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000423372/insert3.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -l -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000423372/ENST00000423372.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000423372/ENST00000423372.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000423372/insert3.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /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/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/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/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/ENST00000571540/ENST00000571540.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000571540/ENST00000571540.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000571540/nmd.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000413103/ENST00000413103.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000413103/ENST00000413103.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000413103/long-deletion.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/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/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/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/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/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/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/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/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: 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/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/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/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/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-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-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-donor7.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -l -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/splice-acceptor-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/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/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-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/frame3.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -l -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/frame3.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/splice-acceptor-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-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/frame1.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -l -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/frame1.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/splice-acceptor-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/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: /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/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/ENST00000318249/ENST00000318249.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000318249/ENST00000318249.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000318249/start-lost.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -l -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000318249/ENST00000318249.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000318249/ENST00000318249.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000318249/start-lost.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/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/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/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/ENST00000285021/ENST00000285021.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000285021/ENST00000285021.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000285021/stop-gained-inframe-indel.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/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/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_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/4Bla9USopM/gtcheck.1.vcf.gz -g /tmp/4Bla9USopM/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/4Bla9USopM/gtcheck.1.vcf.gz -g /tmp/4Bla9USopM/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/4Bla9USopM/gtcheck.1.vcf.gz -g /tmp/4Bla9USopM/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/4Bla9USopM/gtcheck.1.vcf.gz -g /tmp/4Bla9USopM/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/4Bla9USopM/gtcheck.1.vcf.gz -g /tmp/4Bla9USopM/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/4Bla9USopM/gtcheck.1.vcf.gz -g /tmp/4Bla9USopM/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.20/bcftools gtcheck -e 0 /tmp/4Bla9USopM/gtcheck.2.vcf.gz -g /tmp/4Bla9USopM/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.20/bcftools gtcheck -e 0 /tmp/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/gtcheck.1.vcf.gz -g /tmp/4Bla9USopM/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/4Bla9USopM/gtcheck.1.vcf.gz -g /tmp/4Bla9USopM/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/4Bla9USopM/gtcheck.1.vcf.gz -g /tmp/4Bla9USopM/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/4Bla9USopM/gtcheck.1.vcf.gz -g /tmp/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/gtcheck.1.vcf.gz -g /tmp/4Bla9USopM/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/4Bla9USopM/gtcheck.1.vcf.gz -g /tmp/4Bla9USopM/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/4Bla9USopM/gtcheck.1.vcf.gz -g /tmp/4Bla9USopM/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/4Bla9USopM/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.20/bcftools gtcheck /tmp/4Bla9USopM/gtcheck.ntop.vcf.gz -g /tmp/4Bla9USopM/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/4Bla9USopM/gtcheck.ntop.vcf.gz -g /tmp/4Bla9USopM/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.20/bcftools gtcheck /tmp/4Bla9USopM/gtcheck.5.vcf.gz -g /tmp/4Bla9USopM/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/4Bla9USopM/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/4Bla9USopM/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok Number of tests: total .. 1745 passed .. 1745 failed .. 0 make[2]: Leaving directory '/build/reproducible-path/bcftools-1.20' make[1]: Leaving directory '/build/reproducible-path/bcftools-1.20' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/bcftools/ make -j42 install DESTDIR=/build/reproducible-path/bcftools-1.20/debian/bcftools AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/bcftools-1.20' mkdir -p -m 755 /build/reproducible-path/bcftools-1.20/debian/bcftools/usr/bin /build/reproducible-path/bcftools-1.20/debian/bcftools/usr/share/man/man1 /build/reproducible-path/bcftools-1.20/debian/bcftools/usr/lib/x86_64-linux-gnu/bcftools install -p bcftools /build/reproducible-path/bcftools-1.20/debian/bcftools/usr/bin install -p misc/color-chrs.pl misc/gff2gff.py misc/guess-ploidy.py misc/plot-vcfstats misc/plot-roh.py misc/run-roh.pl misc/vcfutils.pl /build/reproducible-path/bcftools-1.20/debian/bcftools/usr/bin install -p -m 644 doc/bcftools.1 /build/reproducible-path/bcftools-1.20/debian/bcftools/usr/share/man/man1 install -p plugins/*.so /build/reproducible-path/bcftools-1.20/debian/bcftools/usr/lib/x86_64-linux-gnu/bcftools make[1]: Leaving directory '/build/reproducible-path/bcftools-1.20' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/bcftools-1.20' dh_install # Fix Perl interpreter PATH for pscript in `grep -Rl '#!/usr/bin/env \+perl' debian/*` ; do \ sed -i '1s?#!/usr/bin/env \+perl?#!/usr/bin/perl?' ${pscript} ; \ done make[1]: Leaving directory '/build/reproducible-path/bcftools-1.20' dh_installdocs dh_installchangelogs debian/rules override_dh_installman make[1]: Entering directory '/build/reproducible-path/bcftools-1.20' dh_installman --language=C make[1]: Leaving directory '/build/reproducible-path/bcftools-1.20' dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dpkg-gencontrol: warning: package bcftools: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package bcftools: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'bcftools' in '../bcftools_1.20-1_amd64.deb'. dpkg-deb: building package 'bcftools-dbgsym' in '../bcftools-dbgsym_1.20-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../bcftools_1.20-1_amd64.buildinfo dpkg-genchanges --build=binary -O../bcftools_1.20-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/4183933 and its subdirectories I: Current time: Tue Jun 10 10:57:41 -12 2025 I: pbuilder-time-stamp: 1749596261 Wed May 8 16:34:41 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos1-amd64.debian.net. Wed May 8 16:34:41 UTC 2024 I: Preparing to do remote build '2' on ionos1-amd64.debian.net. Wed May 8 16:39:44 UTC 2024 I: Deleting $TMPDIR on ionos1-amd64.debian.net. Wed May 8 16:39:45 UTC 2024 I: bcftools_1.20-1_amd64.changes: Format: 1.8 Date: Thu, 18 Apr 2024 17:14:39 +0200 Source: bcftools Binary: bcftools bcftools-dbgsym Architecture: amd64 Version: 1.20-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: bcftools - genomic variant calling and manipulation of VCF/BCF files Closes: 1069234 Changes: bcftools (1.20-1) unstable; urgency=medium . [ Charles Plessy ] * Team upload. * New upstream version . [ Andreas Tille ] * Add missing Depends Closes: #1069234 * Standards-Version: 4.7.0 (routine-update) Checksums-Sha1: 740ac0edb55ef64610842ab74c77507372a5b549 2155356 bcftools-dbgsym_1.20-1_amd64.deb d6774e0d6227c75c4aa829636fcf2c87863f4786 6257 bcftools_1.20-1_amd64.buildinfo 2f27875cc22ddb07fa4bcec420a4adf42e4bc687 760100 bcftools_1.20-1_amd64.deb Checksums-Sha256: 647a0511e3a041ce6a21341bebe42cd69eefc5f97f045afb1ecb8c90b892608f 2155356 bcftools-dbgsym_1.20-1_amd64.deb 21081b3f733d80d4a3833f75dd5a22fea555963db97cc72a4b907b46331c60f4 6257 bcftools_1.20-1_amd64.buildinfo 6cf87b9b9f8c4fd8cf05dd3c571c766f35c9caf7d2642a13c015a2017e4bf7ce 760100 bcftools_1.20-1_amd64.deb Files: e3d416f1ce5abaf6c8c2e417b91f908f 2155356 debug optional bcftools-dbgsym_1.20-1_amd64.deb 8e6d512d749ad8bbde28b1c005d8efb9 6257 science optional bcftools_1.20-1_amd64.buildinfo 0d7c2d4db41d3290397900743062b082 760100 science optional bcftools_1.20-1_amd64.deb Wed May 8 16:39:46 UTC 2024 I: diffoscope 265 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_4-20125.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.ktNlkeuK/bcftools_1.20-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.ktNlkeuK/bcftools_1.20-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.ktNlkeuK/bcftools_1.20-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.ktNlkeuK/b1/bcftools_1.20-1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.ktNlkeuK/b2/bcftools_1.20-1_amd64.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: 0.399s) 0.399s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.047s) 0.047s 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: 750ms CPU time consumed: 747ms Wed May 8 16:39:47 UTC 2024 I: diffoscope 265 found no differences in the changes files, and a .buildinfo file also exists. Wed May 8 16:39:47 UTC 2024 I: bcftools from unstable built successfully and reproducibly on amd64. Wed May 8 16:39:48 UTC 2024 I: Submitting .buildinfo files to external archives: Wed May 8 16:39:48 UTC 2024 I: Submitting 8.0K b1/bcftools_1.20-1_amd64.buildinfo.asc Wed May 8 16:39:50 UTC 2024 I: Submitting 8.0K b2/bcftools_1.20-1_amd64.buildinfo.asc Wed May 8 16:39:52 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Wed May 8 16:39:52 UTC 2024 I: Done submitting .buildinfo files. Wed May 8 16:39:52 UTC 2024 I: Removing signed bcftools_1.20-1_amd64.buildinfo.asc files: removed './b1/bcftools_1.20-1_amd64.buildinfo.asc' removed './b2/bcftools_1.20-1_amd64.buildinfo.asc'