Sun May 12 13:50:30 UTC 2024 I: starting to build bcftools/unstable/arm64 on jenkins on '2024-05-12 13:50' Sun May 12 13:50:30 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_20/18095/console.log Sun May 12 13:50:30 UTC 2024 I: Downloading source for unstable/bcftools=1.20-1 --2024-05-12 13:50:30-- 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% 233M=0s 2024-05-12 13:50:30 (233 MB/s) - ‘bcftools_1.20-1.dsc’ saved [2150/2150] Sun May 12 13:50:30 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----- Sun May 12 13:50:30 UTC 2024 I: Checking whether the package is not for us Sun May 12 13:50:30 UTC 2024 I: Starting 1st build on remote node codethink02-arm64.debian.net. Sun May 12 13:50:30 UTC 2024 I: Preparing to do remote build '1' on codethink02-arm64.debian.net. Sun May 12 13:52:23 UTC 2024 I: Deleting $TMPDIR on codethink02-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun May 12 01:50:33 -12 2024 I: pbuilder-time-stamp: 1715521833 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/846407/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='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='c8297a109a1d4f1a8315b6a18511e4a5' 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='846407' 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.KvuBaBJk/pbuilderrc_iQoA --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.KvuBaBJk/b1 --logfile b1/build.log bcftools_1.20-1.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink02-arm64 6.1.0-21-cloud-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 11 07:42 /bin -> usr/bin I: user script /srv/workspace/pbuilder/846407/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: arm64 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 ... 19744 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 26.9 MB of archives. After unpacking 108 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.22 [22.4 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3 [43.0 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.21-14+b1 [160 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-4 [1130 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40-8 [93.0 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.7-2 [36.5 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.12.1-1 [1394 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.21-14 [496 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libtool all 2.4.7-7 [517 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 23 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.191-1+b1 [187 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-4+b1 [9224 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.9.14+dfsg-1.3+b3 [624 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.21-14+b1 [1249 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.15.3 [901 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b3 [295 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 libbz2-dev arm64 1.0.8-5.1 [31.8 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.1~rc2-1 [22.5 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.20.1-6+b1 [33.0 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.20.1-6+b1 [80.5 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-3 [9112 B] Get: 37 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.20.1-6+b1 [315 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.20.1-6+b1 [124 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-6 [20.1 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-6 [55.3 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 libldap-2.5-0 arm64 2.5.17+dfsg-1 [173 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 libnghttp2-14 arm64 1.61.0-1+b1 [71.0 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 libpsl5t64 arm64 0.21.2-1.1 [56.8 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b4 [56.7 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 libssh2-1t64 arm64 1.11.0-4.1+b2 [207 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 libcurl3t64-gnutls arm64 8.7.1-5 [405 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 libcurl4-gnutls-dev arm64 8.7.1-5 [524 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 libdeflate0 arm64 1.20-1 [41.5 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 libdeflate-dev arm64 1.20-1 [50.5 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 libgslcblas0 arm64 2.7.1+dfsg-6+b1 [72.7 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 libgsl27 arm64 2.7.1+dfsg-6+b1 [822 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 libgsl-dev arm64 2.7.1+dfsg-6+b1 [1039 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 libhtscodecs2 arm64 1.6.0-1+b1 [71.6 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 libhts3t64 arm64 1.19+ds-1.1+b1 [413 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 liblzma-dev arm64 5.6.1+really5.4.5-1 [289 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1 [916 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 libhts-dev arm64 1.19+ds-1.1+b1 [1604 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 libio-pty-perl arm64 1:1.20-1+b1 [34.0 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 tabix arm64 1.19+ds-1.1+b1 [445 kB] Fetched 26.9 MB in 0s (126 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 ... 19744 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_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3_arm64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-14+b1_arm64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-4_arm64.deb ... Unpacking groff-base (1.23.0-4) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40-8_arm64.deb ... Unpacking bsdextrautils (2.40-8) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../08-libpipeline1_1.5.7-2_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.12.1-1_arm64.deb ... Unpacking man-db (2.12.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_arm64.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:arm64. Preparing to unpack .../22-libelf1t64_0.191-1+b1_arm64.deb ... Unpacking libelf1t64:arm64 (0.191-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../24-libicu72_72.1-4+b1_arm64.deb ... Unpacking libicu72:arm64 (72.1-4+b1) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../25-libxml2_2.9.14+dfsg-1.3+b3_arm64.deb ... Unpacking libxml2:arm64 (2.9.14+dfsg-1.3+b3) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.21-14+b1_arm64.deb ... Unpacking gettext (0.21-14+b1) ... Selecting previously unselected package intltool-debian. 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/bcftools-1.20/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../bcftools_1.20-1_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 arm64 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 -j12 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/aarch64-linux-gnu/bcftools ./configure --build=aarch64-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/aarch64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system --enable-gsl --with-cblas=gslcblas --with-bcf-plugin-dir=/usr/lib/aarch64-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 -j12 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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o consensus.o 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DPLUGINPATH='"/usr/lib/aarch64-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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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 -mbranch-protection=standard -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/D2PQpyhQgh/merge.a.vcf.gz 2:3199812-3199812 .. ok test_tabix: /build/reproducible-path/bcftools-1.20/bcftools view -H /tmp/D2PQpyhQgh/merge.a.bcf 2:3199812-3199812 .. ok test_tabix: tabix /tmp/D2PQpyhQgh/merge.a.vcf.gz 1:3000151-3000151 .. ok test_tabix: /build/reproducible-path/bcftools-1.20/bcftools view -H /tmp/D2PQpyhQgh/merge.a.bcf 1:3000151-3000151 .. ok test_index: /build/reproducible-path/bcftools-1.20/bcftools view -H /tmp/D2PQpyhQgh/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /build/reproducible-path/bcftools-1.20/bcftools view -H /tmp/D2PQpyhQgh/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/reproducible-path/bcftools-1.20/bcftools view -H /tmp/D2PQpyhQgh/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/reproducible-path/bcftools-1.20/bcftools view -H /tmp/D2PQpyhQgh/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /build/reproducible-path/bcftools-1.20/bcftools view -H /tmp/D2PQpyhQgh/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/reproducible-path/bcftools-1.20/bcftools view -H /tmp/D2PQpyhQgh/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /build/reproducible-path/bcftools-1.20/bcftools view -H /tmp/D2PQpyhQgh/large_chrom_csi_limit.bcf chr20 .. ok test_index: /build/reproducible-path/bcftools-1.20/bcftools view -H /tmp/D2PQpyhQgh/large_chrom_csi_limit.bcf chr20 .. ok test_index: /build/reproducible-path/bcftools-1.20/bcftools view -H /tmp/D2PQpyhQgh/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /build/reproducible-path/bcftools-1.20/bcftools view -H /tmp/D2PQpyhQgh/large_chrom_csi_limit.bcf chr20 .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.20/bcftools index -s /tmp/D2PQpyhQgh/idx.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.20/bcftools index -s /tmp/D2PQpyhQgh/idx.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.20/bcftools index -s /tmp/D2PQpyhQgh/idx.bcf .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.20/bcftools index -n /tmp/D2PQpyhQgh/idx.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.20/bcftools index -n /tmp/D2PQpyhQgh/idx.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.20/bcftools index -n /tmp/D2PQpyhQgh/idx.vcf.gz.csi .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.20/bcftools index -n /tmp/D2PQpyhQgh/idx.bcf .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.20/bcftools index -n /tmp/D2PQpyhQgh/idx.bcf.csi .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.20/bcftools index -s /tmp/D2PQpyhQgh/empty.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.20/bcftools index -s /tmp/D2PQpyhQgh/empty.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.20/bcftools index -s /tmp/D2PQpyhQgh/empty.bcf .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.20/bcftools index -n /tmp/D2PQpyhQgh/empty.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.20/bcftools index -n /tmp/D2PQpyhQgh/empty.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.20/bcftools index -n /tmp/D2PQpyhQgh/empty.vcf.gz.csi .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.20/bcftools index -n /tmp/D2PQpyhQgh/empty.bcf .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.20/bcftools index -n /tmp/D2PQpyhQgh/empty.bcf.csi .. ok test_vcf_check: /build/reproducible-path/bcftools-1.20/bcftools stats -s - /tmp/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/check.1.chk /tmp/D2PQpyhQgh/check.2.chk /tmp/D2PQpyhQgh/check.3.chk /tmp/D2PQpyhQgh/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/D2PQpyhQgh/stats.a.vcf.gz /tmp/D2PQpyhQgh/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/reproducible-path/bcftools-1.20/bcftools stats -s B /tmp/D2PQpyhQgh/stats.a.vcf.gz /tmp/D2PQpyhQgh/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/reproducible-path/bcftools-1.20/bcftools stats -s - /tmp/D2PQpyhQgh/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/D2PQpyhQgh/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/reproducible-path/bcftools-1.20/bcftools stats -s - /tmp/D2PQpyhQgh/stats.vaf.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.20/bcftools isec -n =2 /tmp/D2PQpyhQgh/isec.a.vcf.gz /tmp/D2PQpyhQgh/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.20/bcftools isec -Ob -n =2 /tmp/D2PQpyhQgh/isec.a.vcf.gz /tmp/D2PQpyhQgh/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.20/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/D2PQpyhQgh/isec.a.vcf.gz /tmp/D2PQpyhQgh/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.20/bcftools isec -Ob -n =2 -i"STRLEN(REF)==2" /tmp/D2PQpyhQgh/isec.a.vcf.gz /tmp/D2PQpyhQgh/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.20/bcftools isec -n =2 -c both /tmp/D2PQpyhQgh/isec.a.vcf.gz /tmp/D2PQpyhQgh/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.20/bcftools isec -Ob -n =2 -c both /tmp/D2PQpyhQgh/isec.a.vcf.gz /tmp/D2PQpyhQgh/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.20/bcftools isec -n =2 -c any /tmp/D2PQpyhQgh/isec.a.vcf.gz /tmp/D2PQpyhQgh/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.20/bcftools isec -Ob -n =2 -c any /tmp/D2PQpyhQgh/isec.a.vcf.gz /tmp/D2PQpyhQgh/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.20/bcftools isec -C -c any /tmp/D2PQpyhQgh/isec.a.vcf.gz /tmp/D2PQpyhQgh/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.20/bcftools isec -Ob -C -c any /tmp/D2PQpyhQgh/isec.a.vcf.gz /tmp/D2PQpyhQgh/isec.b.vcf.gz .. ok test_vcf_isec2: /build/reproducible-path/bcftools-1.20/bcftools isec --no-version -T /tmp/D2PQpyhQgh/isec.tab.gz /tmp/D2PQpyhQgh/isec.a.vcf.gz .. ok test_vcf_isec2: /build/reproducible-path/bcftools-1.20/bcftools isec -Ob -T /tmp/D2PQpyhQgh/isec.tab.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/isec-miss.1.1.vcf.gz /tmp/D2PQpyhQgh/isec-miss.1.2.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/isec-miss.1.1.vcf.gz /tmp/D2PQpyhQgh/isec-miss.1.2.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/isec-miss.1.1.vcf.gz /tmp/D2PQpyhQgh/isec-miss.1.2.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/isec-miss.1.1.vcf.gz /tmp/D2PQpyhQgh/isec-miss.1.2.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/isec-miss.2.1.vcf.gz /tmp/D2PQpyhQgh/isec-miss.2.2.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/isec-miss.2.1.vcf.gz /tmp/D2PQpyhQgh/isec-miss.2.2.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/isec-miss.2.1.vcf.gz /tmp/D2PQpyhQgh/isec-miss.2.2.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/isec-miss.2.1.vcf.gz /tmp/D2PQpyhQgh/isec-miss.2.2.vcf.gz /tmp/D2PQpyhQgh/isec-miss.2.3.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -i AF:join /tmp/D2PQpyhQgh/merge.join.a.vcf.gz /tmp/D2PQpyhQgh/merge.join.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob -i AF:join /tmp/D2PQpyhQgh/merge.join.a.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.join.a.bcf /tmp/D2PQpyhQgh/merge.join.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob -i AF:join /tmp/D2PQpyhQgh/merge.join.a.bcf /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.LPL.a.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-single /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.LPL.a.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-single /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.LPL.a.vcf.gz /tmp/D2PQpyhQgh/merge.LPL.b.vcf.gz /tmp/D2PQpyhQgh/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples /tmp/D2PQpyhQgh/merge.LPL.a.vcf.gz /tmp/D2PQpyhQgh/merge.LPL.b.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.LPL.a.bcf /tmp/D2PQpyhQgh/merge.LPL.b.bcf /tmp/D2PQpyhQgh/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples /tmp/D2PQpyhQgh/merge.LPL.a.bcf /tmp/D2PQpyhQgh/merge.LPL.b.bcf /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.LPL.a.vcf.gz /tmp/D2PQpyhQgh/merge.LPL.b.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.LPL.a.vcf.gz /tmp/D2PQpyhQgh/merge.LPL.b.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.LPL.a.bcf /tmp/D2PQpyhQgh/merge.LPL.b.bcf /tmp/D2PQpyhQgh/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -L 1 /tmp/D2PQpyhQgh/merge.LPL.a.bcf /tmp/D2PQpyhQgh/merge.LPL.b.bcf /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.LPL.a.vcf.gz /tmp/D2PQpyhQgh/merge.LPL.b.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.LPL.a.vcf.gz /tmp/D2PQpyhQgh/merge.LPL.b.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.LPL.a.bcf /tmp/D2PQpyhQgh/merge.LPL.b.bcf /tmp/D2PQpyhQgh/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -L 2 /tmp/D2PQpyhQgh/merge.LPL.a.bcf /tmp/D2PQpyhQgh/merge.LPL.b.bcf /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.LPL.a.vcf.gz /tmp/D2PQpyhQgh/merge.LPL.b.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.LPL.a.vcf.gz /tmp/D2PQpyhQgh/merge.LPL.b.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.LPL.a.bcf /tmp/D2PQpyhQgh/merge.LPL.b.bcf /tmp/D2PQpyhQgh/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -L 3 /tmp/D2PQpyhQgh/merge.LPL.a.bcf /tmp/D2PQpyhQgh/merge.LPL.b.bcf /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.LPL.a.vcf.gz /tmp/D2PQpyhQgh/merge.LPL.b.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.LPL.a.vcf.gz /tmp/D2PQpyhQgh/merge.LPL.b.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.LPL.a.bcf /tmp/D2PQpyhQgh/merge.LPL.b.bcf /tmp/D2PQpyhQgh/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -L 4 /tmp/D2PQpyhQgh/merge.LPL.a.bcf /tmp/D2PQpyhQgh/merge.LPL.b.bcf /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.LPL.a.vcf.gz /tmp/D2PQpyhQgh/merge.LPL.b.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.LPL.a.vcf.gz /tmp/D2PQpyhQgh/merge.LPL.b.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.LPL.a.bcf /tmp/D2PQpyhQgh/merge.LPL.b.bcf /tmp/D2PQpyhQgh/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -L 5 /tmp/D2PQpyhQgh/merge.LPL.a.bcf /tmp/D2PQpyhQgh/merge.LPL.b.bcf /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.a.vcf.gz /tmp/D2PQpyhQgh/merge.b.vcf.gz /tmp/D2PQpyhQgh/merge.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples /tmp/D2PQpyhQgh/merge.a.vcf.gz /tmp/D2PQpyhQgh/merge.b.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.a.bcf /tmp/D2PQpyhQgh/merge.b.bcf /tmp/D2PQpyhQgh/merge.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples /tmp/D2PQpyhQgh/merge.a.bcf /tmp/D2PQpyhQgh/merge.b.bcf /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.a.vcf.gz /tmp/D2PQpyhQgh/merge.b.vcf.gz /tmp/D2PQpyhQgh/merge.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -Fx /tmp/D2PQpyhQgh/merge.a.vcf.gz /tmp/D2PQpyhQgh/merge.b.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.a.bcf /tmp/D2PQpyhQgh/merge.b.bcf /tmp/D2PQpyhQgh/merge.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -Fx /tmp/D2PQpyhQgh/merge.a.bcf /tmp/D2PQpyhQgh/merge.b.bcf /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.a.vcf.gz /tmp/D2PQpyhQgh/merge.b.vcf.gz /tmp/D2PQpyhQgh/merge.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -0 /tmp/D2PQpyhQgh/merge.a.vcf.gz /tmp/D2PQpyhQgh/merge.b.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.a.bcf /tmp/D2PQpyhQgh/merge.b.bcf /tmp/D2PQpyhQgh/merge.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -0 /tmp/D2PQpyhQgh/merge.a.bcf /tmp/D2PQpyhQgh/merge.b.bcf /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.2.a.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.2.a.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.2.a.bcf /tmp/D2PQpyhQgh/merge.2.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -m none /tmp/D2PQpyhQgh/merge.2.a.bcf /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.2.a.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.2.a.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.2.a.bcf /tmp/D2PQpyhQgh/merge.2.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -m both /tmp/D2PQpyhQgh/merge.2.a.bcf /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.2.a.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.2.a.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.2.a.bcf /tmp/D2PQpyhQgh/merge.2.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -m all /tmp/D2PQpyhQgh/merge.2.a.bcf /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.3.a.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.3.a.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.3.a.bcf /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.3.a.bcf /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.4.a.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.4.a.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.4.a.bcf /tmp/D2PQpyhQgh/merge.4.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples -m id /tmp/D2PQpyhQgh/merge.4.a.bcf /tmp/D2PQpyhQgh/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/D2PQpyhQgh/gvcf.merge.1.vcf.gz /tmp/D2PQpyhQgh/gvcf.merge.2.vcf.gz /tmp/D2PQpyhQgh/gvcf.merge.3.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/D2PQpyhQgh/gvcf.merge.1.vcf.gz /tmp/D2PQpyhQgh/gvcf.merge.2.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/gvcf.merge.1.bcf /tmp/D2PQpyhQgh/gvcf.merge.2.bcf /tmp/D2PQpyhQgh/gvcf.merge.3.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/D2PQpyhQgh/gvcf.merge.1.bcf /tmp/D2PQpyhQgh/gvcf.merge.2.bcf /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.gvcf.2.a.vcf.gz /tmp/D2PQpyhQgh/merge.gvcf.2.b.vcf.gz /tmp/D2PQpyhQgh/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/D2PQpyhQgh/merge.gvcf.2.a.vcf.gz /tmp/D2PQpyhQgh/merge.gvcf.2.b.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.gvcf.2.a.vcf.gz /tmp/D2PQpyhQgh/merge.gvcf.2.b.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.gvcf.2.a.vcf.gz /tmp/D2PQpyhQgh/merge.gvcf.2.b.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.gvcf.2.a.vcf.gz /tmp/D2PQpyhQgh/merge.gvcf.2.b.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.gvcf.2.a.vcf.gz /tmp/D2PQpyhQgh/merge.gvcf.2.b.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.gvcf.3.a.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.gvcf.3.a.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.gvcf.4.a.vcf.gz /tmp/D2PQpyhQgh/merge.gvcf.4.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/D2PQpyhQgh/merge.gvcf.4.a.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.gvcf.4.a.bcf /tmp/D2PQpyhQgh/merge.gvcf.4.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/D2PQpyhQgh/merge.gvcf.4.a.bcf /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.5.a.vcf.gz /tmp/D2PQpyhQgh/merge.5.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob /tmp/D2PQpyhQgh/merge.5.a.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.5.a.bcf /tmp/D2PQpyhQgh/merge.5.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob /tmp/D2PQpyhQgh/merge.5.a.bcf /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.6.a.vcf.gz /tmp/D2PQpyhQgh/merge.6.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob /tmp/D2PQpyhQgh/merge.6.a.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.6.a.bcf /tmp/D2PQpyhQgh/merge.6.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob /tmp/D2PQpyhQgh/merge.6.a.bcf /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.gvcf.7.a.vcf.gz /tmp/D2PQpyhQgh/merge.gvcf.7.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/D2PQpyhQgh/merge.gvcf.7.a.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.gvcf.7.a.bcf /tmp/D2PQpyhQgh/merge.gvcf.7.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/D2PQpyhQgh/merge.gvcf.7.a.bcf /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.gvcf.8.a.vcf.gz /tmp/D2PQpyhQgh/merge.gvcf.8.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/D2PQpyhQgh/merge.gvcf.8.a.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.gvcf.8.a.bcf /tmp/D2PQpyhQgh/merge.gvcf.8.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/D2PQpyhQgh/merge.gvcf.8.a.bcf /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.7.a.vcf.gz /tmp/D2PQpyhQgh/merge.7.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples /tmp/D2PQpyhQgh/merge.7.a.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.7.a.bcf /tmp/D2PQpyhQgh/merge.7.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --force-samples /tmp/D2PQpyhQgh/merge.7.a.bcf /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.gvcf.9a.vcf.gz /tmp/D2PQpyhQgh/merge.gvcf.9b.vcf.gz /tmp/D2PQpyhQgh/merge.gvcf.9c.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.gvcf.9a.vcf.gz /tmp/D2PQpyhQgh/merge.gvcf.9b.vcf.gz /tmp/D2PQpyhQgh/merge.gvcf.9c.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.gvcf.9a.bcf /tmp/D2PQpyhQgh/merge.gvcf.9b.bcf /tmp/D2PQpyhQgh/merge.gvcf.9c.bcf /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.gvcf.9a.bcf /tmp/D2PQpyhQgh/merge.gvcf.9b.bcf /tmp/D2PQpyhQgh/merge.gvcf.9c.bcf /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.gvcf.9a.vcf.gz /tmp/D2PQpyhQgh/merge.gvcf.9b.vcf.gz /tmp/D2PQpyhQgh/merge.gvcf.9c.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.gvcf.9a.vcf.gz /tmp/D2PQpyhQgh/merge.gvcf.9b.vcf.gz /tmp/D2PQpyhQgh/merge.gvcf.9c.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.gvcf.9a.bcf /tmp/D2PQpyhQgh/merge.gvcf.9b.bcf /tmp/D2PQpyhQgh/merge.gvcf.9c.bcf /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.gvcf.9a.bcf /tmp/D2PQpyhQgh/merge.gvcf.9b.bcf /tmp/D2PQpyhQgh/merge.gvcf.9c.bcf /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.gvcf.9a.vcf.gz /tmp/D2PQpyhQgh/merge.gvcf.9b.vcf.gz /tmp/D2PQpyhQgh/merge.gvcf.9c.vcf.gz /tmp/D2PQpyhQgh/merge.gvcf.9d.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.gvcf.9a.vcf.gz /tmp/D2PQpyhQgh/merge.gvcf.9b.vcf.gz /tmp/D2PQpyhQgh/merge.gvcf.9c.vcf.gz /tmp/D2PQpyhQgh/merge.gvcf.9d.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.gvcf.9a.bcf /tmp/D2PQpyhQgh/merge.gvcf.9b.bcf /tmp/D2PQpyhQgh/merge.gvcf.9c.bcf /tmp/D2PQpyhQgh/merge.gvcf.9d.bcf /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.gvcf.9a.bcf /tmp/D2PQpyhQgh/merge.gvcf.9b.bcf /tmp/D2PQpyhQgh/merge.gvcf.9c.bcf /tmp/D2PQpyhQgh/merge.gvcf.9d.bcf /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.gvcf.9a.vcf.gz /tmp/D2PQpyhQgh/merge.gvcf.9b.vcf.gz /tmp/D2PQpyhQgh/merge.gvcf.9c.vcf.gz /tmp/D2PQpyhQgh/merge.gvcf.9d.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.gvcf.9a.vcf.gz /tmp/D2PQpyhQgh/merge.gvcf.9b.vcf.gz /tmp/D2PQpyhQgh/merge.gvcf.9c.vcf.gz /tmp/D2PQpyhQgh/merge.gvcf.9d.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.gvcf.9a.bcf /tmp/D2PQpyhQgh/merge.gvcf.9b.bcf /tmp/D2PQpyhQgh/merge.gvcf.9c.bcf /tmp/D2PQpyhQgh/merge.gvcf.9d.bcf /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.gvcf.9a.bcf /tmp/D2PQpyhQgh/merge.gvcf.9b.bcf /tmp/D2PQpyhQgh/merge.gvcf.9c.bcf /tmp/D2PQpyhQgh/merge.gvcf.9d.bcf /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.gvcf.10.a.vcf.gz /tmp/D2PQpyhQgh/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob /tmp/D2PQpyhQgh/merge.gvcf.10.a.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.gvcf.10.a.bcf /tmp/D2PQpyhQgh/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob /tmp/D2PQpyhQgh/merge.gvcf.10.a.bcf /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.gvcf.10.a.vcf.gz /tmp/D2PQpyhQgh/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob -m none /tmp/D2PQpyhQgh/merge.gvcf.10.a.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.gvcf.10.a.bcf /tmp/D2PQpyhQgh/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob -m none /tmp/D2PQpyhQgh/merge.gvcf.10.a.bcf /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.gvcf.10.a.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.gvcf.10.a.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.gvcf.10.a.bcf /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.gvcf.10.a.bcf /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.gvcf.10.a.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.gvcf.10.a.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.gvcf.10.a.bcf /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.gvcf.10.a.bcf /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.noidx.a.vcf.gz /tmp/D2PQpyhQgh/merge.noidx.b.vcf.gz /tmp/D2PQpyhQgh/merge.noidx.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob /tmp/D2PQpyhQgh/merge.noidx.a.vcf.gz /tmp/D2PQpyhQgh/merge.noidx.b.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.noidx.a.bcf /tmp/D2PQpyhQgh/merge.noidx.b.bcf /tmp/D2PQpyhQgh/merge.noidx.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob /tmp/D2PQpyhQgh/merge.noidx.a.bcf /tmp/D2PQpyhQgh/merge.noidx.b.bcf /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.noidx.a.bcf /tmp/D2PQpyhQgh/merge.noidx.b.bcf /tmp/D2PQpyhQgh/merge.noidx.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --no-index /tmp/D2PQpyhQgh/merge.noidx.a.bcf /tmp/D2PQpyhQgh/merge.noidx.b.bcf /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.8.a.vcf.gz /tmp/D2PQpyhQgh/merge.8.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob /tmp/D2PQpyhQgh/merge.8.a.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.8.a.bcf /tmp/D2PQpyhQgh/merge.8.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob /tmp/D2PQpyhQgh/merge.8.a.bcf /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.8.a.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.8.a.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.8.a.bcf /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.8.a.bcf /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.9.a.vcf.gz /tmp/D2PQpyhQgh/merge.9.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob /tmp/D2PQpyhQgh/merge.9.a.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.9.a.bcf /tmp/D2PQpyhQgh/merge.9.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob /tmp/D2PQpyhQgh/merge.9.a.bcf /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.9.a.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.9.a.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.9.a.bcf /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.9.a.bcf /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.10.a.vcf.gz /tmp/D2PQpyhQgh/merge.10.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob -m none /tmp/D2PQpyhQgh/merge.10.a.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.10.a.bcf /tmp/D2PQpyhQgh/merge.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob -m none /tmp/D2PQpyhQgh/merge.10.a.bcf /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.10.a.vcf.gz /tmp/D2PQpyhQgh/merge.10.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob -m both /tmp/D2PQpyhQgh/merge.10.a.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.10.a.bcf /tmp/D2PQpyhQgh/merge.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob -m both /tmp/D2PQpyhQgh/merge.10.a.bcf /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.10.a.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.10.a.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.10.a.bcf /tmp/D2PQpyhQgh/merge.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob -m snp-ins-del /tmp/D2PQpyhQgh/merge.10.a.bcf /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.mrules.1.a.vcf.gz /tmp/D2PQpyhQgh/merge.mrules.1.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/D2PQpyhQgh/merge.mrules.1.a.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.mrules.1.a.bcf /tmp/D2PQpyhQgh/merge.mrules.1.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/D2PQpyhQgh/merge.mrules.1.a.bcf /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.mrules.1.a.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.mrules.1.a.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.mrules.1.a.bcf /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.mrules.1.a.bcf /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.gvcf.5.a.vcf.gz /tmp/D2PQpyhQgh/merge.gvcf.5.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/D2PQpyhQgh/merge.gvcf.5.a.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.gvcf.5.a.bcf /tmp/D2PQpyhQgh/merge.gvcf.5.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/D2PQpyhQgh/merge.gvcf.5.a.bcf /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.gvcf.5.a.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.gvcf.5.a.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.gvcf.5.a.bcf /tmp/D2PQpyhQgh/merge.gvcf.5.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - --merge none /tmp/D2PQpyhQgh/merge.gvcf.5.a.bcf /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.gvcf.11.a.vcf.gz /tmp/D2PQpyhQgh/merge.gvcf.11.b.vcf.gz /tmp/D2PQpyhQgh/merge.gvcf.11.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/D2PQpyhQgh/merge.gvcf.11.a.vcf.gz /tmp/D2PQpyhQgh/merge.gvcf.11.b.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/merge.gvcf.11.a.bcf /tmp/D2PQpyhQgh/merge.gvcf.11.b.bcf /tmp/D2PQpyhQgh/merge.gvcf.11.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.20/bcftools merge --no-version -Ob --gvcf - /tmp/D2PQpyhQgh/merge.gvcf.11.a.bcf /tmp/D2PQpyhQgh/merge.gvcf.11.b.bcf /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.string.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.string.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.string.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.string.2.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.string.2.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.variantkey.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/view.vectors.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.2.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.filter-type.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.filter-type.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.filter-type.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.filter-type.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.filter-type.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/filter-missing-floats.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/filter-missing-floats.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.filter.2.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.filter.3.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.filter.3.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.filter.3.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.filter.4.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/view.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.negative.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.negative.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.negative.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.negative.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.filter.6.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.filter.8.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.filter.8.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.filter.9.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.filter.9.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.filter.13.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.filter.10.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.filter.10.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.filter.id.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.filter.id.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/filter.10.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/filter.13.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.filter-or.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/query.filter-or.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/norm.split.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m- /tmp/D2PQpyhQgh/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/D2PQpyhQgh/norm.split.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m- /tmp/D2PQpyhQgh/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/D2PQpyhQgh/norm.split.3.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m- --force /tmp/D2PQpyhQgh/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/D2PQpyhQgh/norm.split.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m- /tmp/D2PQpyhQgh/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/D2PQpyhQgh/norm.split.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m- --keep-sum AD /tmp/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/norm.merge.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m+ /tmp/D2PQpyhQgh/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/D2PQpyhQgh/norm.merge.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m+ /tmp/D2PQpyhQgh/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/D2PQpyhQgh/norm.merge.3.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m+ /tmp/D2PQpyhQgh/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/D2PQpyhQgh/norm.merge.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m+ -s /tmp/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -d snps /tmp/D2PQpyhQgh/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/D2PQpyhQgh/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -d indels /tmp/D2PQpyhQgh/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/D2PQpyhQgh/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -d both /tmp/D2PQpyhQgh/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/D2PQpyhQgh/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -d all /tmp/D2PQpyhQgh/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/D2PQpyhQgh/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -d none /tmp/D2PQpyhQgh/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/D2PQpyhQgh/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -d exact /tmp/D2PQpyhQgh/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/D2PQpyhQgh/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -d none /tmp/D2PQpyhQgh/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/D2PQpyhQgh/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -d exact /tmp/D2PQpyhQgh/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/D2PQpyhQgh/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -d indels /tmp/D2PQpyhQgh/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/D2PQpyhQgh/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -d any /tmp/D2PQpyhQgh/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/D2PQpyhQgh/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -d both /tmp/D2PQpyhQgh/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/D2PQpyhQgh/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -d snps /tmp/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/atomize.split.3.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version --atomize --atom-overlaps . /tmp/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/norm.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m +both /tmp/D2PQpyhQgh/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/D2PQpyhQgh/norm.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m +any /tmp/D2PQpyhQgh/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/D2PQpyhQgh/norm.5.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m - --multi-overlaps 0 /tmp/D2PQpyhQgh/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/D2PQpyhQgh/norm.5.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m - --multi-overlaps . /tmp/D2PQpyhQgh/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/D2PQpyhQgh/norm.m-any.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m -any /tmp/D2PQpyhQgh/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/D2PQpyhQgh/norm.phased-split.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m -any /tmp/D2PQpyhQgh/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/D2PQpyhQgh/norm.phased-join.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m +any /tmp/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/norm.string-tags.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m -any /tmp/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/norm.merge.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m +any /tmp/D2PQpyhQgh/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/D2PQpyhQgh/norm.merge.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.20/bcftools norm --no-version -m +both /tmp/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/merge.gvcf.2.a.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -HAA /tmp/D2PQpyhQgh/merge.gvcf.2.a.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version /tmp/D2PQpyhQgh/weird-chr-names.vcf.gz -r 1 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/weird-chr-names.vcf.gz -r 1:1-2 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/weird-chr-names.vcf.gz -r 1:1,1:2 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/weird-chr-names.vcf.gz -r 1:1-1 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/weird-chr-names.vcf.gz -r {1:1} .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/weird-chr-names.vcf.gz -r {1:1}:1-2 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/weird-chr-names.vcf.gz -r {1:1}:1-1 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/weird-chr-names.vcf.gz -r {1:1-1} .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/D2PQpyhQgh/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/D2PQpyhQgh/view.vcf.gz -r20,Y .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -f PASS -Xks NA00003 /tmp/D2PQpyhQgh/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/D2PQpyhQgh/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -xs NA00003 /tmp/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -p /tmp/D2PQpyhQgh/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/D2PQpyhQgh/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -P /tmp/D2PQpyhQgh/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/D2PQpyhQgh/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/D2PQpyhQgh/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/D2PQpyhQgh/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -GVsnps /tmp/D2PQpyhQgh/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -GVsnps /tmp/D2PQpyhQgh/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/D2PQpyhQgh/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/D2PQpyhQgh/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/D2PQpyhQgh/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -s ^NA00003 /tmp/D2PQpyhQgh/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/D2PQpyhQgh/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -G /tmp/D2PQpyhQgh/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/D2PQpyhQgh/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -a /tmp/D2PQpyhQgh/many.alleles.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -a /tmp/D2PQpyhQgh/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/D2PQpyhQgh/view.vectors.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -asA /tmp/D2PQpyhQgh/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/D2PQpyhQgh/view.vectors.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -asB /tmp/D2PQpyhQgh/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/D2PQpyhQgh/view.vectors.2.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -asA /tmp/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/view.filter.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -H -i'TXT0="text"' /tmp/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/filter.2.vcf.gz 1:3062917-3157410 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view -Ob -i 'POS>=3062917' /tmp/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/idx.4.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -Ht 2 /tmp/D2PQpyhQgh/view-t.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -Ht 3 /tmp/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -H -c6:nonmajor /tmp/D2PQpyhQgh/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -H -q0.3:major /tmp/D2PQpyhQgh/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/view.filter.annovar.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -H -a /tmp/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/mpileup.2.vcf.gz .. ok test_vcf_head2: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/mpileup.2.vcf.gz .. ok test_vcf_head2: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/mpileup.2.vcf.gz .. ok test_vcf_head2: /build/reproducible-path/bcftools-1.20/bcftools view --no-version -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.20/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/D2PQpyhQgh/regions.tab.gz /tmp/D2PQpyhQgh/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/regions.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/D2PQpyhQgh/regions.tab.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.20/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/D2PQpyhQgh/regions.tab.gz /tmp/D2PQpyhQgh/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.20/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/D2PQpyhQgh/regions.bed /tmp/D2PQpyhQgh/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/regions.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/D2PQpyhQgh/regions.bed .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.20/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/D2PQpyhQgh/regions.bed /tmp/D2PQpyhQgh/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.20/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/D2PQpyhQgh/regions.bed.gz /tmp/D2PQpyhQgh/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/regions.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/D2PQpyhQgh/regions.bed.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.20/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/D2PQpyhQgh/regions.bed.gz /tmp/D2PQpyhQgh/regions.vcf.gz .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.20/bcftools annotate -a /tmp/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/D2PQpyhQgh/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/D2PQpyhQgh/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/D2PQpyhQgh/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/D2PQpyhQgh/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/D2PQpyhQgh/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/D2PQpyhQgh/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/D2PQpyhQgh/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/D2PQpyhQgh/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/D2PQpyhQgh/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/D2PQpyhQgh/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/D2PQpyhQgh/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/D2PQpyhQgh/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/D2PQpyhQgh/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/D2PQpyhQgh/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/D2PQpyhQgh/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/D2PQpyhQgh/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/D2PQpyhQgh/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/D2PQpyhQgh/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/D2PQpyhQgh/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/D2PQpyhQgh/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/D2PQpyhQgh/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/D2PQpyhQgh/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/D2PQpyhQgh/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/D2PQpyhQgh/annots4.vcf.gz -c +INFO /tmp/D2PQpyhQgh/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/D2PQpyhQgh/annots4.vcf.gz -c +INFO /tmp/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/D2PQpyhQgh/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/D2PQpyhQgh/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/D2PQpyhQgh/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/D2PQpyhQgh/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/D2PQpyhQgh/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/D2PQpyhQgh/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/D2PQpyhQgh/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/D2PQpyhQgh/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/D2PQpyhQgh/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/D2PQpyhQgh/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/D2PQpyhQgh/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/D2PQpyhQgh/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/D2PQpyhQgh/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/D2PQpyhQgh/annots11.vcf.gz -c FMT /tmp/D2PQpyhQgh/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/D2PQpyhQgh/annots11.vcf.gz -c FMT /tmp/D2PQpyhQgh/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/D2PQpyhQgh/annots2.vcf.gz -c FMT/newGT:=GT /tmp/D2PQpyhQgh/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/D2PQpyhQgh/annots2.vcf.gz -c FMT/newGT:=GT /tmp/D2PQpyhQgh/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/D2PQpyhQgh/annots12.vcf.gz -c FMT/GT:=newGT /tmp/D2PQpyhQgh/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/D2PQpyhQgh/annots12.vcf.gz -c FMT/GT:=newGT /tmp/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/D2PQpyhQgh/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/D2PQpyhQgh/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/D2PQpyhQgh/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/D2PQpyhQgh/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/D2PQpyhQgh/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/D2PQpyhQgh/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/D2PQpyhQgh/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/D2PQpyhQgh/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/D2PQpyhQgh/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/D2PQpyhQgh/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/D2PQpyhQgh/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/D2PQpyhQgh/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER /tmp/D2PQpyhQgh/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/D2PQpyhQgh/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER /tmp/D2PQpyhQgh/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/D2PQpyhQgh/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER /tmp/D2PQpyhQgh/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/D2PQpyhQgh/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER /tmp/D2PQpyhQgh/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/D2PQpyhQgh/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER,FILTER /tmp/D2PQpyhQgh/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/D2PQpyhQgh/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER,FILTER /tmp/D2PQpyhQgh/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/D2PQpyhQgh/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=./FILTER /tmp/D2PQpyhQgh/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/D2PQpyhQgh/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=./FILTER /tmp/D2PQpyhQgh/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/D2PQpyhQgh/annotate20.src.vcf.gz -c FMT/GT /tmp/D2PQpyhQgh/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/D2PQpyhQgh/annotate20.src.vcf.gz -c FMT/GT /tmp/D2PQpyhQgh/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/D2PQpyhQgh/annotate20.src.vcf.gz -c +FMT/GT /tmp/D2PQpyhQgh/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/D2PQpyhQgh/annotate20.src.vcf.gz -c +FMT/GT /tmp/D2PQpyhQgh/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/D2PQpyhQgh/annotate20.src.vcf.gz -c -FMT/GT /tmp/D2PQpyhQgh/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/D2PQpyhQgh/annotate20.src.vcf.gz -c -FMT/GT /tmp/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/D2PQpyhQgh/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/D2PQpyhQgh/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/annotate24.src.vcf.gz -c XX /tmp/D2PQpyhQgh/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/D2PQpyhQgh/annotate24.src.vcf.gz -c XX /tmp/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/annots.id.vcf.gz -c ALT /tmp/D2PQpyhQgh/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/D2PQpyhQgh/annots.id.vcf.gz -c ALT /tmp/D2PQpyhQgh/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/D2PQpyhQgh/annots.id.vcf.gz -c +ALT /tmp/D2PQpyhQgh/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/D2PQpyhQgh/annots.id.vcf.gz -c +ALT /tmp/D2PQpyhQgh/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/D2PQpyhQgh/annots.id.2.vcf.gz --pair-logic some -c +ID /tmp/D2PQpyhQgh/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/D2PQpyhQgh/annots.id.2.vcf.gz --pair-logic some -c +ID /tmp/D2PQpyhQgh/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/D2PQpyhQgh/annots.id.2.vcf.gz --pair-logic any -c +ID /tmp/D2PQpyhQgh/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/D2PQpyhQgh/annots.id.2.vcf.gz --pair-logic any -c +ID /tmp/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/concat.1.a.vcf.gz /tmp/D2PQpyhQgh/concat.1.b.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat -Ob /tmp/D2PQpyhQgh/concat.1.a.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/concat.1.a.bcf /tmp/D2PQpyhQgh/concat.1.b.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat -Ob /tmp/D2PQpyhQgh/concat.1.a.bcf /tmp/D2PQpyhQgh/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/D2PQpyhQgh/concat.2.a.vcf.gz /tmp/D2PQpyhQgh/concat.2.b.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat -Ob -a /tmp/D2PQpyhQgh/concat.2.a.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/concat.2.a.bcf /tmp/D2PQpyhQgh/concat.2.b.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat -Ob -a /tmp/D2PQpyhQgh/concat.2.a.bcf /tmp/D2PQpyhQgh/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/D2PQpyhQgh/concat.2.a.vcf.gz /tmp/D2PQpyhQgh/concat.2.b.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat -Ob -aD /tmp/D2PQpyhQgh/concat.2.a.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/concat.2.a.bcf /tmp/D2PQpyhQgh/concat.2.b.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat -Ob -aD /tmp/D2PQpyhQgh/concat.2.a.bcf /tmp/D2PQpyhQgh/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/D2PQpyhQgh/concat.3.a.vcf.gz /tmp/D2PQpyhQgh/concat.3.b.vcf.gz /tmp/D2PQpyhQgh/concat.3.0.vcf.gz /tmp/D2PQpyhQgh/concat.3.c.vcf.gz /tmp/D2PQpyhQgh/concat.3.d.vcf.gz /tmp/D2PQpyhQgh/concat.3.e.vcf.gz /tmp/D2PQpyhQgh/concat.3.f.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat -Ob -l --ligate-warn /tmp/D2PQpyhQgh/concat.3.a.vcf.gz /tmp/D2PQpyhQgh/concat.3.b.vcf.gz /tmp/D2PQpyhQgh/concat.3.0.vcf.gz /tmp/D2PQpyhQgh/concat.3.c.vcf.gz /tmp/D2PQpyhQgh/concat.3.d.vcf.gz /tmp/D2PQpyhQgh/concat.3.e.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/concat.3.a.bcf /tmp/D2PQpyhQgh/concat.3.b.bcf /tmp/D2PQpyhQgh/concat.3.0.bcf /tmp/D2PQpyhQgh/concat.3.c.bcf /tmp/D2PQpyhQgh/concat.3.d.bcf /tmp/D2PQpyhQgh/concat.3.e.bcf /tmp/D2PQpyhQgh/concat.3.f.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat -Ob -l --ligate-warn /tmp/D2PQpyhQgh/concat.3.a.bcf /tmp/D2PQpyhQgh/concat.3.b.bcf /tmp/D2PQpyhQgh/concat.3.0.bcf /tmp/D2PQpyhQgh/concat.3.c.bcf /tmp/D2PQpyhQgh/concat.3.d.bcf /tmp/D2PQpyhQgh/concat.3.e.bcf /tmp/D2PQpyhQgh/concat.3.f.bcf | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools_ Random seed for test_naive_concat: 1445650462 .. ok test_naive_concat: /build/reproducible-path/bcftools-1.20/bcftools concat --naive-force /tmp/D2PQpyhQgh/naive_concat.0.bcf /tmp/D2PQpyhQgh/naive_concat.1.bcf /tmp/D2PQpyhQgh/naive_concat.2.bcf /tmp/D2PQpyhQgh/naive_concat.3.bcf /tmp/D2PQpyhQgh/naive_concat.4.bcf /tmp/D2PQpyhQgh/naive_concat.5.bcf /tmp/D2PQpyhQgh/naive_concat.6.bcf /tmp/D2PQpyhQgh/naive_concat.7.bcf /tmp/D2PQpyhQgh/naive_concat.8.bcf /tmp/D2PQpyhQgh/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/D2PQpyhQgh/naive_concat.0.vcf.gz /tmp/D2PQpyhQgh/naive_concat.1.vcf.gz /tmp/D2PQpyhQgh/naive_concat.2.vcf.gz /tmp/D2PQpyhQgh/naive_concat.3.vcf.gz /tmp/D2PQpyhQgh/naive_concat.4.vcf.gz /tmp/D2PQpyhQgh/naive_concat.5.vcf.gz /tmp/D2PQpyhQgh/naive_concat.6.vcf.gz /tmp/D2PQpyhQgh/naive_concat.7.vcf.gz /tmp/D2PQpyhQgh/naive_concat.8.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/concat.4.a.vcf.gz /tmp/D2PQpyhQgh/concat.4.b.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat -Ob -l /tmp/D2PQpyhQgh/concat.4.a.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/concat.4.a.bcf /tmp/D2PQpyhQgh/concat.4.b.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat -Ob -l /tmp/D2PQpyhQgh/concat.4.a.bcf /tmp/D2PQpyhQgh/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/D2PQpyhQgh/concat.5.a.vcf.gz /tmp/D2PQpyhQgh/concat.5.b.vcf.gz /tmp/D2PQpyhQgh/concat.5.c.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat -Ob -l --ligate-warn /tmp/D2PQpyhQgh/concat.5.a.vcf.gz /tmp/D2PQpyhQgh/concat.5.b.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/concat.5.a.bcf /tmp/D2PQpyhQgh/concat.5.b.bcf /tmp/D2PQpyhQgh/concat.5.c.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat -Ob -l --ligate-warn /tmp/D2PQpyhQgh/concat.5.a.bcf /tmp/D2PQpyhQgh/concat.5.b.bcf /tmp/D2PQpyhQgh/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/D2PQpyhQgh/concat.5.a.bcf /tmp/D2PQpyhQgh/concat.5.b.bcf /tmp/D2PQpyhQgh/concat.5.c.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat -Ob -l --ligate-force /tmp/D2PQpyhQgh/concat.5.a.bcf /tmp/D2PQpyhQgh/concat.5.b.bcf /tmp/D2PQpyhQgh/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/D2PQpyhQgh/concat.5.a.vcf.gz /tmp/D2PQpyhQgh/concat.5.b.vcf.gz /tmp/D2PQpyhQgh/concat.5.c.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat -Ob -G -a -D /tmp/D2PQpyhQgh/concat.5.a.vcf.gz /tmp/D2PQpyhQgh/concat.5.b.vcf.gz /tmp/D2PQpyhQgh/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/D2PQpyhQgh/concat.5.a.bcf /tmp/D2PQpyhQgh/concat.5.b.bcf /tmp/D2PQpyhQgh/concat.5.c.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.20/bcftools concat -Ob -G -a -D /tmp/D2PQpyhQgh/concat.5.a.bcf /tmp/D2PQpyhQgh/concat.5.b.bcf /tmp/D2PQpyhQgh/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/D2PQpyhQgh/reheader.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/D2PQpyhQgh/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/D2PQpyhQgh/reheader.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/D2PQpyhQgh/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/D2PQpyhQgh/reheader.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/D2PQpyhQgh/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/D2PQpyhQgh/reheader.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/D2PQpyhQgh/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/D2PQpyhQgh/reheader.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/D2PQpyhQgh/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/D2PQpyhQgh/reheader.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/D2PQpyhQgh/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/D2PQpyhQgh/reheader.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/D2PQpyhQgh/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/D2PQpyhQgh/reheader.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/D2PQpyhQgh/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/D2PQpyhQgh/reheader.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/D2PQpyhQgh/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/D2PQpyhQgh/reheader.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/D2PQpyhQgh/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/D2PQpyhQgh/empty.bcf | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/D2PQpyhQgh/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/D2PQpyhQgh/empty.vcf.gz | /build/reproducible-path/bcftools-1.20/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/rename.map -Ov /tmp/D2PQpyhQgh/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/D2PQpyhQgh/rename.map -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/convert.hap-missing.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/convert.gvcf.vcf.gz .. ok test_vcf_convert_gvcf: /build/reproducible-path/bcftools-1.20/bcftools view -Ob /tmp/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/consensus.1.chain.new >/dev/null; cat /tmp/D2PQpyhQgh/consensus.1.chain.new .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/consensus.2.chain.new >/dev/null; cat /tmp/D2PQpyhQgh/consensus.2.chain.new .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/consensus.3.chain.new >/dev/null; cat /tmp/D2PQpyhQgh/consensus.3.chain.new .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.20/test/consensus.fa -H 1 -c /tmp/D2PQpyhQgh/consensus.4.chain.new >/dev/null; cat /tmp/D2PQpyhQgh/consensus.4.chain.new .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.20/bcftools consensus /tmp/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/mpileup.cram.urllist | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a DP,DV -r17:100-600 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a DP,DV -r17:100-600 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a DP,DV -r17:100-600 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a DP,DV -r17:100-600 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.bam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.cram | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -r17:100-150 -S /build/reproducible-path/bcftools-1.20/test/mplp.samples -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -r17:100-150 -S /build/reproducible-path/bcftools-1.20/test/mplp.samples -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -r17:100-150 -S /build/reproducible-path/bcftools-1.20/test/mplp.samples -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -r17:100-150 -S /build/reproducible-path/bcftools-1.20/test/mplp.samples -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -r17:100-150 -S ^/build/reproducible-path/bcftools-1.20/test/mplp.samples -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -r17:100-150 -S ^/build/reproducible-path/bcftools-1.20/test/mplp.samples -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -r17:100-150 -S ^/build/reproducible-path/bcftools-1.20/test/mplp.samples -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -r17:100-150 -S ^/build/reproducible-path/bcftools-1.20/test/mplp.samples -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -t17:100-150 -S /build/reproducible-path/bcftools-1.20/test/mplp.9.samples -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.sam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.sam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -t17:100-150 -S /build/reproducible-path/bcftools-1.20/test/mplp.9.samples -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.sam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.sam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.sam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -t17:100-150 -S /build/reproducible-path/bcftools-1.20/test/mplp.9.samples -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -t17:100-150 -S /build/reproducible-path/bcftools-1.20/test/mplp.9.samples -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -t17:100-150 -S /build/reproducible-path/bcftools-1.20/test/mplp.9.samples -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -t17:100-150 -S /build/reproducible-path/bcftools-1.20/test/mplp.9.samples -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -t17:100-150 -G /build/reproducible-path/bcftools-1.20/test/mplp.10.samples -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.sam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.sam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -t17:100-150 -G /build/reproducible-path/bcftools-1.20/test/mplp.10.samples -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.sam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.sam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.sam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -t17:100-150 -G /build/reproducible-path/bcftools-1.20/test/mplp.10.samples -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -t17:100-150 -G /build/reproducible-path/bcftools-1.20/test/mplp.10.samples -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -t17:100-150 -G /build/reproducible-path/bcftools-1.20/test/mplp.10.samples -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -t17:100-150 -G /build/reproducible-path/bcftools-1.20/test/mplp.10.samples -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.sam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -s HG00102 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.sam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -s HG00102 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.sam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.4.sam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -s HG00102 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -s HG00102 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.4.bam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -s HG00102 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -s HG00102 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.4.cram | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -s ^HG99999 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.sam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -s ^HG99999 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.sam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.4.sam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -s ^HG99999 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -s ^HG99999 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.4.bam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -s ^HG99999 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -s ^HG99999 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.4.cram | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -G /build/reproducible-path/bcftools-1.20/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.sam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -G /build/reproducible-path/bcftools-1.20/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.sam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.4.sam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -G /build/reproducible-path/bcftools-1.20/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -G /build/reproducible-path/bcftools-1.20/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.4.bam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -G /build/reproducible-path/bcftools-1.20/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -G /build/reproducible-path/bcftools-1.20/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.4.cram | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -G /build/reproducible-path/bcftools-1.20/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.sam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -G /build/reproducible-path/bcftools-1.20/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.sam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.4.sam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -G /build/reproducible-path/bcftools-1.20/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -G /build/reproducible-path/bcftools-1.20/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.bam /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.4.bam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -G /build/reproducible-path/bcftools-1.20/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -G /build/reproducible-path/bcftools-1.20/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.3.cram /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup.4.cram | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a AD -f /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.1.fa /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.1.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a AD -f /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.1.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.1.sam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a AD -f /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.1.fa /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a AD -f /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.1.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.1.bam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a AD -f /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.1.fa /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.1.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a AD -f /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.1.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.1.cram | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a AD --indels-cns -f /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.1.fa /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.1.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a AD --indels-cns -f /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.1.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.1.sam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a AD --indels-cns -f /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.1.fa /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a AD --indels-cns -f /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.1.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.1.bam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a AD --indels-cns -f /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.1.fa /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.1.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a AD --indels-cns -f /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.1.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.1.cram | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a AD -r 11:75 -f /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.2.fa /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a AD -r 11:75 -f /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.2.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.2.bam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a AD -r 11:75 -f /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.2.fa /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a AD -r 11:75 -f /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.2.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.2.cram | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.2.fa /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.2.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.2.bam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.2.fa /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.2.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.2.cram | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.2.fa /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.2.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.2.bam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.2.fa /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.2.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/indel-AD.2.cram | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a INFO/SCR,FMT/SCR -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup-SCR.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup-SCR.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a INFO/SCR,FMT/SCR -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup-SCR.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup-SCR.bam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a INFO/SCR,FMT/SCR -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup-SCR.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup-SCR.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a INFO/SCR,FMT/SCR -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup-SCR.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup-SCR.cram | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -t 1:100 --skip-all-set PAIRED,PROPER_PAIR,MREVERSE -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup-SCR.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -t 1:100 --skip-all-set PAIRED,PROPER_PAIR,MREVERSE -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup-SCR.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup-filter.sam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -t 1:100 --skip-any-set READ1 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup-SCR.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -t 1:100 --skip-any-set READ1 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup-SCR.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup-filter.sam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -t 1:100 --skip-all-unset READ1 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup-SCR.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -t 1:100 --skip-all-unset READ1 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup-SCR.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup-filter.sam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -t 1:100 --skip-any-unset READ1 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup-SCR.fa /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -t 1:100 --skip-any-unset READ1 -f /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup-SCR.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/mpileup-filter.sam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a INFO/NMBZ -r chr19:69-99 -f /build/reproducible-path/bcftools-1.20/test/mpileup/annot-NMBZ.1.fa /build/reproducible-path/bcftools-1.20/test/mpileup/annot-NMBZ.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a INFO/NMBZ -r chr19:69-99 -f /build/reproducible-path/bcftools-1.20/test/mpileup/annot-NMBZ.1.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/annot-NMBZ.1.bam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a INFO/NMBZ -r chr6:75 -f /build/reproducible-path/bcftools-1.20/test/mpileup/annot-NMBZ.2.fa /build/reproducible-path/bcftools-1.20/test/mpileup/annot-NMBZ.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a INFO/NMBZ -r chr6:75 -f /build/reproducible-path/bcftools-1.20/test/mpileup/annot-NMBZ.2.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/annot-NMBZ.2.bam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a INFO/NMBZ -r chr16:75 -f /build/reproducible-path/bcftools-1.20/test/mpileup/annot-NMBZ.3.fa /build/reproducible-path/bcftools-1.20/test/mpileup/annot-NMBZ.3.1.bam /build/reproducible-path/bcftools-1.20/test/mpileup/annot-NMBZ.3.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.20/bcftools mpileup -a INFO/NMBZ -r chr16:75 -f /build/reproducible-path/bcftools-1.20/test/mpileup/annot-NMBZ.3.fa -Ob /build/reproducible-path/bcftools-1.20/test/mpileup/annot-NMBZ.3.1.bam /build/reproducible-path/bcftools-1.20/test/mpileup/annot-NMBZ.3.2.bam | /build/reproducible-path/bcftools-1.20/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_csq: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq.fa -g /build/reproducible-path/bcftools-1.20/test/csq.gff3 /build/reproducible-path/bcftools-1.20/test/csq.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq.fa -g /build/reproducible-path/bcftools-1.20/test/csq.chr.gff3 /build/reproducible-path/bcftools-1.20/test/csq.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq.fa -g /build/reproducible-path/bcftools-1.20/test/csq.2.gff /build/reproducible-path/bcftools-1.20/test/csq.2.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq.fa -g /build/reproducible-path/bcftools-1.20/test/csq.2.gff --ncsq 64 /build/reproducible-path/bcftools-1.20/test/csq.2.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq.nchr.fa -g /build/reproducible-path/bcftools-1.20/test/csq.nchr.gff /build/reproducible-path/bcftools-1.20/test/csq.nchr.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq.ychr.fa -g /build/reproducible-path/bcftools-1.20/test/csq.nchr.gff /build/reproducible-path/bcftools-1.20/test/csq.nchr.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq.nchr.fa -g /build/reproducible-path/bcftools-1.20/test/csq.ychr.gff /build/reproducible-path/bcftools-1.20/test/csq.nchr.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq.ychr.fa -g /build/reproducible-path/bcftools-1.20/test/csq.ychr.gff /build/reproducible-path/bcftools-1.20/test/csq.nchr.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq.ychr.fa -g /build/reproducible-path/bcftools-1.20/test/csq.ychr.gff /build/reproducible-path/bcftools-1.20/test/csq.ychr.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq.ychr.fa -g /build/reproducible-path/bcftools-1.20/test/csq.nchr.gff /build/reproducible-path/bcftools-1.20/test/csq.ychr.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq.nchr.fa -g /build/reproducible-path/bcftools-1.20/test/csq.ychr.gff /build/reproducible-path/bcftools-1.20/test/csq.ychr.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq.nchr.fa -g /build/reproducible-path/bcftools-1.20/test/csq.nchr.gff /build/reproducible-path/bcftools-1.20/test/csq.ychr.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/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/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: 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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/ENST00000423372/ENST00000423372.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000423372/ENST00000423372.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000423372/snps.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -l -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000423372/ENST00000423372.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000423372/ENST00000423372.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000423372/snps.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000423372/ENST00000423372.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000423372/ENST00000423372.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000423372/insert3.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -l -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000423372/ENST00000423372.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000423372/ENST00000423372.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000423372/insert3.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.20/test/csq/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/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/ENST00000420190/ENST00000420190.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000420190/ENST00000420190.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000420190/abort-in-csq-push.vcf | /build/reproducible-path/bcftools-1.20/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/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/ENST00000410009/ENST00000410009.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000410009/ENST00000410009.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000410009/frameshift.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.20/test/csq/ENST00000410009 && /build/reproducible-path/bcftools-1.20/bcftools csq -B 5 -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.20/test/csq/ENST00000410009 && /build/reproducible-path/bcftools-1.20/bcftools csq -lb -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: 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/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/ENST00000400151/ENST00000400151.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000400151/ENST00000400151.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000400151/long-del.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000390520/ENST00000390520.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000390520/ENST00000390520.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000390520/deletion-overlap.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/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/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: 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/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/ENST00000375992/ENST00000375992.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000375992/ENST00000375992.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000375992/incorrect-synon-del-not-start-lost.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000373833/ENST00000373833.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000373833/ENST00000373833.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000373833/boundary-insertion.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -l -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000373833/ENST00000373833.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000373833/ENST00000373833.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000373833/boundary-insertion.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000368801/ENST00000368801.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000368801/ENST00000368801.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000368801/compound-lost.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/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/ENST00000360372/ENST00000360372.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000360372/ENST00000360372.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000360372/mnp.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000357367/ENST00000357367.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000357367/ENST00000357367.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000357367/stop-retained.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -l -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/splice-acceptor-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-donor5.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -l -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/splice-acceptor-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-donor3.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -l -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -l -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/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/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/frame3.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -l -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/frame3.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/frame2.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -l -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/frame2.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000341065/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/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/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/ENST00000318249.2/ENST00000318249.2.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000318249.2/ENST00000318249.2.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000318249.2/synonymous-start-lost.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/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/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/ENST00000295641/ENST00000295641.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000295641/ENST00000295641.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000295641/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -l -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000295641/ENST00000295641.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000295641/ENST00000295641.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000295641/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000294661/ENST00000294661.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000294661/ENST00000294661.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000294661/non-coding-boundary.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -l -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000294661/ENST00000294661.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000294661/ENST00000294661.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000294661/non-coding-boundary.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/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/ENST00000271583/ENST00000271583.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000271583/ENST00000271583.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000271583/splice-acceptor.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000269081/ENST00000269081.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000269081/ENST00000269081.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000269081/stop-gained-not-inframe-insertion.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/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/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/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/ENST00000227471/ENST00000227471.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000227471/ENST00000227471.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000227471/insert-splice-vs-frameshift.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000218032/ENST00000218032.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000218032/ENST00000218032.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000218032/start-lost.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -l -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000218032/ENST00000218032.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000218032/ENST00000218032.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000218032/start-lost.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/ENST00000218032/ENST00000218032.fa -g /build/reproducible-path/bcftools-1.20/test/csq/ENST00000218032/ENST00000218032.gff /build/reproducible-path/bcftools-1.20/test/csq/ENST00000218032/start-lost-del.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: 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/ENSMUST00000133836 && /build/reproducible-path/bcftools-1.20/bcftools csq -f ENSMUST00000133836.fa -g ENSMUST00000133836.gff filter-problem.vcf -i 'FILTER="PASS"' --phase m | ../sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.20/test/csq/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!=25496' --phase m | ../sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.20/test/csq/ENSMUST00000121418 && /build/reproducible-path/bcftools-1.20/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25105' --phase m | ../sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /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: cd /build/reproducible-path/bcftools-1.20/test/csq/EMN908947 && /build/reproducible-path/bcftools-1.20/bcftools csq -f EMN908947.fa -g simple.gff simple.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.20/test/csq/EMN908947 && /build/reproducible-path/bcftools-1.20/bcftools csq -f EMN908947.fa -g ribosomal-slippage.gff ribosomal-slippage.vcf --force | ../sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/EDUMMY0003/EDUMMY0003.fa -g /build/reproducible-path/bcftools-1.20/test/csq/EDUMMY0003/EDUMMY0003.gff /build/reproducible-path/bcftools-1.20/test/csq/EDUMMY0003/long-del.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -f /build/reproducible-path/bcftools-1.20/test/csq/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/EDUMMY0001/EDUMMY0001.fa -g /build/reproducible-path/bcftools-1.20/test/csq/EDUMMY0001/EDUMMY0001.gff /build/reproducible-path/bcftools-1.20/test/csq/EDUMMY0001/starts-with-1.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.20/bcftools csq -l -f /build/reproducible-path/bcftools-1.20/test/csq/EDUMMY0001/EDUMMY0001.fa -g /build/reproducible-path/bcftools-1.20/test/csq/EDUMMY0001/EDUMMY0001.gff /build/reproducible-path/bcftools-1.20/test/csq/EDUMMY0001/starts-with-1.vcf | /build/reproducible-path/bcftools-1.20/test/csq/sort-csq | /build/reproducible-path/bcftools-1.20/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_roh: /build/reproducible-path/bcftools-1.20/bcftools roh /build/reproducible-path/bcftools-1.20/test/roh.1.vcf.gz -Or -G30 --AF-dflt 0.4| grep -v ^# .. ok test_roh: /build/reproducible-path/bcftools-1.20/bcftools roh /build/reproducible-path/bcftools-1.20/test/roh.1.vcf.gz -Or -G30 --AF-file /build/reproducible-path/bcftools-1.20/test/roh.1.tab.gz| grep -v ^# .. ok test_roh: /build/reproducible-path/bcftools-1.20/bcftools roh /build/reproducible-path/bcftools-1.20/test/roh.1.vcf.gz -Or -G30 --AF-file /build/reproducible-path/bcftools-1.20/test/roh.1.tab.gz --ignore-homref| grep -v ^# .. ok test_roh: /build/reproducible-path/bcftools-1.20/bcftools roh /build/reproducible-path/bcftools-1.20/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245| grep -v ^# .. ok test_roh: /build/reproducible-path/bcftools-1.20/bcftools roh /build/reproducible-path/bcftools-1.20/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --ignore-homref| grep -v ^# .. ok test_roh: /build/reproducible-path/bcftools-1.20/bcftools roh /build/reproducible-path/bcftools-1.20/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --ignore-homref --include-noalt| grep -v ^# .. ok test_roh: /build/reproducible-path/bcftools-1.20/bcftools roh /build/reproducible-path/bcftools-1.20/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --include-noalt| grep -v ^# .. ok test_gtcheck: /build/reproducible-path/bcftools-1.20/bcftools gtcheck -e 0 /tmp/D2PQpyhQgh/gtcheck.1.vcf.gz -g /tmp/D2PQpyhQgh/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/D2PQpyhQgh/gtcheck.1.vcf.gz -g /tmp/D2PQpyhQgh/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/D2PQpyhQgh/gtcheck.1.vcf.gz -g /tmp/D2PQpyhQgh/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/D2PQpyhQgh/gtcheck.1.vcf.gz -g /tmp/D2PQpyhQgh/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/D2PQpyhQgh/gtcheck.1.vcf.gz -g /tmp/D2PQpyhQgh/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/D2PQpyhQgh/gtcheck.1.vcf.gz -g /tmp/D2PQpyhQgh/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.20/bcftools gtcheck -e 0 /tmp/D2PQpyhQgh/gtcheck.2.vcf.gz -g /tmp/D2PQpyhQgh/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.20/bcftools gtcheck -e 0 /tmp/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/gtcheck.1.vcf.gz -g /tmp/D2PQpyhQgh/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/D2PQpyhQgh/gtcheck.1.vcf.gz -g /tmp/D2PQpyhQgh/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/D2PQpyhQgh/gtcheck.1.vcf.gz -g /tmp/D2PQpyhQgh/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/D2PQpyhQgh/gtcheck.1.vcf.gz -g /tmp/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/gtcheck.1.vcf.gz -g /tmp/D2PQpyhQgh/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/D2PQpyhQgh/gtcheck.1.vcf.gz -g /tmp/D2PQpyhQgh/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/D2PQpyhQgh/gtcheck.1.vcf.gz -g /tmp/D2PQpyhQgh/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/D2PQpyhQgh/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.20/bcftools gtcheck /tmp/D2PQpyhQgh/gtcheck.ntop.vcf.gz -g /tmp/D2PQpyhQgh/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/D2PQpyhQgh/gtcheck.ntop.vcf.gz -g /tmp/D2PQpyhQgh/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.20/bcftools gtcheck /tmp/D2PQpyhQgh/gtcheck.5.vcf.gz -g /tmp/D2PQpyhQgh/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/D2PQpyhQgh/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/D2PQpyhQgh/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 -j12 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/aarch64-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/aarch64-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_arm64.deb'. dpkg-deb: building package 'bcftools-dbgsym' in '../bcftools-dbgsym_1.20-1_arm64.deb'. dpkg-genbuildinfo --build=binary -O../bcftools_1.20-1_arm64.buildinfo dpkg-genchanges --build=binary -O../bcftools_1.20-1_arm64.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/846407 and its subdirectories I: Current time: Sun May 12 01:52:21 -12 2024 I: pbuilder-time-stamp: 1715521941 Sun May 12 13:52:23 UTC 2024 I: 1st build successful. Starting 2nd build on remote node codethink04-arm64.debian.net. Sun May 12 13:52:23 UTC 2024 I: Preparing to do remote build '2' on codethink04-arm64.debian.net. Sun May 12 13:54:23 UTC 2024 I: Deleting $TMPDIR on codethink04-arm64.debian.net. Sun May 12 13:54:24 UTC 2024 I: bcftools_1.20-1_arm64.changes: Format: 1.8 Date: Thu, 18 Apr 2024 17:14:39 +0200 Source: bcftools Binary: bcftools bcftools-dbgsym Architecture: arm64 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: 9ff206ab2dd8beb9ffd7517bb7c595f2e6a93515 2111992 bcftools-dbgsym_1.20-1_arm64.deb 13d4ddf529e8515a336bca1d29af71d79815242e 6208 bcftools_1.20-1_arm64.buildinfo f05060ca4f26b0c7629075f28c0d39238968de7d 683708 bcftools_1.20-1_arm64.deb Checksums-Sha256: a44f3cb3056a240f58b6c0a5eaf67a19a8b7743f1d94c5bea68e0441bf5bb7ff 2111992 bcftools-dbgsym_1.20-1_arm64.deb 43046551d28a7a1cfcbf91271d1ca014961a2313eb79102d4de39843266e586e 6208 bcftools_1.20-1_arm64.buildinfo 46a708a5942ee9bfb58458cd3a11583f62c1c20f13fab351f5b35e7e6e583dc9 683708 bcftools_1.20-1_arm64.deb Files: c229bd634c71d066d3235e9dfd136e2a 2111992 debug optional bcftools-dbgsym_1.20-1_arm64.deb 9433bd0656567ec61e35738abb00b5c4 6208 science optional bcftools_1.20-1_arm64.buildinfo e1c127889f3b6c49ce2154b093b7f2bd 683708 science optional bcftools_1.20-1_arm64.deb Sun May 12 13:54:26 UTC 2024 I: diffoscope 266 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_20-18095.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.KvuBaBJk/bcftools_1.20-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.KvuBaBJk/bcftools_1.20-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.KvuBaBJk/bcftools_1.20-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.KvuBaBJk/b1/bcftools_1.20-1_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.KvuBaBJk/b2/bcftools_1.20-1_arm64.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: 0.537s) 0.537s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.054s) 0.054s 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: 999ms CPU time consumed: 998ms Sun May 12 14:06:34 UTC 2024 I: diffoscope 266 found no differences in the changes files, and a .buildinfo file also exists. Sun May 12 14:06:34 UTC 2024 I: bcftools from unstable built successfully and reproducibly on arm64. Sun May 12 14:06:38 UTC 2024 I: Submitting .buildinfo files to external archives: Sun May 12 14:06:38 UTC 2024 I: Submitting 8.0K b1/bcftools_1.20-1_arm64.buildinfo.asc Sun May 12 14:06:50 UTC 2024 I: Submitting 8.0K b2/bcftools_1.20-1_arm64.buildinfo.asc Sun May 12 14:07:08 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sun May 12 14:07:08 UTC 2024 I: Done submitting .buildinfo files. Sun May 12 14:07:08 UTC 2024 I: Removing signed bcftools_1.20-1_arm64.buildinfo.asc files: removed './b1/bcftools_1.20-1_arm64.buildinfo.asc' removed './b2/bcftools_1.20-1_arm64.buildinfo.asc'