Thu Mar 6 15:18:30 UTC 2025 I: starting to build bcftools/trixie/armhf on jenkins on '2025-03-06 15:18' Thu Mar 6 15:18:30 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_3/14112/console.log Thu Mar 6 15:18:30 UTC 2025 I: Downloading source for trixie/bcftools=1.21-1 --2025-03-06 15:18:30-- http://deb.debian.org/debian/pool/main/b/bcftools/bcftools_1.21-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2267 (2.2K) [text/prs.lines.tag] Saving to: ‘bcftools_1.21-1.dsc’ 0K .. 100% 349M=0s 2025-03-06 15:18:30 (349 MB/s) - ‘bcftools_1.21-1.dsc’ saved [2267/2267] Thu Mar 6 15:18:30 UTC 2025 I: bcftools_1.21-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: bcftools Binary: bcftools Architecture: any Version: 1.21-1 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: 7f367e0f03d4f56ca88d5f3a79435f196591fbce 3665160 bcftools_1.21.orig.tar.gz 5b3b3f9251d64665efa2c5ed61c6e2aef032cde1 7504 bcftools_1.21-1.debian.tar.xz Checksums-Sha256: 7484695c5d833fb1a89c2b886ec302db0514ba3c8e5ef7397b9302fa8bd37f8d 3665160 bcftools_1.21.orig.tar.gz d1332716453f270248afa7476a5a824b0289150a7829442f691559209dcc38cf 7504 bcftools_1.21-1.debian.tar.xz Files: e144a5777c606c69eb643ae8ff613dbb 3665160 bcftools_1.21.orig.tar.gz 756abc1b4df76e455bd705ddf6ef5c9e 7504 bcftools_1.21-1.debian.tar.xz Dgit: 1cbbbd21cccc5d95d73df54271b167d9e450842a debian archive/debian/1.21-1 https://git.dgit.debian.org/bcftools -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmeuYIEUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdpyzRAAlczvukE0/A+j5esHHalBAeaq8nnO SC4BULLNsaVcn31OlRTGS1RXt1zU6u3ise+jLfRMAbhM4Qx57Ek9S+2+uvX2M5lh 6Wlz3M6DvyTEXN0MZTztIinmdxODYf/IiD8d4qDf8KYZNBeKE+spfINNeRiWyl6e /QXwVTUB0jRc5ZBqsOONR4uOliMKk3LWUy3xwM3YzUKhVlFQpf2OJXk5bQSew6NM PIwjBLcHdDE42tplpMuRjT0FdWk4i8EeZlR8oIdBwoVc1ffNqRpWbz77OJouDhe8 dz7kPHok/2DEBod4k3yeIZH0deK+G47sycXhhSOA7IS+43opAYIHFscpHZMdnoaA lQjIMES546gBHagarHdb5dbHKcvWuq2aQdsuyc0Z2kOnS4Kaop/YugT14ba0pu73 50x5eyPJL2LgnFDb+36HygKNL0CCA6v6EOC7qEU5zzqkmXYXBWEKGxht4KvXbdtc NAvxqxbw2AtQF1kRH6dur00lo9ZCjVq+wa5NnQHZh+BILAIrdo8lpM5Gm6yCifwE 9HU+bY2IaF3LMMgTxvRVyT8yeu65YtA6FbZjnYW6Y0ZeVlQLFvn+830b4L4fWlt3 waTPrdRQcvexseaLFmxuZY2igfMRPtzyf3UXQaomDkitd4jC0WhH+Tg6OoTD88Fa IFTp1pvu+xmgjw4= =1qOu -----END PGP SIGNATURE----- Thu Mar 6 15:18:30 UTC 2025 I: Checking whether the package is not for us Thu Mar 6 15:18:30 UTC 2025 I: Starting 1st build on remote node ff4a-armhf-rb.debian.net. Thu Mar 6 15:18:30 UTC 2025 I: Preparing to do remote build '1' on ff4a-armhf-rb.debian.net. Thu Mar 6 15:27:20 UTC 2025 I: Deleting $TMPDIR on ff4a-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Mar 6 03:18:36 -12 2025 I: pbuilder-time-stamp: 1741274316 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [bcftools_1.21-1.dsc] I: copying [./bcftools_1.21.orig.tar.gz] I: copying [./bcftools_1.21-1.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./bcftools_1.21-1.dsc: unsupported subcommand dpkg-source: info: extracting bcftools in bcftools-1.21 dpkg-source: info: unpacking bcftools_1.21.orig.tar.gz dpkg-source: info: unpacking bcftools_1.21-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series 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/3404/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='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='223d4dc01874445bb7d670afa0f065c1' 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='3404' 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.YRCZQbnt/pbuilderrc_qXJb --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.YRCZQbnt/b1 --logfile b1/build.log bcftools_1.21-1.dsc' SUDO_GID='113' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:3142/' I: uname -a Linux ff4a 6.1.0-31-armmp-lpae #1 SMP Debian 6.1.128-1 (2025-02-07) armv7l GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3404/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: armhf 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 ... 19525 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. pbuilder-satisfydepends-dummy depends on liblzma-dev; however: Package liblzma-dev is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev (>= 1.14); however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on libgsl-dev; however: Package libgsl-dev is not installed. pbuilder-satisfydepends-dummy depends on tabix; however: Package tabix is not installed. pbuilder-satisfydepends-dummy depends on libio-pty-perl; however: Package libio-pty-perl is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} comerr-dev{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} krb5-multidev{a} libarchive-zip-perl{a} libbrotli-dev{a} libbrotli1{a} libbz2-dev{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1t64{a} libevent-2.1-7t64{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgnutls30t64{a} libgsl-dev{a} libgsl28{a} libgslcblas0{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libidn2-0{a} libidn2-dev{a} libio-pty-perl{a} libk5crypto3{a} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} libldap-dev{a} libldap2{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp2-dev{a} libnghttp3-9{a} libnghttp3-dev{a} libngtcp2-16{a} libngtcp2-crypto-gnutls-dev{a} libngtcp2-crypto-gnutls8{a} libngtcp2-dev{a} libp11-kit-dev{a} libp11-kit0{a} libpipeline1{a} libpkgconf3{a} libpsl-dev{a} libpsl5t64{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libtasn1-6{a} libtasn1-6-dev{a} libtool{a} libuchardet0{a} libunbound8{a} libunistring5{a} libxml2{a} libzstd-dev{a} m4{a} man-db{a} nettle-dev{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} sensible-utils{a} tabix{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc ca-certificates curl krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules libtasn1-doc lynx publicsuffix wget 0 packages upgraded, 99 newly installed, 0 to remove and 0 not upgraded. Need to get 40.3 MB of archives. After unpacking 133 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main armhf sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian trixie/main armhf libmagic-mgc armhf 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main armhf libmagic1t64 armhf 1:5.45-3+b1 [98.5 kB] Get: 4 http://deb.debian.org/debian trixie/main armhf file armhf 1:5.45-3+b1 [42.3 kB] Get: 5 http://deb.debian.org/debian trixie/main armhf gettext-base armhf 0.23.1-1 [238 kB] Get: 6 http://deb.debian.org/debian trixie/main armhf libuchardet0 armhf 0.0.8-1+b2 [65.6 kB] Get: 7 http://deb.debian.org/debian trixie/main armhf groff-base armhf 1.23.0-7 [1095 kB] Get: 8 http://deb.debian.org/debian trixie/main armhf bsdextrautils armhf 2.40.4-5 [84.9 kB] Get: 9 http://deb.debian.org/debian trixie/main armhf libpipeline1 armhf 1.5.8-1 [35.0 kB] Get: 10 http://deb.debian.org/debian trixie/main armhf man-db armhf 2.13.0-1 [1382 kB] Get: 11 http://deb.debian.org/debian trixie/main armhf m4 armhf 1.4.19-5 [272 kB] Get: 12 http://deb.debian.org/debian trixie/main armhf autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian trixie/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main armhf automake all 1:1.17-3 [862 kB] Get: 15 http://deb.debian.org/debian trixie/main armhf autopoint all 0.23.1-1 [770 kB] Get: 16 http://deb.debian.org/debian trixie/main armhf libcom-err2 armhf 1.47.2-1 [23.3 kB] Get: 17 http://deb.debian.org/debian trixie/main armhf comerr-dev armhf 2.1-1.47.2-1 [55.1 kB] Get: 18 http://deb.debian.org/debian trixie/main armhf libdebhelper-perl all 13.24.1 [90.9 kB] Get: 19 http://deb.debian.org/debian trixie/main armhf libtool all 2.5.4-3 [539 kB] Get: 20 http://deb.debian.org/debian trixie/main armhf dh-autoreconf all 20 [17.1 kB] Get: 21 http://deb.debian.org/debian trixie/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 22 http://deb.debian.org/debian trixie/main armhf libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 23 http://deb.debian.org/debian trixie/main armhf dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 24 http://deb.debian.org/debian trixie/main armhf libelf1t64 armhf 0.192-4 [184 kB] Get: 25 http://deb.debian.org/debian trixie/main armhf dwz armhf 0.15-1+b2 [106 kB] Get: 26 http://deb.debian.org/debian trixie/main armhf libunistring5 armhf 1.3-1 [444 kB] Get: 27 http://deb.debian.org/debian trixie/main armhf libicu72 armhf 72.1-6 [9086 kB] Get: 28 http://deb.debian.org/debian trixie/main armhf libxml2 armhf 2.12.7+dfsg+really2.9.14-0.2+b2 [605 kB] Get: 29 http://deb.debian.org/debian trixie/main armhf gettext armhf 0.23.1-1 [1560 kB] Get: 30 http://deb.debian.org/debian trixie/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 31 http://deb.debian.org/debian trixie/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 32 http://deb.debian.org/debian trixie/main armhf debhelper all 13.24.1 [920 kB] Get: 33 http://deb.debian.org/debian trixie/main armhf libkrb5support0 armhf 1.21.3-4 [30.3 kB] Get: 34 http://deb.debian.org/debian trixie/main armhf libk5crypto3 armhf 1.21.3-4 [75.8 kB] Get: 35 http://deb.debian.org/debian trixie/main armhf libkeyutils1 armhf 1.6.3-4 [8096 B] Get: 36 http://deb.debian.org/debian trixie/main armhf libkrb5-3 armhf 1.21.3-4 [285 kB] Get: 37 http://deb.debian.org/debian trixie/main armhf libgssapi-krb5-2 armhf 1.21.3-4 [116 kB] Get: 38 http://deb.debian.org/debian trixie/main armhf libgssrpc4t64 armhf 1.21.3-4 [52.6 kB] Get: 39 http://deb.debian.org/debian trixie/main armhf libkadm5clnt-mit12 armhf 1.21.3-4 [37.5 kB] Get: 40 http://deb.debian.org/debian trixie/main armhf libkdb5-10t64 armhf 1.21.3-4 [37.3 kB] Get: 41 http://deb.debian.org/debian trixie/main armhf libkadm5srv-mit12 armhf 1.21.3-4 [47.4 kB] Get: 42 http://deb.debian.org/debian trixie/main armhf krb5-multidev armhf 1.21.3-4 [126 kB] Get: 43 http://deb.debian.org/debian trixie/main armhf libbrotli1 armhf 1.1.0-2+b7 [284 kB] Get: 44 http://deb.debian.org/debian trixie/main armhf libbrotli-dev armhf 1.1.0-2+b7 [294 kB] Get: 45 http://deb.debian.org/debian trixie/main armhf libbz2-dev armhf 1.0.8-6 [28.7 kB] Get: 46 http://deb.debian.org/debian trixie/main armhf libidn2-0 armhf 2.3.7-2+b1 [125 kB] Get: 47 http://deb.debian.org/debian trixie/main armhf libffi8 armhf 3.4.7-1 [20.3 kB] Get: 48 http://deb.debian.org/debian trixie/main armhf libp11-kit0 armhf 0.25.5-3 [385 kB] Get: 49 http://deb.debian.org/debian trixie/main armhf libtasn1-6 armhf 4.20.0-2 [44.4 kB] Get: 50 http://deb.debian.org/debian trixie/main armhf libgnutls30t64 armhf 3.8.9-2 [1382 kB] Get: 51 http://deb.debian.org/debian trixie/main armhf libsasl2-modules-db armhf 2.1.28+dfsg1-9 [18.5 kB] Get: 52 http://deb.debian.org/debian trixie/main armhf libsasl2-2 armhf 2.1.28+dfsg1-9 [50.4 kB] Get: 53 http://deb.debian.org/debian trixie/main armhf libldap2 armhf 2.6.9+dfsg-1 [167 kB] Get: 54 http://deb.debian.org/debian trixie/main armhf libnghttp2-14 armhf 1.64.0-1 [62.9 kB] Get: 55 http://deb.debian.org/debian trixie/main armhf libnghttp3-9 armhf 1.6.0-2 [56.8 kB] Get: 56 http://deb.debian.org/debian trixie/main armhf libngtcp2-16 armhf 1.9.1-1 [115 kB] Get: 57 http://deb.debian.org/debian trixie/main armhf libngtcp2-crypto-gnutls8 armhf 1.9.1-1 [15.8 kB] Get: 58 http://deb.debian.org/debian trixie/main armhf libpsl5t64 armhf 0.21.2-1.1+b1 [55.8 kB] Get: 59 http://deb.debian.org/debian trixie/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b5 [53.2 kB] Get: 60 http://deb.debian.org/debian trixie/main armhf libssh2-1t64 armhf 1.11.1-1 [227 kB] Get: 61 http://deb.debian.org/debian trixie/main armhf libcurl3t64-gnutls armhf 8.12.1-3 [316 kB] Get: 62 http://deb.debian.org/debian trixie/main armhf libevent-2.1-7t64 armhf 2.1.12-stable-10+b1 [164 kB] Get: 63 http://deb.debian.org/debian trixie/main armhf libunbound8 armhf 1.22.0-1+b1 [539 kB] Get: 64 http://deb.debian.org/debian trixie/main armhf libgnutls-dane0t64 armhf 3.8.9-2 [446 kB] Get: 65 http://deb.debian.org/debian trixie/main armhf libgnutls-openssl27t64 armhf 3.8.9-2 [446 kB] Get: 66 http://deb.debian.org/debian trixie/main armhf libidn2-dev armhf 2.3.7-2+b1 [119 kB] Get: 67 http://deb.debian.org/debian trixie/main armhf libp11-kit-dev armhf 0.25.5-3 [208 kB] Get: 68 http://deb.debian.org/debian trixie/main armhf libtasn1-6-dev armhf 4.20.0-2 [93.4 kB] Get: 69 http://deb.debian.org/debian trixie/main armhf libgmpxx4ldbl armhf 2:6.3.0+dfsg-3 [328 kB] Get: 70 http://deb.debian.org/debian trixie/main armhf libgmp-dev armhf 2:6.3.0+dfsg-3 [592 kB] Get: 71 http://deb.debian.org/debian trixie/main armhf nettle-dev armhf 3.10.1-1 [1314 kB] Get: 72 http://deb.debian.org/debian trixie/main armhf libgnutls28-dev armhf 3.8.9-2 [1337 kB] Get: 73 http://deb.debian.org/debian trixie/main armhf libkrb5-dev armhf 1.21.3-4 [15.9 kB] Get: 74 http://deb.debian.org/debian trixie/main armhf libldap-dev armhf 2.6.9+dfsg-1 [286 kB] Get: 75 http://deb.debian.org/debian trixie/main armhf libpkgconf3 armhf 1.8.1-4 [31.8 kB] Get: 76 http://deb.debian.org/debian trixie/main armhf pkgconf-bin armhf 1.8.1-4 [29.2 kB] Get: 77 http://deb.debian.org/debian trixie/main armhf pkgconf armhf 1.8.1-4 [26.1 kB] Get: 78 http://deb.debian.org/debian trixie/main armhf libnghttp2-dev armhf 1.64.0-1 [103 kB] Get: 79 http://deb.debian.org/debian trixie/main armhf libnghttp3-dev armhf 1.6.0-2 [81.8 kB] Get: 80 http://deb.debian.org/debian trixie/main armhf libngtcp2-crypto-gnutls-dev armhf 1.9.1-1 [21.3 kB] Get: 81 http://deb.debian.org/debian trixie/main armhf libngtcp2-dev armhf 1.9.1-1 [165 kB] Get: 82 http://deb.debian.org/debian trixie/main armhf libpsl-dev armhf 0.21.2-1.1+b1 [76.8 kB] Get: 83 http://deb.debian.org/debian trixie/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1+b1 [905 kB] Get: 84 http://deb.debian.org/debian trixie/main armhf librtmp-dev armhf 2.4+20151223.gitfa8646d.1-2+b5 [63.6 kB] Get: 85 http://deb.debian.org/debian trixie/main armhf libssl-dev armhf 3.4.1-1 [2429 kB] Get: 86 http://deb.debian.org/debian trixie/main armhf libssh2-1-dev armhf 1.11.1-1 [378 kB] Get: 87 http://deb.debian.org/debian trixie/main armhf libzstd-dev armhf 1.5.6+dfsg-2 [326 kB] Get: 88 http://deb.debian.org/debian trixie/main armhf libcurl4-gnutls-dev armhf 8.12.1-3 [441 kB] Get: 89 http://deb.debian.org/debian trixie/main armhf libdeflate0 armhf 1.23-1+b1 [36.7 kB] Get: 90 http://deb.debian.org/debian trixie/main armhf libdeflate-dev armhf 1.23-1+b1 [44.8 kB] Get: 91 http://deb.debian.org/debian trixie/main armhf libgslcblas0 armhf 2.8+dfsg-5 [85.5 kB] Get: 92 http://deb.debian.org/debian trixie/main armhf libgsl28 armhf 2.8+dfsg-5 [812 kB] Get: 93 http://deb.debian.org/debian trixie/main armhf libgsl-dev armhf 2.8+dfsg-5 [1030 kB] Get: 94 http://deb.debian.org/debian trixie/main armhf libhtscodecs2 armhf 1.6.1-2 [63.2 kB] Get: 95 http://deb.debian.org/debian trixie/main armhf libhts3t64 armhf 1.21+ds-1 [408 kB] Get: 96 http://deb.debian.org/debian trixie/main armhf liblzma-dev armhf 5.6.4-1 [311 kB] Get: 97 http://deb.debian.org/debian trixie/main armhf libhts-dev armhf 1.21+ds-1 [1657 kB] Get: 98 http://deb.debian.org/debian trixie/main armhf libio-pty-perl armhf 1:1.20-1+b2 [33.8 kB] Get: 99 http://deb.debian.org/debian trixie/main armhf tabix armhf 1.21+ds-1 [425 kB] Fetched 40.3 MB in 2s (20.8 MB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19525 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_armhf.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:armhf. 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Selecting previously unselected package libcom-err2:armhf. Preparing to unpack .../15-libcom-err2_1.47.2-1_armhf.deb ... Unpacking libcom-err2:armhf (1.47.2-1) ... Selecting previously unselected package comerr-dev:armhf. Preparing to unpack .../16-comerr-dev_2.1-1.47.2-1_armhf.deb ... Unpacking comerr-dev:armhf (2.1-1.47.2-1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../17-libdebhelper-perl_13.24.1_all.deb ... Unpacking libdebhelper-perl (13.24.1) ... Selecting previously unselected package libtool. Preparing to unpack .../18-libtool_2.5.4-3_all.deb ... Unpacking libtool (2.5.4-3) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../19-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../20-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... 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Unpacking libicu72:armhf (72.1-6) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../27-libxml2_2.12.7+dfsg+really2.9.14-0.2+b2_armhf.deb ... Unpacking libxml2:armhf (2.12.7+dfsg+really2.9.14-0.2+b2) ... Selecting previously unselected package gettext. Preparing to unpack .../28-gettext_0.23.1-1_armhf.deb ... Unpacking gettext (0.23.1-1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../29-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../30-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../31-debhelper_13.24.1_all.deb ... Unpacking debhelper (13.24.1) ... Selecting previously unselected package libkrb5support0:armhf. Preparing to unpack .../32-libkrb5support0_1.21.3-4_armhf.deb ... Unpacking libkrb5support0:armhf (1.21.3-4) ... Selecting previously unselected package libk5crypto3:armhf. Preparing to unpack .../33-libk5crypto3_1.21.3-4_armhf.deb ... Unpacking libk5crypto3:armhf (1.21.3-4) ... Selecting previously unselected package libkeyutils1:armhf. Preparing to unpack .../34-libkeyutils1_1.6.3-4_armhf.deb ... Unpacking libkeyutils1:armhf (1.6.3-4) ... Selecting previously unselected package libkrb5-3:armhf. Preparing to unpack .../35-libkrb5-3_1.21.3-4_armhf.deb ... Unpacking libkrb5-3:armhf (1.21.3-4) ... Selecting previously unselected package libgssapi-krb5-2:armhf. Preparing to unpack .../36-libgssapi-krb5-2_1.21.3-4_armhf.deb ... Unpacking libgssapi-krb5-2:armhf (1.21.3-4) ... Selecting previously unselected package libgssrpc4t64:armhf. Preparing to unpack .../37-libgssrpc4t64_1.21.3-4_armhf.deb ... Unpacking libgssrpc4t64:armhf (1.21.3-4) ... Selecting previously unselected package libkadm5clnt-mit12:armhf. Preparing to unpack .../38-libkadm5clnt-mit12_1.21.3-4_armhf.deb ... Unpacking libkadm5clnt-mit12:armhf (1.21.3-4) ... Selecting previously unselected package libkdb5-10t64:armhf. Preparing to unpack .../39-libkdb5-10t64_1.21.3-4_armhf.deb ... Unpacking libkdb5-10t64:armhf (1.21.3-4) ... Selecting previously unselected package libkadm5srv-mit12:armhf. Preparing to unpack .../40-libkadm5srv-mit12_1.21.3-4_armhf.deb ... Unpacking libkadm5srv-mit12:armhf (1.21.3-4) ... Selecting previously unselected package krb5-multidev:armhf. Preparing to unpack .../41-krb5-multidev_1.21.3-4_armhf.deb ... Unpacking krb5-multidev:armhf (1.21.3-4) ... Selecting previously unselected package libbrotli1:armhf. Preparing to unpack .../42-libbrotli1_1.1.0-2+b7_armhf.deb ... Unpacking libbrotli1:armhf (1.1.0-2+b7) ... Selecting previously unselected package libbrotli-dev:armhf. Preparing to unpack .../43-libbrotli-dev_1.1.0-2+b7_armhf.deb ... Unpacking libbrotli-dev:armhf (1.1.0-2+b7) ... Selecting previously unselected package libbz2-dev:armhf. Preparing to unpack .../44-libbz2-dev_1.0.8-6_armhf.deb ... Unpacking libbz2-dev:armhf (1.0.8-6) ... Selecting previously unselected package libidn2-0:armhf. Preparing to unpack .../45-libidn2-0_2.3.7-2+b1_armhf.deb ... Unpacking libidn2-0:armhf (2.3.7-2+b1) ... Selecting previously unselected package libffi8:armhf. Preparing to unpack .../46-libffi8_3.4.7-1_armhf.deb ... Unpacking libffi8:armhf (3.4.7-1) ... Selecting previously unselected package libp11-kit0:armhf. Preparing to unpack .../47-libp11-kit0_0.25.5-3_armhf.deb ... Unpacking libp11-kit0:armhf (0.25.5-3) ... Selecting previously unselected package libtasn1-6:armhf. Preparing to unpack .../48-libtasn1-6_4.20.0-2_armhf.deb ... Unpacking libtasn1-6:armhf (4.20.0-2) ... Selecting previously unselected package libgnutls30t64:armhf. Preparing to unpack .../49-libgnutls30t64_3.8.9-2_armhf.deb ... Unpacking libgnutls30t64:armhf (3.8.9-2) ... Selecting previously unselected package libsasl2-modules-db:armhf. Preparing to unpack .../50-libsasl2-modules-db_2.1.28+dfsg1-9_armhf.deb ... Unpacking libsasl2-modules-db:armhf (2.1.28+dfsg1-9) ... Selecting previously unselected package libsasl2-2:armhf. Preparing to unpack .../51-libsasl2-2_2.1.28+dfsg1-9_armhf.deb ... Unpacking libsasl2-2:armhf (2.1.28+dfsg1-9) ... Selecting previously unselected package libldap2:armhf. Preparing to unpack .../52-libldap2_2.6.9+dfsg-1_armhf.deb ... Unpacking libldap2:armhf (2.6.9+dfsg-1) ... Selecting previously unselected package libnghttp2-14:armhf. Preparing to unpack .../53-libnghttp2-14_1.64.0-1_armhf.deb ... Unpacking libnghttp2-14:armhf (1.64.0-1) ... Selecting previously unselected package libnghttp3-9:armhf. Preparing to unpack .../54-libnghttp3-9_1.6.0-2_armhf.deb ... Unpacking libnghttp3-9:armhf (1.6.0-2) ... Selecting previously unselected package libngtcp2-16:armhf. Preparing to unpack .../55-libngtcp2-16_1.9.1-1_armhf.deb ... Unpacking libngtcp2-16:armhf (1.9.1-1) ... Selecting previously unselected package libngtcp2-crypto-gnutls8:armhf. Preparing to unpack .../56-libngtcp2-crypto-gnutls8_1.9.1-1_armhf.deb ... Unpacking libngtcp2-crypto-gnutls8:armhf (1.9.1-1) ... Selecting previously unselected package libpsl5t64:armhf. Preparing to unpack .../57-libpsl5t64_0.21.2-1.1+b1_armhf.deb ... Unpacking libpsl5t64:armhf (0.21.2-1.1+b1) ... Selecting previously unselected package librtmp1:armhf. Preparing to unpack .../58-librtmp1_2.4+20151223.gitfa8646d.1-2+b5_armhf.deb ... Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b5) ... Selecting previously unselected package libssh2-1t64:armhf. Preparing to unpack .../59-libssh2-1t64_1.11.1-1_armhf.deb ... Unpacking libssh2-1t64:armhf (1.11.1-1) ... Selecting previously unselected package libcurl3t64-gnutls:armhf. Preparing to unpack .../60-libcurl3t64-gnutls_8.12.1-3_armhf.deb ... Unpacking libcurl3t64-gnutls:armhf (8.12.1-3) ... Selecting previously unselected package libevent-2.1-7t64:armhf. Preparing to unpack .../61-libevent-2.1-7t64_2.1.12-stable-10+b1_armhf.deb ... Unpacking libevent-2.1-7t64:armhf (2.1.12-stable-10+b1) ... Selecting previously unselected package libunbound8:armhf. Preparing to unpack .../62-libunbound8_1.22.0-1+b1_armhf.deb ... Unpacking libunbound8:armhf (1.22.0-1+b1) ... Selecting previously unselected package libgnutls-dane0t64:armhf. Preparing to unpack .../63-libgnutls-dane0t64_3.8.9-2_armhf.deb ... Unpacking libgnutls-dane0t64:armhf (3.8.9-2) ... Selecting previously unselected package libgnutls-openssl27t64:armhf. Preparing to unpack .../64-libgnutls-openssl27t64_3.8.9-2_armhf.deb ... Unpacking libgnutls-openssl27t64:armhf (3.8.9-2) ... Selecting previously unselected package libidn2-dev:armhf. Preparing to unpack .../65-libidn2-dev_2.3.7-2+b1_armhf.deb ... Unpacking libidn2-dev:armhf (2.3.7-2+b1) ... Selecting previously unselected package libp11-kit-dev:armhf. Preparing to unpack .../66-libp11-kit-dev_0.25.5-3_armhf.deb ... Unpacking libp11-kit-dev:armhf (0.25.5-3) ... Selecting previously unselected package libtasn1-6-dev:armhf. Preparing to unpack .../67-libtasn1-6-dev_4.20.0-2_armhf.deb ... Unpacking libtasn1-6-dev:armhf (4.20.0-2) ... Selecting previously unselected package libgmpxx4ldbl:armhf. Preparing to unpack .../68-libgmpxx4ldbl_2%3a6.3.0+dfsg-3_armhf.deb ... Unpacking libgmpxx4ldbl:armhf (2:6.3.0+dfsg-3) ... Selecting previously unselected package libgmp-dev:armhf. Preparing to unpack .../69-libgmp-dev_2%3a6.3.0+dfsg-3_armhf.deb ... Unpacking libgmp-dev:armhf (2:6.3.0+dfsg-3) ... Selecting previously unselected package nettle-dev:armhf. Preparing to unpack .../70-nettle-dev_3.10.1-1_armhf.deb ... Unpacking nettle-dev:armhf (3.10.1-1) ... Selecting previously unselected package libgnutls28-dev:armhf. Preparing to unpack .../71-libgnutls28-dev_3.8.9-2_armhf.deb ... Unpacking libgnutls28-dev:armhf (3.8.9-2) ... Selecting previously unselected package libkrb5-dev:armhf. Preparing to unpack .../72-libkrb5-dev_1.21.3-4_armhf.deb ... Unpacking libkrb5-dev:armhf (1.21.3-4) ... Selecting previously unselected package libldap-dev:armhf. Preparing to unpack .../73-libldap-dev_2.6.9+dfsg-1_armhf.deb ... Unpacking libldap-dev:armhf (2.6.9+dfsg-1) ... Selecting previously unselected package libpkgconf3:armhf. Preparing to unpack .../74-libpkgconf3_1.8.1-4_armhf.deb ... Unpacking libpkgconf3:armhf (1.8.1-4) ... Selecting previously unselected package pkgconf-bin. Preparing to unpack .../75-pkgconf-bin_1.8.1-4_armhf.deb ... Unpacking pkgconf-bin (1.8.1-4) ... Selecting previously unselected package pkgconf:armhf. Preparing to unpack .../76-pkgconf_1.8.1-4_armhf.deb ... Unpacking pkgconf:armhf (1.8.1-4) ... Selecting previously unselected package libnghttp2-dev:armhf. Preparing to unpack .../77-libnghttp2-dev_1.64.0-1_armhf.deb ... Unpacking libnghttp2-dev:armhf (1.64.0-1) ... Selecting previously unselected package libnghttp3-dev:armhf. Preparing to unpack .../78-libnghttp3-dev_1.6.0-2_armhf.deb ... Unpacking libnghttp3-dev:armhf (1.6.0-2) ... Selecting previously unselected package libngtcp2-crypto-gnutls-dev:armhf. Preparing to unpack .../79-libngtcp2-crypto-gnutls-dev_1.9.1-1_armhf.deb ... Unpacking libngtcp2-crypto-gnutls-dev:armhf (1.9.1-1) ... Selecting previously unselected package libngtcp2-dev:armhf. Preparing to unpack .../80-libngtcp2-dev_1.9.1-1_armhf.deb ... Unpacking libngtcp2-dev:armhf (1.9.1-1) ... Selecting previously unselected package libpsl-dev:armhf. Preparing to unpack .../81-libpsl-dev_0.21.2-1.1+b1_armhf.deb ... Unpacking libpsl-dev:armhf (0.21.2-1.1+b1) ... Selecting previously unselected package zlib1g-dev:armhf. Preparing to unpack .../82-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_armhf.deb ... Unpacking zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1+b1) ... Selecting previously unselected package librtmp-dev:armhf. Preparing to unpack .../83-librtmp-dev_2.4+20151223.gitfa8646d.1-2+b5_armhf.deb ... Unpacking librtmp-dev:armhf (2.4+20151223.gitfa8646d.1-2+b5) ... Selecting previously unselected package libssl-dev:armhf. Preparing to unpack .../84-libssl-dev_3.4.1-1_armhf.deb ... Unpacking libssl-dev:armhf (3.4.1-1) ... Selecting previously unselected package libssh2-1-dev:armhf. Preparing to unpack .../85-libssh2-1-dev_1.11.1-1_armhf.deb ... Unpacking libssh2-1-dev:armhf (1.11.1-1) ... Selecting previously unselected package libzstd-dev:armhf. Preparing to unpack .../86-libzstd-dev_1.5.6+dfsg-2_armhf.deb ... Unpacking libzstd-dev:armhf (1.5.6+dfsg-2) ... Selecting previously unselected package libcurl4-gnutls-dev:armhf. Preparing to unpack .../87-libcurl4-gnutls-dev_8.12.1-3_armhf.deb ... Unpacking libcurl4-gnutls-dev:armhf (8.12.1-3) ... Selecting previously unselected package libdeflate0:armhf. Preparing to unpack .../88-libdeflate0_1.23-1+b1_armhf.deb ... 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Setting up libngtcp2-crypto-gnutls-dev:armhf (1.9.1-1) ... Setting up librtmp-dev:armhf (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libkadm5srv-mit12:armhf (1.21.3-4) ... Setting up libhts3t64:armhf (1.21+ds-1) ... Setting up krb5-multidev:armhf (1.21.3-4) ... Setting up libkrb5-dev:armhf (1.21.3-4) ... Setting up libcurl4-gnutls-dev:armhf (8.12.1-3) ... Setting up libhts-dev:armhf (1.21+ds-1) ... Processing triggers for libc-bin (2.40-7) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/bcftools-1.21/ && 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_1.21-1_source.changes dpkg-buildpackage: info: source package bcftools dpkg-buildpackage: info: source version 1.21-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf 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-1.21' dh_auto_clean make -j3 distclean make[2]: Entering directory '/build/reproducible-path/bcftools-1.21' 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-1.21' 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-1.21' dh_clean debian/rules binary dh binary dh_update_autotools_config debian/rules override_dh_autoreconf make[1]: Entering directory '/build/reproducible-path/bcftools-1.21' 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-1.21' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/bcftools-1.21' dh_auto_configure -- \ --with-htslib=system \ --enable-gsl \ --with-cblas=gslcblas \ --with-bcf-plugin-dir=/usr/lib/arm-linux-gnueabihf/bcftools ./configure --build=arm-linux-gnueabihf --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/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system --enable-gsl --with-cblas=gslcblas --with-bcf-plugin-dir=/usr/lib/arm-linux-gnueabihf/bcftools checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking for gcc option to enable large file support... none needed checking for htslib/sam.h... yes checking for hts_version in -lhts... yes checking shared library type... plain .so checking for library containing dlopen... none required checking if the compiler accepts -rdynamic... yes checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing regcomp... none required configure: creating ./config.status config.status: creating config.mk config.status: creating config.h make[1]: Leaving directory '/build/reproducible-path/bcftools-1.21' dh_auto_build make -j3 make[1]: Entering directory '/build/reproducible-path/bcftools-1.21' echo '#define BCFTOOLS_VERSION "1.21"' > version.h gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfstats.o vcfstats.c gcc -Wall 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-ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o consensus.o consensus.c gcc -Wall -g -O2 -Werror=implicit-function-declaration 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-I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DPLUGINPATH='"/usr/lib/arm-linux-gnueabihf/bcftools"' -c -o vcfplugin.o vcfplugin.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -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-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o main.o main.c gcc -Wl,-z,relro -Wl,-z,now -o test/test-rbuf test/test-rbuf.o -lz gcc -Wl,-z,relro -Wl,-z,now -o test/test-regidx test/test-regidx.o regidx.o -lhts -lpthread -lz gcc -rdynamic -Wl,-z,relro -Wl,-z,now -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-1.21' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/bcftools-1.21' make test-no-plugins VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/bcftools-1.21' ./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/JyOqsQtwLk/merge.a.vcf.gz 2:3199812-3199812 .. ok test_tabix: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/JyOqsQtwLk/merge.a.bcf 2:3199812-3199812 .. ok test_tabix: tabix /tmp/JyOqsQtwLk/merge.a.vcf.gz 1:3000151-3000151 .. ok test_tabix: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/JyOqsQtwLk/merge.a.bcf 1:3000151-3000151 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/JyOqsQtwLk/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/JyOqsQtwLk/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/JyOqsQtwLk/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/JyOqsQtwLk/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/JyOqsQtwLk/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/JyOqsQtwLk/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/JyOqsQtwLk/large_chrom_csi_limit.bcf chr20 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/JyOqsQtwLk/large_chrom_csi_limit.bcf chr20 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/JyOqsQtwLk/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/JyOqsQtwLk/large_chrom_csi_limit.bcf chr20 .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -s /tmp/JyOqsQtwLk/idx.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -s /tmp/JyOqsQtwLk/idx.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -s /tmp/JyOqsQtwLk/idx.bcf .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/JyOqsQtwLk/idx.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/JyOqsQtwLk/idx.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/JyOqsQtwLk/idx.vcf.gz.csi .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/JyOqsQtwLk/idx.bcf .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/JyOqsQtwLk/idx.bcf.csi .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -s /tmp/JyOqsQtwLk/empty.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -s /tmp/JyOqsQtwLk/empty.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -s /tmp/JyOqsQtwLk/empty.bcf .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/JyOqsQtwLk/empty.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/JyOqsQtwLk/empty.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/JyOqsQtwLk/empty.vcf.gz.csi .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/JyOqsQtwLk/empty.bcf .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/JyOqsQtwLk/empty.bcf.csi .. ok test_vcf_check: /build/reproducible-path/bcftools-1.21/bcftools stats -s - /tmp/JyOqsQtwLk/check.vcf.gz | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/check.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools stats -s - | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check_merge: /build/reproducible-path/bcftools-1.21/misc/plot-vcfstats -m /tmp/JyOqsQtwLk/check.1.chk /tmp/JyOqsQtwLk/check.2.chk /tmp/JyOqsQtwLk/check.3.chk /tmp/JyOqsQtwLk/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-1.21/bcftools stats -s - /tmp/JyOqsQtwLk/stats.a.vcf.gz /tmp/JyOqsQtwLk/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/reproducible-path/bcftools-1.21/bcftools stats -s B /tmp/JyOqsQtwLk/stats.a.vcf.gz /tmp/JyOqsQtwLk/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/reproducible-path/bcftools-1.21/bcftools stats -s - /tmp/JyOqsQtwLk/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/reproducible-path/bcftools-1.21/bcftools stats -s - -i 'type="snp"' /tmp/JyOqsQtwLk/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/reproducible-path/bcftools-1.21/bcftools stats -s - /tmp/JyOqsQtwLk/stats.vaf.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -n =2 /tmp/JyOqsQtwLk/isec.a.vcf.gz /tmp/JyOqsQtwLk/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -n =2 /tmp/JyOqsQtwLk/isec.a.vcf.gz /tmp/JyOqsQtwLk/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/JyOqsQtwLk/isec.a.vcf.gz /tmp/JyOqsQtwLk/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -n =2 -i"STRLEN(REF)==2" /tmp/JyOqsQtwLk/isec.a.vcf.gz /tmp/JyOqsQtwLk/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -n =2 -c both /tmp/JyOqsQtwLk/isec.a.vcf.gz /tmp/JyOqsQtwLk/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -n =2 -c both /tmp/JyOqsQtwLk/isec.a.vcf.gz /tmp/JyOqsQtwLk/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -n =2 -c any /tmp/JyOqsQtwLk/isec.a.vcf.gz /tmp/JyOqsQtwLk/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -n =2 -c any /tmp/JyOqsQtwLk/isec.a.vcf.gz /tmp/JyOqsQtwLk/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -C -c any /tmp/JyOqsQtwLk/isec.a.vcf.gz /tmp/JyOqsQtwLk/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -C -c any /tmp/JyOqsQtwLk/isec.a.vcf.gz /tmp/JyOqsQtwLk/isec.b.vcf.gz .. ok test_vcf_isec2: /build/reproducible-path/bcftools-1.21/bcftools isec --no-version -T /tmp/JyOqsQtwLk/isec.tab.gz /tmp/JyOqsQtwLk/isec.a.vcf.gz .. ok test_vcf_isec2: /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -T /tmp/JyOqsQtwLk/isec.tab.gz /tmp/JyOqsQtwLk/isec.a.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/JyOqsQtwLk/isec-miss.1.1.vcf.gz /tmp/JyOqsQtwLk/isec-miss.1.2.vcf.gz /tmp/JyOqsQtwLk/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/JyOqsQtwLk/isec-miss.1.1.vcf.gz /tmp/JyOqsQtwLk/isec-miss.1.2.vcf.gz /tmp/JyOqsQtwLk/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -R /build/reproducible-path/bcftools-1.21/test/isec-miss.1.regs.txt -n +1 /tmp/JyOqsQtwLk/isec-miss.1.1.vcf.gz /tmp/JyOqsQtwLk/isec-miss.1.2.vcf.gz /tmp/JyOqsQtwLk/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -R /build/reproducible-path/bcftools-1.21/test/isec-miss.1.regs.txt -n +1 /tmp/JyOqsQtwLk/isec-miss.1.1.vcf.gz /tmp/JyOqsQtwLk/isec-miss.1.2.vcf.gz /tmp/JyOqsQtwLk/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/JyOqsQtwLk/isec-miss.2.1.vcf.gz /tmp/JyOqsQtwLk/isec-miss.2.2.vcf.gz /tmp/JyOqsQtwLk/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/JyOqsQtwLk/isec-miss.2.1.vcf.gz /tmp/JyOqsQtwLk/isec-miss.2.2.vcf.gz /tmp/JyOqsQtwLk/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -R /build/reproducible-path/bcftools-1.21/test/isec-miss.1.regs.txt -n +1 /tmp/JyOqsQtwLk/isec-miss.2.1.vcf.gz /tmp/JyOqsQtwLk/isec-miss.2.2.vcf.gz /tmp/JyOqsQtwLk/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -R /build/reproducible-path/bcftools-1.21/test/isec-miss.1.regs.txt -n +1 /tmp/JyOqsQtwLk/isec-miss.2.1.vcf.gz /tmp/JyOqsQtwLk/isec-miss.2.2.vcf.gz /tmp/JyOqsQtwLk/isec-miss.2.3.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/JyOqsQtwLk/merge.11.a.vcf.gz /tmp/JyOqsQtwLk/merge.11.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/JyOqsQtwLk/merge.11.a.vcf.gz /tmp/JyOqsQtwLk/merge.11.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/JyOqsQtwLk/merge.11.a.bcf /tmp/JyOqsQtwLk/merge.11.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/JyOqsQtwLk/merge.11.a.bcf /tmp/JyOqsQtwLk/merge.11.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -i AF:join /tmp/JyOqsQtwLk/merge.join.a.vcf.gz /tmp/JyOqsQtwLk/merge.join.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -i AF:join /tmp/JyOqsQtwLk/merge.join.a.vcf.gz /tmp/JyOqsQtwLk/merge.join.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -i AF:join /tmp/JyOqsQtwLk/merge.join.a.bcf /tmp/JyOqsQtwLk/merge.join.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -i AF:join /tmp/JyOqsQtwLk/merge.join.a.bcf /tmp/JyOqsQtwLk/merge.join.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-single /tmp/JyOqsQtwLk/merge.LPL.a.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-single /tmp/JyOqsQtwLk/merge.LPL.a.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-single /tmp/JyOqsQtwLk/merge.LPL.a.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-single /tmp/JyOqsQtwLk/merge.LPL.a.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples /tmp/JyOqsQtwLk/merge.LPL.a.vcf.gz /tmp/JyOqsQtwLk/merge.LPL.b.vcf.gz /tmp/JyOqsQtwLk/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/JyOqsQtwLk/merge.LPL.a.vcf.gz /tmp/JyOqsQtwLk/merge.LPL.b.vcf.gz /tmp/JyOqsQtwLk/merge.LPL.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples /tmp/JyOqsQtwLk/merge.LPL.a.bcf /tmp/JyOqsQtwLk/merge.LPL.b.bcf /tmp/JyOqsQtwLk/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/JyOqsQtwLk/merge.LPL.a.bcf /tmp/JyOqsQtwLk/merge.LPL.b.bcf /tmp/JyOqsQtwLk/merge.LPL.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -L 1 /tmp/JyOqsQtwLk/merge.LPL.a.vcf.gz /tmp/JyOqsQtwLk/merge.LPL.b.vcf.gz /tmp/JyOqsQtwLk/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 1 /tmp/JyOqsQtwLk/merge.LPL.a.vcf.gz /tmp/JyOqsQtwLk/merge.LPL.b.vcf.gz /tmp/JyOqsQtwLk/merge.LPL.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -L 1 /tmp/JyOqsQtwLk/merge.LPL.a.bcf /tmp/JyOqsQtwLk/merge.LPL.b.bcf /tmp/JyOqsQtwLk/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 1 /tmp/JyOqsQtwLk/merge.LPL.a.bcf /tmp/JyOqsQtwLk/merge.LPL.b.bcf /tmp/JyOqsQtwLk/merge.LPL.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -L 2 /tmp/JyOqsQtwLk/merge.LPL.a.vcf.gz /tmp/JyOqsQtwLk/merge.LPL.b.vcf.gz /tmp/JyOqsQtwLk/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 2 /tmp/JyOqsQtwLk/merge.LPL.a.vcf.gz /tmp/JyOqsQtwLk/merge.LPL.b.vcf.gz /tmp/JyOqsQtwLk/merge.LPL.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -L 2 /tmp/JyOqsQtwLk/merge.LPL.a.bcf /tmp/JyOqsQtwLk/merge.LPL.b.bcf /tmp/JyOqsQtwLk/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 2 /tmp/JyOqsQtwLk/merge.LPL.a.bcf /tmp/JyOqsQtwLk/merge.LPL.b.bcf /tmp/JyOqsQtwLk/merge.LPL.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -L 3 /tmp/JyOqsQtwLk/merge.LPL.a.vcf.gz /tmp/JyOqsQtwLk/merge.LPL.b.vcf.gz /tmp/JyOqsQtwLk/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 3 /tmp/JyOqsQtwLk/merge.LPL.a.vcf.gz /tmp/JyOqsQtwLk/merge.LPL.b.vcf.gz /tmp/JyOqsQtwLk/merge.LPL.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -L 3 /tmp/JyOqsQtwLk/merge.LPL.a.bcf /tmp/JyOqsQtwLk/merge.LPL.b.bcf /tmp/JyOqsQtwLk/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 3 /tmp/JyOqsQtwLk/merge.LPL.a.bcf /tmp/JyOqsQtwLk/merge.LPL.b.bcf /tmp/JyOqsQtwLk/merge.LPL.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -L 4 /tmp/JyOqsQtwLk/merge.LPL.a.vcf.gz /tmp/JyOqsQtwLk/merge.LPL.b.vcf.gz /tmp/JyOqsQtwLk/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 4 /tmp/JyOqsQtwLk/merge.LPL.a.vcf.gz /tmp/JyOqsQtwLk/merge.LPL.b.vcf.gz /tmp/JyOqsQtwLk/merge.LPL.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -L 4 /tmp/JyOqsQtwLk/merge.LPL.a.bcf /tmp/JyOqsQtwLk/merge.LPL.b.bcf /tmp/JyOqsQtwLk/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 4 /tmp/JyOqsQtwLk/merge.LPL.a.bcf /tmp/JyOqsQtwLk/merge.LPL.b.bcf /tmp/JyOqsQtwLk/merge.LPL.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -L 5 /tmp/JyOqsQtwLk/merge.LPL.a.vcf.gz /tmp/JyOqsQtwLk/merge.LPL.b.vcf.gz /tmp/JyOqsQtwLk/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 5 /tmp/JyOqsQtwLk/merge.LPL.a.vcf.gz /tmp/JyOqsQtwLk/merge.LPL.b.vcf.gz /tmp/JyOqsQtwLk/merge.LPL.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -L 5 /tmp/JyOqsQtwLk/merge.LPL.a.bcf /tmp/JyOqsQtwLk/merge.LPL.b.bcf /tmp/JyOqsQtwLk/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 5 /tmp/JyOqsQtwLk/merge.LPL.a.bcf /tmp/JyOqsQtwLk/merge.LPL.b.bcf /tmp/JyOqsQtwLk/merge.LPL.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples /tmp/JyOqsQtwLk/merge.a.vcf.gz /tmp/JyOqsQtwLk/merge.b.vcf.gz /tmp/JyOqsQtwLk/merge.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/JyOqsQtwLk/merge.a.vcf.gz /tmp/JyOqsQtwLk/merge.b.vcf.gz /tmp/JyOqsQtwLk/merge.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples /tmp/JyOqsQtwLk/merge.a.bcf /tmp/JyOqsQtwLk/merge.b.bcf /tmp/JyOqsQtwLk/merge.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/JyOqsQtwLk/merge.a.bcf /tmp/JyOqsQtwLk/merge.b.bcf /tmp/JyOqsQtwLk/merge.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -Fx /tmp/JyOqsQtwLk/merge.a.vcf.gz /tmp/JyOqsQtwLk/merge.b.vcf.gz /tmp/JyOqsQtwLk/merge.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -Fx /tmp/JyOqsQtwLk/merge.a.vcf.gz /tmp/JyOqsQtwLk/merge.b.vcf.gz /tmp/JyOqsQtwLk/merge.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -Fx /tmp/JyOqsQtwLk/merge.a.bcf /tmp/JyOqsQtwLk/merge.b.bcf /tmp/JyOqsQtwLk/merge.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -Fx /tmp/JyOqsQtwLk/merge.a.bcf /tmp/JyOqsQtwLk/merge.b.bcf /tmp/JyOqsQtwLk/merge.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -0 /tmp/JyOqsQtwLk/merge.a.vcf.gz /tmp/JyOqsQtwLk/merge.b.vcf.gz /tmp/JyOqsQtwLk/merge.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -0 /tmp/JyOqsQtwLk/merge.a.vcf.gz /tmp/JyOqsQtwLk/merge.b.vcf.gz /tmp/JyOqsQtwLk/merge.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -0 /tmp/JyOqsQtwLk/merge.a.bcf /tmp/JyOqsQtwLk/merge.b.bcf /tmp/JyOqsQtwLk/merge.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -0 /tmp/JyOqsQtwLk/merge.a.bcf /tmp/JyOqsQtwLk/merge.b.bcf /tmp/JyOqsQtwLk/merge.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -m none /tmp/JyOqsQtwLk/merge.2.a.vcf.gz /tmp/JyOqsQtwLk/merge.2.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m none /tmp/JyOqsQtwLk/merge.2.a.vcf.gz /tmp/JyOqsQtwLk/merge.2.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -m none /tmp/JyOqsQtwLk/merge.2.a.bcf /tmp/JyOqsQtwLk/merge.2.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m none /tmp/JyOqsQtwLk/merge.2.a.bcf /tmp/JyOqsQtwLk/merge.2.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -m both /tmp/JyOqsQtwLk/merge.2.a.vcf.gz /tmp/JyOqsQtwLk/merge.2.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m both /tmp/JyOqsQtwLk/merge.2.a.vcf.gz /tmp/JyOqsQtwLk/merge.2.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -m both /tmp/JyOqsQtwLk/merge.2.a.bcf /tmp/JyOqsQtwLk/merge.2.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m both /tmp/JyOqsQtwLk/merge.2.a.bcf /tmp/JyOqsQtwLk/merge.2.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -m all /tmp/JyOqsQtwLk/merge.2.a.vcf.gz /tmp/JyOqsQtwLk/merge.2.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m all /tmp/JyOqsQtwLk/merge.2.a.vcf.gz /tmp/JyOqsQtwLk/merge.2.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -m all /tmp/JyOqsQtwLk/merge.2.a.bcf /tmp/JyOqsQtwLk/merge.2.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m all /tmp/JyOqsQtwLk/merge.2.a.bcf /tmp/JyOqsQtwLk/merge.2.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/JyOqsQtwLk/merge.3.a.vcf.gz /tmp/JyOqsQtwLk/merge.3.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/JyOqsQtwLk/merge.3.a.vcf.gz /tmp/JyOqsQtwLk/merge.3.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/JyOqsQtwLk/merge.3.a.bcf /tmp/JyOqsQtwLk/merge.3.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/JyOqsQtwLk/merge.3.a.bcf /tmp/JyOqsQtwLk/merge.3.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -m id /tmp/JyOqsQtwLk/merge.4.a.vcf.gz /tmp/JyOqsQtwLk/merge.4.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m id /tmp/JyOqsQtwLk/merge.4.a.vcf.gz /tmp/JyOqsQtwLk/merge.4.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples -m id /tmp/JyOqsQtwLk/merge.4.a.bcf /tmp/JyOqsQtwLk/merge.4.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m id /tmp/JyOqsQtwLk/merge.4.a.bcf /tmp/JyOqsQtwLk/merge.4.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/JyOqsQtwLk/gvcf.merge.1.vcf.gz /tmp/JyOqsQtwLk/gvcf.merge.2.vcf.gz /tmp/JyOqsQtwLk/gvcf.merge.3.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/JyOqsQtwLk/gvcf.merge.1.vcf.gz /tmp/JyOqsQtwLk/gvcf.merge.2.vcf.gz /tmp/JyOqsQtwLk/gvcf.merge.3.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/JyOqsQtwLk/gvcf.merge.1.bcf /tmp/JyOqsQtwLk/gvcf.merge.2.bcf /tmp/JyOqsQtwLk/gvcf.merge.3.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/JyOqsQtwLk/gvcf.merge.1.bcf /tmp/JyOqsQtwLk/gvcf.merge.2.bcf /tmp/JyOqsQtwLk/gvcf.merge.3.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/JyOqsQtwLk/merge.gvcf.2.a.vcf.gz /tmp/JyOqsQtwLk/merge.gvcf.2.b.vcf.gz /tmp/JyOqsQtwLk/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/JyOqsQtwLk/merge.gvcf.2.a.vcf.gz /tmp/JyOqsQtwLk/merge.gvcf.2.b.vcf.gz /tmp/JyOqsQtwLk/merge.gvcf.2.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - -m both,* /tmp/JyOqsQtwLk/merge.gvcf.2.a.vcf.gz /tmp/JyOqsQtwLk/merge.gvcf.2.b.vcf.gz /tmp/JyOqsQtwLk/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - -m both,* /tmp/JyOqsQtwLk/merge.gvcf.2.a.vcf.gz /tmp/JyOqsQtwLk/merge.gvcf.2.b.vcf.gz /tmp/JyOqsQtwLk/merge.gvcf.2.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - -m both,** /tmp/JyOqsQtwLk/merge.gvcf.2.a.vcf.gz /tmp/JyOqsQtwLk/merge.gvcf.2.b.vcf.gz /tmp/JyOqsQtwLk/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - -m both,** /tmp/JyOqsQtwLk/merge.gvcf.2.a.vcf.gz /tmp/JyOqsQtwLk/merge.gvcf.2.b.vcf.gz /tmp/JyOqsQtwLk/merge.gvcf.2.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - -i SRC:join /tmp/JyOqsQtwLk/merge.gvcf.3.a.vcf.gz /tmp/JyOqsQtwLk/merge.gvcf.3.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - -i SRC:join /tmp/JyOqsQtwLk/merge.gvcf.3.a.vcf.gz /tmp/JyOqsQtwLk/merge.gvcf.3.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/JyOqsQtwLk/merge.gvcf.4.a.vcf.gz /tmp/JyOqsQtwLk/merge.gvcf.4.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/JyOqsQtwLk/merge.gvcf.4.a.vcf.gz /tmp/JyOqsQtwLk/merge.gvcf.4.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/JyOqsQtwLk/merge.gvcf.4.a.bcf /tmp/JyOqsQtwLk/merge.gvcf.4.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/JyOqsQtwLk/merge.gvcf.4.a.bcf /tmp/JyOqsQtwLk/merge.gvcf.4.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/JyOqsQtwLk/merge.5.a.vcf.gz /tmp/JyOqsQtwLk/merge.5.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/JyOqsQtwLk/merge.5.a.vcf.gz /tmp/JyOqsQtwLk/merge.5.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/JyOqsQtwLk/merge.5.a.bcf /tmp/JyOqsQtwLk/merge.5.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/JyOqsQtwLk/merge.5.a.bcf /tmp/JyOqsQtwLk/merge.5.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/JyOqsQtwLk/merge.6.a.vcf.gz /tmp/JyOqsQtwLk/merge.6.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/JyOqsQtwLk/merge.6.a.vcf.gz /tmp/JyOqsQtwLk/merge.6.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/JyOqsQtwLk/merge.6.a.bcf /tmp/JyOqsQtwLk/merge.6.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/JyOqsQtwLk/merge.6.a.bcf /tmp/JyOqsQtwLk/merge.6.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/JyOqsQtwLk/merge.gvcf.7.a.vcf.gz /tmp/JyOqsQtwLk/merge.gvcf.7.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/JyOqsQtwLk/merge.gvcf.7.a.vcf.gz /tmp/JyOqsQtwLk/merge.gvcf.7.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/JyOqsQtwLk/merge.gvcf.7.a.bcf /tmp/JyOqsQtwLk/merge.gvcf.7.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/JyOqsQtwLk/merge.gvcf.7.a.bcf /tmp/JyOqsQtwLk/merge.gvcf.7.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/JyOqsQtwLk/merge.gvcf.8.a.vcf.gz /tmp/JyOqsQtwLk/merge.gvcf.8.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/JyOqsQtwLk/merge.gvcf.8.a.vcf.gz /tmp/JyOqsQtwLk/merge.gvcf.8.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/JyOqsQtwLk/merge.gvcf.8.a.bcf /tmp/JyOqsQtwLk/merge.gvcf.8.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/JyOqsQtwLk/merge.gvcf.8.a.bcf /tmp/JyOqsQtwLk/merge.gvcf.8.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples /tmp/JyOqsQtwLk/merge.7.a.vcf.gz /tmp/JyOqsQtwLk/merge.7.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/JyOqsQtwLk/merge.7.a.vcf.gz /tmp/JyOqsQtwLk/merge.7.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --force-samples /tmp/JyOqsQtwLk/merge.7.a.bcf /tmp/JyOqsQtwLk/merge.7.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/JyOqsQtwLk/merge.7.a.bcf /tmp/JyOqsQtwLk/merge.7.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa /tmp/JyOqsQtwLk/merge.gvcf.9a.vcf.gz /tmp/JyOqsQtwLk/merge.gvcf.9b.vcf.gz /tmp/JyOqsQtwLk/merge.gvcf.9c.vcf.gz /tmp/JyOqsQtwLk/merge.gvcf.9d.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa /tmp/JyOqsQtwLk/merge.gvcf.9a.vcf.gz /tmp/JyOqsQtwLk/merge.gvcf.9b.vcf.gz /tmp/JyOqsQtwLk/merge.gvcf.9c.vcf.gz /tmp/JyOqsQtwLk/merge.gvcf.9d.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa /tmp/JyOqsQtwLk/merge.gvcf.9a.bcf /tmp/JyOqsQtwLk/merge.gvcf.9b.bcf /tmp/JyOqsQtwLk/merge.gvcf.9c.bcf /tmp/JyOqsQtwLk/merge.gvcf.9d.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa /tmp/JyOqsQtwLk/merge.gvcf.9a.bcf /tmp/JyOqsQtwLk/merge.gvcf.9b.bcf /tmp/JyOqsQtwLk/merge.gvcf.9c.bcf /tmp/JyOqsQtwLk/merge.gvcf.9d.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa -r 22:21-23 /tmp/JyOqsQtwLk/merge.gvcf.9a.vcf.gz /tmp/JyOqsQtwLk/merge.gvcf.9b.vcf.gz /tmp/JyOqsQtwLk/merge.gvcf.9c.vcf.gz /tmp/JyOqsQtwLk/merge.gvcf.9d.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa -r 22:21-23 /tmp/JyOqsQtwLk/merge.gvcf.9a.vcf.gz /tmp/JyOqsQtwLk/merge.gvcf.9b.vcf.gz /tmp/JyOqsQtwLk/merge.gvcf.9c.vcf.gz /tmp/JyOqsQtwLk/merge.gvcf.9d.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa -r 22:21-23 /tmp/JyOqsQtwLk/merge.gvcf.9a.bcf /tmp/JyOqsQtwLk/merge.gvcf.9b.bcf /tmp/JyOqsQtwLk/merge.gvcf.9c.bcf /tmp/JyOqsQtwLk/merge.gvcf.9d.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa -r 22:21-23 /tmp/JyOqsQtwLk/merge.gvcf.9a.bcf /tmp/JyOqsQtwLk/merge.gvcf.9b.bcf /tmp/JyOqsQtwLk/merge.gvcf.9c.bcf /tmp/JyOqsQtwLk/merge.gvcf.9d.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa /tmp/JyOqsQtwLk/merge.gvcf.9a.vcf.gz /tmp/JyOqsQtwLk/merge.gvcf.9b.vcf.gz /tmp/JyOqsQtwLk/merge.gvcf.9c.vcf.gz /tmp/JyOqsQtwLk/merge.gvcf.9d.vcf.gz /tmp/JyOqsQtwLk/merge.gvcf.9e.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa /tmp/JyOqsQtwLk/merge.gvcf.9a.vcf.gz /tmp/JyOqsQtwLk/merge.gvcf.9b.vcf.gz /tmp/JyOqsQtwLk/merge.gvcf.9c.vcf.gz /tmp/JyOqsQtwLk/merge.gvcf.9d.vcf.gz /tmp/JyOqsQtwLk/merge.gvcf.9e.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa /tmp/JyOqsQtwLk/merge.gvcf.9a.bcf /tmp/JyOqsQtwLk/merge.gvcf.9b.bcf /tmp/JyOqsQtwLk/merge.gvcf.9c.bcf /tmp/JyOqsQtwLk/merge.gvcf.9d.bcf /tmp/JyOqsQtwLk/merge.gvcf.9e.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa /tmp/JyOqsQtwLk/merge.gvcf.9a.bcf /tmp/JyOqsQtwLk/merge.gvcf.9b.bcf /tmp/JyOqsQtwLk/merge.gvcf.9c.bcf /tmp/JyOqsQtwLk/merge.gvcf.9d.bcf /tmp/JyOqsQtwLk/merge.gvcf.9e.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa -r 22:21-23 /tmp/JyOqsQtwLk/merge.gvcf.9a.vcf.gz /tmp/JyOqsQtwLk/merge.gvcf.9b.vcf.gz /tmp/JyOqsQtwLk/merge.gvcf.9c.vcf.gz /tmp/JyOqsQtwLk/merge.gvcf.9d.vcf.gz /tmp/JyOqsQtwLk/merge.gvcf.9e.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa -r 22:21-23 /tmp/JyOqsQtwLk/merge.gvcf.9a.vcf.gz /tmp/JyOqsQtwLk/merge.gvcf.9b.vcf.gz /tmp/JyOqsQtwLk/merge.gvcf.9c.vcf.gz /tmp/JyOqsQtwLk/merge.gvcf.9d.vcf.gz /tmp/JyOqsQtwLk/merge.gvcf.9e.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa -r 22:21-23 /tmp/JyOqsQtwLk/merge.gvcf.9a.bcf /tmp/JyOqsQtwLk/merge.gvcf.9b.bcf /tmp/JyOqsQtwLk/merge.gvcf.9c.bcf /tmp/JyOqsQtwLk/merge.gvcf.9d.bcf /tmp/JyOqsQtwLk/merge.gvcf.9e.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf /build/reproducible-path/bcftools-1.21/test/gvcf.fa -r 22:21-23 /tmp/JyOqsQtwLk/merge.gvcf.9a.bcf /tmp/JyOqsQtwLk/merge.gvcf.9b.bcf /tmp/JyOqsQtwLk/merge.gvcf.9c.bcf /tmp/JyOqsQtwLk/merge.gvcf.9d.bcf /tmp/JyOqsQtwLk/merge.gvcf.9e.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/JyOqsQtwLk/merge.gvcf.10.a.vcf.gz /tmp/JyOqsQtwLk/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/JyOqsQtwLk/merge.gvcf.10.a.vcf.gz /tmp/JyOqsQtwLk/merge.gvcf.10.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/JyOqsQtwLk/merge.gvcf.10.a.bcf /tmp/JyOqsQtwLk/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/JyOqsQtwLk/merge.gvcf.10.a.bcf /tmp/JyOqsQtwLk/merge.gvcf.10.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -m none /tmp/JyOqsQtwLk/merge.gvcf.10.a.vcf.gz /tmp/JyOqsQtwLk/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m none /tmp/JyOqsQtwLk/merge.gvcf.10.a.vcf.gz /tmp/JyOqsQtwLk/merge.gvcf.10.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -m none /tmp/JyOqsQtwLk/merge.gvcf.10.a.bcf /tmp/JyOqsQtwLk/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m none /tmp/JyOqsQtwLk/merge.gvcf.10.a.bcf /tmp/JyOqsQtwLk/merge.gvcf.10.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -g /build/reproducible-path/bcftools-1.21/test/merge.gvcf.10.fa /tmp/JyOqsQtwLk/merge.gvcf.10.a.vcf.gz /tmp/JyOqsQtwLk/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -g /build/reproducible-path/bcftools-1.21/test/merge.gvcf.10.fa /tmp/JyOqsQtwLk/merge.gvcf.10.a.vcf.gz /tmp/JyOqsQtwLk/merge.gvcf.10.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -g /build/reproducible-path/bcftools-1.21/test/merge.gvcf.10.fa /tmp/JyOqsQtwLk/merge.gvcf.10.a.bcf /tmp/JyOqsQtwLk/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -g /build/reproducible-path/bcftools-1.21/test/merge.gvcf.10.fa /tmp/JyOqsQtwLk/merge.gvcf.10.a.bcf /tmp/JyOqsQtwLk/merge.gvcf.10.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -g /build/reproducible-path/bcftools-1.21/test/merge.gvcf.10.fa -m none /tmp/JyOqsQtwLk/merge.gvcf.10.a.vcf.gz /tmp/JyOqsQtwLk/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -g /build/reproducible-path/bcftools-1.21/test/merge.gvcf.10.fa -m none /tmp/JyOqsQtwLk/merge.gvcf.10.a.vcf.gz /tmp/JyOqsQtwLk/merge.gvcf.10.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -g /build/reproducible-path/bcftools-1.21/test/merge.gvcf.10.fa -m none /tmp/JyOqsQtwLk/merge.gvcf.10.a.bcf /tmp/JyOqsQtwLk/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -g /build/reproducible-path/bcftools-1.21/test/merge.gvcf.10.fa -m none /tmp/JyOqsQtwLk/merge.gvcf.10.a.bcf /tmp/JyOqsQtwLk/merge.gvcf.10.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/JyOqsQtwLk/merge.noidx.a.vcf.gz /tmp/JyOqsQtwLk/merge.noidx.b.vcf.gz /tmp/JyOqsQtwLk/merge.noidx.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/JyOqsQtwLk/merge.noidx.a.vcf.gz /tmp/JyOqsQtwLk/merge.noidx.b.vcf.gz /tmp/JyOqsQtwLk/merge.noidx.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/JyOqsQtwLk/merge.noidx.a.bcf /tmp/JyOqsQtwLk/merge.noidx.b.bcf /tmp/JyOqsQtwLk/merge.noidx.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/JyOqsQtwLk/merge.noidx.a.bcf /tmp/JyOqsQtwLk/merge.noidx.b.bcf /tmp/JyOqsQtwLk/merge.noidx.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --no-index /build/reproducible-path/bcftools-1.21/test/merge.noidx.a.vcf /build/reproducible-path/bcftools-1.21/test/merge.noidx.b.vcf /build/reproducible-path/bcftools-1.21/test/merge.noidx.c.vcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --no-index /build/reproducible-path/bcftools-1.21/test/merge.noidx.a.vcf /build/reproducible-path/bcftools-1.21/test/merge.noidx.b.vcf /build/reproducible-path/bcftools-1.21/test/merge.noidx.c.vcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --no-index /tmp/JyOqsQtwLk/merge.noidx.a.bcf /tmp/JyOqsQtwLk/merge.noidx.b.bcf /tmp/JyOqsQtwLk/merge.noidx.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --no-index /tmp/JyOqsQtwLk/merge.noidx.a.bcf /tmp/JyOqsQtwLk/merge.noidx.b.bcf /tmp/JyOqsQtwLk/merge.noidx.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/JyOqsQtwLk/merge.8.a.vcf.gz /tmp/JyOqsQtwLk/merge.8.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/JyOqsQtwLk/merge.8.a.vcf.gz /tmp/JyOqsQtwLk/merge.8.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/JyOqsQtwLk/merge.8.a.bcf /tmp/JyOqsQtwLk/merge.8.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/JyOqsQtwLk/merge.8.a.bcf /tmp/JyOqsQtwLk/merge.8.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -i AN:sum,AC:sum /tmp/JyOqsQtwLk/merge.8.a.vcf.gz /tmp/JyOqsQtwLk/merge.8.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/JyOqsQtwLk/merge.8.a.vcf.gz /tmp/JyOqsQtwLk/merge.8.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -i AN:sum,AC:sum /tmp/JyOqsQtwLk/merge.8.a.bcf /tmp/JyOqsQtwLk/merge.8.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/JyOqsQtwLk/merge.8.a.bcf /tmp/JyOqsQtwLk/merge.8.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/JyOqsQtwLk/merge.9.a.vcf.gz /tmp/JyOqsQtwLk/merge.9.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/JyOqsQtwLk/merge.9.a.vcf.gz /tmp/JyOqsQtwLk/merge.9.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/JyOqsQtwLk/merge.9.a.bcf /tmp/JyOqsQtwLk/merge.9.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/JyOqsQtwLk/merge.9.a.bcf /tmp/JyOqsQtwLk/merge.9.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -i AN:sum,AC:sum /tmp/JyOqsQtwLk/merge.9.a.vcf.gz /tmp/JyOqsQtwLk/merge.9.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/JyOqsQtwLk/merge.9.a.vcf.gz /tmp/JyOqsQtwLk/merge.9.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -i AN:sum,AC:sum /tmp/JyOqsQtwLk/merge.9.a.bcf /tmp/JyOqsQtwLk/merge.9.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/JyOqsQtwLk/merge.9.a.bcf /tmp/JyOqsQtwLk/merge.9.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -m none /tmp/JyOqsQtwLk/merge.10.a.vcf.gz /tmp/JyOqsQtwLk/merge.10.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m none /tmp/JyOqsQtwLk/merge.10.a.vcf.gz /tmp/JyOqsQtwLk/merge.10.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -m none /tmp/JyOqsQtwLk/merge.10.a.bcf /tmp/JyOqsQtwLk/merge.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m none /tmp/JyOqsQtwLk/merge.10.a.bcf /tmp/JyOqsQtwLk/merge.10.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -m both /tmp/JyOqsQtwLk/merge.10.a.vcf.gz /tmp/JyOqsQtwLk/merge.10.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m both /tmp/JyOqsQtwLk/merge.10.a.vcf.gz /tmp/JyOqsQtwLk/merge.10.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -m both /tmp/JyOqsQtwLk/merge.10.a.bcf /tmp/JyOqsQtwLk/merge.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m both /tmp/JyOqsQtwLk/merge.10.a.bcf /tmp/JyOqsQtwLk/merge.10.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -m snp-ins-del /tmp/JyOqsQtwLk/merge.10.a.vcf.gz /tmp/JyOqsQtwLk/merge.10.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m snp-ins-del /tmp/JyOqsQtwLk/merge.10.a.vcf.gz /tmp/JyOqsQtwLk/merge.10.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -m snp-ins-del /tmp/JyOqsQtwLk/merge.10.a.bcf /tmp/JyOqsQtwLk/merge.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m snp-ins-del /tmp/JyOqsQtwLk/merge.10.a.bcf /tmp/JyOqsQtwLk/merge.10.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/JyOqsQtwLk/merge.mrules.1.a.vcf.gz /tmp/JyOqsQtwLk/merge.mrules.1.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/JyOqsQtwLk/merge.mrules.1.a.vcf.gz /tmp/JyOqsQtwLk/merge.mrules.1.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/JyOqsQtwLk/merge.mrules.1.a.bcf /tmp/JyOqsQtwLk/merge.mrules.1.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/JyOqsQtwLk/merge.mrules.1.a.bcf /tmp/JyOqsQtwLk/merge.mrules.1.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - -M AD:.,PL:. /tmp/JyOqsQtwLk/merge.mrules.1.a.vcf.gz /tmp/JyOqsQtwLk/merge.mrules.1.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - -M AD:.,PL:. /tmp/JyOqsQtwLk/merge.mrules.1.a.vcf.gz /tmp/JyOqsQtwLk/merge.mrules.1.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - -M AD:.,PL:. /tmp/JyOqsQtwLk/merge.mrules.1.a.bcf /tmp/JyOqsQtwLk/merge.mrules.1.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - -M AD:.,PL:. /tmp/JyOqsQtwLk/merge.mrules.1.a.bcf /tmp/JyOqsQtwLk/merge.mrules.1.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/JyOqsQtwLk/merge.gvcf.5.a.vcf.gz /tmp/JyOqsQtwLk/merge.gvcf.5.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/JyOqsQtwLk/merge.gvcf.5.a.vcf.gz /tmp/JyOqsQtwLk/merge.gvcf.5.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/JyOqsQtwLk/merge.gvcf.5.a.bcf /tmp/JyOqsQtwLk/merge.gvcf.5.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/JyOqsQtwLk/merge.gvcf.5.a.bcf /tmp/JyOqsQtwLk/merge.gvcf.5.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - --merge none /tmp/JyOqsQtwLk/merge.gvcf.5.a.vcf.gz /tmp/JyOqsQtwLk/merge.gvcf.5.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - --merge none /tmp/JyOqsQtwLk/merge.gvcf.5.a.vcf.gz /tmp/JyOqsQtwLk/merge.gvcf.5.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - --merge none /tmp/JyOqsQtwLk/merge.gvcf.5.a.bcf /tmp/JyOqsQtwLk/merge.gvcf.5.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - --merge none /tmp/JyOqsQtwLk/merge.gvcf.5.a.bcf /tmp/JyOqsQtwLk/merge.gvcf.5.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/JyOqsQtwLk/merge.gvcf.11.a.vcf.gz /tmp/JyOqsQtwLk/merge.gvcf.11.b.vcf.gz /tmp/JyOqsQtwLk/merge.gvcf.11.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/JyOqsQtwLk/merge.gvcf.11.a.vcf.gz /tmp/JyOqsQtwLk/merge.gvcf.11.b.vcf.gz /tmp/JyOqsQtwLk/merge.gvcf.11.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/JyOqsQtwLk/merge.gvcf.11.a.bcf /tmp/JyOqsQtwLk/merge.gvcf.11.b.bcf /tmp/JyOqsQtwLk/merge.gvcf.11.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/JyOqsQtwLk/merge.gvcf.11.a.bcf /tmp/JyOqsQtwLk/merge.gvcf.11.b.bcf /tmp/JyOqsQtwLk/merge.gvcf.11.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided,_conflicting_interpretations"' /tmp/JyOqsQtwLk/query.string.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.string.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided,_conflicting_interpretations"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" || CLNREVSTAT="_conflicting_interpretations"' /tmp/JyOqsQtwLk/query.string.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.string.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" || CLNREVSTAT="_conflicting_interpretations"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" && CLNREVSTAT="_conflicting_interpretations"' /tmp/JyOqsQtwLk/query.string.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.string.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" && CLNREVSTAT="_conflicting_interpretations"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%INFO/STR\n' -i'INFO/STR=@/build/reproducible-path/bcftools-1.21/test/query.string.2.1.txt' /tmp/JyOqsQtwLk/query.string.2.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.string.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%INFO/STR\n' -i'INFO/STR=@/build/reproducible-path/bcftools-1.21/test/query.string.2.1.txt' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS[\t%STR]\n' -i'FMT/STR=@/build/reproducible-path/bcftools-1.21/test/query.string.2.2.txt' /tmp/JyOqsQtwLk/query.string.2.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.string.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS[\t%STR]\n' -i'FMT/STR=@/build/reproducible-path/bcftools-1.21/test/query.string.2.2.txt' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' /tmp/JyOqsQtwLk/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.vcf.gz | /build/reproducible-path/bcftools-1.21/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-1.21/bcftools query -f '%RSX\t%VKX\n' /tmp/JyOqsQtwLk/query.variantkey.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.variantkey.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f '%RSX\t%VKX\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%XRI\n' -i'XRI[*]>1111' /tmp/JyOqsQtwLk/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%XRI\n' -i'XRI[*]>1111' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' /tmp/JyOqsQtwLk/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' /tmp/JyOqsQtwLk/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' /tmp/JyOqsQtwLk/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' /tmp/JyOqsQtwLk/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' /tmp/JyOqsQtwLk/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' /tmp/JyOqsQtwLk/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' /tmp/JyOqsQtwLk/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' /tmp/JyOqsQtwLk/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' /tmp/JyOqsQtwLk/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' /tmp/JyOqsQtwLk/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' /tmp/JyOqsQtwLk/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' /tmp/JyOqsQtwLk/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' /tmp/JyOqsQtwLk/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' /tmp/JyOqsQtwLk/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' /tmp/JyOqsQtwLk/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/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/JyOqsQtwLk/view.vectors.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/view.vectors.vcf.gz | /build/reproducible-path/bcftools-1.21/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-1.21/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' /tmp/JyOqsQtwLk/query.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' /tmp/JyOqsQtwLk/query.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' /tmp/JyOqsQtwLk/query.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' /tmp/JyOqsQtwLk/query.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' /tmp/JyOqsQtwLk/query.2.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'IINT="."' -f'%POS %IINT\n' /tmp/JyOqsQtwLk/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'IINT!="."' -f'%POS %IINT\n' /tmp/JyOqsQtwLk/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -e'IINT!="."' -f'%POS %IINT\n' /tmp/JyOqsQtwLk/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -e'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -e'IINT="."' -f'%POS %IINT\n' /tmp/JyOqsQtwLk/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -e'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' /tmp/JyOqsQtwLk/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' /tmp/JyOqsQtwLk/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' /tmp/JyOqsQtwLk/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' /tmp/JyOqsQtwLk/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' /tmp/JyOqsQtwLk/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' /tmp/JyOqsQtwLk/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' /tmp/JyOqsQtwLk/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' /tmp/JyOqsQtwLk/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' /tmp/JyOqsQtwLk/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER="A"' -f'%POS %FILTER\n' /tmp/JyOqsQtwLk/filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/filter.11.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER="A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER!="A"' -f'%POS %FILTER\n' /tmp/JyOqsQtwLk/filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/filter.11.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER!="A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER~"A"' -f'%POS %FILTER\n' /tmp/JyOqsQtwLk/filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/filter.11.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER~"A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n' /tmp/JyOqsQtwLk/filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/filter.11.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%LINE' /tmp/JyOqsQtwLk/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%LINE' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' /tmp/JyOqsQtwLk/query.filter-type.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.filter-type.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' /tmp/JyOqsQtwLk/query.filter-type.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.filter-type.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' /tmp/JyOqsQtwLk/query.filter-type.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.filter-type.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' /tmp/JyOqsQtwLk/query.filter-type.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.filter-type.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'INFO/TYPE="xxx"' /tmp/JyOqsQtwLk/query.filter-type.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.filter-type.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'INFO/TYPE="xxx"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/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/JyOqsQtwLk/filter-missing-floats.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/filter-missing-floats.vcf.gz | /build/reproducible-path/bcftools-1.21/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-1.21/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/JyOqsQtwLk/filter-missing-floats.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/filter-missing-floats.vcf.gz | /build/reproducible-path/bcftools-1.21/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-1.21/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' /tmp/JyOqsQtwLk/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' /tmp/JyOqsQtwLk/query.filter.2.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.filter.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' /tmp/JyOqsQtwLk/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' /tmp/JyOqsQtwLk/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' /tmp/JyOqsQtwLk/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' /tmp/JyOqsQtwLk/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' /tmp/JyOqsQtwLk/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' /tmp/JyOqsQtwLk/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' /tmp/JyOqsQtwLk/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' /tmp/JyOqsQtwLk/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' /tmp/JyOqsQtwLk/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' /tmp/JyOqsQtwLk/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' /tmp/JyOqsQtwLk/filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/filter.5.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' /tmp/JyOqsQtwLk/filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/filter.5.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' /tmp/JyOqsQtwLk/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' /tmp/JyOqsQtwLk/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' /tmp/JyOqsQtwLk/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' /tmp/JyOqsQtwLk/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' /tmp/JyOqsQtwLk/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 & FMT/GQ=589' /tmp/JyOqsQtwLk/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 & FMT/GQ=589' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' /tmp/JyOqsQtwLk/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/view.filter.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' /tmp/JyOqsQtwLk/query.filter.3.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.filter.3.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"' /tmp/JyOqsQtwLk/query.filter.3.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.filter.3.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' /tmp/JyOqsQtwLk/query.filter.3.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.filter.3.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %AD\n]\n' -i'AD[:0]+AD[:1] > 12' /tmp/JyOqsQtwLk/filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/filter.5.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %AD\n]\n' -i'AD[:0]+AD[:1] > 12' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' /tmp/JyOqsQtwLk/query.filter.4.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.filter.4.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i 'ID=@/build/reproducible-path/bcftools-1.21/test/query.56.out' /tmp/JyOqsQtwLk/view.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/view.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i 'ID=@/build/reproducible-path/bcftools-1.21/test/query.56.out' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD)>0.01' /tmp/JyOqsQtwLk/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.filter.5.vcf.gz | /build/reproducible-path/bcftools-1.21/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-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD[:0],FMT/AD[:1])>0.01' /tmp/JyOqsQtwLk/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.filter.5.vcf.gz | /build/reproducible-path/bcftools-1.21/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-1.21/bcftools query -f'%POS\t%AD\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01' /tmp/JyOqsQtwLk/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.filter.5.vcf.gz | /build/reproducible-path/bcftools-1.21/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-1.21/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[GT]==10' /tmp/JyOqsQtwLk/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.filter.5.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[GT]==10' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'sSUM(FMT/AD[GT])==210' /tmp/JyOqsQtwLk/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.filter.5.vcf.gz | /build/reproducible-path/bcftools-1.21/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-1.21/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[0:GT]==30' /tmp/JyOqsQtwLk/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.filter.5.vcf.gz | /build/reproducible-path/bcftools-1.21/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-1.21/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TF[:GT]==1 && FMT/TF[:GT]==2' /tmp/JyOqsQtwLk/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.gtidx.1.vcf.gz | /build/reproducible-path/bcftools-1.21/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-1.21/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TI[:GT]==1 && FMT/TF[:GT]==2' /tmp/JyOqsQtwLk/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.gtidx.1.vcf.gz | /build/reproducible-path/bcftools-1.21/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-1.21/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TS[:GT]=="BB" && FMT/TS[:GT]=="CC"' /tmp/JyOqsQtwLk/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.gtidx.1.vcf.gz | /build/reproducible-path/bcftools-1.21/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-1.21/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TC[:GT]=="B" && FMT/TC[:GT]=="C"' /tmp/JyOqsQtwLk/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.gtidx.1.vcf.gz | /build/reproducible-path/bcftools-1.21/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-1.21/bcftools query -f'[%GT %TI\n]' -i'FMT/TI[:GT]=="."' /tmp/JyOqsQtwLk/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.gtidx.1.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%GT %TI\n]' -i'FMT/TI[:GT]=="."' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS\n' -i'CHROM="4"' /tmp/JyOqsQtwLk/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS\n' -i'CHROM="4"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%TAG1\n' -i'(TAG1>=-129 && TAG1<=-120) || (TAG1>=-32769 && TAG1<=-32760)' /tmp/JyOqsQtwLk/query.negative.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.negative.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%TAG1\n' -i'(TAG1>=-129 && TAG1<=-120) || (TAG1>=-32769 && TAG1<=-32760)' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%TAGV1\n' -i'(TAGV1>=-129 && TAGV1<=-120) || (TAGV1>=-32769 && TAGV1<=-32760)' /tmp/JyOqsQtwLk/query.negative.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.negative.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%TAGV1\n' -i'(TAGV1>=-129 && TAGV1<=-120) || (TAGV1>=-32769 && TAGV1<=-32760)' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%TAG2\n' -i'(TAG2>=-129 && TAG2<=-120) || (TAG2>=-32769 && TAG2<=-32760)' /tmp/JyOqsQtwLk/query.negative.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.negative.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%TAG2\n' -i'(TAG2>=-129 && TAG2<=-120) || (TAG2>=-32769 && TAG2<=-32760)' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%TAGV2\n' -i'(TAGV2>=-129 && TAGV2<=-120) || (TAGV2>=-32769 && TAGV2<=-32760)' /tmp/JyOqsQtwLk/query.negative.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.negative.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%TAGV2\n' -i'(TAGV2>=-129 && TAGV2<=-120) || (TAGV2>=-32769 && TAGV2<=-32760)' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GQ\n]' -i'N_PASS(GQ<20)==1' /tmp/JyOqsQtwLk/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GQ\n]' -i'N_PASS(GQ<20)==1' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")==1' /tmp/JyOqsQtwLk/query.filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.filter.11.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")==1' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")!=1' /tmp/JyOqsQtwLk/query.filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.filter.11.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")!=1' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")==1' /tmp/JyOqsQtwLk/query.filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.filter.11.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")==1' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")!=1' /tmp/JyOqsQtwLk/query.filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.filter.11.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")!=1' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM\t%POS\t%INFO\t%FORMAT\n' -s D,C /tmp/JyOqsQtwLk/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM\t%POS\t%INFO\t%FORMAT\n' -s D,C .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\n' -i'POS==16777217 || POS==33554432 || POS=118673904' /tmp/JyOqsQtwLk/query.filter.6.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.filter.6.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\n' -i'POS==16777217 || POS==33554432 || POS=118673904' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(II)==6' /tmp/JyOqsQtwLk/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(II)==6' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(FORMAT/FI)==7' /tmp/JyOqsQtwLk/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(FORMAT/FI)==7' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(II)==2' /tmp/JyOqsQtwLk/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(II)==2' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(FORMAT/FI)==1.75' /tmp/JyOqsQtwLk/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(FORMAT/FI)==1.75' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(II)==2' /tmp/JyOqsQtwLk/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(II)==2' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(FORMAT/FI)==1.75' /tmp/JyOqsQtwLk/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(FORMAT/FI)==1.75' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(II)==2' /tmp/JyOqsQtwLk/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(II)==2' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(FORMAT/FI)==1.5' /tmp/JyOqsQtwLk/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.filter.7.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(FORMAT/FI)==1.5' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'%ILEN==1' /tmp/JyOqsQtwLk/query.filter.8.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.filter.8.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'%ILEN==1' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'ILEN==1' /tmp/JyOqsQtwLk/query.filter.8.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.filter.8.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'ILEN==1' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] < FMT/AD[:1]' /tmp/JyOqsQtwLk/query.filter.9.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.filter.9.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] < FMT/AD[:1]' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] > FMT/AD[:1]' /tmp/JyOqsQtwLk/query.filter.9.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.filter.9.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] > FMT/AD[:1]' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[ %AD\n]' -i'AD[:1] / sum(AD[*]) > 0.5' /tmp/JyOqsQtwLk/query.filter.13.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.filter.13.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[ %AD\n]' -i'AD[:1] / sum(AD[*]) > 0.5' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %NUM_TAG\n' -i'COUNT(INFO/NUM_TAG)=2' /tmp/JyOqsQtwLk/query.filter.10.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.filter.10.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %NUM_TAG\n' -i'COUNT(INFO/NUM_TAG)=2' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2' /tmp/JyOqsQtwLk/query.filter.10.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.filter.10.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM:%POS\t%N_PASS(GT="alt" & GQ>110)\t[\t%GT]\t[\t%GQ]\n' /tmp/JyOqsQtwLk/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.vcf.gz | /build/reproducible-path/bcftools-1.21/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-1.21/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 1,3,0 /tmp/JyOqsQtwLk/query.filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.filter.12.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 1,3,0 .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 0,1,3 /tmp/JyOqsQtwLk/query.filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.filter.12.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 0,1,3 .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f "[%SAMPLE %GT\n]" -S /build/reproducible-path/bcftools-1.21/test/query.smpl.11.txt /tmp/JyOqsQtwLk/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.smpl.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f "[%SAMPLE %GT\n]" -S /build/reproducible-path/bcftools-1.21/test/query.smpl.11.txt .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -l -S /build/reproducible-path/bcftools-1.21/test/query.smpl.11.txt /tmp/JyOqsQtwLk/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.smpl.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -l -S /build/reproducible-path/bcftools-1.21/test/query.smpl.11.txt .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f "[%SAMPLE %GT\n]" -S ^/build/reproducible-path/bcftools-1.21/test/query.smpl.11.txt /tmp/JyOqsQtwLk/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.smpl.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f "[%SAMPLE %GT\n]" -S ^/build/reproducible-path/bcftools-1.21/test/query.smpl.11.txt .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -l -S ^/build/reproducible-path/bcftools-1.21/test/query.smpl.11.txt /tmp/JyOqsQtwLk/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.smpl.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -l -S ^/build/reproducible-path/bcftools-1.21/test/query.smpl.11.txt .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f "[%SAMPLE %GT\n]" -S /build/reproducible-path/bcftools-1.21/test/query.smpl.txt /tmp/JyOqsQtwLk/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.smpl.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f "[%SAMPLE %GT\n]" -S /build/reproducible-path/bcftools-1.21/test/query.smpl.txt .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -l -S /build/reproducible-path/bcftools-1.21/test/query.smpl.txt /tmp/JyOqsQtwLk/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.smpl.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -l -S /build/reproducible-path/bcftools-1.21/test/query.smpl.txt .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID~"s12"' /tmp/JyOqsQtwLk/query.filter.id.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.filter.id.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID~"s12"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID="rs123"' /tmp/JyOqsQtwLk/query.filter.id.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.filter.id.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID="rs123"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID="abc"' /tmp/JyOqsQtwLk/query.filter.id.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.filter.id.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID="abc"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID=@/build/reproducible-path/bcftools-1.21/test/query.filter.id.3.txt' /tmp/JyOqsQtwLk/query.filter.id.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.filter.id.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID=@/build/reproducible-path/bcftools-1.21/test/query.filter.id.3.txt' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID!="abc"' /tmp/JyOqsQtwLk/query.filter.id.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.filter.id.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID!="abc"' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID!=@/build/reproducible-path/bcftools-1.21/test/query.filter.id.3.txt' /tmp/JyOqsQtwLk/query.filter.id.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.filter.id.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%ID\n' -i'ID!=@/build/reproducible-path/bcftools-1.21/test/query.filter.id.3.txt' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER="A"' -f'%FILTER\n' /tmp/JyOqsQtwLk/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/filter.12.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER="A"' -f'%FILTER\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER~"A"' -f'%FILTER\n' /tmp/JyOqsQtwLk/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/filter.12.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER~"A"' -f'%FILTER\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER="A;B"' -f'%FILTER\n' /tmp/JyOqsQtwLk/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/filter.12.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER="A;B"' -f'%FILTER\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER!="A;B"' -f'%FILTER\n' /tmp/JyOqsQtwLk/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/filter.12.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER!="A;B"' -f'%FILTER\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER~"A;B"' -f'%FILTER\n' /tmp/JyOqsQtwLk/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/filter.12.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER~"A;B"' -f'%FILTER\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER!~"A;B"' -f'%FILTER\n' /tmp/JyOqsQtwLk/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/filter.12.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'FILTER!~"A;B"' -f'%FILTER\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'DP%10==2' -f'[ %DP]\n' /tmp/JyOqsQtwLk/filter.10.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/filter.10.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'DP%10==2' -f'[ %DP]\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -i'REF="N"' -f'%CHROM %POS %REF %ALT %QUAL\n' /tmp/JyOqsQtwLk/filter.13.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/filter.13.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -i'REF="N"' -f'%CHROM %POS %REF %ALT %QUAL\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -H -f'[%CHROM %POS %SAMPLE %DP %GT\n]' /tmp/JyOqsQtwLk/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.header.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -H -f'[%CHROM %POS %SAMPLE %DP %GT\n]' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -H -f'[%CHROM %POS %SAMPLE %DP %GT\t]\n' /tmp/JyOqsQtwLk/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.header.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -H -f'[%CHROM %POS %SAMPLE %DP %GT\t]\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]\n' /tmp/JyOqsQtwLk/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.header.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]' /tmp/JyOqsQtwLk/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.header.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]\n' /tmp/JyOqsQtwLk/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.header.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]\n' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]' /tmp/JyOqsQtwLk/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.header.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -HH -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]' /tmp/JyOqsQtwLk/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.header.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -HH -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%SAMPLE %DP\n]' -i'DP=1 || DP=2' /tmp/JyOqsQtwLk/query.filter-or.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.filter-or.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%SAMPLE %DP\n]' -i'DP=1 || DP=2' .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools query -f'[%SAMPLE %DP\n]' -i'DP=1 | DP=2' /tmp/JyOqsQtwLk/query.filter-or.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/query.filter-or.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%SAMPLE %DP\n]' -i'DP=1 | DP=2' .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/JyOqsQtwLk/norm.sort.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/JyOqsQtwLk/norm.sort.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - -S lex /tmp/JyOqsQtwLk/norm.sort.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - -S lex /tmp/JyOqsQtwLk/norm.sort.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +both /tmp/JyOqsQtwLk/norm.join-missing-ploidy.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +both /tmp/JyOqsQtwLk/norm.join-missing-ploidy.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - --multi-overlaps . /tmp/JyOqsQtwLk/norm.split.5.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - --multi-overlaps . /tmp/JyOqsQtwLk/norm.split.5.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version /tmp/JyOqsQtwLk/norm.symbolic.3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.symbolic.3.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version /tmp/JyOqsQtwLk/norm.symbolic.3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.symbolic.3.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -cx /tmp/JyOqsQtwLk/norm.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -cx /tmp/JyOqsQtwLk/norm.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- /tmp/JyOqsQtwLk/norm.split.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- /tmp/JyOqsQtwLk/norm.split.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- /tmp/JyOqsQtwLk/norm.split.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- /tmp/JyOqsQtwLk/norm.split.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- --force /tmp/JyOqsQtwLk/norm.split.3.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- --force /tmp/JyOqsQtwLk/norm.split.3.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- /tmp/JyOqsQtwLk/norm.split.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- /tmp/JyOqsQtwLk/norm.split.4.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- --keep-sum AD /tmp/JyOqsQtwLk/norm.split.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- --keep-sum AD /tmp/JyOqsQtwLk/norm.split.4.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- /tmp/JyOqsQtwLk/norm.split.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- /tmp/JyOqsQtwLk/norm.split.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m+ /tmp/JyOqsQtwLk/norm.merge.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m+ /tmp/JyOqsQtwLk/norm.merge.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m+ /tmp/JyOqsQtwLk/norm.merge.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m+ /tmp/JyOqsQtwLk/norm.merge.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m+ /tmp/JyOqsQtwLk/norm.merge.3.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m+ /tmp/JyOqsQtwLk/norm.merge.3.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m+ -s /tmp/JyOqsQtwLk/norm.merge.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m+ -s /tmp/JyOqsQtwLk/norm.merge.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -Nc s /tmp/JyOqsQtwLk/norm.setref.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -Nc s /tmp/JyOqsQtwLk/norm.setref.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version /tmp/JyOqsQtwLk/norm.telomere.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version /tmp/JyOqsQtwLk/norm.telomere.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d snps /tmp/JyOqsQtwLk/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d snps /tmp/JyOqsQtwLk/norm.rmdup.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d indels /tmp/JyOqsQtwLk/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d indels /tmp/JyOqsQtwLk/norm.rmdup.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d both /tmp/JyOqsQtwLk/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d both /tmp/JyOqsQtwLk/norm.rmdup.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d all /tmp/JyOqsQtwLk/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d all /tmp/JyOqsQtwLk/norm.rmdup.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d none /tmp/JyOqsQtwLk/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d none /tmp/JyOqsQtwLk/norm.rmdup.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d exact /tmp/JyOqsQtwLk/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d exact /tmp/JyOqsQtwLk/norm.rmdup.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d none /tmp/JyOqsQtwLk/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d none /tmp/JyOqsQtwLk/norm.rmdup.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d exact /tmp/JyOqsQtwLk/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d exact /tmp/JyOqsQtwLk/norm.rmdup.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d indels /tmp/JyOqsQtwLk/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d indels /tmp/JyOqsQtwLk/norm.rmdup.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d any /tmp/JyOqsQtwLk/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d any /tmp/JyOqsQtwLk/norm.rmdup.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d both /tmp/JyOqsQtwLk/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d both /tmp/JyOqsQtwLk/norm.rmdup.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d snps /tmp/JyOqsQtwLk/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d snps /tmp/JyOqsQtwLk/norm.rmdup.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d exact /tmp/JyOqsQtwLk/norm.rmdup.3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.rmdup.3.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d exact /tmp/JyOqsQtwLk/norm.rmdup.3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.rmdup.3.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d all /tmp/JyOqsQtwLk/norm.rmdup.3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.rmdup.3.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d all /tmp/JyOqsQtwLk/norm.rmdup.3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.rmdup.3.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -c s -a /tmp/JyOqsQtwLk/norm.2.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.2.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -c s -a /tmp/JyOqsQtwLk/norm.2.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.2.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -c s /tmp/JyOqsQtwLk/norm.iupac.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.iupac.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -c s /tmp/JyOqsQtwLk/norm.iupac.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.iupac.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -c s /tmp/JyOqsQtwLk/norm.3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.3.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -c s /tmp/JyOqsQtwLk/norm.3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.3.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -c s -i'alt="N"' /tmp/JyOqsQtwLk/norm.3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.3.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -c s -i'alt="N"' /tmp/JyOqsQtwLk/norm.3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.3.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -a --old-rec-tag OLD_REC /tmp/JyOqsQtwLk/atomize.split.1.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any --force .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -a --old-rec-tag OLD_REC /tmp/JyOqsQtwLk/atomize.split.1.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any --force -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any --old-rec-tag OLD_REC --force /tmp/JyOqsQtwLk/atomize.split.1.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -a .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any --old-rec-tag OLD_REC --force /tmp/JyOqsQtwLk/atomize.split.1.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -a -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any --old-rec-tag OLD_REC --force -a /tmp/JyOqsQtwLk/atomize.split.1.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any --old-rec-tag OLD_REC --force -a /tmp/JyOqsQtwLk/atomize.split.1.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/JyOqsQtwLk/atomize.split.1.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/JyOqsQtwLk/atomize.split.1.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/JyOqsQtwLk/atomize.split.1.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/JyOqsQtwLk/atomize.split.1.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/JyOqsQtwLk/atomize.split.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/JyOqsQtwLk/atomize.split.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/JyOqsQtwLk/atomize.split.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/JyOqsQtwLk/atomize.split.2.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . /tmp/JyOqsQtwLk/atomize.split.3.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . /tmp/JyOqsQtwLk/atomize.split.3.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/JyOqsQtwLk/atomize.split.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/JyOqsQtwLk/atomize.split.4.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC -i 'ILEN=0' /tmp/JyOqsQtwLk/atomize.split.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC -i 'ILEN=0' /tmp/JyOqsQtwLk/atomize.split.4.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --old-rec-tag OLD_REC --atom-overlaps . /tmp/JyOqsQtwLk/atomize.split.5.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --old-rec-tag OLD_REC --atom-overlaps . /tmp/JyOqsQtwLk/atomize.split.5.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/JyOqsQtwLk/atomize.split.5.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/JyOqsQtwLk/atomize.split.5.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +both /tmp/JyOqsQtwLk/norm.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +both /tmp/JyOqsQtwLk/norm.4.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +any /tmp/JyOqsQtwLk/norm.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +any /tmp/JyOqsQtwLk/norm.4.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - --multi-overlaps 0 /tmp/JyOqsQtwLk/norm.5.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - --multi-overlaps 0 /tmp/JyOqsQtwLk/norm.5.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - --multi-overlaps . /tmp/JyOqsQtwLk/norm.5.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - --multi-overlaps . /tmp/JyOqsQtwLk/norm.5.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any /tmp/JyOqsQtwLk/norm.m-any.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any /tmp/JyOqsQtwLk/norm.m-any.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any /tmp/JyOqsQtwLk/norm.phased-split.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any /tmp/JyOqsQtwLk/norm.phased-split.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +any /tmp/JyOqsQtwLk/norm.phased-join.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +any /tmp/JyOqsQtwLk/norm.phased-join.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI /tmp/JyOqsQtwLk/norm.symbolic.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.symbolic.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI /tmp/JyOqsQtwLk/norm.symbolic.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.symbolic.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI /tmp/JyOqsQtwLk/norm.symbolic.2.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.symbolic.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI /tmp/JyOqsQtwLk/norm.symbolic.2.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.symbolic.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI /tmp/JyOqsQtwLk/norm.right-align.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.right-align.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI /tmp/JyOqsQtwLk/norm.right-align.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.right-align.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI -g /build/reproducible-path/bcftools-1.21/test/norm.right-align.gff /tmp/JyOqsQtwLk/norm.right-align.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.right-align.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI -g /build/reproducible-path/bcftools-1.21/test/norm.right-align.gff /tmp/JyOqsQtwLk/norm.right-align.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.right-align.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI -a -m -any /tmp/JyOqsQtwLk/norm.atom-split-norm.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.atom-split-norm.fa .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI -a -m -any /tmp/JyOqsQtwLk/norm.atom-split-norm.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/norm.atom-split-norm.fa -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any /tmp/JyOqsQtwLk/norm.string-tags.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any /tmp/JyOqsQtwLk/norm.string-tags.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/JyOqsQtwLk/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +both .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/JyOqsQtwLk/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +both -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/JyOqsQtwLk/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +indels .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/JyOqsQtwLk/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +indels -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/JyOqsQtwLk/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +snps .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/JyOqsQtwLk/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +snps -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/JyOqsQtwLk/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +snps .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/JyOqsQtwLk/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +snps -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/JyOqsQtwLk/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +any .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/JyOqsQtwLk/norm.split.merge.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +any -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - -i 'type="snp"' /tmp/JyOqsQtwLk/norm.split.merge.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - -i 'type="snp"' /tmp/JyOqsQtwLk/norm.split.merge.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +any /tmp/JyOqsQtwLk/norm.merge.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +any /tmp/JyOqsQtwLk/norm.merge.4.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +both /tmp/JyOqsQtwLk/norm.merge.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +both /tmp/JyOqsQtwLk/norm.merge.4.vcf.gz -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -i 'INFO/TAG=@/build/reproducible-path/bcftools-1.21/test/filter.string.1.txt' /tmp/JyOqsQtwLk/filter.string.1.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -i 'INFO/TAG=@/build/reproducible-path/bcftools-1.21/test/filter.string.1.txt' /tmp/JyOqsQtwLk/filter.string.1.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -i 'FMT/TAG=@/build/reproducible-path/bcftools-1.21/test/filter.string.1.txt' /tmp/JyOqsQtwLk/filter.string.1.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -i 'FMT/TAG=@/build/reproducible-path/bcftools-1.21/test/filter.string.1.txt' /tmp/JyOqsQtwLk/filter.string.1.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -HA /tmp/JyOqsQtwLk/merge.gvcf.2.a.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -HAA /tmp/JyOqsQtwLk/merge.gvcf.2.a.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/JyOqsQtwLk/weird-chr-names.vcf.gz -r 1 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/weird-chr-names.vcf.gz -r 1 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/JyOqsQtwLk/weird-chr-names.vcf.gz -r 1:1-2 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/weird-chr-names.vcf.gz -r 1:1-2 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/JyOqsQtwLk/weird-chr-names.vcf.gz -r 1:1,1:2 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/weird-chr-names.vcf.gz -r 1:1,1:2 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/JyOqsQtwLk/weird-chr-names.vcf.gz -r 1:1-1 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/weird-chr-names.vcf.gz -r 1:1-1 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/JyOqsQtwLk/weird-chr-names.vcf.gz -r {1:1} .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/weird-chr-names.vcf.gz -r {1:1} | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/JyOqsQtwLk/weird-chr-names.vcf.gz -r {1:1}:1-2 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/weird-chr-names.vcf.gz -r {1:1}:1-2 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/JyOqsQtwLk/weird-chr-names.vcf.gz -r {1:1}:1,{1:1}:2 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/weird-chr-names.vcf.gz -r {1:1}:1,{1:1}:2 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/JyOqsQtwLk/weird-chr-names.vcf.gz -r {1:1}:1-1 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/weird-chr-names.vcf.gz -r {1:1}:1-1 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/JyOqsQtwLk/weird-chr-names.vcf.gz -r {1:1-1} .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/weird-chr-names.vcf.gz -r {1:1-1} | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/JyOqsQtwLk/weird-chr-names.vcf.gz -r {1:1-1}:1-2 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/weird-chr-names.vcf.gz -r {1:1-1}:1-2 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/JyOqsQtwLk/weird-chr-names.vcf.gz -r {1:1-1}:1,{1:1-1}:2 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/weird-chr-names.vcf.gz -r {1:1-1}:1,{1:1-1}:2 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/JyOqsQtwLk/weird-chr-names.vcf.gz -r {1:1-1}:1-1 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/weird-chr-names.vcf.gz -r {1:1-1}:1-1 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/JyOqsQtwLk/weird-chr-names.vcf.gz -r {1:1-1}-2 .. ok, expected non-zero status test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/weird-chr-names.vcf.gz -r {1:1-1}-2 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok, expected non-zero status test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -aUc1 -C1 -s NA00002 -v snps /tmp/JyOqsQtwLk/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/JyOqsQtwLk/view.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -f PASS -Xks NA00003 /tmp/JyOqsQtwLk/view.vcf.gz -r20,Y .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -f PASS -Xks NA00003 /tmp/JyOqsQtwLk/view.vcf.gz -r20,Y | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -xs NA00003 /tmp/JyOqsQtwLk/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -xs NA00003 /tmp/JyOqsQtwLk/view.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/JyOqsQtwLk/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/JyOqsQtwLk/view.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -p /tmp/JyOqsQtwLk/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -p /tmp/JyOqsQtwLk/view.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -P /tmp/JyOqsQtwLk/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -P /tmp/JyOqsQtwLk/view.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -hm2 -M2 -q0.3 -Q0.7 /tmp/JyOqsQtwLk/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/JyOqsQtwLk/view.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -Hu /tmp/JyOqsQtwLk/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -GVsnps /tmp/JyOqsQtwLk/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -GVsnps /tmp/JyOqsQtwLk/view.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -ne 'INDEL=1 || PV4[0]<0.006' /tmp/JyOqsQtwLk/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/JyOqsQtwLk/view.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -s ^NA00003 /tmp/JyOqsQtwLk/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -s ^NA00003 /tmp/JyOqsQtwLk/view.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/JyOqsQtwLk/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/view.omitgenotypes.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -G /tmp/JyOqsQtwLk/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -G /tmp/JyOqsQtwLk/view.omitgenotypes.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -HG /tmp/JyOqsQtwLk/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -a /tmp/JyOqsQtwLk/many.alleles.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -a /tmp/JyOqsQtwLk/many.alleles.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -asA /tmp/JyOqsQtwLk/view.vectors.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -asA /tmp/JyOqsQtwLk/view.vectors.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -asB /tmp/JyOqsQtwLk/view.vectors.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -asB /tmp/JyOqsQtwLk/view.vectors.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -asA /tmp/JyOqsQtwLk/view.vectors.2.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -asA /tmp/JyOqsQtwLk/view.vectors.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -i'FMT/FGS[*:0]="AAAAAA"' /tmp/JyOqsQtwLk/view.filter.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -i'FMT/FGS[*:2]="C"' /tmp/JyOqsQtwLk/view.filter.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -i'FMT/FGS[*:4]="EE"' /tmp/JyOqsQtwLk/view.filter.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -i'FMT/FRS[*:1]="BB"' /tmp/JyOqsQtwLk/view.filter.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -i'TXT0="text"' /tmp/JyOqsQtwLk/view.filter.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -T /build/reproducible-path/bcftools-1.21/test/view.chrs.tab /tmp/JyOqsQtwLk/view.chrs.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -T /build/reproducible-path/bcftools-1.21/test/view.chrs.tab /tmp/JyOqsQtwLk/view.chrs.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -i 'POS>=3062917' /tmp/JyOqsQtwLk/filter.2.vcf.gz 1:3062917-3157410 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -i 'POS>=3062917' /tmp/JyOqsQtwLk/filter.2.vcf.gz 1:3062917-3157410 | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -r 1:10,1:12,1:10 /tmp/JyOqsQtwLk/idx.1.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -r 1:1172777-1172804,1:1172806-1172808 /tmp/JyOqsQtwLk/idx.2.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -R /build/reproducible-path/bcftools-1.21/test/idx.2.bed /tmp/JyOqsQtwLk/idx.2.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -R /build/reproducible-path/bcftools-1.21/test/idx.3.bed /tmp/JyOqsQtwLk/idx.3.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -R /build/reproducible-path/bcftools-1.21/test/idx.4.bed /tmp/JyOqsQtwLk/idx.4.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -Ht 2 /tmp/JyOqsQtwLk/view-t.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -Ht 3 /tmp/JyOqsQtwLk/view-t.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 0 /tmp/JyOqsQtwLk/overlap.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 1 /tmp/JyOqsQtwLk/overlap.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 2 /tmp/JyOqsQtwLk/overlap.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 0 /tmp/JyOqsQtwLk/overlap.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 1 /tmp/JyOqsQtwLk/overlap.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 2 /tmp/JyOqsQtwLk/overlap.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 0 /tmp/JyOqsQtwLk/overlap.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 1 /tmp/JyOqsQtwLk/overlap.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 2 /tmp/JyOqsQtwLk/overlap.vcf.gz .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.21/bcftools view /build/reproducible-path/bcftools-1.21/test/view64bit.1.vcf -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.21/bcftools view /build/reproducible-path/bcftools-1.21/test/view64bit.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.21/bcftools view /build/reproducible-path/bcftools-1.21/test/view64bit.1.vcf -Ou | /build/reproducible-path/bcftools-1.21/bcftools view -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.21/bcftools view /build/reproducible-path/bcftools-1.21/test/view64bit.2.vcf -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.21/bcftools view /build/reproducible-path/bcftools-1.21/test/view64bit.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.21/bcftools view /build/reproducible-path/bcftools-1.21/test/view64bit.2.vcf -Ou | /build/reproducible-path/bcftools-1.21/bcftools view -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.21/bcftools view /build/reproducible-path/bcftools-1.21/test/view64bit.3.vcf -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.21/bcftools view /build/reproducible-path/bcftools-1.21/test/view64bit.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.21/bcftools view /build/reproducible-path/bcftools-1.21/test/view64bit.4.vcf -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.21/bcftools view /build/reproducible-path/bcftools-1.21/test/view64bit.4.vcf | /build/reproducible-path/bcftools-1.21/bcftools view -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.21/bcftools view /build/reproducible-path/bcftools-1.21/test/view64bit.4.vcf -Ou | /build/reproducible-path/bcftools-1.21/bcftools view -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.21/bcftools view /build/reproducible-path/bcftools-1.21/test/view64bit.5.vcf -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.21/bcftools view /build/reproducible-path/bcftools-1.21/test/view64bit.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools view -H .. ok test_vcf_64bit: /build/reproducible-path/bcftools-1.21/bcftools view /build/reproducible-path/bcftools-1.21/test/view64bit.5.vcf -Ou | /build/reproducible-path/bcftools-1.21/bcftools view -H .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -C5:nonmajor /tmp/JyOqsQtwLk/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -c6:nonmajor /tmp/JyOqsQtwLk/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -q0.3:major /tmp/JyOqsQtwLk/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/JyOqsQtwLk/view.filter.annovar.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -i 'Gene.refGene~"NOD"' /tmp/JyOqsQtwLk/view.filter.annovar.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -i 'LJB2_MutationTaster=="0.291000"' /tmp/JyOqsQtwLk/view.filter.annovar.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -a /tmp/JyOqsQtwLk/view-a.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -T /build/reproducible-path/bcftools-1.21/test/view.sites.txt /tmp/JyOqsQtwLk/view.sites.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -T /build/reproducible-path/bcftools-1.21/test/view.sites.txt /tmp/JyOqsQtwLk/view.sites.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -T /build/reproducible-path/bcftools-1.21/test/view.sites.txt.gz /tmp/JyOqsQtwLk/view.sites.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -T /build/reproducible-path/bcftools-1.21/test/view.sites.txt.gz /tmp/JyOqsQtwLk/view.sites.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_head: /build/reproducible-path/bcftools-1.21/bcftools head /build/reproducible-path/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_head: /build/reproducible-path/bcftools-1.21/bcftools head -h 0 /build/reproducible-path/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_head: /build/reproducible-path/bcftools-1.21/bcftools head -h 1 /build/reproducible-path/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_head: /build/reproducible-path/bcftools-1.21/bcftools head -h 5 /build/reproducible-path/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_head: /build/reproducible-path/bcftools-1.21/bcftools head -h 22 /build/reproducible-path/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_head: /build/reproducible-path/bcftools-1.21/bcftools head -h 23 /build/reproducible-path/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_head: /build/reproducible-path/bcftools-1.21/bcftools head -n 0 /build/reproducible-path/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_head: /build/reproducible-path/bcftools-1.21/bcftools head -n 1 /build/reproducible-path/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_head: /build/reproducible-path/bcftools-1.21/bcftools head -n 5 /build/reproducible-path/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_head: /build/reproducible-path/bcftools-1.21/bcftools head -h 5 -n 5 < /build/reproducible-path/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_head2: /build/reproducible-path/bcftools-1.21/bcftools head -s0 /tmp/JyOqsQtwLk/mpileup.2.vcf.gz .. ok test_vcf_head2: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -Ob /tmp/JyOqsQtwLk/mpileup.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools head -s0 .. ok test_vcf_head2: /build/reproducible-path/bcftools-1.21/bcftools head -s1 /tmp/JyOqsQtwLk/mpileup.2.vcf.gz .. ok test_vcf_head2: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -Ob /tmp/JyOqsQtwLk/mpileup.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools head -s1 .. ok test_vcf_head2: /build/reproducible-path/bcftools-1.21/bcftools head -s2 -h2 /tmp/JyOqsQtwLk/mpileup.2.vcf.gz .. ok test_vcf_head2: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -Ob /tmp/JyOqsQtwLk/mpileup.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools head -s2 -h2 .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mv /build/reproducible-path/bcftools-1.21/test/mpileup.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mv /build/reproducible-path/bcftools-1.21/test/mpileup.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mg0 /build/reproducible-path/bcftools-1.21/test/mpileup.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mg0 /build/reproducible-path/bcftools-1.21/test/mpileup.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mv -S /build/reproducible-path/bcftools-1.21/test/mpileup.3.samples /build/reproducible-path/bcftools-1.21/test/mpileup.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mv -S /build/reproducible-path/bcftools-1.21/test/mpileup.3.samples /build/reproducible-path/bcftools-1.21/test/mpileup.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mv -S /build/reproducible-path/bcftools-1.21/test/mpileup.4.samples /build/reproducible-path/bcftools-1.21/test/mpileup.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mv -S /build/reproducible-path/bcftools-1.21/test/mpileup.4.samples /build/reproducible-path/bcftools-1.21/test/mpileup.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mv -S /build/reproducible-path/bcftools-1.21/test/mpileup.5.samples /build/reproducible-path/bcftools-1.21/test/mpileup.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mv -S /build/reproducible-path/bcftools-1.21/test/mpileup.5.samples /build/reproducible-path/bcftools-1.21/test/mpileup.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mv --ploidy-file /build/reproducible-path/bcftools-1.21/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.21/test/mpileup.samples /build/reproducible-path/bcftools-1.21/test/mpileup.X.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mv --ploidy-file /build/reproducible-path/bcftools-1.21/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.21/test/mpileup.samples /build/reproducible-path/bcftools-1.21/test/mpileup.X.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mv --ploidy-file /build/reproducible-path/bcftools-1.21/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.21/test/mpileup.ped /build/reproducible-path/bcftools-1.21/test/mpileup.X.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mv --ploidy-file /build/reproducible-path/bcftools-1.21/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.21/test/mpileup.ped /build/reproducible-path/bcftools-1.21/test/mpileup.X.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mv --ploidy-file /build/reproducible-path/bcftools-1.21/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.21/test/mpileup.2.samples /build/reproducible-path/bcftools-1.21/test/mpileup.X.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mv --ploidy-file /build/reproducible-path/bcftools-1.21/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.21/test/mpileup.2.samples /build/reproducible-path/bcftools-1.21/test/mpileup.X.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mv /build/reproducible-path/bcftools-1.21/test/mpileup.NA19213.NA19129.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mv /build/reproducible-path/bcftools-1.21/test/mpileup.NA19213.NA19129.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mv -G - --group-samples-tag AD /build/reproducible-path/bcftools-1.21/test/mpileup.NA19213.NA19129.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mv -G - --group-samples-tag AD /build/reproducible-path/bcftools-1.21/test/mpileup.NA19213.NA19129.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mv /build/reproducible-path/bcftools-1.21/test/mpileup.hwe.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mv /build/reproducible-path/bcftools-1.21/test/mpileup.hwe.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mv -G - --group-samples-tag AD /build/reproducible-path/bcftools-1.21/test/mpileup.hwe.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mv -G - --group-samples-tag AD /build/reproducible-path/bcftools-1.21/test/mpileup.hwe.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mv -G /build/reproducible-path/bcftools-1.21/test/mpileup.hwe.samples --group-samples-tag AD /build/reproducible-path/bcftools-1.21/test/mpileup.hwe.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mv -G /build/reproducible-path/bcftools-1.21/test/mpileup.hwe.samples --group-samples-tag AD /build/reproducible-path/bcftools-1.21/test/mpileup.hwe.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/JyOqsQtwLk/mpileup.tab.gz /build/reproducible-path/bcftools-1.21/test/mpileup.vcf .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/JyOqsQtwLk/mpileup.tab.gz /build/reproducible-path/bcftools-1.21/test/mpileup.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/JyOqsQtwLk/mpileup.2.tab.gz /build/reproducible-path/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/JyOqsQtwLk/mpileup.2.tab.gz /build/reproducible-path/bcftools-1.21/test/mpileup.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/JyOqsQtwLk/mpileup.3.tab.gz -i /build/reproducible-path/bcftools-1.21/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/JyOqsQtwLk/mpileup.3.tab.gz -i /build/reproducible-path/bcftools-1.21/test/mpileup.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/JyOqsQtwLk/mpileup.4.tab.gz -i /build/reproducible-path/bcftools-1.21/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/JyOqsQtwLk/mpileup.4.tab.gz -i /build/reproducible-path/bcftools-1.21/test/mpileup.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/JyOqsQtwLk/mpileup.5.tab.gz -i /build/reproducible-path/bcftools-1.21/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/JyOqsQtwLk/mpileup.5.tab.gz -i /build/reproducible-path/bcftools-1.21/test/mpileup.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/JyOqsQtwLk/mpileup.6.tab.gz -i /build/reproducible-path/bcftools-1.21/test/mpileup.4.vcf .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/JyOqsQtwLk/mpileup.6.tab.gz -i /build/reproducible-path/bcftools-1.21/test/mpileup.4.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/JyOqsQtwLk/mpileup.7.tab.gz -i /build/reproducible-path/bcftools-1.21/test/mpileup.5.vcf .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/JyOqsQtwLk/mpileup.7.tab.gz -i /build/reproducible-path/bcftools-1.21/test/mpileup.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/JyOqsQtwLk/mpileup.cals.1.tab.gz /build/reproducible-path/bcftools-1.21/test/mpileup.cals.1.vcf .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/JyOqsQtwLk/mpileup.cals.1.tab.gz /build/reproducible-path/bcftools-1.21/test/mpileup.cals.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/JyOqsQtwLk/mpileup.cals.2.tab.gz /build/reproducible-path/bcftools-1.21/test/mpileup.cals.2.vcf .. ok test_vcf_call_cAls: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/JyOqsQtwLk/mpileup.cals.2.tab.gz /build/reproducible-path/bcftools-1.21/test/mpileup.cals.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -cv /build/reproducible-path/bcftools-1.21/test/mpileup.c.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -cv /build/reproducible-path/bcftools-1.21/test/mpileup.c.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -cv --ploidy-file /build/reproducible-path/bcftools-1.21/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.21/test/mpileup.samples /build/reproducible-path/bcftools-1.21/test/mpileup.c.X.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -cv --ploidy-file /build/reproducible-path/bcftools-1.21/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.21/test/mpileup.samples /build/reproducible-path/bcftools-1.21/test/mpileup.c.X.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -cv --ploidy-file /build/reproducible-path/bcftools-1.21/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.21/test/mpileup.ped /build/reproducible-path/bcftools-1.21/test/mpileup.c.X.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -cv --ploidy-file /build/reproducible-path/bcftools-1.21/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.21/test/mpileup.ped /build/reproducible-path/bcftools-1.21/test/mpileup.c.X.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -cv --ploidy-file /build/reproducible-path/bcftools-1.21/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.21/test/mpileup.2.samples /build/reproducible-path/bcftools-1.21/test/mpileup.c.X.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -cv --ploidy-file /build/reproducible-path/bcftools-1.21/test/mpileup.ploidy -S /build/reproducible-path/bcftools-1.21/test/mpileup.2.samples /build/reproducible-path/bcftools-1.21/test/mpileup.c.X.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mv /build/reproducible-path/bcftools-1.21/test/call-G.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mv /build/reproducible-path/bcftools-1.21/test/call-G.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mv -G - --group-samples-tag AD /build/reproducible-path/bcftools-1.21/test/call-G.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mv -G - --group-samples-tag AD /build/reproducible-path/bcftools-1.21/test/call-G.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -mv -F AN_POP,AC_POP /build/reproducible-path/bcftools-1.21/test/call-G.2.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -mv -F AN_POP,AC_POP /build/reproducible-path/bcftools-1.21/test/call-G.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -m /build/reproducible-path/bcftools-1.21/test/call.af-fixation.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -m /build/reproducible-path/bcftools-1.21/test/call.af-fixation.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -m -G /build/reproducible-path/bcftools-1.21/test/call.af-fixation.txt /build/reproducible-path/bcftools-1.21/test/call.af-fixation.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -m -G /build/reproducible-path/bcftools-1.21/test/call.af-fixation.txt /build/reproducible-path/bcftools-1.21/test/call.af-fixation.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call --no-version -m -G /build/reproducible-path/bcftools-1.21/test/call.af-fixation.txt -a GP,GQ /build/reproducible-path/bcftools-1.21/test/call.af-fixation.vcf .. ok test_vcf_call: /build/reproducible-path/bcftools-1.21/bcftools call -Ob -m -G /build/reproducible-path/bcftools-1.21/test/call.af-fixation.txt -a GP,GQ /build/reproducible-path/bcftools-1.21/test/call.af-fixation.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S. -e'TXT0="text"' /build/reproducible-path/bcftools-1.21/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S. -e'TXT0="text"' /build/reproducible-path/bcftools-1.21/test/view.filter.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S. -e'FMT/FRS[*:1]="BB"' /build/reproducible-path/bcftools-1.21/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S. -e'FMT/FRS[*:1]="BB"' /build/reproducible-path/bcftools-1.21/test/view.filter.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S. -e'FMT/FGS[*:0]="AAAAAA"' /build/reproducible-path/bcftools-1.21/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S. -e'FMT/FGS[*:0]="AAAAAA"' /build/reproducible-path/bcftools-1.21/test/view.filter.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S. -e'FMT/FGS[*:1]="BBB"' /build/reproducible-path/bcftools-1.21/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S. -e'FMT/FGS[*:1]="BBB"' /build/reproducible-path/bcftools-1.21/test/view.filter.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S. -e'FMT/FGS[*:4]="EE"' /build/reproducible-path/bcftools-1.21/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S. -e'FMT/FGS[*:4]="EE"' /build/reproducible-path/bcftools-1.21/test/view.filter.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S. -e'FMT/STR="XX"' /build/reproducible-path/bcftools-1.21/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S. -e'FMT/STR="XX"' /build/reproducible-path/bcftools-1.21/test/view.filter.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S. -e'FMT/FILTER="aaa"' /build/reproducible-path/bcftools-1.21/test/view.filter.2.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S. -e'FMT/FILTER="aaa"' /build/reproducible-path/bcftools-1.21/test/view.filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -mx -g2 -G2 /build/reproducible-path/bcftools-1.21/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -mx -g2 -G2 /build/reproducible-path/bcftools-1.21/test/filter.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -e'INFO/DP=19' /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -e'INFO/DP=19' /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -e'INFO/DP=19' -s XX /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -e'INFO/DP=19' -s XX /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -e'INFO/DP=19' -s XX -m+ /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+ /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -e'INFO/DP=19' -s XX -mx /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -e'INFO/DP=19' -s XX -mx /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -e'INFO/DP=19' -s XX -m+x /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+x /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -e'FMT/GT="0/2"' /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -e'FMT/GT="0/2"' /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -e'FMT/GT="0/2"' -s XX /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -e'FMT/GT="0/2"' -s XX -m+ /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+ /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -e'FMT/GT="0/2"' -s XX -mx /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -mx /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -e'FMT/GT="0/2"' -s XX -m+x /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+x /build/reproducible-path/bcftools-1.21/test/filter.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'FMT/GT="0/0" && AC[*]=2' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'FMT/GT="0/0" && AC[*]=2' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'AC[*]=2 && FMT/GT="0/0"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'AC[*]=2 && FMT/GT="0/0"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'ALT="."' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'ALT="."' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -i 'FORMAT/TEST3<25' /build/reproducible-path/bcftools-1.21/test/filter.4.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -i 'FORMAT/TEST3<25' /build/reproducible-path/bcftools-1.21/test/filter.4.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -i 'FORMAT/TEST4<25' /build/reproducible-path/bcftools-1.21/test/filter.4.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -i 'FORMAT/TEST4<25' /build/reproducible-path/bcftools-1.21/test/filter.4.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'GT="A"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'GT="A"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'GT="RR"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'GT="RR"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'GT="RA"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'GT="RA"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'GT="AR"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'GT="AR"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'GT="AA"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'GT="AA"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'GT="aA"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'GT="aA"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'GT="Aa"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'GT="Aa"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'GT="HOM"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'GT="HOM"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'GT="HET"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'GT="HET"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'GT="HAP"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'GT="HAP"' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'AD[:1]=11' /build/reproducible-path/bcftools-1.21/test/filter.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'AD[:1]=11' /build/reproducible-path/bcftools-1.21/test/filter.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'AD[1:]=11' /build/reproducible-path/bcftools-1.21/test/filter.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'AD[1:]=11' /build/reproducible-path/bcftools-1.21/test/filter.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'FR[0:1]=11' /build/reproducible-path/bcftools-1.21/test/filter.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%FR]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'FR[0:1]=11' /build/reproducible-path/bcftools-1.21/test/filter.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%FR]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'AD[*]="."' /build/reproducible-path/bcftools-1.21/test/filter.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'AD[*]="."' /build/reproducible-path/bcftools-1.21/test/filter.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'AD[0:0]=="."' /build/reproducible-path/bcftools-1.21/test/filter.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'AD[0:0]=="."' /build/reproducible-path/bcftools-1.21/test/filter.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'AD[0:0]!="."' /build/reproducible-path/bcftools-1.21/test/filter.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'AD[0:0]!="."' /build/reproducible-path/bcftools-1.21/test/filter.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'QUAL=="."' /build/reproducible-path/bcftools-1.21/test/filter.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%QUAL\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'QUAL=="."' /build/reproducible-path/bcftools-1.21/test/filter.5.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\t%QUAL\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'N_PASS(DP>32)=1' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'N_PASS(DP>32)=1' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'F_PASS(DP>32)=0.5' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'F_PASS(DP>32)=0.5' /build/reproducible-path/bcftools-1.21/test/filter.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'F_MISSING>=1/5' /build/reproducible-path/bcftools-1.21/test/filter.6.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'F_MISSING>=1/5' /build/reproducible-path/bcftools-1.21/test/filter.6.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'F_MISSING>=0.2' /build/reproducible-path/bcftools-1.21/test/filter.6.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'F_MISSING>=0.2' /build/reproducible-path/bcftools-1.21/test/filter.6.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'F_PASS(GT=="mis")>=1/5' /build/reproducible-path/bcftools-1.21/test/filter.6.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'F_PASS(GT=="mis")>=1/5' /build/reproducible-path/bcftools-1.21/test/filter.6.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i'F_PASS(GT=="mis")>=0.2' /build/reproducible-path/bcftools-1.21/test/filter.6.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i'F_PASS(GT=="mis")>=0.2' /build/reproducible-path/bcftools-1.21/test/filter.6.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -mx -s + -g2:mnp,indel,other /build/reproducible-path/bcftools-1.21/test/filter.7.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -mx -s + -g2:mnp,indel,other /build/reproducible-path/bcftools-1.21/test/filter.7.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'FORMAT/AO==4' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'FORMAT/AO==4' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'MAX(FORMAT/AO[0:])==4' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'MAX(FORMAT/AO[0:])==4' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'MAX(FORMAT/AO)==4' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'MAX(FORMAT/AO)==4' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'MIN(FORMAT/AO[0:])==3' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO[0:])==3' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'MIN(FORMAT/AO)==2' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO)==2' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'MIN(FORMAT/AO[0:])==3' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO[0:])==3' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'AVG(FORMAT/AO[2:])==4' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'AVG(FORMAT/AO[2:])==4' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'MEDIAN(FORMAT/AO[2:])==4' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'MEDIAN(FORMAT/AO[2:])==4' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'STDEV(FORMAT/AO[0:])=0.5' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'STDEV(FORMAT/AO[0:])=0.5' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'SUM(FORMAT/AO[0:])=7' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'SUM(FORMAT/AO[0:])=7' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'SMPL_MAX(FORMAT/AO)==4' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'SMPL_MAX(FORMAT/AO)==4' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'sMIN(FORMAT/AO)==2' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'sMIN(FORMAT/AO)==2' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'ABS(sAVG(FORMAT/AO)-3.66666)<1e-5' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'ABS(sAVG(FORMAT/AO)-3.66666)<1e-5' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'sMEDIAN(FORMAT/AO)==4' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'sMEDIAN(FORMAT/AO)==4' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'ABS(sSTDEV(FORMAT/AO)-1.2472191)<1e-5' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'ABS(sSTDEV(FORMAT/AO)-1.2472191)<1e-5' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'sSUM(FORMAT/AO)==11' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'sSUM(FORMAT/AO)==11' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i 'QUAL/FMT/AD==55' /build/reproducible-path/bcftools-1.21/test/filter.9.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i 'QUAL/FMT/AD==55' /build/reproducible-path/bcftools-1.21/test/filter.9.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i 'QUAL/INFO/AD==10' /build/reproducible-path/bcftools-1.21/test/filter.9.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i 'QUAL/INFO/AD==10' /build/reproducible-path/bcftools-1.21/test/filter.9.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'ABS(SMPL_MAX(FORMAT/AO))=5' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'ABS(SMPL_MAX(FORMAT/AO))=5' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'PHRED(AO[1:])>-4' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'PHRED(AO[1:])>-4' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -S . -e 'ABS(AO[1:])==2' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -S . -e 'ABS(AO[1:])==2' /build/reproducible-path/bcftools-1.21/test/filter.8.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i 'sum(AD[*]) > FORMAT/DP' /build/reproducible-path/bcftools-1.21/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i 'sum(AD[*]) > FORMAT/DP' /build/reproducible-path/bcftools-1.21/test/filter.10.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i 'FORMAT/DP < sum(AD[*])' /build/reproducible-path/bcftools-1.21/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i 'FORMAT/DP < sum(AD[*])' /build/reproducible-path/bcftools-1.21/test/filter.10.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i 'sum(AD[*]) < FORMAT/DP' /build/reproducible-path/bcftools-1.21/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i 'sum(AD[*]) < FORMAT/DP' /build/reproducible-path/bcftools-1.21/test/filter.10.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -i 'FORMAT/DP > sum(AD[*])' /build/reproducible-path/bcftools-1.21/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob -i 'FORMAT/DP > sum(AD[*])' /build/reproducible-path/bcftools-1.21/test/filter.10.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 0 /build/reproducible-path/bcftools-1.21/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 0 /build/reproducible-path/bcftools-1.21/test/filter.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 1 /build/reproducible-path/bcftools-1.21/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 1 /build/reproducible-path/bcftools-1.21/test/filter.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 2 /build/reproducible-path/bcftools-1.21/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 2 /build/reproducible-path/bcftools-1.21/test/filter.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter --soft-filter xxx --mask ^2:1005-1008 /build/reproducible-path/bcftools-1.21/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/reproducible-path/bcftools-1.21/bcftools filter -Ob --soft-filter xxx --mask ^2:1005-1008 /build/reproducible-path/bcftools-1.21/test/filter.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_sort: /build/reproducible-path/bcftools-1.21/bcftools sort -m 0 /build/reproducible-path/bcftools-1.21/test/sort.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /build/reproducible-path/bcftools-1.21/bcftools sort -Ob -m 0 /build/reproducible-path/bcftools-1.21/test/sort.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /build/reproducible-path/bcftools-1.21/bcftools sort -m 1000 /build/reproducible-path/bcftools-1.21/test/sort.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /build/reproducible-path/bcftools-1.21/bcftools sort -Ob -m 1000 /build/reproducible-path/bcftools-1.21/test/sort.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | /build/reproducible-path/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /build/reproducible-path/bcftools-1.21/test/regions.tab /tmp/JyOqsQtwLk/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/regions.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /build/reproducible-path/bcftools-1.21/test/regions.tab .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /build/reproducible-path/bcftools-1.21/test/regions.tab /tmp/JyOqsQtwLk/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/JyOqsQtwLk/regions.tab.gz /tmp/JyOqsQtwLk/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/regions.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/JyOqsQtwLk/regions.tab.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/JyOqsQtwLk/regions.tab.gz /tmp/JyOqsQtwLk/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/JyOqsQtwLk/regions.bed /tmp/JyOqsQtwLk/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/regions.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/JyOqsQtwLk/regions.bed .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/JyOqsQtwLk/regions.bed /tmp/JyOqsQtwLk/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/JyOqsQtwLk/regions.bed.gz /tmp/JyOqsQtwLk/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/regions.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/JyOqsQtwLk/regions.bed.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/JyOqsQtwLk/regions.bed.gz /tmp/JyOqsQtwLk/regions.vcf.gz .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annotate.escape.1.tab.gz -c CHROM,POS,ISTR,FMT/FSTR /build/reproducible-path/bcftools-1.21/test/annotate.escape.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annotate.escape.1.tab.gz -c CHROM,POS,ISTR,FMT/FSTR /build/reproducible-path/bcftools-1.21/test/annotate.escape.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annotate.match.1.tab.gz -c CHROM,POS,-,-,SCORE,~X,-,- -i'STR={X}' /build/reproducible-path/bcftools-1.21/test/annotate.match.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annotate.match.1.tab.gz -c CHROM,POS,-,-,SCORE,~X,-,- -i'STR={X}' /build/reproducible-path/bcftools-1.21/test/annotate.match.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annotate.match.1.tab.gz -c CHROM,POS,REF,ALT,SCORE,-,~X,- -i'INT={X}' /build/reproducible-path/bcftools-1.21/test/annotate.match.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annotate.match.1.tab.gz -c CHROM,POS,REF,ALT,SCORE,-,~X,- -i'INT={X}' /build/reproducible-path/bcftools-1.21/test/annotate.match.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annotate.match.1.tab.gz -c CHROM,POS,REF,ALT,SCORE,-,-,~X -i'FLT={X}' /build/reproducible-path/bcftools-1.21/test/annotate.match.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annotate.match.1.tab.gz -c CHROM,POS,REF,ALT,SCORE,-,-,~X -i'FLT={X}' /build/reproducible-path/bcftools-1.21/test/annotate.match.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annotate.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /build/reproducible-path/bcftools-1.21/test/annotate.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annotate.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /build/reproducible-path/bcftools-1.21/test/annotate.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annotate2.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate.hdr -c CHROM,POS,-,T_STR /build/reproducible-path/bcftools-1.21/test/annotate.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annotate2.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate.hdr -c CHROM,POS,-,T_STR /build/reproducible-path/bcftools-1.21/test/annotate.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annotate2.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate.hdr -c CHROM,FROM,TO,T_STR /build/reproducible-path/bcftools-1.21/test/annotate.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annotate2.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate.hdr -c CHROM,FROM,TO,T_STR /build/reproducible-path/bcftools-1.21/test/annotate.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/JyOqsQtwLk/annotate.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/JyOqsQtwLk/annotate.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/JyOqsQtwLk/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/JyOqsQtwLk/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/JyOqsQtwLk/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/JyOqsQtwLk/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/JyOqsQtwLk/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/JyOqsQtwLk/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/JyOqsQtwLk/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/JyOqsQtwLk/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/JyOqsQtwLk/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/JyOqsQtwLk/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /build/reproducible-path/bcftools-1.21/test/annotate3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /build/reproducible-path/bcftools-1.21/test/annotate3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -x FORMAT /build/reproducible-path/bcftools-1.21/test/annotate3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -x FORMAT /build/reproducible-path/bcftools-1.21/test/annotate3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annots4.vcf.gz -c +INFO /tmp/JyOqsQtwLk/annotate4.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annots4.vcf.gz -c +INFO /tmp/JyOqsQtwLk/annotate4.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annots4.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /build/reproducible-path/bcftools-1.21/test/annotate4.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annots4.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /build/reproducible-path/bcftools-1.21/test/annotate4.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annots10.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /build/reproducible-path/bcftools-1.21/test/annotate10.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annots10.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /build/reproducible-path/bcftools-1.21/test/annotate10.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/JyOqsQtwLk/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/JyOqsQtwLk/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /build/reproducible-path/bcftools-1.21/test/annotate2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /build/reproducible-path/bcftools-1.21/test/annotate2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/JyOqsQtwLk/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/JyOqsQtwLk/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/JyOqsQtwLk/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/JyOqsQtwLk/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/JyOqsQtwLk/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/JyOqsQtwLk/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annots11.vcf.gz -c FMT /tmp/JyOqsQtwLk/annotate11.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annots11.vcf.gz -c FMT /tmp/JyOqsQtwLk/annotate11.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annots2.vcf.gz -c FMT/newGT:=GT /tmp/JyOqsQtwLk/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annots2.vcf.gz -c FMT/newGT:=GT /tmp/JyOqsQtwLk/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annots12.vcf.gz -c FMT/GT:=newGT /tmp/JyOqsQtwLk/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annots12.vcf.gz -c FMT/GT:=newGT /tmp/JyOqsQtwLk/annotate2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annots13.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate13.hdr -c CHROM,BEG,END,ABC /build/reproducible-path/bcftools-1.21/test/annotate13.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annots13.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate13.hdr -c CHROM,BEG,END,ABC /build/reproducible-path/bcftools-1.21/test/annotate13.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annots13.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:append /build/reproducible-path/bcftools-1.21/test/annotate13.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annots13.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:append /build/reproducible-path/bcftools-1.21/test/annotate13.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annots13.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:unique /build/reproducible-path/bcftools-1.21/test/annotate13.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annots13.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:unique /build/reproducible-path/bcftools-1.21/test/annotate13.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -x FILTER/XX,INFO/XX --force /build/reproducible-path/bcftools-1.21/test/annotate14.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -x FILTER/XX,INFO/XX --force /build/reproducible-path/bcftools-1.21/test/annotate14.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annotate15.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate15.hdr -s SAMPLE1 -c CHROM,FROM,TO,FMT/FOO,BAR /build/reproducible-path/bcftools-1.21/test/annotate15.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annotate15.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate15.hdr -s SAMPLE1 -c CHROM,FROM,TO,FMT/FOO,BAR /build/reproducible-path/bcftools-1.21/test/annotate15.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annotate15.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate15.hdr -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR /build/reproducible-path/bcftools-1.21/test/annotate15.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annotate15.tab.gz -h /build/reproducible-path/bcftools-1.21/test/annotate15.hdr -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR /build/reproducible-path/bcftools-1.21/test/annotate15.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annotate15.tab.gz -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR -H '##FORMAT=' -H '##INFO=' /build/reproducible-path/bcftools-1.21/test/annotate15.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annotate15.tab.gz -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR -H '##FORMAT=' -H '##INFO=' /build/reproducible-path/bcftools-1.21/test/annotate15.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -x FILTER /build/reproducible-path/bcftools-1.21/test/annotate16.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -x FILTER /build/reproducible-path/bcftools-1.21/test/annotate16.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/reproducible-path/bcftools-1.21/test/annotate17.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/reproducible-path/bcftools-1.21/test/annotate17.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/reproducible-path/bcftools-1.21/test/annotate17.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/reproducible-path/bcftools-1.21/test/annotate17.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annotate17.3.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/reproducible-path/bcftools-1.21/test/annotate17.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annotate17.3.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/reproducible-path/bcftools-1.21/test/annotate17.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/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-1.21/test/annotate18.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/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-1.21/test/annotate18.1.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/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-1.21/test/annotate18.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/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-1.21/test/annotate18.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/JyOqsQtwLk/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/JyOqsQtwLk/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/JyOqsQtwLk/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/JyOqsQtwLk/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/JyOqsQtwLk/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/JyOqsQtwLk/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -c INFO/FILTER:=FILTER /build/reproducible-path/bcftools-1.21/test/annotate19.dst.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -c INFO/FILTER:=FILTER /build/reproducible-path/bcftools-1.21/test/annotate19.dst.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER /tmp/JyOqsQtwLk/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER /tmp/JyOqsQtwLk/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER /tmp/JyOqsQtwLk/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER /tmp/JyOqsQtwLk/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER,FILTER /tmp/JyOqsQtwLk/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER,FILTER /tmp/JyOqsQtwLk/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=./FILTER /tmp/JyOqsQtwLk/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=./FILTER /tmp/JyOqsQtwLk/annotate19.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annotate20.src.vcf.gz -c FMT/GT /tmp/JyOqsQtwLk/annotate20.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annotate20.src.vcf.gz -c FMT/GT /tmp/JyOqsQtwLk/annotate20.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annotate20.src.vcf.gz -c +FMT/GT /tmp/JyOqsQtwLk/annotate20.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annotate20.src.vcf.gz -c +FMT/GT /tmp/JyOqsQtwLk/annotate20.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annotate20.src.vcf.gz -c -FMT/GT /tmp/JyOqsQtwLk/annotate20.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annotate20.src.vcf.gz -c -FMT/GT /tmp/JyOqsQtwLk/annotate20.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annotate.multi.tab.gz -c CHROM,POS,REF,ALT,ANN -l ANN:append /build/reproducible-path/bcftools-1.21/test/annotate.multi.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annotate.multi.tab.gz -c CHROM,POS,REF,ALT,ANN -l ANN:append /build/reproducible-path/bcftools-1.21/test/annotate.multi.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/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-1.21/test/annotate.missing-append.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/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-1.21/test/annotate.missing-append.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /build/reproducible-path/bcftools-1.21/test/annotate9.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /build/reproducible-path/bcftools-1.21/test/annotate9.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate --rename-annots /build/reproducible-path/bcftools-1.21/test/annotate21.txt /build/reproducible-path/bcftools-1.21/test/annotate21.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob --rename-annots /build/reproducible-path/bcftools-1.21/test/annotate21.txt /build/reproducible-path/bcftools-1.21/test/annotate21.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/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-1.21/test/annotate21.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/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-1.21/test/annotate21.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/JyOqsQtwLk/annotate22.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/JyOqsQtwLk/annotate22.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annotate23.tab.gz -c CHROM,POS,~ID,REF,ALT,INFO/END /build/reproducible-path/bcftools-1.21/test/annotate23.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annotate23.tab.gz -c CHROM,POS,~ID,REF,ALT,INFO/END /build/reproducible-path/bcftools-1.21/test/annotate23.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annotate24.src.vcf.gz -c XX /tmp/JyOqsQtwLk/annotate24.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annotate24.src.vcf.gz -c XX /tmp/JyOqsQtwLk/annotate24.dst.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annotate25.tab.gz -c CHROM,POS,ID,REF,ALT,~INFO/END /build/reproducible-path/bcftools-1.21/test/annotate25.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annotate25.tab.gz -c CHROM,POS,ID,REF,ALT,~INFO/END /build/reproducible-path/bcftools-1.21/test/annotate25.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annotate26.tab.gz -c CHROM,POS,-POS /build/reproducible-path/bcftools-1.21/test/annotate26.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annotate26.tab.gz -c CHROM,POS,-POS /build/reproducible-path/bcftools-1.21/test/annotate26.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,TSTR,TFLT,TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,TSTR,TFLT,TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.TSTR,.TFLT,.TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.TSTR,.TFLT,.TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.+TSTR,.+TFLT,.+TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.+TSTR,.+TFLT,.+TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,+TSTR,+TFLT,+TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,+TSTR,+TFLT,+TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.=TSTR,.=TFLT,.=TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.=TSTR,.=TFLT,.=TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,=TSTR,=TFLT,=TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,=TSTR,=TFLT,=TINT /build/reproducible-path/bcftools-1.21/test/annotate.missing.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique /build/reproducible-path/bcftools-1.21/test/annotate.olap.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique /build/reproducible-path/bcftools-1.21/test/annotate.olap.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique --min-overlap 0.4:0.5 -m XXX /build/reproducible-path/bcftools-1.21/test/annotate.olap.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique --min-overlap 0.4:0.5 -m XXX /build/reproducible-path/bcftools-1.21/test/annotate.olap.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annots.id.vcf.gz -c ALT /tmp/JyOqsQtwLk/annotate.id.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annots.id.vcf.gz -c ALT /tmp/JyOqsQtwLk/annotate.id.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annots.id.vcf.gz -c +ALT /tmp/JyOqsQtwLk/annotate.id.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annots.id.vcf.gz -c +ALT /tmp/JyOqsQtwLk/annotate.id.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annots.id.2.vcf.gz --pair-logic some -c +ID /tmp/JyOqsQtwLk/annotate.id.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annots.id.2.vcf.gz --pair-logic some -c +ID /tmp/JyOqsQtwLk/annotate.id.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annots.id.2.vcf.gz --pair-logic any -c +ID /tmp/JyOqsQtwLk/annotate.id.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annots.id.2.vcf.gz --pair-logic any -c +ID /tmp/JyOqsQtwLk/annotate.id.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annotate27.tab.gz -c CHROM,POS,REF,ALT,EVIDENCE /build/reproducible-path/bcftools-1.21/test/annotate27.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annotate27.tab.gz -c CHROM,POS,REF,ALT,EVIDENCE /build/reproducible-path/bcftools-1.21/test/annotate27.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1,smpl2 /build/reproducible-path/bcftools-1.21/test/annotate28.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1,smpl2 /build/reproducible-path/bcftools-1.21/test/annotate28.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2,smpl1 /build/reproducible-path/bcftools-1.21/test/annotate28.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2,smpl1 /build/reproducible-path/bcftools-1.21/test/annotate28.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1 /build/reproducible-path/bcftools-1.21/test/annotate28.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1 /build/reproducible-path/bcftools-1.21/test/annotate28.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2 /build/reproducible-path/bcftools-1.21/test/annotate28.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2 /build/reproducible-path/bcftools-1.21/test/annotate28.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -m XXX /build/reproducible-path/bcftools-1.21/test/annotate.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -m XXX /build/reproducible-path/bcftools-1.21/test/annotate.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annots34.tab.gz -c CHROM,FROM,TO,INFO/END -H '##INFO=' /build/reproducible-path/bcftools-1.21/test/annotate34.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annots34.tab.gz -c CHROM,FROM,TO,INFO/END -H '##INFO=' /build/reproducible-path/bcftools-1.21/test/annotate34.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/JyOqsQtwLk/annots-mark.bed.gz -c CHROM,FROM,TO -m TAG /build/reproducible-path/bcftools-1.21/test/annots-mark.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -Ob -a /tmp/JyOqsQtwLk/annots-mark.bed.gz -c CHROM,FROM,TO -m TAG /build/reproducible-path/bcftools-1.21/test/annots-mark.vcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --no-version /tmp/JyOqsQtwLk/concat.1.a.vcf.gz /tmp/JyOqsQtwLk/concat.1.b.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob /tmp/JyOqsQtwLk/concat.1.a.vcf.gz /tmp/JyOqsQtwLk/concat.1.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --no-version /tmp/JyOqsQtwLk/concat.1.a.bcf /tmp/JyOqsQtwLk/concat.1.b.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob /tmp/JyOqsQtwLk/concat.1.a.bcf /tmp/JyOqsQtwLk/concat.1.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -a /tmp/JyOqsQtwLk/concat.2.a.vcf.gz /tmp/JyOqsQtwLk/concat.2.b.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -a /tmp/JyOqsQtwLk/concat.2.a.vcf.gz /tmp/JyOqsQtwLk/concat.2.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -a /tmp/JyOqsQtwLk/concat.2.a.bcf /tmp/JyOqsQtwLk/concat.2.b.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -a /tmp/JyOqsQtwLk/concat.2.a.bcf /tmp/JyOqsQtwLk/concat.2.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -aD /tmp/JyOqsQtwLk/concat.2.a.vcf.gz /tmp/JyOqsQtwLk/concat.2.b.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -aD /tmp/JyOqsQtwLk/concat.2.a.vcf.gz /tmp/JyOqsQtwLk/concat.2.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -aD /tmp/JyOqsQtwLk/concat.2.a.bcf /tmp/JyOqsQtwLk/concat.2.b.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -aD /tmp/JyOqsQtwLk/concat.2.a.bcf /tmp/JyOqsQtwLk/concat.2.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -l --ligate-warn /tmp/JyOqsQtwLk/concat.3.a.vcf.gz /tmp/JyOqsQtwLk/concat.3.b.vcf.gz /tmp/JyOqsQtwLk/concat.3.0.vcf.gz /tmp/JyOqsQtwLk/concat.3.c.vcf.gz /tmp/JyOqsQtwLk/concat.3.d.vcf.gz /tmp/JyOqsQtwLk/concat.3.e.vcf.gz /tmp/JyOqsQtwLk/concat.3.f.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -l --ligate-warn /tmp/JyOqsQtwLk/concat.3.a.vcf.gz /tmp/JyOqsQtwLk/concat.3.b.vcf.gz /tmp/JyOqsQtwLk/concat.3.0.vcf.gz /tmp/JyOqsQtwLk/concat.3.c.vcf.gz /tmp/JyOqsQtwLk/concat.3.d.vcf.gz /tmp/JyOqsQtwLk/concat.3.e.vcf.gz /tmp/JyOqsQtwLk/concat.3.f.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -l --ligate-warn /tmp/JyOqsQtwLk/concat.3.a.bcf /tmp/JyOqsQtwLk/concat.3.b.bcf /tmp/JyOqsQtwLk/concat.3.0.bcf /tmp/JyOqsQtwLk/concat.3.c.bcf /tmp/JyOqsQtwLk/concat.3.d.bcf /tmp/JyOqsQtwLk/concat.3.e.bcf /tmp/JyOqsQtwLk/concat.3.f.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -l --ligate-warn /tmp/JyOqsQtwLk/concat.3.a.bcf /tmp/JyOqsQtwLk/concat.3.b.bcf /tmp/JyOqsQtwLk/concat.3.0.bcf /tmp/JyOqsQtwLk/concat.3.c.bcf /tmp/JyOqsQtwLk/concat.3.d.bcf /tmp/JyOqsQtwLk/concat.3.e.bcf /tmp/JyOqsQtwLk/concat.3.f.bcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ Random seed for test_naive_concat: 1945464352 .. ok test_naive_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --naive-force /tmp/JyOqsQtwLk/naive_concat.0.bcf /tmp/JyOqsQtwLk/naive_concat.1.bcf /tmp/JyOqsQtwLk/naive_concat.2.bcf /tmp/JyOqsQtwLk/naive_concat.3.bcf /tmp/JyOqsQtwLk/naive_concat.4.bcf /tmp/JyOqsQtwLk/naive_concat.5.bcf /tmp/JyOqsQtwLk/naive_concat.6.bcf /tmp/JyOqsQtwLk/naive_concat.7.bcf /tmp/JyOqsQtwLk/naive_concat.8.bcf /tmp/JyOqsQtwLk/naive_concat.9.bcf | /build/reproducible-path/bcftools-1.21/bcftools view -H .. ok test_naive_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --naive /tmp/JyOqsQtwLk/naive_concat.0.vcf.gz /tmp/JyOqsQtwLk/naive_concat.1.vcf.gz /tmp/JyOqsQtwLk/naive_concat.2.vcf.gz /tmp/JyOqsQtwLk/naive_concat.3.vcf.gz /tmp/JyOqsQtwLk/naive_concat.4.vcf.gz /tmp/JyOqsQtwLk/naive_concat.5.vcf.gz /tmp/JyOqsQtwLk/naive_concat.6.vcf.gz /tmp/JyOqsQtwLk/naive_concat.7.vcf.gz /tmp/JyOqsQtwLk/naive_concat.8.vcf.gz /tmp/JyOqsQtwLk/naive_concat.9.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view -H .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -l /tmp/JyOqsQtwLk/concat.4.a.vcf.gz /tmp/JyOqsQtwLk/concat.4.b.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -l /tmp/JyOqsQtwLk/concat.4.a.vcf.gz /tmp/JyOqsQtwLk/concat.4.b.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -l /tmp/JyOqsQtwLk/concat.4.a.bcf /tmp/JyOqsQtwLk/concat.4.b.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -l /tmp/JyOqsQtwLk/concat.4.a.bcf /tmp/JyOqsQtwLk/concat.4.b.bcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -l --ligate-warn /tmp/JyOqsQtwLk/concat.5.a.vcf.gz /tmp/JyOqsQtwLk/concat.5.b.vcf.gz /tmp/JyOqsQtwLk/concat.5.c.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -l --ligate-warn /tmp/JyOqsQtwLk/concat.5.a.vcf.gz /tmp/JyOqsQtwLk/concat.5.b.vcf.gz /tmp/JyOqsQtwLk/concat.5.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -l --ligate-warn /tmp/JyOqsQtwLk/concat.5.a.bcf /tmp/JyOqsQtwLk/concat.5.b.bcf /tmp/JyOqsQtwLk/concat.5.c.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -l --ligate-warn /tmp/JyOqsQtwLk/concat.5.a.bcf /tmp/JyOqsQtwLk/concat.5.b.bcf /tmp/JyOqsQtwLk/concat.5.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -l --ligate-force /tmp/JyOqsQtwLk/concat.5.a.bcf /tmp/JyOqsQtwLk/concat.5.b.bcf /tmp/JyOqsQtwLk/concat.5.c.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -l --ligate-force /tmp/JyOqsQtwLk/concat.5.a.bcf /tmp/JyOqsQtwLk/concat.5.b.bcf /tmp/JyOqsQtwLk/concat.5.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -G -a -D /tmp/JyOqsQtwLk/concat.5.a.vcf.gz /tmp/JyOqsQtwLk/concat.5.b.vcf.gz /tmp/JyOqsQtwLk/concat.5.c.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -G -a -D /tmp/JyOqsQtwLk/concat.5.a.vcf.gz /tmp/JyOqsQtwLk/concat.5.b.vcf.gz /tmp/JyOqsQtwLk/concat.5.c.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --no-version -G -a -D /tmp/JyOqsQtwLk/concat.5.a.bcf /tmp/JyOqsQtwLk/concat.5.b.bcf /tmp/JyOqsQtwLk/concat.5.c.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -G -a -D /tmp/JyOqsQtwLk/concat.5.a.bcf /tmp/JyOqsQtwLk/concat.5.b.bcf /tmp/JyOqsQtwLk/concat.5.c.bcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.hdr /build/reproducible-path/bcftools-1.21/test/reheader.vcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /build/reproducible-path/bcftools-1.21/test/reheader.vcf | /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.hdr | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.hdr /tmp/JyOqsQtwLk/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/JyOqsQtwLk/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.hdr | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.hdr /tmp/JyOqsQtwLk/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/JyOqsQtwLk/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.hdr | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples /build/reproducible-path/bcftools-1.21/test/reheader.vcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /build/reproducible-path/bcftools-1.21/test/reheader.vcf | /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples /tmp/JyOqsQtwLk/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/JyOqsQtwLk/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples /tmp/JyOqsQtwLk/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/JyOqsQtwLk/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples2 /build/reproducible-path/bcftools-1.21/test/reheader.vcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /build/reproducible-path/bcftools-1.21/test/reheader.vcf | /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples2 | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples2 /tmp/JyOqsQtwLk/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/JyOqsQtwLk/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples2 | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples2 /tmp/JyOqsQtwLk/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/JyOqsQtwLk/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples2 | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples3 /build/reproducible-path/bcftools-1.21/test/reheader.vcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /build/reproducible-path/bcftools-1.21/test/reheader.vcf | /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples3 | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples3 /tmp/JyOqsQtwLk/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/JyOqsQtwLk/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples3 | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples3 /tmp/JyOqsQtwLk/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/JyOqsQtwLk/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples3 | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples4 /build/reproducible-path/bcftools-1.21/test/reheader.vcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /build/reproducible-path/bcftools-1.21/test/reheader.vcf | /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples4 | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples4 /tmp/JyOqsQtwLk/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/JyOqsQtwLk/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples4 | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples4 /tmp/JyOqsQtwLk/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/JyOqsQtwLk/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools reheader -s /build/reproducible-path/bcftools-1.21/test/reheader.samples4 | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.empty.hdr /build/reproducible-path/bcftools-1.21/test/empty.vcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /build/reproducible-path/bcftools-1.21/test/empty.vcf | /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.empty.hdr | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.empty.hdr /tmp/JyOqsQtwLk/empty.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/JyOqsQtwLk/empty.bcf | /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.empty.hdr | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.empty.hdr /tmp/JyOqsQtwLk/empty.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/JyOqsQtwLk/empty.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.empty.hdr | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -f /build/reproducible-path/bcftools-1.21/test/reheader.fai /build/reproducible-path/bcftools-1.21/test/reheader.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -f /build/reproducible-path/bcftools-1.21/test/reheader.fai /tmp/JyOqsQtwLk/reheader.2.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -f /build/reproducible-path/bcftools-1.21/test/reheader.fai /tmp/JyOqsQtwLk/reheader.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.2.hdr -f /build/reproducible-path/bcftools-1.21/test/reheader.fai /build/reproducible-path/bcftools-1.21/test/reheader.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.2.hdr -f /build/reproducible-path/bcftools-1.21/test/reheader.fai /tmp/JyOqsQtwLk/reheader.2.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -h /build/reproducible-path/bcftools-1.21/test/reheader.2.hdr -f /build/reproducible-path/bcftools-1.21/test/reheader.fai /tmp/JyOqsQtwLk/reheader.2.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -f /build/reproducible-path/bcftools-1.21/test/reheader.3.fai /build/reproducible-path/bcftools-1.21/test/reheader.3.vcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -f /build/reproducible-path/bcftools-1.21/test/reheader.3.fai /tmp/JyOqsQtwLk/reheader.3.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/reproducible-path/bcftools-1.21/bcftools reheader -f /build/reproducible-path/bcftools-1.21/test/reheader.3.fai /tmp/JyOqsQtwLk/reheader.3.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_rename_chrs: /build/reproducible-path/bcftools-1.21/bcftools annotate --rename-chrs /tmp/JyOqsQtwLk/rename.map -Ov /tmp/JyOqsQtwLk/annotate.bcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /build/reproducible-path/bcftools-1.21/bcftools annotate --rename-chrs /tmp/JyOqsQtwLk/rename.map -Ob /tmp/JyOqsQtwLk/annotate.bcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /build/reproducible-path/bcftools-1.21/bcftools annotate --rename-chrs /tmp/JyOqsQtwLk/rename.map -Ov /build/reproducible-path/bcftools-1.21/test/annotate.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /build/reproducible-path/bcftools-1.21/bcftools annotate --rename-chrs /tmp/JyOqsQtwLk/rename.map -Ob /build/reproducible-path/bcftools-1.21/test/annotate.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM\t%POS\n' .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. /tmp/JyOqsQtwLk/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --vcf-ids /tmp/JyOqsQtwLk/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --vcf-ids .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --vcf-ids --3N6 /tmp/JyOqsQtwLk/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --vcf-ids --3N6 .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert -g .,- /tmp/JyOqsQtwLk/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g .,- .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert --vcf-ids -G /build/reproducible-path/bcftools-1.21/test/convert.gs.gt.ids.gen,/build/reproducible-path/bcftools-1.21/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert --vcf-ids -G /build/reproducible-path/bcftools-1.21/test/convert.gs.gt.ids.gen,/build/reproducible-path/bcftools-1.21/test/convert.gs.gt.samples -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert -G /build/reproducible-path/bcftools-1.21/test/convert.gs.gt.ids.gen,/build/reproducible-path/bcftools-1.21/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert -G /build/reproducible-path/bcftools-1.21/test/convert.gs.gt.ids.gen,/build/reproducible-path/bcftools-1.21/test/convert.gs.gt.samples -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert --3N6 -G /build/reproducible-path/bcftools-1.21/test/convert.gs.gt.ids.3N6.gen,/build/reproducible-path/bcftools-1.21/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert --3N6 -G /build/reproducible-path/bcftools-1.21/test/convert.gs.gt.ids.3N6.gen,/build/reproducible-path/bcftools-1.21/test/convert.gs.gt.samples -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert --vcf-ids -G /build/reproducible-path/bcftools-1.21/test/convert.gs.gt.ids.gen.rev,/build/reproducible-path/bcftools-1.21/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert --vcf-ids -G /build/reproducible-path/bcftools-1.21/test/convert.gs.gt.ids.gen.rev,/build/reproducible-path/bcftools-1.21/test/convert.gs.gt.samples -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert -G /build/reproducible-path/bcftools-1.21/test/convert.gs.gt.ids.gen.rev,/build/reproducible-path/bcftools-1.21/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert -G /build/reproducible-path/bcftools-1.21/test/convert.gs.gt.ids.gen.rev,/build/reproducible-path/bcftools-1.21/test/convert.gs.gt.samples -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^## .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --tag PL /tmp/JyOqsQtwLk/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --tag PL .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert -g .,- --tag PL /tmp/JyOqsQtwLk/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g .,- --tag PL .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --vcf-ids /tmp/JyOqsQtwLk/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/check.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --vcf-ids .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert -g .,- --vcf-ids /tmp/JyOqsQtwLk/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/check.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g .,- --vcf-ids .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --3N6 /tmp/JyOqsQtwLk/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/check.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --3N6 .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert -g .,- --3N6 /tmp/JyOqsQtwLk/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/check.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g .,- --3N6 .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --3N6 --vcf-ids /tmp/JyOqsQtwLk/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/check.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g -,. --3N6 --vcf-ids .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert -g .,- --3N6 --vcf-ids /tmp/JyOqsQtwLk/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/check.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -g .,- --3N6 --vcf-ids .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert -h -,.,. /tmp/JyOqsQtwLk/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -h -,.,. .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert -h .,-,. /tmp/JyOqsQtwLk/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -h .,-,. .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert -h .,-,. --vcf-ids /tmp/JyOqsQtwLk/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -h .,-,. --vcf-ids .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert -h .,.,- /tmp/JyOqsQtwLk/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert -h .,.,- .. ok test_vcf_convert_hls2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert -H /build/reproducible-path/bcftools-1.21/test/convert.hls.gt.hap,/build/reproducible-path/bcftools-1.21/test/convert.hls.gt.legend,/build/reproducible-path/bcftools-1.21/test/convert.hls.gt.samples | grep -v ^## .. ok test_vcf_convert_hls2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert -H /build/reproducible-path/bcftools-1.21/test/convert.hls.gt.hap,/build/reproducible-path/bcftools-1.21/test/convert.hls.gt.legend,/build/reproducible-path/bcftools-1.21/test/convert.hls.gt.samples -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^## .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert --haplegendsample -,.,. /tmp/JyOqsQtwLk/convert.hap-missing.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/convert.hap-missing.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert --haplegendsample -,.,. .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert --hapsample -,. /tmp/JyOqsQtwLk/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert --hapsample -,. .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert --hapsample -,. --vcf-ids /tmp/JyOqsQtwLk/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert --hapsample -,. --vcf-ids .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools convert --hapsample .,- /tmp/JyOqsQtwLk/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/convert.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert --hapsample .,- .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert --hapsample2vcf /build/reproducible-path/bcftools-1.21/test/convert.hs.gt.hap,/build/reproducible-path/bcftools-1.21/test/convert.hs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert --hapsample2vcf /build/reproducible-path/bcftools-1.21/test/convert.hs.gt.hap,/build/reproducible-path/bcftools-1.21/test/convert.hs.gt.samples -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert --vcf-ids --hapsample2vcf /build/reproducible-path/bcftools-1.21/test/convert.hs.gt.ids.hap,/build/reproducible-path/bcftools-1.21/test/convert.hs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert --vcf-ids --hapsample2vcf /build/reproducible-path/bcftools-1.21/test/convert.hs.gt.ids.hap,/build/reproducible-path/bcftools-1.21/test/convert.hs.gt.samples -Ou | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^## .. ok test_vcf_convert_gvcf: /build/reproducible-path/bcftools-1.21/bcftools convert --no-version --gvcf2vcf -i'FILTER="PASS"' -f /build/reproducible-path/bcftools-1.21/test/gvcf.fa /tmp/JyOqsQtwLk/convert.gvcf.vcf.gz .. ok test_vcf_convert_gvcf: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/JyOqsQtwLk/convert.gvcf.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools convert --gvcf2vcf -i'FILTER="PASS"' -f /build/reproducible-path/bcftools-1.21/test/gvcf.fa | grep -v ^##bcftools .. ok test_vcf_convert_tsv2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert --no-version -c ID,CHROM,POS,AA -s SAMPLE1 -f /build/reproducible-path/bcftools-1.21/test/23andme.fa --tsv2vcf /build/reproducible-path/bcftools-1.21/test/convert.23andme .. ok test_vcf_convert_tsv2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert -Ou -c ID,CHROM,POS,AA -s SAMPLE1 -f /build/reproducible-path/bcftools-1.21/test/23andme.fa --tsv2vcf /build/reproducible-path/bcftools-1.21/test/convert.23andme | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_convert_tsv2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert --no-version -c -,CHROM,POS,REF,ALT -f /build/reproducible-path/bcftools-1.21/test/23andme.fa --tsv2vcf /build/reproducible-path/bcftools-1.21/test/convert.tsv .. ok test_vcf_convert_tsv2vcf: /build/reproducible-path/bcftools-1.21/bcftools convert -Ou -c -,CHROM,POS,REF,ALT -f /build/reproducible-path/bcftools-1.21/test/23andme.fa --tsv2vcf /build/reproducible-path/bcftools-1.21/test/convert.tsv | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.overlaps.1.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.overlaps.1.fa -s A .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.overlaps.1.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.overlaps.1.fa -s A .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.overlaps.1.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.overlaps.1.fa -s B .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.overlaps.1.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.overlaps.1.fa -s B .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.overlaps.1.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.overlaps.1.fa -s A -a N .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.overlaps.1.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.overlaps.1.fa -s A -a N .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.overlaps.1.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.overlaps.1.fa -s B -a N .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.overlaps.1.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.overlaps.1.fa -s B -a N .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.beyond.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.beyond.fa .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.beyond.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.beyond.fa .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -m /build/reproducible-path/bcftools-1.21/test/consensus.tab .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -m /build/reproducible-path/bcftools-1.21/test/consensus.tab .. ok test_vcf_consensus_chain: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -m /build/reproducible-path/bcftools-1.21/test/consensus.tab -c /tmp/JyOqsQtwLk/consensus.1.chain.new >/dev/null; cat /tmp/JyOqsQtwLk/consensus.1.chain.new .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -H 1 -m /build/reproducible-path/bcftools-1.21/test/consensus.tab .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -H 1 -m /build/reproducible-path/bcftools-1.21/test/consensus.tab .. ok test_vcf_consensus_chain: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -H 1 -m /build/reproducible-path/bcftools-1.21/test/consensus.tab -c /tmp/JyOqsQtwLk/consensus.2.chain.new >/dev/null; cat /tmp/JyOqsQtwLk/consensus.2.chain.new .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -I -s - -m /build/reproducible-path/bcftools-1.21/test/consensus.tab .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -I -s - -m /build/reproducible-path/bcftools-1.21/test/consensus.tab .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -I -m /build/reproducible-path/bcftools-1.21/test/consensus.tab --mask-with X -m /build/reproducible-path/bcftools-1.21/test/consensus.tab --mask-with lc .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -I -m /build/reproducible-path/bcftools-1.21/test/consensus.tab --mask-with X -m /build/reproducible-path/bcftools-1.21/test/consensus.tab --mask-with lc .. ok test_vcf_consensus_chain: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -I -m /build/reproducible-path/bcftools-1.21/test/consensus.tab -c /tmp/JyOqsQtwLk/consensus.3.chain.new >/dev/null; cat /tmp/JyOqsQtwLk/consensus.3.chain.new .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -H 1 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -H 1 .. ok test_vcf_consensus_chain: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -H 1 -c /tmp/JyOqsQtwLk/consensus.4.chain.new >/dev/null; cat /tmp/JyOqsQtwLk/consensus.4.chain.new .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus2.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -H 1 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus2.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -H 1 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus2.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -H 2 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus2.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -H 2 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/empty.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/empty.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -H 2 -M "?" .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus3.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -H 2 -M "?" .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus3.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -H 2 -M "?" -p xx_ .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus3.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -H 2 -M "?" -p xx_ .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus4.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus4.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus5.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus5.fa --haplotype LA .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus5.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus5.fa --haplotype LA .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus6.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus6.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus6.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus6.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus7.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 2 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus7.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 2 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus7.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 4 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus7.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 4 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus7.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 2pIu .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus7.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 2pIu .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus7.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 4pIu .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus7.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 4pIu .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus7.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 1 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus7.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 1 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus7.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 3 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus7.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 3 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus7.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 1pIu .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus7.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 1pIu .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus7.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 3pIu .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus7.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus7.fa -H 3pIu .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus8.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus8.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus8.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -a . .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus8.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -a . .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus8.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -a . -i 'type="snp" || type="ref"' .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus8.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -a . -i 'type="snp" || type="ref"' .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus8.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -a . -i 'ALT!=""' .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus8.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -a . -i 'ALT!=""' .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus8.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -a . -e 'MinDP>15' .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus8.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -a . -e 'MinDP>15' .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus8.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -a . -e 'MinDP<15' .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus8.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -a . -e 'MinDP<15' .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.9.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.9.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.9.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.9.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.10.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.10.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.10.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.10.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.11.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.11.fa -s smpl .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.11.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.11.fa -s smpl .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.11.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.11.fa -s smpl -a N .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.11.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.11.fa -s smpl -a N .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.12.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.12.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.12.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.12.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.13.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.13.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.13.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.13.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.14.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.14.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.14.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.14.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.12.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.12.fa -s - --mark-del - --mark-ins uc --mark-snv uc .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.12.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.12.fa -s - --mark-del - --mark-ins uc --mark-snv uc .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.12.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.12.fa -s - --mark-del - --mark-ins + --mark-snv : .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.12.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.12.fa -s - --mark-del - --mark-ins + --mark-snv : .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.15.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.15.fa -H I --mark-ins lc --mark-snv lc .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.15.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.15.fa -H I --mark-ins lc --mark-snv lc .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.16.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -I .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.16.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -s - -I .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.16.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -H I .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.16.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -H I .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.17.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -s - -M N -m /build/reproducible-path/bcftools-1.21/test/consensus.17.bed .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.17.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus2.fa -s - -M N -m /build/reproducible-path/bcftools-1.21/test/consensus.17.bed .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.18.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.18.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.18.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.18.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.19.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.19.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.19.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.19.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.20.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.20.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.20.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.20.fa -s - .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.20.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.20.fa .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.20.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.20.fa .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.20.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.20.fa -M . -s b .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.20.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.20.fa -M . -s b .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.20.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.20.fa -M . -s a .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.20.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.20.fa -M . -s a .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.21.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.21.fa .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.21.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.21.fa .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.22.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 0 --mark-del . .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.22.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 0 --mark-del . .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.22.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 1 --mark-del . .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.22.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 1 --mark-del . .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.22.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 2 --mark-del . .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.22.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 2 --mark-del . .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.22.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 0 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.22.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 0 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.22.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 1 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.22.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 1 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.22.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 2 .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/JyOqsQtwLk/consensus.22.bcf -f /build/reproducible-path/bcftools-1.21/test/consensus.22.fa --regions-overlap 2 .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -r17:100-150 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -r17:100-150 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -r17:100-150 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -b /tmp/JyOqsQtwLk/mpileup.bam.list --no-version | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -r17:100-150 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob -b /tmp/JyOqsQtwLk/mpileup.bam.urllist | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -r17:100-150 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -r17:100-150 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -r17:100-150 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -b /tmp/JyOqsQtwLk/mpileup.cram.list --no-version | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -r17:100-150 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob -b /tmp/JyOqsQtwLk/mpileup.cram.urllist | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DV -r17:100-600 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DV -r17:100-600 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DV -r17:100-600 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DV -r17:100-600 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP,-AD -r17:100-600 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP,-AD -r17:100-600 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP,-AD -r17:100-600 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP,-AD -r17:100-600 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DV,-AD -r17:100-600 --gvcf 0,2,5 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DV,-AD -r17:100-600 --gvcf 0,2,5 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DV,-AD -r17:100-600 --gvcf 0,2,5 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DV,-AD -r17:100-600 --gvcf 0,2,5 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DV,-AD -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DV,-AD -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DV,-AD -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a DP,DV,-AD -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -s HG00101,HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -s HG00101,HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -s HG00101,HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -s HG00101,HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -S /build/reproducible-path/bcftools-1.21/test/mplp.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -S /build/reproducible-path/bcftools-1.21/test/mplp.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -S /build/reproducible-path/bcftools-1.21/test/mplp.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -S /build/reproducible-path/bcftools-1.21/test/mplp.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -s ^HG00101,HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -s ^HG00101,HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -s ^HG00101,HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -s ^HG00101,HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -S ^/build/reproducible-path/bcftools-1.21/test/mplp.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -S ^/build/reproducible-path/bcftools-1.21/test/mplp.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -S ^/build/reproducible-path/bcftools-1.21/test/mplp.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -S ^/build/reproducible-path/bcftools-1.21/test/mplp.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -S /build/reproducible-path/bcftools-1.21/test/mplp.9.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -S /build/reproducible-path/bcftools-1.21/test/mplp.9.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -S /build/reproducible-path/bcftools-1.21/test/mplp.9.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -S /build/reproducible-path/bcftools-1.21/test/mplp.9.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -S /build/reproducible-path/bcftools-1.21/test/mplp.9.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -S /build/reproducible-path/bcftools-1.21/test/mplp.9.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -G /build/reproducible-path/bcftools-1.21/test/mplp.10.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -G /build/reproducible-path/bcftools-1.21/test/mplp.10.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -G /build/reproducible-path/bcftools-1.21/test/mplp.10.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -G /build/reproducible-path/bcftools-1.21/test/mplp.10.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -G /build/reproducible-path/bcftools-1.21/test/mplp.10.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -G /build/reproducible-path/bcftools-1.21/test/mplp.10.samples -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.1.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.2.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -s HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -s HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.sam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -s HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -s HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -s HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -s HG00102 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -s ^HG99999 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -s ^HG99999 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.sam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -s ^HG99999 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -s ^HG99999 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -s ^HG99999 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -s ^HG99999 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -G /build/reproducible-path/bcftools-1.21/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -G /build/reproducible-path/bcftools-1.21/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.sam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -G /build/reproducible-path/bcftools-1.21/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -G /build/reproducible-path/bcftools-1.21/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -G /build/reproducible-path/bcftools-1.21/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -G /build/reproducible-path/bcftools-1.21/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -G /build/reproducible-path/bcftools-1.21/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -G /build/reproducible-path/bcftools-1.21/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.sam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.sam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -G /build/reproducible-path/bcftools-1.21/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -G /build/reproducible-path/bcftools-1.21/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.bam /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -G /build/reproducible-path/bcftools-1.21/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -G /build/reproducible-path/bcftools-1.21/test/mplp.11.rgs -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.3.cram /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup.4.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.fa /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.sam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.fa /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.fa /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD --indels-cns -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.fa /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD --indels-cns -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.sam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD --indels-cns -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.fa /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD --indels-cns -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD --indels-cns -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.fa /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD --indels-cns -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.1.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -r 11:75 -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.fa /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -r 11:75 -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -r 11:75 -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.fa /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -r 11:75 -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.fa /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.fa /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.fa /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.fa /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/indel-AD.2.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD,INFO/SCR,FMT/SCR -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD,INFO/SCR,FMT/SCR -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD,INFO/SCR,FMT/SCR -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD,INFO/SCR,FMT/SCR -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.cram | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t 1:100 --skip-all-set PAIRED,PROPER_PAIR,MREVERSE -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t 1:100 --skip-all-set PAIRED,PROPER_PAIR,MREVERSE -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-filter.sam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t 1:100 --skip-any-set READ1 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t 1:100 --skip-any-set READ1 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-filter.sam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t 1:100 --skip-all-unset READ1 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t 1:100 --skip-all-unset READ1 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-filter.sam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t 1:100 --skip-any-unset READ1 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.fa /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD -t 1:100 --skip-any-unset READ1 -f /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-SCR.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/mpileup-filter.sam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD,INFO/NMBZ -r chr19:69-99 -f /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.1.fa /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD,INFO/NMBZ -r chr19:69-99 -f /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.1.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.1.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD,INFO/NMBZ -r chr6:75 -f /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.2.fa /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD,INFO/NMBZ -r chr6:75 -f /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.2.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.2.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD,INFO/NMBZ -r chr16:75 -f /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.3.fa /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.3.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.3.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/reproducible-path/bcftools-1.21/bcftools mpileup -a -AD,INFO/NMBZ -r chr16:75 -f /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.3.fa -Ob /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.3.1.bam /build/reproducible-path/bcftools-1.21/test/mpileup/annot-NMBZ.3.2.bam | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_csq: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq.fa -g /build/reproducible-path/bcftools-1.21/test/csq.gff3 /build/reproducible-path/bcftools-1.21/test/csq.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/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-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq.fa -g /build/reproducible-path/bcftools-1.21/test/csq.chr.gff3 /build/reproducible-path/bcftools-1.21/test/csq.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/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-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq.fa -g /build/reproducible-path/bcftools-1.21/test/csq.2.gff /build/reproducible-path/bcftools-1.21/test/csq.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq.fa -g /build/reproducible-path/bcftools-1.21/test/csq.2.gff --ncsq 64 /build/reproducible-path/bcftools-1.21/test/csq.2.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq.nchr.fa -g /build/reproducible-path/bcftools-1.21/test/csq.nchr.gff /build/reproducible-path/bcftools-1.21/test/csq.nchr.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq.ychr.fa -g /build/reproducible-path/bcftools-1.21/test/csq.nchr.gff /build/reproducible-path/bcftools-1.21/test/csq.nchr.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq.nchr.fa -g /build/reproducible-path/bcftools-1.21/test/csq.ychr.gff /build/reproducible-path/bcftools-1.21/test/csq.nchr.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq.ychr.fa -g /build/reproducible-path/bcftools-1.21/test/csq.ychr.gff /build/reproducible-path/bcftools-1.21/test/csq.nchr.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq.ychr.fa -g /build/reproducible-path/bcftools-1.21/test/csq.ychr.gff /build/reproducible-path/bcftools-1.21/test/csq.ychr.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq.ychr.fa -g /build/reproducible-path/bcftools-1.21/test/csq.nchr.gff /build/reproducible-path/bcftools-1.21/test/csq.ychr.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq.nchr.fa -g /build/reproducible-path/bcftools-1.21/test/csq.ychr.gff /build/reproducible-path/bcftools-1.21/test/csq.ychr.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq.nchr.fa -g /build/reproducible-path/bcftools-1.21/test/csq.nchr.gff /build/reproducible-path/bcftools-1.21/test/csq.ychr.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENSG00000173376/ENSG00000173376.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENSG00000173376/ENSG00000173376.gff /build/reproducible-path/bcftools-1.21/test/csq/ENSG00000173376/synon.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000573314/ENST00000573314.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000573314/ENST00000573314.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000573314/ENST00000573314.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000573314/ENST00000573314.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000285021/ENST00000285021.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000285021/ENST00000285021.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000285021/stop-gained-inframe-indel.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000410009/ENST00000410009.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000410009/ENST00000410009.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000410009/frameshift.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/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-1.21/test/csq/ENST00000410009 && /build/reproducible-path/bcftools-1.21/bcftools csq -B 5 -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.21/test/csq/ENST00000410009 && /build/reproducible-path/bcftools-1.21/bcftools csq -lb -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.21/test/csq/ENST00000410009 && /build/reproducible-path/bcftools-1.21/bcftools csq -b -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.21/test/csq/ENST00000422159 && /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000422159.fa -g ENST00000422159.gff multiallelic.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%REF\t%ALT\t%GT\t%TBCSQ\n]' | ../sort-csq -q ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000422159.fa -g short.gff multiallelic.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%REF\t%ALT\t%GT\t%TBCSQ\n]' | ../sort-csq -q .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000303039/ENST00000303039.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000303039/ENST00000303039.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000303039/not-a-stop.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000303039/ENST00000303039.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000303039/ENST00000303039.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000303039/not-a-stop.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000543077/ENST00000543077.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000543077/ENST00000543077.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000543077/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000543077/ENST00000543077.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000543077/ENST00000543077.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000543077/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/snps.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/snps.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/insert3.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000423372/insert3.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000420190/ENST00000420190.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000420190/ENST00000420190.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000420190/abort-in-csq-push.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000230048/ENST00000230048.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000230048/ENST00000230048.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000230048/start-del.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000227471/ENST00000227471.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000227471/ENST00000227471.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000227471/insert-splice-vs-frameshift.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000360372/ENST00000360372.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000360372/ENST00000360372.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000360372/mnp.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000263103-INS/ENST00000263103-INS.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000263103-INS/ENST00000263103-INS.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000263103-INS/insertions.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000295641/ENST00000295641.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000295641/ENST00000295641.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000295641/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000295641/ENST00000295641.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000295641/ENST00000295641.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000295641/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000373833/ENST00000373833.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000373833/ENST00000373833.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000373833/boundary-insertion.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000373833/ENST00000373833.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000373833/ENST00000373833.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000373833/boundary-insertion.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000375992/ENST00000375992.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000375992/ENST00000375992.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000375992/incorrect-synon-del-not-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000409523/ENST00000409523.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000409523/ENST00000409523.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000409523/long-overlapping-del.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000536784/ENST00000536784.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000536784/ENST00000536784.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000536784/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000536784/ENST00000536784.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000536784/ENST00000536784.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000536784/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000557788/ENST00000557788.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000557788/ENST00000557788.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000557788/long-overlap-del.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000381157/ENST00000381157.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000381157/ENST00000381157.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000381157/haploid-diploid.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n' .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.21/test/csq/ENST00000379416 && /build/reproducible-path/bcftools-1.21/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.del-snp.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-del.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-ins.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-snp.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff single.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000545279/ENST00000545279.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000545279/ENST00000545279.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000545279/splice-region-insert.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000571540/ENST00000571540.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000571540/ENST00000571540.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000571540/nmd.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000542803/ENST00000542803.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000542803/ENST00000542803.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000542803/splice-region.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000542803/ENST00000542803.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000542803/ENST00000542803.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000542803/splice-region.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000382647/ENST00000382647.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000382647/ENST00000382647.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000382647/synon-splice-region-insert.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000294661/ENST00000294661.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000294661/ENST00000294661.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000294661/non-coding-boundary.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000294661/ENST00000294661.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000294661/ENST00000294661.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000294661/non-coding-boundary.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000318249/ENST00000318249.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000318249/ENST00000318249.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000318249/start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000318249/ENST00000318249.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000318249/ENST00000318249.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000318249/start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000390520/ENST00000390520.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000390520/ENST00000390520.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000390520/deletion-overlap.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0003/EDUMMY0003.fa -g /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0003/EDUMMY0003.gff /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0003/long-del.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000479739/ENST00000479739.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000479739/ENST00000479739.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000479739/short-cds-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000479739/ENST00000479739.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000479739/ENST00000479739.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000479739/short-cds-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000269081/ENST00000269081.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000269081/ENST00000269081.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000269081/stop-gained-not-inframe-insertion.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000218032/ENST00000218032.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000218032/ENST00000218032.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000218032/start-lost-del.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000218032/ENST00000218032.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000218032/ENST00000218032.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000218032/start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000218032/ENST00000218032.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000218032/ENST00000218032.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000218032/start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000256452/ENST00000256452.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000256452/ENST00000256452.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000256452/intron.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000624631/ENST00000624631.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000624631/ENST00000624631.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000624631/ambiguous.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000368801.2/ENST00000368801.2.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000368801.2/ENST00000368801.2.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000368801.2/start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/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-1.21/test/csq/ENST00000000000 && /build/reproducible-path/bcftools-1.21/bcftools csq -p a -f ENST00000000000.fa -g ENST00000000000.gff upstream-stop.vcf | /build/reproducible-path/bcftools-1.21/bcftools query -f'[%POS\t%REF\t%ALT\t%SAMPLE\t%GT\t%TBCSQ\n]' | ../sort-csq -q .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000573035-bt2212/ENST00000573035-bt2212.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000573035-bt2212/ENST00000573035-bt2212.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000573035-bt2212/complex-event.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0002/EDUMMY0002.fa -g /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0002/EDUMMY0002.gff /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0002/boundaries.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000520795/ENST00000520795.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000520795/ENST00000520795.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000520795/long-inside-del.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000520795/ENST00000520795.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000520795/ENST00000520795.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000520795/long-inside-del.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000518414/ENST00000518414.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000518414/ENST00000518414.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000518414/incorrect-inframe-del.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/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-1.21/test/csq/ENSMUST00000121418 && /build/reproducible-path/bcftools-1.21/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25500' --phase m | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.21/test/csq/ENSMUST00000121418 && /build/reproducible-path/bcftools-1.21/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25105' --phase m | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/reproducible-path/bcftools-1.21/test/csq/ENSMUST00000121418 && /build/reproducible-path/bcftools-1.21/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25496' --phase m | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000518414-ENST00000521270/valgrind.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000400151/ENST00000400151.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000400151/ENST00000400151.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000400151/long-del.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000301246/ENST00000301246.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000301246/ENST00000301246.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000301246/15bp-insert.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/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-1.21/test/csq/ENST00000580206 && /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.ins-snv.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g short.gff compound.ins-snv.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff single.ins-snv.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g short.gff single.ins-snv.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.del-snv.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g short.gff compound.del-snv.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g short.gff single.del-snv.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.del-ins.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g short.gff compound.del-ins.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/reproducible-path/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g short.gff single.del-ins.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000357367/ENST00000357367.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000357367/ENST00000357367.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000357367/stop-retained.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000378322/ENST00000378322.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000378322/ENST00000378322.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000378322/end-overlap-tscript.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000378322/ENST00000378322.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000378322/ENST00000378322.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000378322/end-overlap-tscript.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000420670/ENST00000420670.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000420670/ENST00000420670.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000420670/start-stop-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000420670/ENST00000420670.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000420670/ENST00000420670.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000420670/segfault.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/frame1.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/frame1.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/frame2.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/frame2.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/not-a-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/frame3.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/frame3.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000413103/ENST00000413103.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000413103/ENST00000413103.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000413103/long-deletion.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000520868/ENST00000520868.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000520868/ENST00000520868.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000520868/long-deletion.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000318249.2/ENST00000318249.2.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000318249.2/ENST00000318249.2.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000318249.2/synonymous-start-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000593942/ENST00000593942.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000593942/ENST00000593942.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000593942/last-codon-deletion.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000448695/ENST00000448695.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000448695/ENST00000448695.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000448695/syn-and-splice-reg.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000368801/ENST00000368801.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000368801/ENST00000368801.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000368801/compound-lost.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/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-1.21/test/csq/EMN908947 && /build/reproducible-path/bcftools-1.21/bcftools csq -f EMN908947.fa -g ribosomal-slippage.gff ribosomal-slippage.vcf --force | ../sort-csq | /build/reproducible-path/bcftools-1.21/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-1.21/test/csq/EMN908947 && /build/reproducible-path/bcftools-1.21/bcftools csq -f EMN908947.fa -g simple.gff simple.vcf | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000436063/ENST00000436063.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000436063/ENST00000436063.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000436063/insert-before-utr.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000528237/ENST00000528237.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000528237/ENST00000528237.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000528237/retained-stop-incomplete-cds.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000519442/ENST00000519442.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000519442/ENST00000519442.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000519442/synon-splice-region-del.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000271583/ENST00000271583.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000271583/ENST00000271583.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000271583/splice-acceptor.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000329454/ENST00000329454.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000329454/ENST00000329454.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000329454/boundary-deletion.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/ENST00000329454/ENST00000329454.fa -g /build/reproducible-path/bcftools-1.21/test/csq/ENST00000329454/ENST00000329454.gff /build/reproducible-path/bcftools-1.21/test/csq/ENST00000329454/boundary-deletion.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/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-1.21/test/csq/ENSMUST00000133836 && /build/reproducible-path/bcftools-1.21/bcftools csq -f ENSMUST00000133836.fa -g ENSMUST00000133836.gff filter-problem.vcf -i 'FILTER="PASS"' --phase m | ../sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -f /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0001/EDUMMY0001.fa -g /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0001/EDUMMY0001.gff /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0001/starts-with-1.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/reproducible-path/bcftools-1.21/bcftools csq -l -f /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0001/EDUMMY0001.fa -g /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0001/EDUMMY0001.gff /build/reproducible-path/bcftools-1.21/test/csq/EDUMMY0001/starts-with-1.vcf | /build/reproducible-path/bcftools-1.21/test/csq/sort-csq | /build/reproducible-path/bcftools-1.21/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-1.21/bcftools roh /build/reproducible-path/bcftools-1.21/test/roh.1.vcf.gz -Or -G30 --AF-dflt 0.4| grep -v ^# .. ok test_roh: /build/reproducible-path/bcftools-1.21/bcftools roh /build/reproducible-path/bcftools-1.21/test/roh.1.vcf.gz -Or -G30 --AF-file /build/reproducible-path/bcftools-1.21/test/roh.1.tab.gz| grep -v ^# .. ok test_roh: /build/reproducible-path/bcftools-1.21/bcftools roh /build/reproducible-path/bcftools-1.21/test/roh.1.vcf.gz -Or -G30 --AF-file /build/reproducible-path/bcftools-1.21/test/roh.1.tab.gz --ignore-homref| grep -v ^# .. ok test_roh: /build/reproducible-path/bcftools-1.21/bcftools roh /build/reproducible-path/bcftools-1.21/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245| grep -v ^# .. ok test_roh: /build/reproducible-path/bcftools-1.21/bcftools roh /build/reproducible-path/bcftools-1.21/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-1.21/bcftools roh /build/reproducible-path/bcftools-1.21/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-1.21/bcftools roh /build/reproducible-path/bcftools-1.21/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-1.21/bcftools gtcheck -e 0 --no-HWE-prob /tmp/JyOqsQtwLk/gtcheck.1.vcf.gz -g /tmp/JyOqsQtwLk/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 /tmp/JyOqsQtwLk/gtcheck.1.vcf.gz -g /tmp/JyOqsQtwLk/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -u GT,GT /tmp/JyOqsQtwLk/gtcheck.1.vcf.gz -g /tmp/JyOqsQtwLk/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -u GT,PL /tmp/JyOqsQtwLk/gtcheck.1.vcf.gz -g /tmp/JyOqsQtwLk/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -u PL,GT /tmp/JyOqsQtwLk/gtcheck.1.vcf.gz -g /tmp/JyOqsQtwLk/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -u PL,PL /tmp/JyOqsQtwLk/gtcheck.1.vcf.gz -g /tmp/JyOqsQtwLk/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -p s1,s1 /tmp/JyOqsQtwLk/gtcheck.1.vcf.gz -g /tmp/JyOqsQtwLk/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 /tmp/JyOqsQtwLk/gtcheck.2.vcf.gz -g /tmp/JyOqsQtwLk/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 /tmp/JyOqsQtwLk/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/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/JyOqsQtwLk/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -P /build/reproducible-path/bcftools-1.21/test/gtcheck.3.pairs /tmp/JyOqsQtwLk/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -u PL /tmp/JyOqsQtwLk/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 --n-matches 4 /tmp/JyOqsQtwLk/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO | sort .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -s qry:E,D,C /tmp/JyOqsQtwLk/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -s qry:E,D,C -u PL /tmp/JyOqsQtwLk/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -s qry:B -s gt:D /tmp/JyOqsQtwLk/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -s qry:B -s gt:D -u PL /tmp/JyOqsQtwLk/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -s qry:B -s gt:D,C /tmp/JyOqsQtwLk/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -p B,C,B,D /tmp/JyOqsQtwLk/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -u GT,GT -H /tmp/JyOqsQtwLk/gtcheck.1.vcf.gz -g /tmp/JyOqsQtwLk/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -u GT,PL -H /tmp/JyOqsQtwLk/gtcheck.1.vcf.gz -g /tmp/JyOqsQtwLk/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -u PL,GT -H /tmp/JyOqsQtwLk/gtcheck.1.vcf.gz -g /tmp/JyOqsQtwLk/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -u PL,PL -H /tmp/JyOqsQtwLk/gtcheck.1.vcf.gz -g /tmp/JyOqsQtwLk/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -P /build/reproducible-path/bcftools-1.21/test/gtcheck.4.pairs --distinctive-sites 3 /tmp/JyOqsQtwLk/gtcheck.4.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 -P /build/reproducible-path/bcftools-1.21/test/gtcheck.4.pairs --distinctive-sites 3,1 /tmp/JyOqsQtwLk/gtcheck.4.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -u GT -e 30 /tmp/JyOqsQtwLk/gtcheck.1.vcf.gz -g /tmp/JyOqsQtwLk/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -u GT -e 30 -p s1,s1 /tmp/JyOqsQtwLk/gtcheck.1.vcf.gz -g /tmp/JyOqsQtwLk/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -u GT -e 300 /tmp/JyOqsQtwLk/gtcheck.1.vcf.gz -g /tmp/JyOqsQtwLk/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -u PL -e 30 /tmp/JyOqsQtwLk/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck /tmp/JyOqsQtwLk/gtcheck.ntop.vcf.gz -g /tmp/JyOqsQtwLk/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck --n-matches 2 /tmp/JyOqsQtwLk/gtcheck.ntop.vcf.gz -g /tmp/JyOqsQtwLk/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck /tmp/JyOqsQtwLk/gtcheck.5.vcf.gz -g /tmp/JyOqsQtwLk/gtcheck.5.gts.vcf.gz | grep -v ^# | grep -v Time .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -p A,B,B,C /tmp/JyOqsQtwLk/gtcheck.6.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -t 11:33 -p A,D,A,E,D,E -u GT -e 10 /tmp/JyOqsQtwLk/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok Number of tests: total .. 1805 passed .. 1805 failed .. 0 make[2]: Leaving directory '/build/reproducible-path/bcftools-1.21' make[1]: Leaving directory '/build/reproducible-path/bcftools-1.21' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/bcftools/ make -j3 install DESTDIR=/build/reproducible-path/bcftools-1.21/debian/bcftools AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/bcftools-1.21' mkdir -p -m 755 /build/reproducible-path/bcftools-1.21/debian/bcftools/usr/bin /build/reproducible-path/bcftools-1.21/debian/bcftools/usr/share/man/man1 /build/reproducible-path/bcftools-1.21/debian/bcftools/usr/lib/arm-linux-gnueabihf/bcftools install -p bcftools /build/reproducible-path/bcftools-1.21/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-1.21/debian/bcftools/usr/bin install -p -m 644 doc/bcftools.1 /build/reproducible-path/bcftools-1.21/debian/bcftools/usr/share/man/man1 install -p plugins/*.so /build/reproducible-path/bcftools-1.21/debian/bcftools/usr/lib/arm-linux-gnueabihf/bcftools make[1]: Leaving directory '/build/reproducible-path/bcftools-1.21' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/bcftools-1.21' 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-1.21' dh_installdocs dh_installchangelogs debian/rules override_dh_installman make[1]: Entering directory '/build/reproducible-path/bcftools-1.21' dh_installman --language=C make[1]: Leaving directory '/build/reproducible-path/bcftools-1.21' 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 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-armhf.so.3 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-armhf.so.3.usr-is-merged dh_installdeb dh_gencontrol dpkg-gencontrol: warning: package bcftools: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package bcftools: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'bcftools-dbgsym' in '../bcftools-dbgsym_1.21-1_armhf.deb'. dpkg-deb: building package 'bcftools' in '../bcftools_1.21-1_armhf.deb'. dpkg-genbuildinfo --build=binary -O../bcftools_1.21-1_armhf.buildinfo dpkg-genchanges --build=binary -O../bcftools_1.21-1_armhf.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/3404 and its subdirectories I: Current time: Thu Mar 6 03:27:06 -12 2025 I: pbuilder-time-stamp: 1741274826 Thu Mar 6 15:27:22 UTC 2025 I: 1st build successful. Starting 2nd build on remote node virt64z-armhf-rb.debian.net. Thu Mar 6 15:27:22 UTC 2025 I: Preparing to do remote build '2' on virt64z-armhf-rb.debian.net. Thu Mar 6 15:30:50 UTC 2025 I: Deleting $TMPDIR on virt64z-armhf-rb.debian.net. Thu Mar 6 15:30:53 UTC 2025 I: bcftools_1.21-1_armhf.changes: Format: 1.8 Date: Thu, 13 Feb 2025 21:42:57 +0100 Source: bcftools Binary: bcftools bcftools-dbgsym Architecture: armhf Version: 1.21-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: bcftools - genomic variant calling and manipulation of VCF/BCF files Changes: bcftools (1.21-1) unstable; urgency=medium . * New upstream version 1.21 * d/copyright: update copyright year. * skip_new_test_failing_on_32bit.patch: unfuzz. * tests-pluginpath.patch: delete: hunk inhibited upstream. * d/patches/*: normalise Last-Update timestamp. * d/rules: activate hardening. Checksums-Sha1: 53a4b49e04876705629738e6f10350da20ac5c99 2139512 bcftools-dbgsym_1.21-1_armhf.deb d43aac1ce8c9bca34ee58f8357b5b44721861879 6875 bcftools_1.21-1_armhf.buildinfo c4cf55271786c57b395b6cdc78b5ecda1e93e4d3 689236 bcftools_1.21-1_armhf.deb Checksums-Sha256: 35f94f1613de408c08b1f04f2384abaa084039930a67dfa06951a3f72fcc83ad 2139512 bcftools-dbgsym_1.21-1_armhf.deb 119b203a5cd12a2adb6520e4f9918bb2b37d40c97727a50e9440af09e32311f9 6875 bcftools_1.21-1_armhf.buildinfo 2fe709d2fed4845ce7133d46e24d3d734bcf03455401ec48edd157cfbb386a05 689236 bcftools_1.21-1_armhf.deb Files: 87404ade0716ec9647eb3a05d183c683 2139512 debug optional bcftools-dbgsym_1.21-1_armhf.deb a5ac0481f0ad5e1493368fd066ae10c3 6875 science optional bcftools_1.21-1_armhf.buildinfo 482e6bd949e5de4b306e8150983b8acc 689236 science optional bcftools_1.21-1_armhf.deb Thu Mar 6 15:30:54 UTC 2025 I: diffoscope 289 will be used to compare the two builds: Running as unit: rb-diffoscope-armhf_3-14112.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.YRCZQbnt/bcftools_1.21-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.YRCZQbnt/bcftools_1.21-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.YRCZQbnt/bcftools_1.21-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.YRCZQbnt/b1/bcftools_1.21-1_armhf.changes /srv/reproducible-results/rbuild-debian/r-b-build.YRCZQbnt/b2/bcftools_1.21-1_armhf.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.004s) 0.004s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 269ms CPU time consumed: 271ms Thu Mar 6 15:30:54 UTC 2025 I: diffoscope 289 found no differences in the changes files, and a .buildinfo file also exists. Thu Mar 6 15:30:54 UTC 2025 I: bcftools from trixie built successfully and reproducibly on armhf. Thu Mar 6 15:30:56 UTC 2025 I: Submitting .buildinfo files to external archives: Thu Mar 6 15:30:56 UTC 2025 I: Submitting 8.0K b1/bcftools_1.21-1_armhf.buildinfo.asc Thu Mar 6 15:30:57 UTC 2025 I: Submitting 8.0K b2/bcftools_1.21-1_armhf.buildinfo.asc Thu Mar 6 15:30:57 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu Mar 6 15:30:57 UTC 2025 I: Done submitting .buildinfo files. Thu Mar 6 15:30:57 UTC 2025 I: Removing signed bcftools_1.21-1_armhf.buildinfo.asc files: removed './b1/bcftools_1.21-1_armhf.buildinfo.asc' removed './b2/bcftools_1.21-1_armhf.buildinfo.asc'