I: pbuilder: network access will be disabled during build I: Current time: Sat Feb 15 19:44:12 -12 2025 I: pbuilder-time-stamp: 1739691852 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: using eatmydata during job 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/50672/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=11 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='ba247ba73dfa49fd8fe855dc9fc8e391' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='50672' 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.VcjNPGdC/pbuilderrc_gP38 --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.VcjNPGdC/b1 --logfile b1/build.log bcftools_1.21-1.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos2-i386 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/50672/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: i386 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), zlib1g-dev, libbz2-dev, liblzma-dev, libhts-dev (>= 1.14), libgsl-dev, tabix, libio-pty-perl dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19794 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 43.7 MB of archives. After unpacking 152 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main i386 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian unstable/main i386 libmagic-mgc i386 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian unstable/main i386 libmagic1t64 i386 1:5.45-3+b1 [115 kB] Get: 4 http://deb.debian.org/debian unstable/main i386 file i386 1:5.45-3+b1 [43.2 kB] Get: 5 http://deb.debian.org/debian unstable/main i386 gettext-base i386 0.23.1-1 [245 kB] Get: 6 http://deb.debian.org/debian unstable/main i386 libuchardet0 i386 0.0.8-1+b2 [69.2 kB] Get: 7 http://deb.debian.org/debian unstable/main i386 groff-base i386 1.23.0-7 [1199 kB] Get: 8 http://deb.debian.org/debian unstable/main i386 bsdextrautils i386 2.40.4-3 [96.2 kB] Get: 9 http://deb.debian.org/debian unstable/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB] Get: 10 http://deb.debian.org/debian unstable/main i386 man-db i386 2.13.0-1 [1428 kB] Get: 11 http://deb.debian.org/debian unstable/main i386 m4 i386 1.4.19-5 [301 kB] Get: 12 http://deb.debian.org/debian unstable/main i386 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian unstable/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian unstable/main i386 automake all 1:1.17-3 [862 kB] Get: 15 http://deb.debian.org/debian unstable/main i386 autopoint all 0.23.1-1 [770 kB] Get: 16 http://deb.debian.org/debian unstable/main i386 libcom-err2 i386 1.47.2-1 [24.3 kB] Get: 17 http://deb.debian.org/debian unstable/main i386 comerr-dev i386 2.1-1.47.2-1 [56.2 kB] Get: 18 http://deb.debian.org/debian unstable/main i386 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 19 http://deb.debian.org/debian unstable/main i386 libtool all 2.5.4-3 [539 kB] Get: 20 http://deb.debian.org/debian unstable/main i386 dh-autoreconf all 20 [17.1 kB] Get: 21 http://deb.debian.org/debian unstable/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 22 http://deb.debian.org/debian unstable/main i386 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 23 http://deb.debian.org/debian unstable/main i386 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 24 http://deb.debian.org/debian unstable/main i386 libelf1t64 i386 0.192-4 [195 kB] Get: 25 http://deb.debian.org/debian unstable/main i386 dwz i386 0.15-1+b1 [116 kB] Get: 26 http://deb.debian.org/debian unstable/main i386 libunistring5 i386 1.3-1 [458 kB] Get: 27 http://deb.debian.org/debian unstable/main i386 libicu72 i386 72.1-6 [9582 kB] Get: 28 http://deb.debian.org/debian unstable/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.2+b1 [734 kB] Get: 29 http://deb.debian.org/debian unstable/main i386 gettext i386 0.23.1-1 [1714 kB] Get: 30 http://deb.debian.org/debian unstable/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 31 http://deb.debian.org/debian unstable/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 32 http://deb.debian.org/debian unstable/main i386 debhelper all 13.24.1 [920 kB] Get: 33 http://deb.debian.org/debian unstable/main i386 libkrb5support0 i386 1.21.3-4 [35.0 kB] Get: 34 http://deb.debian.org/debian unstable/main i386 libk5crypto3 i386 1.21.3-4 [83.7 kB] Get: 35 http://deb.debian.org/debian unstable/main i386 libkeyutils1 i386 1.6.3-4 [9600 B] Get: 36 http://deb.debian.org/debian unstable/main i386 libkrb5-3 i386 1.21.3-4 [354 kB] Get: 37 http://deb.debian.org/debian unstable/main i386 libgssapi-krb5-2 i386 1.21.3-4 [149 kB] Get: 38 http://deb.debian.org/debian unstable/main i386 libgssrpc4t64 i386 1.21.3-4 [63.4 kB] Get: 39 http://deb.debian.org/debian unstable/main i386 libkadm5clnt-mit12 i386 1.21.3-4 [44.1 kB] Get: 40 http://deb.debian.org/debian unstable/main i386 libkdb5-10t64 i386 1.21.3-4 [45.3 kB] Get: 41 http://deb.debian.org/debian unstable/main i386 libkadm5srv-mit12 i386 1.21.3-4 [57.7 kB] Get: 42 http://deb.debian.org/debian unstable/main i386 krb5-multidev i386 1.21.3-4 [126 kB] Get: 43 http://deb.debian.org/debian unstable/main i386 libbrotli1 i386 1.1.0-2+b6 [308 kB] Get: 44 http://deb.debian.org/debian unstable/main i386 libbrotli-dev i386 1.1.0-2+b6 [313 kB] Get: 45 http://deb.debian.org/debian unstable/main i386 libbz2-dev i386 1.0.8-6 [32.1 kB] Get: 46 http://deb.debian.org/debian unstable/main i386 libidn2-0 i386 2.3.7-2+b1 [130 kB] Get: 47 http://deb.debian.org/debian unstable/main i386 libffi8 i386 3.4.7-1 [21.4 kB] Get: 48 http://deb.debian.org/debian unstable/main i386 libp11-kit0 i386 0.25.5-3 [423 kB] Get: 49 http://deb.debian.org/debian unstable/main i386 libtasn1-6 i386 4.20.0-2 [51.6 kB] Get: 50 http://deb.debian.org/debian unstable/main i386 libgnutls30t64 i386 3.8.9-2 [1462 kB] Get: 51 http://deb.debian.org/debian unstable/main i386 libsasl2-modules-db i386 2.1.28+dfsg1-8+b1 [20.9 kB] Get: 52 http://deb.debian.org/debian unstable/main i386 libsasl2-2 i386 2.1.28+dfsg1-8+b1 [61.3 kB] Get: 53 http://deb.debian.org/debian unstable/main i386 libldap2 i386 2.6.9+dfsg-1 [205 kB] Get: 54 http://deb.debian.org/debian unstable/main i386 libnghttp2-14 i386 1.64.0-1 [82.4 kB] Get: 55 http://deb.debian.org/debian unstable/main i386 libnghttp3-9 i386 1.6.0-2 [75.9 kB] Get: 56 http://deb.debian.org/debian unstable/main i386 libngtcp2-16 i386 1.9.1-1 [151 kB] Get: 57 http://deb.debian.org/debian unstable/main i386 libngtcp2-crypto-gnutls8 i386 1.9.1-1 [19.1 kB] Get: 58 http://deb.debian.org/debian unstable/main i386 libpsl5t64 i386 0.21.2-1.1+b1 [57.7 kB] Get: 59 http://deb.debian.org/debian unstable/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b5 [62.4 kB] Get: 60 http://deb.debian.org/debian unstable/main i386 libssh2-1t64 i386 1.11.1-1 [256 kB] Get: 61 http://deb.debian.org/debian unstable/main i386 libcurl3t64-gnutls i386 8.12.1-2 [411 kB] Get: 62 http://deb.debian.org/debian unstable/main i386 libevent-2.1-7t64 i386 2.1.12-stable-10+b1 [195 kB] Get: 63 http://deb.debian.org/debian unstable/main i386 libunbound8 i386 1.22.0-1+b1 [633 kB] Get: 64 http://deb.debian.org/debian unstable/main i386 libgnutls-dane0t64 i386 3.8.9-2 [453 kB] Get: 65 http://deb.debian.org/debian unstable/main i386 libgnutls-openssl27t64 i386 3.8.9-2 [453 kB] Get: 66 http://deb.debian.org/debian unstable/main i386 libidn2-dev i386 2.3.7-2+b1 [126 kB] Get: 67 http://deb.debian.org/debian unstable/main i386 libp11-kit-dev i386 0.25.5-3 [208 kB] Get: 68 http://deb.debian.org/debian unstable/main i386 libtasn1-6-dev i386 4.20.0-2 [103 kB] Get: 69 http://deb.debian.org/debian unstable/main i386 libgmpxx4ldbl i386 2:6.3.0+dfsg-3 [329 kB] Get: 70 http://deb.debian.org/debian unstable/main i386 libgmp-dev i386 2:6.3.0+dfsg-3 [661 kB] Get: 71 http://deb.debian.org/debian unstable/main i386 nettle-dev i386 3.10-1+b1 [1334 kB] Get: 72 http://deb.debian.org/debian unstable/main i386 libgnutls28-dev i386 3.8.9-2 [1464 kB] Get: 73 http://deb.debian.org/debian unstable/main i386 libkrb5-dev i386 1.21.3-4 [15.9 kB] Get: 74 http://deb.debian.org/debian unstable/main i386 libldap-dev i386 2.6.9+dfsg-1 [328 kB] Get: 75 http://deb.debian.org/debian unstable/main i386 libpkgconf3 i386 1.8.1-4 [38.4 kB] Get: 76 http://deb.debian.org/debian unstable/main i386 pkgconf-bin i386 1.8.1-4 [30.6 kB] Get: 77 http://deb.debian.org/debian unstable/main i386 pkgconf i386 1.8.1-4 [26.2 kB] Get: 78 http://deb.debian.org/debian unstable/main i386 libnghttp2-dev i386 1.64.0-1 [123 kB] Get: 79 http://deb.debian.org/debian unstable/main i386 libnghttp3-dev i386 1.6.0-2 [101 kB] Get: 80 http://deb.debian.org/debian unstable/main i386 libngtcp2-crypto-gnutls-dev i386 1.9.1-1 [24.0 kB] Get: 81 http://deb.debian.org/debian unstable/main i386 libngtcp2-dev i386 1.9.1-1 [202 kB] Get: 82 http://deb.debian.org/debian unstable/main i386 libpsl-dev i386 0.21.2-1.1+b1 [78.4 kB] Get: 83 http://deb.debian.org/debian unstable/main i386 zlib1g-dev i386 1:1.3.dfsg+really1.3.1-1+b1 [916 kB] Get: 84 http://deb.debian.org/debian unstable/main i386 librtmp-dev i386 2.4+20151223.gitfa8646d.1-2+b5 [72.3 kB] Get: 85 http://deb.debian.org/debian unstable/main i386 libssl-dev i386 3.4.1-1 [2837 kB] Get: 86 http://deb.debian.org/debian unstable/main i386 libssh2-1-dev i386 1.11.1-1 [407 kB] Get: 87 http://deb.debian.org/debian unstable/main i386 libzstd-dev i386 1.5.6+dfsg-2 [354 kB] Get: 88 http://deb.debian.org/debian unstable/main i386 libcurl4-gnutls-dev i386 8.12.1-2 [542 kB] Get: 89 http://deb.debian.org/debian unstable/main i386 libdeflate0 i386 1.23-1+b1 [48.4 kB] Get: 90 http://deb.debian.org/debian unstable/main i386 libdeflate-dev i386 1.23-1+b1 [57.5 kB] Get: 91 http://deb.debian.org/debian unstable/main i386 libgslcblas0 i386 2.8+dfsg-5 [106 kB] Get: 92 http://deb.debian.org/debian unstable/main i386 libgsl28 i386 2.8+dfsg-5 [978 kB] Get: 93 http://deb.debian.org/debian unstable/main i386 libgsl-dev i386 2.8+dfsg-5 [1240 kB] Get: 94 http://deb.debian.org/debian unstable/main i386 libhtscodecs2 i386 1.6.1-1 [70.8 kB] Get: 95 http://deb.debian.org/debian unstable/main i386 libhts3t64 i386 1.21+ds-1 [506 kB] Get: 96 http://deb.debian.org/debian unstable/main i386 liblzma-dev i386 5.6.3-1+b1 [328 kB] Get: 97 http://deb.debian.org/debian unstable/main i386 libhts-dev i386 1.21+ds-1 [1725 kB] Get: 98 http://deb.debian.org/debian unstable/main i386 libio-pty-perl i386 1:1.20-1+b3 [35.8 kB] Get: 99 http://deb.debian.org/debian unstable/main i386 tabix i386 1.21+ds-1 [541 kB] Fetched 43.7 MB in 3s (16.7 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 ... 19794 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_i386.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:i386. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_i386.deb ... Unpacking libmagic1t64:i386 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3+b1_i386.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-1_i386.deb ... Unpacking gettext-base (0.23.1-1) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_i386.deb ... Unpacking libuchardet0:i386 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-7_i386.deb ... Unpacking groff-base (1.23.0-7) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.4-3_i386.deb ... Unpacking bsdextrautils (2.40.4-3) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../08-libpipeline1_1.5.8-1_i386.deb ... Unpacking libpipeline1:i386 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.0-1_i386.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-5_i386.deb ... Unpacking m4 (1.4.19-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.17-3_all.deb ... Unpacking automake (1:1.17-3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.23.1-1_all.deb ... Unpacking autopoint (0.23.1-1) ... Selecting previously unselected package libcom-err2:i386. Preparing to unpack .../15-libcom-err2_1.47.2-1_i386.deb ... Unpacking libcom-err2:i386 (1.47.2-1) ... Selecting previously unselected package comerr-dev:i386. Preparing to unpack .../16-comerr-dev_2.1-1.47.2-1_i386.deb ... Unpacking comerr-dev:i386 (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) ... Selecting previously unselected package libfile-stripnondeterminism-perl. 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Setting up libmagic1t64:i386 (1:5.45-3+b1) ... Setting up libnghttp2-14:i386 (1.64.0-1) ... Setting up libdeflate0:i386 (1.23-1+b1) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-5) ... Setting up libevent-2.1-7t64:i386 (2.1.12-stable-10+b1) ... Setting up libcom-err2:i386 (1.47.2-1) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:i386 (0.192-4) ... Setting up libkrb5support0:i386 (1.21.3-4) ... Setting up libsasl2-modules-db:i386 (2.1.28+dfsg1-8+b1) ... Setting up autotools-dev (20220109.1) ... Setting up libunbound8:i386 (1.22.0-1+b1) ... Setting up libpkgconf3:i386 (1.8.1-4) ... Setting up libgmpxx4ldbl:i386 (2:6.3.0+dfsg-3) ... Setting up comerr-dev:i386 (2.1-1.47.2-1) ... Setting up libunistring5:i386 (1.3-1) ... Setting up libssl-dev:i386 (3.4.1-1) ... Setting up autopoint (0.23.1-1) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libk5crypto3:i386 (1.21.3-4) ... Setting up libsasl2-2:i386 (2.1.28+dfsg1-8+b1) ... Setting up autoconf (2.72-3) ... Setting up libnghttp3-9:i386 (1.6.0-2) ... Setting up libnghttp3-dev:i386 (1.6.0-2) ... Setting up liblzma-dev:i386 (5.6.3-1+b1) ... Setting up zlib1g-dev:i386 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libffi8:i386 (3.4.7-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:i386 (0.0.8-1+b2) ... Setting up libtasn1-6:i386 (4.20.0-2) ... Setting up libngtcp2-16:i386 (1.9.1-1) ... Setting up libkrb5-3:i386 (1.21.3-4) ... Setting up libssh2-1t64:i386 (1.11.1-1) ... Setting up libgsl28:i386 (2.8+dfsg-5) ... Setting up libtasn1-6-dev:i386 (4.20.0-2) ... Setting up libdeflate-dev:i386 (1.23-1+b1) ... Setting up tabix (1.21+ds-1) ... Setting up libxml2:i386 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up libldap2:i386 (2.6.9+dfsg-1) ... Setting up libbrotli-dev:i386 (1.1.0-2+b6) ... Setting up libbz2-dev:i386 (1.0.8-6) ... Setting up automake (1:1.17-3) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up gettext (0.23.1-1) ... Setting up libgsl-dev (2.8+dfsg-5) ... Setting up libgmp-dev:i386 (2:6.3.0+dfsg-3) ... Setting up nettle-dev:i386 (3.10-1+b1) ... Setting up libtool (2.5.4-3) ... Setting up libidn2-0:i386 (2.3.7-2+b1) ... Setting up libngtcp2-dev:i386 (1.9.1-1) ... Setting up pkgconf:i386 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libldap-dev:i386 (2.6.9+dfsg-1) ... Setting up libp11-kit0:i386 (0.25.5-3) ... Setting up libgssapi-krb5-2:i386 (1.21.3-4) ... Setting up libssh2-1-dev:i386 (1.11.1-1) ... Setting up libidn2-dev:i386 (2.3.7-2+b1) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-7) ... Setting up libp11-kit-dev:i386 (0.25.5-3) ... Setting up libgnutls30t64:i386 (3.8.9-2) ... Setting up libgnutls-openssl27t64:i386 (3.8.9-2) ... Setting up libnghttp2-dev:i386 (1.64.0-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpsl5t64:i386 (0.21.2-1.1+b1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libpsl-dev:i386 (0.21.2-1.1+b1) ... Setting up libgnutls-dane0t64:i386 (3.8.9-2) ... Setting up librtmp1:i386 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libgssrpc4t64:i386 (1.21.3-4) ... Setting up libngtcp2-crypto-gnutls8:i386 (1.9.1-1) ... Setting up libkadm5clnt-mit12:i386 (1.21.3-4) ... Setting up libgnutls28-dev:i386 (3.8.9-2) ... Setting up libkdb5-10t64:i386 (1.21.3-4) ... Setting up libcurl3t64-gnutls:i386 (8.12.1-2) ... Setting up debhelper (13.24.1) ... Setting up libngtcp2-crypto-gnutls-dev:i386 (1.9.1-1) ... Setting up librtmp-dev:i386 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libkadm5srv-mit12:i386 (1.21.3-4) ... Setting up libhts3t64:i386 (1.21+ds-1) ... Setting up krb5-multidev:i386 (1.21.3-4) ... Setting up libkrb5-dev:i386 (1.21.3-4) ... Setting up libcurl4-gnutls-dev:i386 (8.12.1-2) ... Setting up libhts-dev:i386 (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 i386 debian/rules clean rm -f config.mk && touch config.mk dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/bcftools-1.21' dh_auto_clean make -j11 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/i386-linux-gnu/bcftools ./configure --build=i686-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/i386-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system --enable-gsl --with-cblas=gslcblas --with-bcf-plugin-dir=/usr/lib/i386-linux-gnu/bcftools checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking for gcc option to enable large file support... -D_FILE_OFFSET_BITS=64 checking for htslib/sam.h... yes checking for hts_version in -lhts... yes checking shared library type... plain .so checking for library containing dlopen... none required checking if the compiler accepts -rdynamic... yes checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing regcomp... none required configure: creating ./config.status config.status: creating config.mk config.status: creating config.h make[1]: Leaving directory '/build/reproducible-path/bcftools-1.21' dh_auto_build make -j11 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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfindex.o vcfindex.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tabix.o tabix.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfstats.o vcfstats.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time 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-Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfview.o vcfview.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfannotate.o vcfannotate.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfroh.o vcfroh.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfconcat.o vcfconcat.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcall.o vcfcall.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mcall.o mcall.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcmp.o vcmp.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gvcf.o gvcf.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o reheader.o reheader.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o convert.o convert.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfconvert.o vcfconvert.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tsv2vcf.o tsv2vcf.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcnv.o vcfcnv.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfhead.o vcfhead.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o HMM.o HMM.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o consensus.o consensus.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ploidy.o ploidy.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bin.o bin.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hclust.o hclust.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o version.o version.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o regidx.o regidx.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o smpl_ilist.o smpl_ilist.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o csq.o csq.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfbuf.o vcfbuf.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mpileup.o mpileup.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_iaux.o bam2bcf_iaux.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_edlib.o bam2bcf_edlib.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o read_consensus.o read_consensus.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sample.o bam_sample.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfsort.o vcfsort.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cols.o cols.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o extsort.o extsort.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dist.o dist.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o abuf.o abuf.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ccall.o ccall.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o em.o em.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o prob1.o prob1.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kmin.o kmin.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o str_finder.o str_finder.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gff.o gff.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o edlib.o edlib.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DPLUGINPATH='"/usr/lib/i386-linux-gnu/bcftools"' -c -o vcfplugin.o vcfplugin.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-rbuf.o test/test-rbuf.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-regidx.o test/test-regidx.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/bcftools-1.21=. -fstack-protector-strong -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -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 -Wformat -Werror=format-security -mfpmath=sse -msse2 -I. -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/w1hDG0Hw69/merge.a.vcf.gz 2:3199812-3199812 .. ok test_tabix: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/w1hDG0Hw69/merge.a.bcf 2:3199812-3199812 .. ok test_tabix: tabix /tmp/w1hDG0Hw69/merge.a.vcf.gz 1:3000151-3000151 .. ok test_tabix: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/w1hDG0Hw69/merge.a.bcf 1:3000151-3000151 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/w1hDG0Hw69/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/w1hDG0Hw69/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/w1hDG0Hw69/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/w1hDG0Hw69/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/w1hDG0Hw69/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/w1hDG0Hw69/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/w1hDG0Hw69/large_chrom_csi_limit.bcf chr20 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/w1hDG0Hw69/large_chrom_csi_limit.bcf chr20 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/w1hDG0Hw69/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /build/reproducible-path/bcftools-1.21/bcftools view -H /tmp/w1hDG0Hw69/large_chrom_csi_limit.bcf chr20 .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -s /tmp/w1hDG0Hw69/idx.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -s /tmp/w1hDG0Hw69/idx.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -s /tmp/w1hDG0Hw69/idx.bcf .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/w1hDG0Hw69/idx.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/w1hDG0Hw69/idx.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/w1hDG0Hw69/idx.vcf.gz.csi .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/w1hDG0Hw69/idx.bcf .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/w1hDG0Hw69/idx.bcf.csi .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -s /tmp/w1hDG0Hw69/empty.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -s /tmp/w1hDG0Hw69/empty.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -s /tmp/w1hDG0Hw69/empty.bcf .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/w1hDG0Hw69/empty.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/w1hDG0Hw69/empty.vcf.gz .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/w1hDG0Hw69/empty.vcf.gz.csi .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/w1hDG0Hw69/empty.bcf .. ok test_vcf_idxstats: /build/reproducible-path/bcftools-1.21/bcftools index -n /tmp/w1hDG0Hw69/empty.bcf.csi .. ok test_vcf_check: /build/reproducible-path/bcftools-1.21/bcftools stats -s - /tmp/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/check.1.chk /tmp/w1hDG0Hw69/check.2.chk /tmp/w1hDG0Hw69/check.3.chk /tmp/w1hDG0Hw69/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/w1hDG0Hw69/stats.a.vcf.gz /tmp/w1hDG0Hw69/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/reproducible-path/bcftools-1.21/bcftools stats -s B /tmp/w1hDG0Hw69/stats.a.vcf.gz /tmp/w1hDG0Hw69/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/reproducible-path/bcftools-1.21/bcftools stats -s - /tmp/w1hDG0Hw69/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/w1hDG0Hw69/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/reproducible-path/bcftools-1.21/bcftools stats -s - /tmp/w1hDG0Hw69/stats.vaf.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -n =2 /tmp/w1hDG0Hw69/isec.a.vcf.gz /tmp/w1hDG0Hw69/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -n =2 /tmp/w1hDG0Hw69/isec.a.vcf.gz /tmp/w1hDG0Hw69/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/w1hDG0Hw69/isec.a.vcf.gz /tmp/w1hDG0Hw69/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -n =2 -i"STRLEN(REF)==2" /tmp/w1hDG0Hw69/isec.a.vcf.gz /tmp/w1hDG0Hw69/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -n =2 -c both /tmp/w1hDG0Hw69/isec.a.vcf.gz /tmp/w1hDG0Hw69/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -n =2 -c both /tmp/w1hDG0Hw69/isec.a.vcf.gz /tmp/w1hDG0Hw69/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -n =2 -c any /tmp/w1hDG0Hw69/isec.a.vcf.gz /tmp/w1hDG0Hw69/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -n =2 -c any /tmp/w1hDG0Hw69/isec.a.vcf.gz /tmp/w1hDG0Hw69/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -C -c any /tmp/w1hDG0Hw69/isec.a.vcf.gz /tmp/w1hDG0Hw69/isec.b.vcf.gz .. ok test_vcf_isec: /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -C -c any /tmp/w1hDG0Hw69/isec.a.vcf.gz /tmp/w1hDG0Hw69/isec.b.vcf.gz .. ok test_vcf_isec2: /build/reproducible-path/bcftools-1.21/bcftools isec --no-version -T /tmp/w1hDG0Hw69/isec.tab.gz /tmp/w1hDG0Hw69/isec.a.vcf.gz .. ok test_vcf_isec2: /build/reproducible-path/bcftools-1.21/bcftools isec -Ob -T /tmp/w1hDG0Hw69/isec.tab.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/isec-miss.1.1.vcf.gz /tmp/w1hDG0Hw69/isec-miss.1.2.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/isec-miss.1.1.vcf.gz /tmp/w1hDG0Hw69/isec-miss.1.2.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/isec-miss.1.1.vcf.gz /tmp/w1hDG0Hw69/isec-miss.1.2.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/isec-miss.1.1.vcf.gz /tmp/w1hDG0Hw69/isec-miss.1.2.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/isec-miss.2.1.vcf.gz /tmp/w1hDG0Hw69/isec-miss.2.2.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/isec-miss.2.1.vcf.gz /tmp/w1hDG0Hw69/isec-miss.2.2.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/isec-miss.2.1.vcf.gz /tmp/w1hDG0Hw69/isec-miss.2.2.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/isec-miss.2.1.vcf.gz /tmp/w1hDG0Hw69/isec-miss.2.2.vcf.gz /tmp/w1hDG0Hw69/isec-miss.2.3.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version /tmp/w1hDG0Hw69/merge.11.a.vcf.gz /tmp/w1hDG0Hw69/merge.11.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/w1hDG0Hw69/merge.11.a.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.11.a.bcf /tmp/w1hDG0Hw69/merge.11.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/w1hDG0Hw69/merge.11.a.bcf /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.join.a.vcf.gz /tmp/w1hDG0Hw69/merge.join.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -i AF:join /tmp/w1hDG0Hw69/merge.join.a.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.join.a.bcf /tmp/w1hDG0Hw69/merge.join.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -i AF:join /tmp/w1hDG0Hw69/merge.join.a.bcf /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.LPL.a.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-single /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.LPL.a.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-single /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.LPL.a.vcf.gz /tmp/w1hDG0Hw69/merge.LPL.b.vcf.gz /tmp/w1hDG0Hw69/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/w1hDG0Hw69/merge.LPL.a.vcf.gz /tmp/w1hDG0Hw69/merge.LPL.b.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.LPL.a.bcf /tmp/w1hDG0Hw69/merge.LPL.b.bcf /tmp/w1hDG0Hw69/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/w1hDG0Hw69/merge.LPL.a.bcf /tmp/w1hDG0Hw69/merge.LPL.b.bcf /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.LPL.a.vcf.gz /tmp/w1hDG0Hw69/merge.LPL.b.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.LPL.a.vcf.gz /tmp/w1hDG0Hw69/merge.LPL.b.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.LPL.a.bcf /tmp/w1hDG0Hw69/merge.LPL.b.bcf /tmp/w1hDG0Hw69/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 1 /tmp/w1hDG0Hw69/merge.LPL.a.bcf /tmp/w1hDG0Hw69/merge.LPL.b.bcf /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.LPL.a.vcf.gz /tmp/w1hDG0Hw69/merge.LPL.b.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.LPL.a.vcf.gz /tmp/w1hDG0Hw69/merge.LPL.b.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.LPL.a.bcf /tmp/w1hDG0Hw69/merge.LPL.b.bcf /tmp/w1hDG0Hw69/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 2 /tmp/w1hDG0Hw69/merge.LPL.a.bcf /tmp/w1hDG0Hw69/merge.LPL.b.bcf /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.LPL.a.vcf.gz /tmp/w1hDG0Hw69/merge.LPL.b.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.LPL.a.vcf.gz /tmp/w1hDG0Hw69/merge.LPL.b.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.LPL.a.bcf /tmp/w1hDG0Hw69/merge.LPL.b.bcf /tmp/w1hDG0Hw69/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 3 /tmp/w1hDG0Hw69/merge.LPL.a.bcf /tmp/w1hDG0Hw69/merge.LPL.b.bcf /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.LPL.a.vcf.gz /tmp/w1hDG0Hw69/merge.LPL.b.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.LPL.a.vcf.gz /tmp/w1hDG0Hw69/merge.LPL.b.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.LPL.a.bcf /tmp/w1hDG0Hw69/merge.LPL.b.bcf /tmp/w1hDG0Hw69/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 4 /tmp/w1hDG0Hw69/merge.LPL.a.bcf /tmp/w1hDG0Hw69/merge.LPL.b.bcf /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.LPL.a.vcf.gz /tmp/w1hDG0Hw69/merge.LPL.b.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.LPL.a.vcf.gz /tmp/w1hDG0Hw69/merge.LPL.b.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.LPL.a.bcf /tmp/w1hDG0Hw69/merge.LPL.b.bcf /tmp/w1hDG0Hw69/merge.LPL.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 5 /tmp/w1hDG0Hw69/merge.LPL.a.bcf /tmp/w1hDG0Hw69/merge.LPL.b.bcf /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.a.vcf.gz /tmp/w1hDG0Hw69/merge.b.vcf.gz /tmp/w1hDG0Hw69/merge.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/w1hDG0Hw69/merge.a.vcf.gz /tmp/w1hDG0Hw69/merge.b.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.a.bcf /tmp/w1hDG0Hw69/merge.b.bcf /tmp/w1hDG0Hw69/merge.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/w1hDG0Hw69/merge.a.bcf /tmp/w1hDG0Hw69/merge.b.bcf /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.a.vcf.gz /tmp/w1hDG0Hw69/merge.b.vcf.gz /tmp/w1hDG0Hw69/merge.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -Fx /tmp/w1hDG0Hw69/merge.a.vcf.gz /tmp/w1hDG0Hw69/merge.b.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.a.bcf /tmp/w1hDG0Hw69/merge.b.bcf /tmp/w1hDG0Hw69/merge.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -Fx /tmp/w1hDG0Hw69/merge.a.bcf /tmp/w1hDG0Hw69/merge.b.bcf /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.a.vcf.gz /tmp/w1hDG0Hw69/merge.b.vcf.gz /tmp/w1hDG0Hw69/merge.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -0 /tmp/w1hDG0Hw69/merge.a.vcf.gz /tmp/w1hDG0Hw69/merge.b.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.a.bcf /tmp/w1hDG0Hw69/merge.b.bcf /tmp/w1hDG0Hw69/merge.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -0 /tmp/w1hDG0Hw69/merge.a.bcf /tmp/w1hDG0Hw69/merge.b.bcf /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.2.a.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.2.a.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.2.a.bcf /tmp/w1hDG0Hw69/merge.2.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m none /tmp/w1hDG0Hw69/merge.2.a.bcf /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.2.a.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.2.a.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.2.a.bcf /tmp/w1hDG0Hw69/merge.2.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m both /tmp/w1hDG0Hw69/merge.2.a.bcf /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.2.a.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.2.a.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.2.a.bcf /tmp/w1hDG0Hw69/merge.2.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m all /tmp/w1hDG0Hw69/merge.2.a.bcf /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.3.a.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.3.a.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.3.a.bcf /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.3.a.bcf /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.4.a.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.4.a.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.4.a.bcf /tmp/w1hDG0Hw69/merge.4.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m id /tmp/w1hDG0Hw69/merge.4.a.bcf /tmp/w1hDG0Hw69/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/w1hDG0Hw69/gvcf.merge.1.vcf.gz /tmp/w1hDG0Hw69/gvcf.merge.2.vcf.gz /tmp/w1hDG0Hw69/gvcf.merge.3.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/w1hDG0Hw69/gvcf.merge.1.vcf.gz /tmp/w1hDG0Hw69/gvcf.merge.2.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/gvcf.merge.1.bcf /tmp/w1hDG0Hw69/gvcf.merge.2.bcf /tmp/w1hDG0Hw69/gvcf.merge.3.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/w1hDG0Hw69/gvcf.merge.1.bcf /tmp/w1hDG0Hw69/gvcf.merge.2.bcf /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.gvcf.2.a.vcf.gz /tmp/w1hDG0Hw69/merge.gvcf.2.b.vcf.gz /tmp/w1hDG0Hw69/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/w1hDG0Hw69/merge.gvcf.2.a.vcf.gz /tmp/w1hDG0Hw69/merge.gvcf.2.b.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.gvcf.2.a.vcf.gz /tmp/w1hDG0Hw69/merge.gvcf.2.b.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.gvcf.2.a.vcf.gz /tmp/w1hDG0Hw69/merge.gvcf.2.b.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.gvcf.2.a.vcf.gz /tmp/w1hDG0Hw69/merge.gvcf.2.b.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.gvcf.2.a.vcf.gz /tmp/w1hDG0Hw69/merge.gvcf.2.b.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.gvcf.3.a.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.gvcf.3.a.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.gvcf.4.a.vcf.gz /tmp/w1hDG0Hw69/merge.gvcf.4.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/w1hDG0Hw69/merge.gvcf.4.a.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.gvcf.4.a.bcf /tmp/w1hDG0Hw69/merge.gvcf.4.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/w1hDG0Hw69/merge.gvcf.4.a.bcf /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.5.a.vcf.gz /tmp/w1hDG0Hw69/merge.5.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/w1hDG0Hw69/merge.5.a.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.5.a.bcf /tmp/w1hDG0Hw69/merge.5.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/w1hDG0Hw69/merge.5.a.bcf /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.6.a.vcf.gz /tmp/w1hDG0Hw69/merge.6.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/w1hDG0Hw69/merge.6.a.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.6.a.bcf /tmp/w1hDG0Hw69/merge.6.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/w1hDG0Hw69/merge.6.a.bcf /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.gvcf.7.a.vcf.gz /tmp/w1hDG0Hw69/merge.gvcf.7.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/w1hDG0Hw69/merge.gvcf.7.a.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.gvcf.7.a.bcf /tmp/w1hDG0Hw69/merge.gvcf.7.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/w1hDG0Hw69/merge.gvcf.7.a.bcf /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.gvcf.8.a.vcf.gz /tmp/w1hDG0Hw69/merge.gvcf.8.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/w1hDG0Hw69/merge.gvcf.8.a.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.gvcf.8.a.bcf /tmp/w1hDG0Hw69/merge.gvcf.8.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/w1hDG0Hw69/merge.gvcf.8.a.bcf /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.7.a.vcf.gz /tmp/w1hDG0Hw69/merge.7.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/w1hDG0Hw69/merge.7.a.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.7.a.bcf /tmp/w1hDG0Hw69/merge.7.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/w1hDG0Hw69/merge.7.a.bcf /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.gvcf.9a.vcf.gz /tmp/w1hDG0Hw69/merge.gvcf.9b.vcf.gz /tmp/w1hDG0Hw69/merge.gvcf.9c.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.gvcf.9a.vcf.gz /tmp/w1hDG0Hw69/merge.gvcf.9b.vcf.gz /tmp/w1hDG0Hw69/merge.gvcf.9c.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.gvcf.9a.bcf /tmp/w1hDG0Hw69/merge.gvcf.9b.bcf /tmp/w1hDG0Hw69/merge.gvcf.9c.bcf /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.gvcf.9a.bcf /tmp/w1hDG0Hw69/merge.gvcf.9b.bcf /tmp/w1hDG0Hw69/merge.gvcf.9c.bcf /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.gvcf.9a.vcf.gz /tmp/w1hDG0Hw69/merge.gvcf.9b.vcf.gz /tmp/w1hDG0Hw69/merge.gvcf.9c.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.gvcf.9a.vcf.gz /tmp/w1hDG0Hw69/merge.gvcf.9b.vcf.gz /tmp/w1hDG0Hw69/merge.gvcf.9c.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.gvcf.9a.bcf /tmp/w1hDG0Hw69/merge.gvcf.9b.bcf /tmp/w1hDG0Hw69/merge.gvcf.9c.bcf /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.gvcf.9a.bcf /tmp/w1hDG0Hw69/merge.gvcf.9b.bcf /tmp/w1hDG0Hw69/merge.gvcf.9c.bcf /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.gvcf.9a.vcf.gz /tmp/w1hDG0Hw69/merge.gvcf.9b.vcf.gz /tmp/w1hDG0Hw69/merge.gvcf.9c.vcf.gz /tmp/w1hDG0Hw69/merge.gvcf.9d.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.gvcf.9a.vcf.gz /tmp/w1hDG0Hw69/merge.gvcf.9b.vcf.gz /tmp/w1hDG0Hw69/merge.gvcf.9c.vcf.gz /tmp/w1hDG0Hw69/merge.gvcf.9d.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.gvcf.9a.bcf /tmp/w1hDG0Hw69/merge.gvcf.9b.bcf /tmp/w1hDG0Hw69/merge.gvcf.9c.bcf /tmp/w1hDG0Hw69/merge.gvcf.9d.bcf /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.gvcf.9a.bcf /tmp/w1hDG0Hw69/merge.gvcf.9b.bcf /tmp/w1hDG0Hw69/merge.gvcf.9c.bcf /tmp/w1hDG0Hw69/merge.gvcf.9d.bcf /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.gvcf.9a.vcf.gz /tmp/w1hDG0Hw69/merge.gvcf.9b.vcf.gz /tmp/w1hDG0Hw69/merge.gvcf.9c.vcf.gz /tmp/w1hDG0Hw69/merge.gvcf.9d.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.gvcf.9a.vcf.gz /tmp/w1hDG0Hw69/merge.gvcf.9b.vcf.gz /tmp/w1hDG0Hw69/merge.gvcf.9c.vcf.gz /tmp/w1hDG0Hw69/merge.gvcf.9d.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.gvcf.9a.bcf /tmp/w1hDG0Hw69/merge.gvcf.9b.bcf /tmp/w1hDG0Hw69/merge.gvcf.9c.bcf /tmp/w1hDG0Hw69/merge.gvcf.9d.bcf /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.gvcf.9a.bcf /tmp/w1hDG0Hw69/merge.gvcf.9b.bcf /tmp/w1hDG0Hw69/merge.gvcf.9c.bcf /tmp/w1hDG0Hw69/merge.gvcf.9d.bcf /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.gvcf.10.a.vcf.gz /tmp/w1hDG0Hw69/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/w1hDG0Hw69/merge.gvcf.10.a.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.gvcf.10.a.bcf /tmp/w1hDG0Hw69/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/w1hDG0Hw69/merge.gvcf.10.a.bcf /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.gvcf.10.a.vcf.gz /tmp/w1hDG0Hw69/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m none /tmp/w1hDG0Hw69/merge.gvcf.10.a.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.gvcf.10.a.bcf /tmp/w1hDG0Hw69/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m none /tmp/w1hDG0Hw69/merge.gvcf.10.a.bcf /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.gvcf.10.a.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.gvcf.10.a.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.gvcf.10.a.bcf /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.gvcf.10.a.bcf /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.gvcf.10.a.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.gvcf.10.a.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.gvcf.10.a.bcf /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.gvcf.10.a.bcf /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.noidx.a.vcf.gz /tmp/w1hDG0Hw69/merge.noidx.b.vcf.gz /tmp/w1hDG0Hw69/merge.noidx.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/w1hDG0Hw69/merge.noidx.a.vcf.gz /tmp/w1hDG0Hw69/merge.noidx.b.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.noidx.a.bcf /tmp/w1hDG0Hw69/merge.noidx.b.bcf /tmp/w1hDG0Hw69/merge.noidx.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/w1hDG0Hw69/merge.noidx.a.bcf /tmp/w1hDG0Hw69/merge.noidx.b.bcf /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.noidx.a.bcf /tmp/w1hDG0Hw69/merge.noidx.b.bcf /tmp/w1hDG0Hw69/merge.noidx.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --no-index /tmp/w1hDG0Hw69/merge.noidx.a.bcf /tmp/w1hDG0Hw69/merge.noidx.b.bcf /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.8.a.vcf.gz /tmp/w1hDG0Hw69/merge.8.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/w1hDG0Hw69/merge.8.a.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.8.a.bcf /tmp/w1hDG0Hw69/merge.8.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/w1hDG0Hw69/merge.8.a.bcf /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.8.a.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.8.a.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.8.a.bcf /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.8.a.bcf /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.9.a.vcf.gz /tmp/w1hDG0Hw69/merge.9.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/w1hDG0Hw69/merge.9.a.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.9.a.bcf /tmp/w1hDG0Hw69/merge.9.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob /tmp/w1hDG0Hw69/merge.9.a.bcf /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.9.a.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.9.a.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.9.a.bcf /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.9.a.bcf /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.10.a.vcf.gz /tmp/w1hDG0Hw69/merge.10.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m none /tmp/w1hDG0Hw69/merge.10.a.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.10.a.bcf /tmp/w1hDG0Hw69/merge.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m none /tmp/w1hDG0Hw69/merge.10.a.bcf /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.10.a.vcf.gz /tmp/w1hDG0Hw69/merge.10.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m both /tmp/w1hDG0Hw69/merge.10.a.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.10.a.bcf /tmp/w1hDG0Hw69/merge.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m both /tmp/w1hDG0Hw69/merge.10.a.bcf /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.10.a.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.10.a.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.10.a.bcf /tmp/w1hDG0Hw69/merge.10.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob -m snp-ins-del /tmp/w1hDG0Hw69/merge.10.a.bcf /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.mrules.1.a.vcf.gz /tmp/w1hDG0Hw69/merge.mrules.1.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/w1hDG0Hw69/merge.mrules.1.a.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.mrules.1.a.bcf /tmp/w1hDG0Hw69/merge.mrules.1.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/w1hDG0Hw69/merge.mrules.1.a.bcf /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.mrules.1.a.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.mrules.1.a.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.mrules.1.a.bcf /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.mrules.1.a.bcf /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.gvcf.5.a.vcf.gz /tmp/w1hDG0Hw69/merge.gvcf.5.b.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/w1hDG0Hw69/merge.gvcf.5.a.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.gvcf.5.a.bcf /tmp/w1hDG0Hw69/merge.gvcf.5.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/w1hDG0Hw69/merge.gvcf.5.a.bcf /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.gvcf.5.a.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.gvcf.5.a.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.gvcf.5.a.bcf /tmp/w1hDG0Hw69/merge.gvcf.5.b.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - --merge none /tmp/w1hDG0Hw69/merge.gvcf.5.a.bcf /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.gvcf.11.a.vcf.gz /tmp/w1hDG0Hw69/merge.gvcf.11.b.vcf.gz /tmp/w1hDG0Hw69/merge.gvcf.11.c.vcf.gz .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/w1hDG0Hw69/merge.gvcf.11.a.vcf.gz /tmp/w1hDG0Hw69/merge.gvcf.11.b.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/merge.gvcf.11.a.bcf /tmp/w1hDG0Hw69/merge.gvcf.11.b.bcf /tmp/w1hDG0Hw69/merge.gvcf.11.c.bcf .. ok test_vcf_merge: /build/reproducible-path/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/w1hDG0Hw69/merge.gvcf.11.a.bcf /tmp/w1hDG0Hw69/merge.gvcf.11.b.bcf /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.string.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.string.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.string.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.string.2.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.string.2.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.variantkey.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/view.vectors.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.2.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.filter-type.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.filter-type.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.filter-type.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.filter-type.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.filter-type.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/filter-missing-floats.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/filter-missing-floats.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/missing.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.filter.2.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/view.filter.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.filter.3.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.filter.3.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.filter.3.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.filter.4.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/view.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.filter.5.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.negative.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.negative.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.negative.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.negative.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.filter.11.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.filter.6.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.filter.7.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.filter.8.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.filter.8.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.filter.9.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.filter.9.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.filter.13.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.filter.10.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.filter.10.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.smpl.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.filter.id.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.filter.id.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.filter.id.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.filter.id.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.filter.id.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.filter.id.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/filter.12.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/filter.10.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/filter.13.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.header.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.filter-or.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/query.filter-or.vcf.gz .. ok test_vcf_query: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/norm.sort.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - /tmp/w1hDG0Hw69/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/w1hDG0Hw69/norm.sort.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - -S lex /tmp/w1hDG0Hw69/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/w1hDG0Hw69/norm.join-missing-ploidy.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +both /tmp/w1hDG0Hw69/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/w1hDG0Hw69/norm.split.5.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - --multi-overlaps . /tmp/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/norm.split.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- /tmp/w1hDG0Hw69/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/w1hDG0Hw69/norm.split.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- /tmp/w1hDG0Hw69/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/w1hDG0Hw69/norm.split.3.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- --force /tmp/w1hDG0Hw69/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/w1hDG0Hw69/norm.split.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- /tmp/w1hDG0Hw69/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/w1hDG0Hw69/norm.split.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m- --keep-sum AD /tmp/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/norm.merge.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m+ /tmp/w1hDG0Hw69/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/w1hDG0Hw69/norm.merge.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m+ /tmp/w1hDG0Hw69/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/w1hDG0Hw69/norm.merge.3.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m+ /tmp/w1hDG0Hw69/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/w1hDG0Hw69/norm.merge.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m+ -s /tmp/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d snps /tmp/w1hDG0Hw69/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/w1hDG0Hw69/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d indels /tmp/w1hDG0Hw69/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/w1hDG0Hw69/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d both /tmp/w1hDG0Hw69/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/w1hDG0Hw69/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d all /tmp/w1hDG0Hw69/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/w1hDG0Hw69/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d none /tmp/w1hDG0Hw69/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/w1hDG0Hw69/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d exact /tmp/w1hDG0Hw69/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/w1hDG0Hw69/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d none /tmp/w1hDG0Hw69/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/w1hDG0Hw69/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d exact /tmp/w1hDG0Hw69/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/w1hDG0Hw69/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d indels /tmp/w1hDG0Hw69/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/w1hDG0Hw69/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d any /tmp/w1hDG0Hw69/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/w1hDG0Hw69/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d both /tmp/w1hDG0Hw69/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/w1hDG0Hw69/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -d snps /tmp/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/atomize.split.3.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . /tmp/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/norm.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +both /tmp/w1hDG0Hw69/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/w1hDG0Hw69/norm.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +any /tmp/w1hDG0Hw69/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/w1hDG0Hw69/norm.5.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - --multi-overlaps 0 /tmp/w1hDG0Hw69/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/w1hDG0Hw69/norm.5.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - --multi-overlaps . /tmp/w1hDG0Hw69/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/w1hDG0Hw69/norm.m-any.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any /tmp/w1hDG0Hw69/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/w1hDG0Hw69/norm.phased-split.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any /tmp/w1hDG0Hw69/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/w1hDG0Hw69/norm.phased-join.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +any /tmp/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/norm.string-tags.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m -any /tmp/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/norm.split.merge.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m - -i 'type="snp"' /tmp/w1hDG0Hw69/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/w1hDG0Hw69/norm.merge.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +any /tmp/w1hDG0Hw69/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/w1hDG0Hw69/norm.merge.4.vcf.gz .. ok test_vcf_norm: /build/reproducible-path/bcftools-1.21/bcftools norm --no-version -m +both /tmp/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/merge.gvcf.2.a.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -HAA /tmp/w1hDG0Hw69/merge.gvcf.2.a.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version /tmp/w1hDG0Hw69/weird-chr-names.vcf.gz -r 1 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/weird-chr-names.vcf.gz -r 1:1-2 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/weird-chr-names.vcf.gz -r 1:1,1:2 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/weird-chr-names.vcf.gz -r 1:1-1 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/weird-chr-names.vcf.gz -r {1:1} .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/weird-chr-names.vcf.gz -r {1:1}:1-2 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/weird-chr-names.vcf.gz -r {1:1}:1-1 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/weird-chr-names.vcf.gz -r {1:1-1} .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/w1hDG0Hw69/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/w1hDG0Hw69/view.vcf.gz -r20,Y .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -f PASS -Xks NA00003 /tmp/w1hDG0Hw69/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/w1hDG0Hw69/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -xs NA00003 /tmp/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -p /tmp/w1hDG0Hw69/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/w1hDG0Hw69/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -P /tmp/w1hDG0Hw69/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/w1hDG0Hw69/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/w1hDG0Hw69/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/w1hDG0Hw69/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -GVsnps /tmp/w1hDG0Hw69/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -GVsnps /tmp/w1hDG0Hw69/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/w1hDG0Hw69/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/w1hDG0Hw69/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/w1hDG0Hw69/view.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -s ^NA00003 /tmp/w1hDG0Hw69/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/w1hDG0Hw69/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -G /tmp/w1hDG0Hw69/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/w1hDG0Hw69/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -a /tmp/w1hDG0Hw69/many.alleles.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -a /tmp/w1hDG0Hw69/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/w1hDG0Hw69/view.vectors.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -asA /tmp/w1hDG0Hw69/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/w1hDG0Hw69/view.vectors.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -asB /tmp/w1hDG0Hw69/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/w1hDG0Hw69/view.vectors.2.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -asA /tmp/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/view.filter.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -i'TXT0="text"' /tmp/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/filter.2.vcf.gz 1:3062917-3157410 .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view -Ob -i 'POS>=3062917' /tmp/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/idx.4.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -Ht 2 /tmp/w1hDG0Hw69/view-t.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -Ht 3 /tmp/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -c6:nonmajor /tmp/w1hDG0Hw69/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -q0.3:major /tmp/w1hDG0Hw69/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/view.filter.annovar.vcf.gz .. ok test_vcf_view: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -H -a /tmp/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/mpileup.2.vcf.gz .. ok test_vcf_head2: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/mpileup.2.vcf.gz .. ok test_vcf_head2: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/mpileup.2.vcf.gz .. ok test_vcf_head2: /build/reproducible-path/bcftools-1.21/bcftools view --no-version -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/w1hDG0Hw69/regions.tab.gz /tmp/w1hDG0Hw69/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/regions.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/w1hDG0Hw69/regions.tab.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/w1hDG0Hw69/regions.tab.gz /tmp/w1hDG0Hw69/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/w1hDG0Hw69/regions.bed /tmp/w1hDG0Hw69/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/regions.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/w1hDG0Hw69/regions.bed .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/w1hDG0Hw69/regions.bed /tmp/w1hDG0Hw69/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/w1hDG0Hw69/regions.bed.gz /tmp/w1hDG0Hw69/regions.vcf.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/regions.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/w1hDG0Hw69/regions.bed.gz .. ok test_vcf_regions: /build/reproducible-path/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/w1hDG0Hw69/regions.bed.gz /tmp/w1hDG0Hw69/regions.vcf.gz .. ok test_vcf_annotate: /build/reproducible-path/bcftools-1.21/bcftools annotate -a /tmp/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/w1hDG0Hw69/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/w1hDG0Hw69/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/w1hDG0Hw69/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/w1hDG0Hw69/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/w1hDG0Hw69/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/w1hDG0Hw69/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/w1hDG0Hw69/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/w1hDG0Hw69/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/w1hDG0Hw69/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/w1hDG0Hw69/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/w1hDG0Hw69/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/w1hDG0Hw69/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/w1hDG0Hw69/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/w1hDG0Hw69/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/w1hDG0Hw69/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/w1hDG0Hw69/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/w1hDG0Hw69/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/w1hDG0Hw69/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/w1hDG0Hw69/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/w1hDG0Hw69/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/w1hDG0Hw69/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/w1hDG0Hw69/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/w1hDG0Hw69/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/w1hDG0Hw69/annots4.vcf.gz -c +INFO /tmp/w1hDG0Hw69/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/w1hDG0Hw69/annots4.vcf.gz -c +INFO /tmp/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/w1hDG0Hw69/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/w1hDG0Hw69/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/w1hDG0Hw69/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/w1hDG0Hw69/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/w1hDG0Hw69/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/w1hDG0Hw69/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/w1hDG0Hw69/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/w1hDG0Hw69/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/w1hDG0Hw69/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/w1hDG0Hw69/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/w1hDG0Hw69/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/w1hDG0Hw69/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/w1hDG0Hw69/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/w1hDG0Hw69/annots11.vcf.gz -c FMT /tmp/w1hDG0Hw69/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/w1hDG0Hw69/annots11.vcf.gz -c FMT /tmp/w1hDG0Hw69/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/w1hDG0Hw69/annots2.vcf.gz -c FMT/newGT:=GT /tmp/w1hDG0Hw69/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/w1hDG0Hw69/annots2.vcf.gz -c FMT/newGT:=GT /tmp/w1hDG0Hw69/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/w1hDG0Hw69/annots12.vcf.gz -c FMT/GT:=newGT /tmp/w1hDG0Hw69/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/w1hDG0Hw69/annots12.vcf.gz -c FMT/GT:=newGT /tmp/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/w1hDG0Hw69/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/w1hDG0Hw69/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/w1hDG0Hw69/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/w1hDG0Hw69/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/w1hDG0Hw69/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/w1hDG0Hw69/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/w1hDG0Hw69/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/w1hDG0Hw69/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/w1hDG0Hw69/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/w1hDG0Hw69/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/w1hDG0Hw69/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/w1hDG0Hw69/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER /tmp/w1hDG0Hw69/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/w1hDG0Hw69/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER /tmp/w1hDG0Hw69/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/w1hDG0Hw69/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER /tmp/w1hDG0Hw69/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/w1hDG0Hw69/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER /tmp/w1hDG0Hw69/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/w1hDG0Hw69/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER,FILTER /tmp/w1hDG0Hw69/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/w1hDG0Hw69/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER,FILTER /tmp/w1hDG0Hw69/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/w1hDG0Hw69/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=./FILTER /tmp/w1hDG0Hw69/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/w1hDG0Hw69/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=./FILTER /tmp/w1hDG0Hw69/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/w1hDG0Hw69/annotate20.src.vcf.gz -c FMT/GT /tmp/w1hDG0Hw69/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/w1hDG0Hw69/annotate20.src.vcf.gz -c FMT/GT /tmp/w1hDG0Hw69/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/w1hDG0Hw69/annotate20.src.vcf.gz -c +FMT/GT /tmp/w1hDG0Hw69/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/w1hDG0Hw69/annotate20.src.vcf.gz -c +FMT/GT /tmp/w1hDG0Hw69/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/w1hDG0Hw69/annotate20.src.vcf.gz -c -FMT/GT /tmp/w1hDG0Hw69/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/w1hDG0Hw69/annotate20.src.vcf.gz -c -FMT/GT /tmp/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/w1hDG0Hw69/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/w1hDG0Hw69/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/annotate24.src.vcf.gz -c XX /tmp/w1hDG0Hw69/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/w1hDG0Hw69/annotate24.src.vcf.gz -c XX /tmp/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/annots.id.vcf.gz -c ALT /tmp/w1hDG0Hw69/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/w1hDG0Hw69/annots.id.vcf.gz -c ALT /tmp/w1hDG0Hw69/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/w1hDG0Hw69/annots.id.vcf.gz -c +ALT /tmp/w1hDG0Hw69/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/w1hDG0Hw69/annots.id.vcf.gz -c +ALT /tmp/w1hDG0Hw69/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/w1hDG0Hw69/annots.id.2.vcf.gz --pair-logic some -c +ID /tmp/w1hDG0Hw69/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/w1hDG0Hw69/annots.id.2.vcf.gz --pair-logic some -c +ID /tmp/w1hDG0Hw69/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/w1hDG0Hw69/annots.id.2.vcf.gz --pair-logic any -c +ID /tmp/w1hDG0Hw69/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/w1hDG0Hw69/annots.id.2.vcf.gz --pair-logic any -c +ID /tmp/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/concat.1.a.vcf.gz /tmp/w1hDG0Hw69/concat.1.b.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob /tmp/w1hDG0Hw69/concat.1.a.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/concat.1.a.bcf /tmp/w1hDG0Hw69/concat.1.b.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob /tmp/w1hDG0Hw69/concat.1.a.bcf /tmp/w1hDG0Hw69/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/w1hDG0Hw69/concat.2.a.vcf.gz /tmp/w1hDG0Hw69/concat.2.b.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -a /tmp/w1hDG0Hw69/concat.2.a.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/concat.2.a.bcf /tmp/w1hDG0Hw69/concat.2.b.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -a /tmp/w1hDG0Hw69/concat.2.a.bcf /tmp/w1hDG0Hw69/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/w1hDG0Hw69/concat.2.a.vcf.gz /tmp/w1hDG0Hw69/concat.2.b.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -aD /tmp/w1hDG0Hw69/concat.2.a.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/concat.2.a.bcf /tmp/w1hDG0Hw69/concat.2.b.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -aD /tmp/w1hDG0Hw69/concat.2.a.bcf /tmp/w1hDG0Hw69/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/w1hDG0Hw69/concat.3.a.vcf.gz /tmp/w1hDG0Hw69/concat.3.b.vcf.gz /tmp/w1hDG0Hw69/concat.3.0.vcf.gz /tmp/w1hDG0Hw69/concat.3.c.vcf.gz /tmp/w1hDG0Hw69/concat.3.d.vcf.gz /tmp/w1hDG0Hw69/concat.3.e.vcf.gz /tmp/w1hDG0Hw69/concat.3.f.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -l --ligate-warn /tmp/w1hDG0Hw69/concat.3.a.vcf.gz /tmp/w1hDG0Hw69/concat.3.b.vcf.gz /tmp/w1hDG0Hw69/concat.3.0.vcf.gz /tmp/w1hDG0Hw69/concat.3.c.vcf.gz /tmp/w1hDG0Hw69/concat.3.d.vcf.gz /tmp/w1hDG0Hw69/concat.3.e.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/concat.3.a.bcf /tmp/w1hDG0Hw69/concat.3.b.bcf /tmp/w1hDG0Hw69/concat.3.0.bcf /tmp/w1hDG0Hw69/concat.3.c.bcf /tmp/w1hDG0Hw69/concat.3.d.bcf /tmp/w1hDG0Hw69/concat.3.e.bcf /tmp/w1hDG0Hw69/concat.3.f.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -l --ligate-warn /tmp/w1hDG0Hw69/concat.3.a.bcf /tmp/w1hDG0Hw69/concat.3.b.bcf /tmp/w1hDG0Hw69/concat.3.0.bcf /tmp/w1hDG0Hw69/concat.3.c.bcf /tmp/w1hDG0Hw69/concat.3.d.bcf /tmp/w1hDG0Hw69/concat.3.e.bcf /tmp/w1hDG0Hw69/concat.3.f.bcf | /build/reproducible-path/bcftools-1.21/bcftools view | grep -v ^##bcftools_ Random seed for test_naive_concat: 3299428478 .. ok test_naive_concat: /build/reproducible-path/bcftools-1.21/bcftools concat --naive-force /tmp/w1hDG0Hw69/naive_concat.0.bcf /tmp/w1hDG0Hw69/naive_concat.1.bcf /tmp/w1hDG0Hw69/naive_concat.2.bcf /tmp/w1hDG0Hw69/naive_concat.3.bcf /tmp/w1hDG0Hw69/naive_concat.4.bcf /tmp/w1hDG0Hw69/naive_concat.5.bcf /tmp/w1hDG0Hw69/naive_concat.6.bcf /tmp/w1hDG0Hw69/naive_concat.7.bcf /tmp/w1hDG0Hw69/naive_concat.8.bcf /tmp/w1hDG0Hw69/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/w1hDG0Hw69/naive_concat.0.vcf.gz /tmp/w1hDG0Hw69/naive_concat.1.vcf.gz /tmp/w1hDG0Hw69/naive_concat.2.vcf.gz /tmp/w1hDG0Hw69/naive_concat.3.vcf.gz /tmp/w1hDG0Hw69/naive_concat.4.vcf.gz /tmp/w1hDG0Hw69/naive_concat.5.vcf.gz /tmp/w1hDG0Hw69/naive_concat.6.vcf.gz /tmp/w1hDG0Hw69/naive_concat.7.vcf.gz /tmp/w1hDG0Hw69/naive_concat.8.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/concat.4.a.vcf.gz /tmp/w1hDG0Hw69/concat.4.b.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -l /tmp/w1hDG0Hw69/concat.4.a.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/concat.4.a.bcf /tmp/w1hDG0Hw69/concat.4.b.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -l /tmp/w1hDG0Hw69/concat.4.a.bcf /tmp/w1hDG0Hw69/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/w1hDG0Hw69/concat.5.a.vcf.gz /tmp/w1hDG0Hw69/concat.5.b.vcf.gz /tmp/w1hDG0Hw69/concat.5.c.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -l --ligate-warn /tmp/w1hDG0Hw69/concat.5.a.vcf.gz /tmp/w1hDG0Hw69/concat.5.b.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/concat.5.a.bcf /tmp/w1hDG0Hw69/concat.5.b.bcf /tmp/w1hDG0Hw69/concat.5.c.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -l --ligate-warn /tmp/w1hDG0Hw69/concat.5.a.bcf /tmp/w1hDG0Hw69/concat.5.b.bcf /tmp/w1hDG0Hw69/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/w1hDG0Hw69/concat.5.a.bcf /tmp/w1hDG0Hw69/concat.5.b.bcf /tmp/w1hDG0Hw69/concat.5.c.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -l --ligate-force /tmp/w1hDG0Hw69/concat.5.a.bcf /tmp/w1hDG0Hw69/concat.5.b.bcf /tmp/w1hDG0Hw69/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/w1hDG0Hw69/concat.5.a.vcf.gz /tmp/w1hDG0Hw69/concat.5.b.vcf.gz /tmp/w1hDG0Hw69/concat.5.c.vcf.gz .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -G -a -D /tmp/w1hDG0Hw69/concat.5.a.vcf.gz /tmp/w1hDG0Hw69/concat.5.b.vcf.gz /tmp/w1hDG0Hw69/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/w1hDG0Hw69/concat.5.a.bcf /tmp/w1hDG0Hw69/concat.5.b.bcf /tmp/w1hDG0Hw69/concat.5.c.bcf .. ok test_vcf_concat: /build/reproducible-path/bcftools-1.21/bcftools concat -Ob -G -a -D /tmp/w1hDG0Hw69/concat.5.a.bcf /tmp/w1hDG0Hw69/concat.5.b.bcf /tmp/w1hDG0Hw69/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/w1hDG0Hw69/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/w1hDG0Hw69/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/w1hDG0Hw69/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/w1hDG0Hw69/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/w1hDG0Hw69/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/w1hDG0Hw69/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/w1hDG0Hw69/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/w1hDG0Hw69/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/w1hDG0Hw69/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/w1hDG0Hw69/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/w1hDG0Hw69/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/w1hDG0Hw69/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/w1hDG0Hw69/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/w1hDG0Hw69/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/w1hDG0Hw69/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/w1hDG0Hw69/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/w1hDG0Hw69/reheader.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/w1hDG0Hw69/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/w1hDG0Hw69/reheader.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/w1hDG0Hw69/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/w1hDG0Hw69/empty.bcf | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/w1hDG0Hw69/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/w1hDG0Hw69/empty.vcf.gz | /build/reproducible-path/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/rename.map -Ov /tmp/w1hDG0Hw69/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/w1hDG0Hw69/rename.map -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/check.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/convert.hap-missing.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/convert.vcf.gz .. ok test_vcf_convert: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/convert.gvcf.vcf.gz .. ok test_vcf_convert_gvcf: /build/reproducible-path/bcftools-1.21/bcftools view -Ob /tmp/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/consensus.1.chain.new >/dev/null; cat /tmp/w1hDG0Hw69/consensus.1.chain.new .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/consensus.2.chain.new >/dev/null; cat /tmp/w1hDG0Hw69/consensus.2.chain.new .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/consensus.3.chain.new >/dev/null; cat /tmp/w1hDG0Hw69/consensus.3.chain.new .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/consensus.vcf.gz -f /build/reproducible-path/bcftools-1.21/test/consensus.fa -H 1 -c /tmp/w1hDG0Hw69/consensus.4.chain.new >/dev/null; cat /tmp/w1hDG0Hw69/consensus.4.chain.new .. ok test_vcf_consensus: /build/reproducible-path/bcftools-1.21/bcftools consensus /tmp/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/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/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/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_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/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/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/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/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/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/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: 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: 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/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/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/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/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/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/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/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/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/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: /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/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/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/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: /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/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/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/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: 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/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/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/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/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: /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/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: 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/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/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/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/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-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-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-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-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/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-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-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/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/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/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/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/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/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/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/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/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/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/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: 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 -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: /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 -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: /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: 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/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/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/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/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/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/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!=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!=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/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/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/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/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/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/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: /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/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_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/w1hDG0Hw69/gtcheck.1.vcf.gz -g /tmp/w1hDG0Hw69/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 /tmp/w1hDG0Hw69/gtcheck.1.vcf.gz -g /tmp/w1hDG0Hw69/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/w1hDG0Hw69/gtcheck.1.vcf.gz -g /tmp/w1hDG0Hw69/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/w1hDG0Hw69/gtcheck.1.vcf.gz -g /tmp/w1hDG0Hw69/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/w1hDG0Hw69/gtcheck.1.vcf.gz -g /tmp/w1hDG0Hw69/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/w1hDG0Hw69/gtcheck.1.vcf.gz -g /tmp/w1hDG0Hw69/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/w1hDG0Hw69/gtcheck.1.vcf.gz -g /tmp/w1hDG0Hw69/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 /tmp/w1hDG0Hw69/gtcheck.2.vcf.gz -g /tmp/w1hDG0Hw69/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck -e 0 /tmp/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/gtcheck.1.vcf.gz -g /tmp/w1hDG0Hw69/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/w1hDG0Hw69/gtcheck.1.vcf.gz -g /tmp/w1hDG0Hw69/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/w1hDG0Hw69/gtcheck.1.vcf.gz -g /tmp/w1hDG0Hw69/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/w1hDG0Hw69/gtcheck.1.vcf.gz -g /tmp/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/gtcheck.1.vcf.gz -g /tmp/w1hDG0Hw69/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/w1hDG0Hw69/gtcheck.1.vcf.gz -g /tmp/w1hDG0Hw69/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/w1hDG0Hw69/gtcheck.1.vcf.gz -g /tmp/w1hDG0Hw69/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/w1hDG0Hw69/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck /tmp/w1hDG0Hw69/gtcheck.ntop.vcf.gz -g /tmp/w1hDG0Hw69/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/w1hDG0Hw69/gtcheck.ntop.vcf.gz -g /tmp/w1hDG0Hw69/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/reproducible-path/bcftools-1.21/bcftools gtcheck /tmp/w1hDG0Hw69/gtcheck.5.vcf.gz -g /tmp/w1hDG0Hw69/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/w1hDG0Hw69/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/w1hDG0Hw69/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 -j11 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/i386-linux-gnu/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/i386-linux-gnu/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 dh_installdeb dh_gencontrol dpkg-gencontrol: warning: package bcftools: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package bcftools: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'bcftools' in '../bcftools_1.21-1_i386.deb'. dpkg-deb: building package 'bcftools-dbgsym' in '../bcftools-dbgsym_1.21-1_i386.deb'. dpkg-genbuildinfo --build=binary -O../bcftools_1.21-1_i386.buildinfo dpkg-genchanges --build=binary -O../bcftools_1.21-1_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: 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/50672 and its subdirectories I: Current time: Sat Feb 15 19:54:52 -12 2025 I: pbuilder-time-stamp: 1739692492