I: pbuilder: network access will be disabled during build I: Current time: Wed Jul 10 03:28:30 -12 2024 I: pbuilder-time-stamp: 1720625310 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [bcftools_1.16-1.dsc] I: copying [./bcftools_1.16.orig.tar.gz] I: copying [./bcftools_1.16-1.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Sep 29 21:56:19 2022 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./bcftools_1.16-1.dsc: no acceptable signature found dpkg-source: info: extracting bcftools in bcftools-1.16 dpkg-source: info: unpacking bcftools_1.16.orig.tar.gz dpkg-source: info: unpacking bcftools_1.16-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying tests-pluginpath.patch dpkg-source: info: applying skip_new_test_failing_on_32bit.patch dpkg-source: info: applying 2to3.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1489716/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16 ' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='d308204bd6cb4aa0b6687fa565114b69' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='1489716' 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.r21ocxVz/pbuilderrc_wEsm --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.r21ocxVz/b1 --logfile b1/build.log bcftools_1.16-1.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://85.184.249.68:3128' I: uname -a Linux ionos5-amd64 6.1.0-0.deb11.7-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.20-2~bpo11+1 (2023-04-23) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Apr 23 2023 bash -rwxr-xr-x 3 root root 39224 Sep 18 2022 bunzip2 -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzip2 -rwxr-xr-x 1 root root 14568 Sep 18 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore -rwxr-xr-x 1 root root 44016 Sep 20 2022 cat -rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod -rwxr-xr-x 1 root root 72752 Sep 20 2022 chown -rwxr-xr-x 1 root root 151152 Sep 20 2022 cp -rwxr-xr-x 1 root root 125640 Jan 5 2023 dash -rwxr-xr-x 1 root root 121904 Sep 20 2022 date -rwxr-xr-x 1 root root 89240 Sep 20 2022 dd -rwxr-xr-x 1 root root 102200 Sep 20 2022 df -rwxr-xr-x 1 root root 151344 Sep 20 2022 dir -rwxr-xr-x 1 root root 88656 Mar 22 2023 dmesg lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep -rwxr-xr-x 1 root root 35664 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep -rwxr-xr-x 1 root root 85600 Mar 22 2023 findmnt -rwsr-xr-x 1 root root 35128 Mar 22 2023 fusermount -rwxr-xr-x 1 root root 203152 Jan 24 2023 grep -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe -rwxr-xr-x 1 root root 98136 Apr 9 2022 gzip -rwxr-xr-x 1 root root 22680 Dec 19 2022 hostname -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln -rwxr-xr-x 1 root root 53024 Mar 23 2023 login -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls -rwxr-xr-x 1 root root 207168 Mar 22 2023 lsblk -rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod -rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 59712 Mar 22 2023 more -rwsr-xr-x 1 root root 59704 Mar 22 2023 mount -rwxr-xr-x 1 root root 18744 Mar 22 2023 mountpoint -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 2 2023 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Apr 23 2023 rbash -> bash -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 27560 Nov 2 2022 run-parts -rwxr-xr-x 1 root root 126424 Jan 5 2023 sed lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty -rwsr-xr-x 1 root root 72000 Mar 22 2023 su -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync -rwxr-xr-x 1 root root 531984 Apr 6 2023 tar -rwxr-xr-x 1 root root 14520 Nov 2 2022 tempfile -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch -rwxr-xr-x 1 root root 35664 Sep 20 2022 true -rwxr-xr-x 1 root root 14568 Mar 22 2023 ulockmgr_server -rwsr-xr-x 1 root root 35128 Mar 22 2023 umount -rwxr-xr-x 1 root root 43888 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir -rwxr-xr-x 1 root root 72024 Mar 22 2023 wdctl lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew I: user script /srv/workspace/pbuilder/1489716/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), zlib1g-dev, libbz2-dev, liblzma-dev, libhts-dev (>= 1.14), libgsl-dev, tabix, libio-pty-perl dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19591 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. pbuilder-satisfydepends-dummy depends on liblzma-dev; however: Package liblzma-dev is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev (>= 1.14); however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on libgsl-dev; however: Package libgsl-dev is not installed. pbuilder-satisfydepends-dummy depends on tabix; however: Package tabix is not installed. pbuilder-satisfydepends-dummy depends on libio-pty-perl; however: Package libio-pty-perl is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbrotli1{a} libbz2-dev{a} libcurl3-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1{a} libfile-stripnondeterminism-perl{a} libgsl-dev{a} libgsl27{a} libgslcblas0{a} libhts-dev{a} libhts3{a} libhtscodecs2{a} libicu72{a} libio-pty-perl{a} libldap-2.5-0{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libnghttp2-14{a} libpipeline1{a} libpsl5{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} tabix{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc ca-certificates curl libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix wget 0 packages upgraded, 53 newly installed, 0 to remove and 0 not upgraded. Need to get 26.6 MB of archives. After unpacking 101 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 2 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get: 3 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get: 4 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB] Get: 5 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB] Get: 6 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 7 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get: 8 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get: 9 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get: 10 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get: 11 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB] Get: 12 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB] Get: 16 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 17 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB] Get: 18 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get: 21 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 22 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 23 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get: 24 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB] Get: 25 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get: 26 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.2 [687 kB] Get: 27 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB] Get: 28 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] Get: 31 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB] Get: 32 http://deb.debian.org/debian bookworm/main amd64 libbz2-dev amd64 1.0.8-5+b1 [30.9 kB] Get: 33 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-10 [20.3 kB] Get: 34 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB] Get: 35 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB] Get: 36 http://deb.debian.org/debian bookworm/main amd64 libnghttp2-14 amd64 1.52.0-1 [72.3 kB] Get: 37 http://deb.debian.org/debian bookworm/main amd64 libpsl5 amd64 0.21.2-1 [58.7 kB] Get: 38 http://deb.debian.org/debian bookworm/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get: 39 http://deb.debian.org/debian bookworm/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB] Get: 40 http://deb.debian.org/debian bookworm/main amd64 libcurl3-gnutls amd64 7.88.1-10 [381 kB] Get: 41 http://deb.debian.org/debian bookworm/main amd64 libcurl4-gnutls-dev amd64 7.88.1-10 [481 kB] Get: 42 http://deb.debian.org/debian bookworm/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB] Get: 43 http://deb.debian.org/debian bookworm/main amd64 libdeflate-dev amd64 1.14-1 [53.3 kB] Get: 44 http://deb.debian.org/debian bookworm/main amd64 libgslcblas0 amd64 2.7.1+dfsg-5 [108 kB] Get: 45 http://deb.debian.org/debian bookworm/main amd64 libgsl27 amd64 2.7.1+dfsg-5 [941 kB] Get: 46 http://deb.debian.org/debian bookworm/main amd64 libgsl-dev amd64 2.7.1+dfsg-5 [1152 kB] Get: 47 http://deb.debian.org/debian bookworm/main amd64 libhtscodecs2 amd64 1.3.0-4 [87.5 kB] Get: 48 http://deb.debian.org/debian bookworm/main amd64 libhts3 amd64 1.16+ds-3 [430 kB] Get: 49 http://deb.debian.org/debian bookworm/main amd64 liblzma-dev amd64 5.4.1-0.2 [260 kB] Get: 50 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB] Get: 51 http://deb.debian.org/debian bookworm/main amd64 libhts-dev amd64 1.16+ds-3 [1601 kB] Get: 52 http://deb.debian.org/debian bookworm/main amd64 libio-pty-perl amd64 1:1.17-1 [34.9 kB] Get: 53 http://deb.debian.org/debian bookworm/main amd64 tabix amd64 1.16+ds-3 [457 kB] Fetched 26.6 MB in 0s (56.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19591 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.44-3_amd64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../02-libmagic1_1%3a5.44-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.44-3_amd64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-12_amd64.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.22.4-10_amd64.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.38.1-5+b1_amd64.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.7-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.11.2-2_amd64.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-3_amd64.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.11.4_all.deb ... Unpacking libdebhelper-perl (13.11.4) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-5_all.deb ... Unpacking libtool (2.4.7-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../19-libsub-override-perl_0.09-4_all.deb ... Unpacking libsub-override-perl (0.09-4) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../22-libelf1_0.188-2.1_amd64.deb ... Unpacking libelf1:amd64 (0.188-2.1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1_amd64.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../24-libicu72_72.1-3_amd64.deb ... Unpacking libicu72:amd64 (72.1-3) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../25-libxml2_2.9.14+dfsg-1.2_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.2) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.21-12_amd64.deb ... Unpacking gettext (0.21-12) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-intltool-debian_0.35.0+20060710.6_all.deb ... 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Setting up m4 (1.4.19-3) ... Setting up file (1:5.44-3) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg-10) ... Setting up autotools-dev (20220109.1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up autopoint (0.21-12) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg-10) ... Setting up autoconf (2.71-3) ... Setting up liblzma-dev:amd64 (5.4.1-0.2) ... Setting up zlib1g-dev:amd64 (1:1.2.13.dfsg-1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libssh2-1:amd64 (1.10.0-3+b1) ... Setting up libdeflate-dev:amd64 (1.14-1) ... Setting up tabix (1.16+ds-3) ... Setting up libelf1:amd64 (0.188-2.1) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.2) ... Setting up libbz2-dev:amd64 (1.0.8-5+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up gettext (0.21-12) ... Setting up libgsl-dev (2.7.1+dfsg-5) ... Setting up libtool (2.4.7-5) ... Setting up libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-10) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3-gnutls:amd64 (7.88.1-10) ... Setting up libcurl4-gnutls-dev:amd64 (7.88.1-10) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libhts3:amd64 (1.16+ds-3) ... Setting up libhts-dev:amd64 (1.16+ds-3) ... Setting up debhelper (13.11.4) ... Processing triggers for libc-bin (2.36-9) ... 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/bcftools-1.16/ && 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_1.16-1_source.changes dpkg-buildpackage: info: source package bcftools dpkg-buildpackage: info: source version 1.16-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean rm -f config.mk && touch config.mk dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/bcftools-1.16' dh_auto_clean make -j16 distclean make[2]: Entering directory '/build/bcftools-1.16' rm -f test/*.o test/*.fa.fai test/*~ test/test-rbuf test/test-regidx rm -f plugins/*.so plugins/*.P rm -f test/*.unsorted.hex test/*.unsorted.tsv rm -rf plugins/*.dSYM rm -f gmon.out *.o *.a *~ bcftools version.h rm -rf *.dSYM test/*.dSYM rm -f config.cache config.h config.log config.mk config.status rm -rf autom4te.cache rm -f TAGS make[2]: Leaving directory '/build/bcftools-1.16' 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/bcftools-1.16' dh_clean debian/rules binary dh binary dh_update_autotools_config debian/rules override_dh_autoreconf make[1]: Entering directory '/build/bcftools-1.16' 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/bcftools-1.16' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/bcftools-1.16' dh_auto_configure -- \ --with-htslib=system \ --enable-gsl \ --with-cblas=gslcblas \ --with-bcf-plugin-dir=/usr/lib/x86_64-linux-gnu/bcftools ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system --enable-gsl --with-cblas=gslcblas --with-bcf-plugin-dir=/usr/lib/x86_64-linux-gnu/bcftools checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking for grep that handles long lines and -e... /bin/grep checking for C compiler warning flags... -Wall checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for htslib/sam.h... yes checking for hts_version in -lhts... yes checking shared library type... plain .so checking for library containing dlopen... none required checking if the compiler accepts -rdynamic... yes checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing regcomp... none required configure: creating ./config.status config.status: creating config.mk config.status: creating config.h make[1]: Leaving directory '/build/bcftools-1.16' dh_auto_build make -j16 make[1]: Entering directory '/build/bcftools-1.16' echo '#define BCFTOOLS_VERSION "1.16"' > version.h gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfindex.o vcfindex.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tabix.o tabix.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfstats.o vcfstats.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfisec.o vcfisec.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfmerge.o vcfmerge.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfquery.o vcfquery.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcffilter.o vcffilter.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o filter.o filter.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfsom.o vcfsom.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfnorm.o vcfnorm.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfgtcheck.o vcfgtcheck.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfview.o vcfview.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfannotate.o vcfannotate.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfroh.o vcfroh.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfconcat.o vcfconcat.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcall.o vcfcall.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mcall.o mcall.c gcc -Wall -g -O2 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-D_FORTIFY_SOURCE=2 -c -o tsv2vcf.o tsv2vcf.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcnv.o vcfcnv.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfhead.o vcfhead.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o HMM.o HMM.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o consensus.o consensus.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ploidy.o ploidy.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bin.o bin.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hclust.o hclust.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o version.o version.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o regidx.o regidx.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o smpl_ilist.o smpl_ilist.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o csq.o csq.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfbuf.o vcfbuf.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mpileup.o mpileup.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sample.o bam_sample.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfsort.o vcfsort.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cols.o cols.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o extsort.o extsort.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dist.o dist.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o abuf.o abuf.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ccall.o ccall.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o em.o em.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o prob1.o prob1.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kmin.o kmin.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o str_finder.o str_finder.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DPLUGINPATH='"/usr/lib/x86_64-linux-gnu/bcftools"' -c -o vcfplugin.o vcfplugin.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-rbuf.o test/test-rbuf.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-regidx.o test/test-regidx.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/GTisec.so version.c plugins/GTisec.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/GTsubset.so version.c plugins/GTsubset.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/ad-bias.so convert.c version.c plugins/ad-bias.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/add-variantkey.so version.c plugins/add-variantkey.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/af-dist.so bin.c version.c plugins/af-dist.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/allele-length.so version.c plugins/allele-length.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/check-ploidy.so version.c plugins/check-ploidy.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/check-sparsity.so version.c plugins/check-sparsity.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/color-chrs.so HMM.c version.c plugins/color-chrs.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/contrast.so version.c plugins/contrast.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/counts.so version.c plugins/counts.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/dosage.so version.c plugins/dosage.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fill-AN-AC.so version.c plugins/fill-AN-AC.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fill-from-fasta.so filter.c version.c plugins/fill-from-fasta.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fill-tags.so version.c plugins/fill-tags.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fixploidy.so ploidy.c regidx.c version.c plugins/fixploidy.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fixref.so version.c plugins/fixref.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/frameshifts.so version.c plugins/frameshifts.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/guess-ploidy.so version.c plugins/guess-ploidy.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/gvcfz.so version.c plugins/gvcfz.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/impute-info.so version.c plugins/impute-info.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/indel-stats.so version.c plugins/indel-stats.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/isecGT.so smpl_ilist.c version.c plugins/isecGT.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/mendelian.so version.c plugins/mendelian.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/missing2ref.so version.c plugins/missing2ref.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/parental-origin.so version.c plugins/parental-origin.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/prune.so version.c plugins/prune.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/remove-overlaps.so version.c plugins/remove-overlaps.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/scatter.so version.c plugins/scatter.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/setGT.so version.c plugins/setGT.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/smpl-stats.so version.c plugins/smpl-stats.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/split-vep.so version.c plugins/split-vep.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/split.so version.c plugins/split.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/tag2tag.so version.c plugins/tag2tag.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/trio-dnm2.so version.c plugins/trio-dnm2.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/trio-stats.so version.c plugins/trio-stats.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/trio-switch-rate.so version.c plugins/trio-switch-rate.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/variant-distance.so version.c plugins/variant-distance.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/variantkey-hex.so version.c plugins/variantkey-hex.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o main.o main.c gcc -Wl,-z,relro -o test/test-rbuf test/test-rbuf.o -lz gcc -Wl,-z,relro -o test/test-regidx test/test-regidx.o regidx.o -lhts -lpthread -lz gcc -rdynamic -Wl,-z,relro -o bcftools main.o vcfindex.o tabix.o vcfstats.o vcfisec.o vcfmerge.o vcfquery.o vcffilter.o filter.o vcfsom.o vcfnorm.o vcfgtcheck.o vcfview.o vcfannotate.o vcfroh.o vcfconcat.o vcfcall.o mcall.o vcmp.o gvcf.o reheader.o convert.o vcfconvert.o tsv2vcf.o vcfcnv.o vcfhead.o HMM.o consensus.o ploidy.o bin.o hclust.o version.o regidx.o smpl_ilist.o csq.o vcfbuf.o mpileup.o bam2bcf.o bam2bcf_indel.o bam_sample.o vcfsort.o cols.o extsort.o dist.o abuf.o ccall.o em.o prob1.o kmin.o str_finder.o vcfplugin.o -lhts -lm -lz -lpthread make[1]: Leaving directory '/build/bcftools-1.16' debian/rules override_dh_auto_test make[1]: Entering directory '/build/bcftools-1.16' make test-no-plugins VERBOSE=1 make[2]: Entering directory '/build/bcftools-1.16' ./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/vabHikq0lF/merge.a.vcf.gz 2:3199812-3199812 .. ok test_tabix: /build/bcftools-1.16/bcftools view -H /tmp/vabHikq0lF/merge.a.bcf 2:3199812-3199812 .. ok test_tabix: tabix /tmp/vabHikq0lF/merge.a.vcf.gz 1:3000151-3000151 .. ok test_tabix: /build/bcftools-1.16/bcftools view -H /tmp/vabHikq0lF/merge.a.bcf 1:3000151-3000151 .. ok test_index: /build/bcftools-1.16/bcftools view -H /tmp/vabHikq0lF/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /build/bcftools-1.16/bcftools view -H /tmp/vabHikq0lF/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/bcftools-1.16/bcftools view -H /tmp/vabHikq0lF/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/bcftools-1.16/bcftools view -H /tmp/vabHikq0lF/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /build/bcftools-1.16/bcftools view -H /tmp/vabHikq0lF/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/bcftools-1.16/bcftools view -H /tmp/vabHikq0lF/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /build/bcftools-1.16/bcftools view -H /tmp/vabHikq0lF/large_chrom_csi_limit.bcf chr20 .. ok test_index: /build/bcftools-1.16/bcftools view -H /tmp/vabHikq0lF/large_chrom_csi_limit.bcf chr20 .. ok test_index: /build/bcftools-1.16/bcftools view -H /tmp/vabHikq0lF/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /build/bcftools-1.16/bcftools view -H /tmp/vabHikq0lF/large_chrom_csi_limit.bcf chr20 .. ok test_vcf_idxstats: /build/bcftools-1.16/bcftools index -s /tmp/vabHikq0lF/idx.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.16/bcftools index -s /tmp/vabHikq0lF/idx.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.16/bcftools index -s /tmp/vabHikq0lF/idx.bcf .. ok test_vcf_idxstats: /build/bcftools-1.16/bcftools index -n /tmp/vabHikq0lF/idx.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.16/bcftools index -n /tmp/vabHikq0lF/idx.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.16/bcftools index -n /tmp/vabHikq0lF/idx.vcf.gz.csi .. ok test_vcf_idxstats: /build/bcftools-1.16/bcftools index -n /tmp/vabHikq0lF/idx.bcf .. ok test_vcf_idxstats: /build/bcftools-1.16/bcftools index -n /tmp/vabHikq0lF/idx.bcf.csi .. ok test_vcf_idxstats: /build/bcftools-1.16/bcftools index -s /tmp/vabHikq0lF/empty.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.16/bcftools index -s /tmp/vabHikq0lF/empty.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.16/bcftools index -s /tmp/vabHikq0lF/empty.bcf .. ok test_vcf_idxstats: /build/bcftools-1.16/bcftools index -n /tmp/vabHikq0lF/empty.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.16/bcftools index -n /tmp/vabHikq0lF/empty.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.16/bcftools index -n /tmp/vabHikq0lF/empty.vcf.gz.csi .. ok test_vcf_idxstats: /build/bcftools-1.16/bcftools index -n /tmp/vabHikq0lF/empty.bcf .. ok test_vcf_idxstats: /build/bcftools-1.16/bcftools index -n /tmp/vabHikq0lF/empty.bcf.csi .. ok test_vcf_check: /build/bcftools-1.16/bcftools stats -s - /tmp/vabHikq0lF/check.vcf.gz | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/check.vcf.gz | /build/bcftools-1.16/bcftools stats -s - | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check_merge: /build/bcftools-1.16/misc/plot-vcfstats -m /tmp/vabHikq0lF/check.1.chk /tmp/vabHikq0lF/check.2.chk /tmp/vabHikq0lF/check.3.chk /tmp/vabHikq0lF/check.4.chk | grep -v 'plot-vcfstats' | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_stats: /build/bcftools-1.16/bcftools stats -s - /tmp/vabHikq0lF/stats.a.vcf.gz /tmp/vabHikq0lF/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/bcftools-1.16/bcftools stats -s B /tmp/vabHikq0lF/stats.a.vcf.gz /tmp/vabHikq0lF/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/bcftools-1.16/bcftools stats -s - /tmp/vabHikq0lF/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_isec: /build/bcftools-1.16/bcftools isec -n =2 /tmp/vabHikq0lF/isec.a.vcf.gz /tmp/vabHikq0lF/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.16/bcftools isec -Ob -n =2 /tmp/vabHikq0lF/isec.a.vcf.gz /tmp/vabHikq0lF/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.16/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/vabHikq0lF/isec.a.vcf.gz /tmp/vabHikq0lF/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.16/bcftools isec -Ob -n =2 -i"STRLEN(REF)==2" /tmp/vabHikq0lF/isec.a.vcf.gz /tmp/vabHikq0lF/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.16/bcftools isec -n =2 -c both /tmp/vabHikq0lF/isec.a.vcf.gz /tmp/vabHikq0lF/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.16/bcftools isec -Ob -n =2 -c both /tmp/vabHikq0lF/isec.a.vcf.gz /tmp/vabHikq0lF/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.16/bcftools isec -n =2 -c any /tmp/vabHikq0lF/isec.a.vcf.gz /tmp/vabHikq0lF/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.16/bcftools isec -Ob -n =2 -c any /tmp/vabHikq0lF/isec.a.vcf.gz /tmp/vabHikq0lF/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.16/bcftools isec -C -c any /tmp/vabHikq0lF/isec.a.vcf.gz /tmp/vabHikq0lF/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.16/bcftools isec -Ob -C -c any /tmp/vabHikq0lF/isec.a.vcf.gz /tmp/vabHikq0lF/isec.b.vcf.gz .. ok test_vcf_isec2: /build/bcftools-1.16/bcftools isec --no-version -T /tmp/vabHikq0lF/isec.tab.gz /tmp/vabHikq0lF/isec.a.vcf.gz .. ok test_vcf_isec2: /build/bcftools-1.16/bcftools isec -Ob -T /tmp/vabHikq0lF/isec.tab.gz /tmp/vabHikq0lF/isec.a.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_isec: /build/bcftools-1.16/bcftools isec -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/vabHikq0lF/isec-miss.1.1.vcf.gz /tmp/vabHikq0lF/isec-miss.1.2.vcf.gz /tmp/vabHikq0lF/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.16/bcftools isec -Ob -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/vabHikq0lF/isec-miss.1.1.vcf.gz /tmp/vabHikq0lF/isec-miss.1.2.vcf.gz /tmp/vabHikq0lF/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.16/bcftools isec -R /build/bcftools-1.16/test/isec-miss.1.regs.txt -n +1 /tmp/vabHikq0lF/isec-miss.1.1.vcf.gz /tmp/vabHikq0lF/isec-miss.1.2.vcf.gz /tmp/vabHikq0lF/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.16/bcftools isec -Ob -R /build/bcftools-1.16/test/isec-miss.1.regs.txt -n +1 /tmp/vabHikq0lF/isec-miss.1.1.vcf.gz /tmp/vabHikq0lF/isec-miss.1.2.vcf.gz /tmp/vabHikq0lF/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.16/bcftools isec -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/vabHikq0lF/isec-miss.2.1.vcf.gz /tmp/vabHikq0lF/isec-miss.2.2.vcf.gz /tmp/vabHikq0lF/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.16/bcftools isec -Ob -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/vabHikq0lF/isec-miss.2.1.vcf.gz /tmp/vabHikq0lF/isec-miss.2.2.vcf.gz /tmp/vabHikq0lF/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.16/bcftools isec -R /build/bcftools-1.16/test/isec-miss.1.regs.txt -n +1 /tmp/vabHikq0lF/isec-miss.2.1.vcf.gz /tmp/vabHikq0lF/isec-miss.2.2.vcf.gz /tmp/vabHikq0lF/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.16/bcftools isec -Ob -R /build/bcftools-1.16/test/isec-miss.1.regs.txt -n +1 /tmp/vabHikq0lF/isec-miss.2.1.vcf.gz /tmp/vabHikq0lF/isec-miss.2.2.vcf.gz /tmp/vabHikq0lF/isec-miss.2.3.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version -i AF:join /tmp/vabHikq0lF/merge.join.a.vcf.gz /tmp/vabHikq0lF/merge.join.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob -i AF:join /tmp/vabHikq0lF/merge.join.a.vcf.gz /tmp/vabHikq0lF/merge.join.b.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version -i AF:join /tmp/vabHikq0lF/merge.join.a.bcf /tmp/vabHikq0lF/merge.join.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob -i AF:join /tmp/vabHikq0lF/merge.join.a.bcf /tmp/vabHikq0lF/merge.join.b.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --force-samples /tmp/vabHikq0lF/merge.LPL.a.vcf.gz /tmp/vabHikq0lF/merge.LPL.b.vcf.gz /tmp/vabHikq0lF/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples /tmp/vabHikq0lF/merge.LPL.a.vcf.gz /tmp/vabHikq0lF/merge.LPL.b.vcf.gz /tmp/vabHikq0lF/merge.LPL.c.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --force-samples /tmp/vabHikq0lF/merge.LPL.a.bcf /tmp/vabHikq0lF/merge.LPL.b.bcf /tmp/vabHikq0lF/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples /tmp/vabHikq0lF/merge.LPL.a.bcf /tmp/vabHikq0lF/merge.LPL.b.bcf /tmp/vabHikq0lF/merge.LPL.c.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --force-samples -L 1 /tmp/vabHikq0lF/merge.LPL.a.vcf.gz /tmp/vabHikq0lF/merge.LPL.b.vcf.gz /tmp/vabHikq0lF/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -L 1 /tmp/vabHikq0lF/merge.LPL.a.vcf.gz /tmp/vabHikq0lF/merge.LPL.b.vcf.gz /tmp/vabHikq0lF/merge.LPL.c.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --force-samples -L 1 /tmp/vabHikq0lF/merge.LPL.a.bcf /tmp/vabHikq0lF/merge.LPL.b.bcf /tmp/vabHikq0lF/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -L 1 /tmp/vabHikq0lF/merge.LPL.a.bcf /tmp/vabHikq0lF/merge.LPL.b.bcf /tmp/vabHikq0lF/merge.LPL.c.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --force-samples -L 2 /tmp/vabHikq0lF/merge.LPL.a.vcf.gz /tmp/vabHikq0lF/merge.LPL.b.vcf.gz /tmp/vabHikq0lF/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -L 2 /tmp/vabHikq0lF/merge.LPL.a.vcf.gz /tmp/vabHikq0lF/merge.LPL.b.vcf.gz /tmp/vabHikq0lF/merge.LPL.c.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --force-samples -L 2 /tmp/vabHikq0lF/merge.LPL.a.bcf /tmp/vabHikq0lF/merge.LPL.b.bcf /tmp/vabHikq0lF/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -L 2 /tmp/vabHikq0lF/merge.LPL.a.bcf /tmp/vabHikq0lF/merge.LPL.b.bcf /tmp/vabHikq0lF/merge.LPL.c.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --force-samples -L 3 /tmp/vabHikq0lF/merge.LPL.a.vcf.gz /tmp/vabHikq0lF/merge.LPL.b.vcf.gz /tmp/vabHikq0lF/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -L 3 /tmp/vabHikq0lF/merge.LPL.a.vcf.gz /tmp/vabHikq0lF/merge.LPL.b.vcf.gz /tmp/vabHikq0lF/merge.LPL.c.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --force-samples -L 3 /tmp/vabHikq0lF/merge.LPL.a.bcf /tmp/vabHikq0lF/merge.LPL.b.bcf /tmp/vabHikq0lF/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -L 3 /tmp/vabHikq0lF/merge.LPL.a.bcf /tmp/vabHikq0lF/merge.LPL.b.bcf /tmp/vabHikq0lF/merge.LPL.c.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --force-samples -L 4 /tmp/vabHikq0lF/merge.LPL.a.vcf.gz /tmp/vabHikq0lF/merge.LPL.b.vcf.gz /tmp/vabHikq0lF/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -L 4 /tmp/vabHikq0lF/merge.LPL.a.vcf.gz /tmp/vabHikq0lF/merge.LPL.b.vcf.gz /tmp/vabHikq0lF/merge.LPL.c.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --force-samples -L 4 /tmp/vabHikq0lF/merge.LPL.a.bcf /tmp/vabHikq0lF/merge.LPL.b.bcf /tmp/vabHikq0lF/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -L 4 /tmp/vabHikq0lF/merge.LPL.a.bcf /tmp/vabHikq0lF/merge.LPL.b.bcf /tmp/vabHikq0lF/merge.LPL.c.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --force-samples -L 5 /tmp/vabHikq0lF/merge.LPL.a.vcf.gz /tmp/vabHikq0lF/merge.LPL.b.vcf.gz /tmp/vabHikq0lF/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -L 5 /tmp/vabHikq0lF/merge.LPL.a.vcf.gz /tmp/vabHikq0lF/merge.LPL.b.vcf.gz /tmp/vabHikq0lF/merge.LPL.c.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --force-samples -L 5 /tmp/vabHikq0lF/merge.LPL.a.bcf /tmp/vabHikq0lF/merge.LPL.b.bcf /tmp/vabHikq0lF/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -L 5 /tmp/vabHikq0lF/merge.LPL.a.bcf /tmp/vabHikq0lF/merge.LPL.b.bcf /tmp/vabHikq0lF/merge.LPL.c.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --force-samples /tmp/vabHikq0lF/merge.a.vcf.gz /tmp/vabHikq0lF/merge.b.vcf.gz /tmp/vabHikq0lF/merge.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples /tmp/vabHikq0lF/merge.a.vcf.gz /tmp/vabHikq0lF/merge.b.vcf.gz /tmp/vabHikq0lF/merge.c.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --force-samples /tmp/vabHikq0lF/merge.a.bcf /tmp/vabHikq0lF/merge.b.bcf /tmp/vabHikq0lF/merge.c.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples /tmp/vabHikq0lF/merge.a.bcf /tmp/vabHikq0lF/merge.b.bcf /tmp/vabHikq0lF/merge.c.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --force-samples -Fx /tmp/vabHikq0lF/merge.a.vcf.gz /tmp/vabHikq0lF/merge.b.vcf.gz /tmp/vabHikq0lF/merge.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -Fx /tmp/vabHikq0lF/merge.a.vcf.gz /tmp/vabHikq0lF/merge.b.vcf.gz /tmp/vabHikq0lF/merge.c.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --force-samples -Fx /tmp/vabHikq0lF/merge.a.bcf /tmp/vabHikq0lF/merge.b.bcf /tmp/vabHikq0lF/merge.c.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -Fx /tmp/vabHikq0lF/merge.a.bcf /tmp/vabHikq0lF/merge.b.bcf /tmp/vabHikq0lF/merge.c.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --force-samples -0 /tmp/vabHikq0lF/merge.a.vcf.gz /tmp/vabHikq0lF/merge.b.vcf.gz /tmp/vabHikq0lF/merge.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -0 /tmp/vabHikq0lF/merge.a.vcf.gz /tmp/vabHikq0lF/merge.b.vcf.gz /tmp/vabHikq0lF/merge.c.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --force-samples -0 /tmp/vabHikq0lF/merge.a.bcf /tmp/vabHikq0lF/merge.b.bcf /tmp/vabHikq0lF/merge.c.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -0 /tmp/vabHikq0lF/merge.a.bcf /tmp/vabHikq0lF/merge.b.bcf /tmp/vabHikq0lF/merge.c.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --force-samples -m none /tmp/vabHikq0lF/merge.2.a.vcf.gz /tmp/vabHikq0lF/merge.2.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -m none /tmp/vabHikq0lF/merge.2.a.vcf.gz /tmp/vabHikq0lF/merge.2.b.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --force-samples -m none /tmp/vabHikq0lF/merge.2.a.bcf /tmp/vabHikq0lF/merge.2.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -m none /tmp/vabHikq0lF/merge.2.a.bcf /tmp/vabHikq0lF/merge.2.b.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --force-samples -m both /tmp/vabHikq0lF/merge.2.a.vcf.gz /tmp/vabHikq0lF/merge.2.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -m both /tmp/vabHikq0lF/merge.2.a.vcf.gz /tmp/vabHikq0lF/merge.2.b.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --force-samples -m both /tmp/vabHikq0lF/merge.2.a.bcf /tmp/vabHikq0lF/merge.2.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -m both /tmp/vabHikq0lF/merge.2.a.bcf /tmp/vabHikq0lF/merge.2.b.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --force-samples -m all /tmp/vabHikq0lF/merge.2.a.vcf.gz /tmp/vabHikq0lF/merge.2.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -m all /tmp/vabHikq0lF/merge.2.a.vcf.gz /tmp/vabHikq0lF/merge.2.b.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --force-samples -m all /tmp/vabHikq0lF/merge.2.a.bcf /tmp/vabHikq0lF/merge.2.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -m all /tmp/vabHikq0lF/merge.2.a.bcf /tmp/vabHikq0lF/merge.2.b.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/vabHikq0lF/merge.3.a.vcf.gz /tmp/vabHikq0lF/merge.3.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/vabHikq0lF/merge.3.a.vcf.gz /tmp/vabHikq0lF/merge.3.b.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/vabHikq0lF/merge.3.a.bcf /tmp/vabHikq0lF/merge.3.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/vabHikq0lF/merge.3.a.bcf /tmp/vabHikq0lF/merge.3.b.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --force-samples -m id /tmp/vabHikq0lF/merge.4.a.vcf.gz /tmp/vabHikq0lF/merge.4.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -m id /tmp/vabHikq0lF/merge.4.a.vcf.gz /tmp/vabHikq0lF/merge.4.b.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --force-samples -m id /tmp/vabHikq0lF/merge.4.a.bcf /tmp/vabHikq0lF/merge.4.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -m id /tmp/vabHikq0lF/merge.4.a.bcf /tmp/vabHikq0lF/merge.4.b.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --gvcf - /tmp/vabHikq0lF/gvcf.merge.1.vcf.gz /tmp/vabHikq0lF/gvcf.merge.2.vcf.gz /tmp/vabHikq0lF/gvcf.merge.3.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --gvcf - /tmp/vabHikq0lF/gvcf.merge.1.vcf.gz /tmp/vabHikq0lF/gvcf.merge.2.vcf.gz /tmp/vabHikq0lF/gvcf.merge.3.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --gvcf - /tmp/vabHikq0lF/gvcf.merge.1.bcf /tmp/vabHikq0lF/gvcf.merge.2.bcf /tmp/vabHikq0lF/gvcf.merge.3.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --gvcf - /tmp/vabHikq0lF/gvcf.merge.1.bcf /tmp/vabHikq0lF/gvcf.merge.2.bcf /tmp/vabHikq0lF/gvcf.merge.3.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --gvcf - /tmp/vabHikq0lF/merge.gvcf.2.a.vcf.gz /tmp/vabHikq0lF/merge.gvcf.2.b.vcf.gz /tmp/vabHikq0lF/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --gvcf - /tmp/vabHikq0lF/merge.gvcf.2.a.vcf.gz /tmp/vabHikq0lF/merge.gvcf.2.b.vcf.gz /tmp/vabHikq0lF/merge.gvcf.2.c.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --gvcf - -i SRC:join /tmp/vabHikq0lF/merge.gvcf.3.a.vcf.gz /tmp/vabHikq0lF/merge.gvcf.3.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --gvcf - -i SRC:join /tmp/vabHikq0lF/merge.gvcf.3.a.vcf.gz /tmp/vabHikq0lF/merge.gvcf.3.b.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --gvcf - /tmp/vabHikq0lF/merge.gvcf.4.a.vcf.gz /tmp/vabHikq0lF/merge.gvcf.4.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --gvcf - /tmp/vabHikq0lF/merge.gvcf.4.a.vcf.gz /tmp/vabHikq0lF/merge.gvcf.4.b.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --gvcf - /tmp/vabHikq0lF/merge.gvcf.4.a.bcf /tmp/vabHikq0lF/merge.gvcf.4.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --gvcf - /tmp/vabHikq0lF/merge.gvcf.4.a.bcf /tmp/vabHikq0lF/merge.gvcf.4.b.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version /tmp/vabHikq0lF/merge.5.a.vcf.gz /tmp/vabHikq0lF/merge.5.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob /tmp/vabHikq0lF/merge.5.a.vcf.gz /tmp/vabHikq0lF/merge.5.b.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version /tmp/vabHikq0lF/merge.5.a.bcf /tmp/vabHikq0lF/merge.5.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob /tmp/vabHikq0lF/merge.5.a.bcf /tmp/vabHikq0lF/merge.5.b.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version /tmp/vabHikq0lF/merge.6.a.vcf.gz /tmp/vabHikq0lF/merge.6.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob /tmp/vabHikq0lF/merge.6.a.vcf.gz /tmp/vabHikq0lF/merge.6.b.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version /tmp/vabHikq0lF/merge.6.a.bcf /tmp/vabHikq0lF/merge.6.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob /tmp/vabHikq0lF/merge.6.a.bcf /tmp/vabHikq0lF/merge.6.b.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --gvcf - /tmp/vabHikq0lF/merge.gvcf.7.a.vcf.gz /tmp/vabHikq0lF/merge.gvcf.7.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --gvcf - /tmp/vabHikq0lF/merge.gvcf.7.a.vcf.gz /tmp/vabHikq0lF/merge.gvcf.7.b.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --gvcf - /tmp/vabHikq0lF/merge.gvcf.7.a.bcf /tmp/vabHikq0lF/merge.gvcf.7.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --gvcf - /tmp/vabHikq0lF/merge.gvcf.7.a.bcf /tmp/vabHikq0lF/merge.gvcf.7.b.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --gvcf - /tmp/vabHikq0lF/merge.gvcf.8.a.vcf.gz /tmp/vabHikq0lF/merge.gvcf.8.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --gvcf - /tmp/vabHikq0lF/merge.gvcf.8.a.vcf.gz /tmp/vabHikq0lF/merge.gvcf.8.b.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --gvcf - /tmp/vabHikq0lF/merge.gvcf.8.a.bcf /tmp/vabHikq0lF/merge.gvcf.8.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --gvcf - /tmp/vabHikq0lF/merge.gvcf.8.a.bcf /tmp/vabHikq0lF/merge.gvcf.8.b.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --force-samples /tmp/vabHikq0lF/merge.7.a.vcf.gz /tmp/vabHikq0lF/merge.7.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples /tmp/vabHikq0lF/merge.7.a.vcf.gz /tmp/vabHikq0lF/merge.7.b.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --force-samples /tmp/vabHikq0lF/merge.7.a.bcf /tmp/vabHikq0lF/merge.7.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples /tmp/vabHikq0lF/merge.7.a.bcf /tmp/vabHikq0lF/merge.7.b.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --gvcf /build/bcftools-1.16/test/gvcf.fa /tmp/vabHikq0lF/merge.gvcf.9a.vcf.gz /tmp/vabHikq0lF/merge.gvcf.9b.vcf.gz /tmp/vabHikq0lF/merge.gvcf.9c.vcf.gz /tmp/vabHikq0lF/merge.gvcf.9d.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --gvcf /build/bcftools-1.16/test/gvcf.fa /tmp/vabHikq0lF/merge.gvcf.9a.vcf.gz /tmp/vabHikq0lF/merge.gvcf.9b.vcf.gz /tmp/vabHikq0lF/merge.gvcf.9c.vcf.gz /tmp/vabHikq0lF/merge.gvcf.9d.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --gvcf /build/bcftools-1.16/test/gvcf.fa /tmp/vabHikq0lF/merge.gvcf.9a.bcf /tmp/vabHikq0lF/merge.gvcf.9b.bcf /tmp/vabHikq0lF/merge.gvcf.9c.bcf /tmp/vabHikq0lF/merge.gvcf.9d.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --gvcf /build/bcftools-1.16/test/gvcf.fa /tmp/vabHikq0lF/merge.gvcf.9a.bcf /tmp/vabHikq0lF/merge.gvcf.9b.bcf /tmp/vabHikq0lF/merge.gvcf.9c.bcf /tmp/vabHikq0lF/merge.gvcf.9d.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --gvcf /build/bcftools-1.16/test/gvcf.fa -r 22:21-23 /tmp/vabHikq0lF/merge.gvcf.9a.vcf.gz /tmp/vabHikq0lF/merge.gvcf.9b.vcf.gz /tmp/vabHikq0lF/merge.gvcf.9c.vcf.gz /tmp/vabHikq0lF/merge.gvcf.9d.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --gvcf /build/bcftools-1.16/test/gvcf.fa -r 22:21-23 /tmp/vabHikq0lF/merge.gvcf.9a.vcf.gz /tmp/vabHikq0lF/merge.gvcf.9b.vcf.gz /tmp/vabHikq0lF/merge.gvcf.9c.vcf.gz /tmp/vabHikq0lF/merge.gvcf.9d.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --gvcf /build/bcftools-1.16/test/gvcf.fa -r 22:21-23 /tmp/vabHikq0lF/merge.gvcf.9a.bcf /tmp/vabHikq0lF/merge.gvcf.9b.bcf /tmp/vabHikq0lF/merge.gvcf.9c.bcf /tmp/vabHikq0lF/merge.gvcf.9d.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --gvcf /build/bcftools-1.16/test/gvcf.fa -r 22:21-23 /tmp/vabHikq0lF/merge.gvcf.9a.bcf /tmp/vabHikq0lF/merge.gvcf.9b.bcf /tmp/vabHikq0lF/merge.gvcf.9c.bcf /tmp/vabHikq0lF/merge.gvcf.9d.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --gvcf /build/bcftools-1.16/test/gvcf.fa /tmp/vabHikq0lF/merge.gvcf.9a.vcf.gz /tmp/vabHikq0lF/merge.gvcf.9b.vcf.gz /tmp/vabHikq0lF/merge.gvcf.9c.vcf.gz /tmp/vabHikq0lF/merge.gvcf.9d.vcf.gz /tmp/vabHikq0lF/merge.gvcf.9e.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --gvcf /build/bcftools-1.16/test/gvcf.fa /tmp/vabHikq0lF/merge.gvcf.9a.vcf.gz /tmp/vabHikq0lF/merge.gvcf.9b.vcf.gz /tmp/vabHikq0lF/merge.gvcf.9c.vcf.gz /tmp/vabHikq0lF/merge.gvcf.9d.vcf.gz /tmp/vabHikq0lF/merge.gvcf.9e.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --gvcf /build/bcftools-1.16/test/gvcf.fa /tmp/vabHikq0lF/merge.gvcf.9a.bcf /tmp/vabHikq0lF/merge.gvcf.9b.bcf /tmp/vabHikq0lF/merge.gvcf.9c.bcf /tmp/vabHikq0lF/merge.gvcf.9d.bcf /tmp/vabHikq0lF/merge.gvcf.9e.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --gvcf /build/bcftools-1.16/test/gvcf.fa /tmp/vabHikq0lF/merge.gvcf.9a.bcf /tmp/vabHikq0lF/merge.gvcf.9b.bcf /tmp/vabHikq0lF/merge.gvcf.9c.bcf /tmp/vabHikq0lF/merge.gvcf.9d.bcf /tmp/vabHikq0lF/merge.gvcf.9e.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --gvcf /build/bcftools-1.16/test/gvcf.fa -r 22:21-23 /tmp/vabHikq0lF/merge.gvcf.9a.vcf.gz /tmp/vabHikq0lF/merge.gvcf.9b.vcf.gz /tmp/vabHikq0lF/merge.gvcf.9c.vcf.gz /tmp/vabHikq0lF/merge.gvcf.9d.vcf.gz /tmp/vabHikq0lF/merge.gvcf.9e.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --gvcf /build/bcftools-1.16/test/gvcf.fa -r 22:21-23 /tmp/vabHikq0lF/merge.gvcf.9a.vcf.gz /tmp/vabHikq0lF/merge.gvcf.9b.vcf.gz /tmp/vabHikq0lF/merge.gvcf.9c.vcf.gz /tmp/vabHikq0lF/merge.gvcf.9d.vcf.gz /tmp/vabHikq0lF/merge.gvcf.9e.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --gvcf /build/bcftools-1.16/test/gvcf.fa -r 22:21-23 /tmp/vabHikq0lF/merge.gvcf.9a.bcf /tmp/vabHikq0lF/merge.gvcf.9b.bcf /tmp/vabHikq0lF/merge.gvcf.9c.bcf /tmp/vabHikq0lF/merge.gvcf.9d.bcf /tmp/vabHikq0lF/merge.gvcf.9e.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --gvcf /build/bcftools-1.16/test/gvcf.fa -r 22:21-23 /tmp/vabHikq0lF/merge.gvcf.9a.bcf /tmp/vabHikq0lF/merge.gvcf.9b.bcf /tmp/vabHikq0lF/merge.gvcf.9c.bcf /tmp/vabHikq0lF/merge.gvcf.9d.bcf /tmp/vabHikq0lF/merge.gvcf.9e.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version /tmp/vabHikq0lF/merge.gvcf.10.a.vcf.gz /tmp/vabHikq0lF/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob /tmp/vabHikq0lF/merge.gvcf.10.a.vcf.gz /tmp/vabHikq0lF/merge.gvcf.10.b.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version /tmp/vabHikq0lF/merge.gvcf.10.a.bcf /tmp/vabHikq0lF/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob /tmp/vabHikq0lF/merge.gvcf.10.a.bcf /tmp/vabHikq0lF/merge.gvcf.10.b.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version -m none /tmp/vabHikq0lF/merge.gvcf.10.a.vcf.gz /tmp/vabHikq0lF/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob -m none /tmp/vabHikq0lF/merge.gvcf.10.a.vcf.gz /tmp/vabHikq0lF/merge.gvcf.10.b.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version -m none /tmp/vabHikq0lF/merge.gvcf.10.a.bcf /tmp/vabHikq0lF/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob -m none /tmp/vabHikq0lF/merge.gvcf.10.a.bcf /tmp/vabHikq0lF/merge.gvcf.10.b.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version -g /build/bcftools-1.16/test/merge.gvcf.10.fa /tmp/vabHikq0lF/merge.gvcf.10.a.vcf.gz /tmp/vabHikq0lF/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob -g /build/bcftools-1.16/test/merge.gvcf.10.fa /tmp/vabHikq0lF/merge.gvcf.10.a.vcf.gz /tmp/vabHikq0lF/merge.gvcf.10.b.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version -g /build/bcftools-1.16/test/merge.gvcf.10.fa /tmp/vabHikq0lF/merge.gvcf.10.a.bcf /tmp/vabHikq0lF/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob -g /build/bcftools-1.16/test/merge.gvcf.10.fa /tmp/vabHikq0lF/merge.gvcf.10.a.bcf /tmp/vabHikq0lF/merge.gvcf.10.b.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version -g /build/bcftools-1.16/test/merge.gvcf.10.fa -m none /tmp/vabHikq0lF/merge.gvcf.10.a.vcf.gz /tmp/vabHikq0lF/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob -g /build/bcftools-1.16/test/merge.gvcf.10.fa -m none /tmp/vabHikq0lF/merge.gvcf.10.a.vcf.gz /tmp/vabHikq0lF/merge.gvcf.10.b.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version -g /build/bcftools-1.16/test/merge.gvcf.10.fa -m none /tmp/vabHikq0lF/merge.gvcf.10.a.bcf /tmp/vabHikq0lF/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob -g /build/bcftools-1.16/test/merge.gvcf.10.fa -m none /tmp/vabHikq0lF/merge.gvcf.10.a.bcf /tmp/vabHikq0lF/merge.gvcf.10.b.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version -g /build/bcftools-1.16/test/merge.gvcf.10.fa /tmp/vabHikq0lF/merge.gvcf.10.b.vcf.gz /tmp/vabHikq0lF/merge.gvcf.10.a.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob -g /build/bcftools-1.16/test/merge.gvcf.10.fa /tmp/vabHikq0lF/merge.gvcf.10.b.vcf.gz /tmp/vabHikq0lF/merge.gvcf.10.a.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version -g /build/bcftools-1.16/test/merge.gvcf.10.fa /tmp/vabHikq0lF/merge.gvcf.10.b.bcf /tmp/vabHikq0lF/merge.gvcf.10.a.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob -g /build/bcftools-1.16/test/merge.gvcf.10.fa /tmp/vabHikq0lF/merge.gvcf.10.b.bcf /tmp/vabHikq0lF/merge.gvcf.10.a.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version -g /build/bcftools-1.16/test/merge.gvcf.10.fa -m none /tmp/vabHikq0lF/merge.gvcf.10.b.vcf.gz /tmp/vabHikq0lF/merge.gvcf.10.a.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob -g /build/bcftools-1.16/test/merge.gvcf.10.fa -m none /tmp/vabHikq0lF/merge.gvcf.10.b.vcf.gz /tmp/vabHikq0lF/merge.gvcf.10.a.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version -g /build/bcftools-1.16/test/merge.gvcf.10.fa -m none /tmp/vabHikq0lF/merge.gvcf.10.b.bcf /tmp/vabHikq0lF/merge.gvcf.10.a.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob -g /build/bcftools-1.16/test/merge.gvcf.10.fa -m none /tmp/vabHikq0lF/merge.gvcf.10.b.bcf /tmp/vabHikq0lF/merge.gvcf.10.a.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version /tmp/vabHikq0lF/merge.noidx.a.vcf.gz /tmp/vabHikq0lF/merge.noidx.b.vcf.gz /tmp/vabHikq0lF/merge.noidx.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob /tmp/vabHikq0lF/merge.noidx.a.vcf.gz /tmp/vabHikq0lF/merge.noidx.b.vcf.gz /tmp/vabHikq0lF/merge.noidx.c.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version /tmp/vabHikq0lF/merge.noidx.a.bcf /tmp/vabHikq0lF/merge.noidx.b.bcf /tmp/vabHikq0lF/merge.noidx.c.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob /tmp/vabHikq0lF/merge.noidx.a.bcf /tmp/vabHikq0lF/merge.noidx.b.bcf /tmp/vabHikq0lF/merge.noidx.c.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --no-index /build/bcftools-1.16/test/merge.noidx.a.vcf /build/bcftools-1.16/test/merge.noidx.b.vcf /build/bcftools-1.16/test/merge.noidx.c.vcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --no-index /build/bcftools-1.16/test/merge.noidx.a.vcf /build/bcftools-1.16/test/merge.noidx.b.vcf /build/bcftools-1.16/test/merge.noidx.c.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --no-index /tmp/vabHikq0lF/merge.noidx.a.bcf /tmp/vabHikq0lF/merge.noidx.b.bcf /tmp/vabHikq0lF/merge.noidx.c.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --no-index /tmp/vabHikq0lF/merge.noidx.a.bcf /tmp/vabHikq0lF/merge.noidx.b.bcf /tmp/vabHikq0lF/merge.noidx.c.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version /tmp/vabHikq0lF/merge.8.a.vcf.gz /tmp/vabHikq0lF/merge.8.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob /tmp/vabHikq0lF/merge.8.a.vcf.gz /tmp/vabHikq0lF/merge.8.b.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version /tmp/vabHikq0lF/merge.8.a.bcf /tmp/vabHikq0lF/merge.8.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob /tmp/vabHikq0lF/merge.8.a.bcf /tmp/vabHikq0lF/merge.8.b.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version -i AN:sum,AC:sum /tmp/vabHikq0lF/merge.8.a.vcf.gz /tmp/vabHikq0lF/merge.8.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob -i AN:sum,AC:sum /tmp/vabHikq0lF/merge.8.a.vcf.gz /tmp/vabHikq0lF/merge.8.b.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version -i AN:sum,AC:sum /tmp/vabHikq0lF/merge.8.a.bcf /tmp/vabHikq0lF/merge.8.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob -i AN:sum,AC:sum /tmp/vabHikq0lF/merge.8.a.bcf /tmp/vabHikq0lF/merge.8.b.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version /tmp/vabHikq0lF/merge.9.a.vcf.gz /tmp/vabHikq0lF/merge.9.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob /tmp/vabHikq0lF/merge.9.a.vcf.gz /tmp/vabHikq0lF/merge.9.b.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version /tmp/vabHikq0lF/merge.9.a.bcf /tmp/vabHikq0lF/merge.9.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob /tmp/vabHikq0lF/merge.9.a.bcf /tmp/vabHikq0lF/merge.9.b.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version -i AN:sum,AC:sum /tmp/vabHikq0lF/merge.9.a.vcf.gz /tmp/vabHikq0lF/merge.9.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob -i AN:sum,AC:sum /tmp/vabHikq0lF/merge.9.a.vcf.gz /tmp/vabHikq0lF/merge.9.b.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version -i AN:sum,AC:sum /tmp/vabHikq0lF/merge.9.a.bcf /tmp/vabHikq0lF/merge.9.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob -i AN:sum,AC:sum /tmp/vabHikq0lF/merge.9.a.bcf /tmp/vabHikq0lF/merge.9.b.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version -m none /tmp/vabHikq0lF/merge.10.a.vcf.gz /tmp/vabHikq0lF/merge.10.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob -m none /tmp/vabHikq0lF/merge.10.a.vcf.gz /tmp/vabHikq0lF/merge.10.b.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version -m none /tmp/vabHikq0lF/merge.10.a.bcf /tmp/vabHikq0lF/merge.10.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob -m none /tmp/vabHikq0lF/merge.10.a.bcf /tmp/vabHikq0lF/merge.10.b.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version -m both /tmp/vabHikq0lF/merge.10.a.vcf.gz /tmp/vabHikq0lF/merge.10.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob -m both /tmp/vabHikq0lF/merge.10.a.vcf.gz /tmp/vabHikq0lF/merge.10.b.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version -m both /tmp/vabHikq0lF/merge.10.a.bcf /tmp/vabHikq0lF/merge.10.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob -m both /tmp/vabHikq0lF/merge.10.a.bcf /tmp/vabHikq0lF/merge.10.b.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version -m snp-ins-del /tmp/vabHikq0lF/merge.10.a.vcf.gz /tmp/vabHikq0lF/merge.10.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob -m snp-ins-del /tmp/vabHikq0lF/merge.10.a.vcf.gz /tmp/vabHikq0lF/merge.10.b.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version -m snp-ins-del /tmp/vabHikq0lF/merge.10.a.bcf /tmp/vabHikq0lF/merge.10.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob -m snp-ins-del /tmp/vabHikq0lF/merge.10.a.bcf /tmp/vabHikq0lF/merge.10.b.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided,_conflicting_interpretations"' /tmp/vabHikq0lF/query.string.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.string.vcf.gz | /build/bcftools-1.16/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided,_conflicting_interpretations"' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" || CLNREVSTAT="_conflicting_interpretations"' /tmp/vabHikq0lF/query.string.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.string.vcf.gz | /build/bcftools-1.16/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" || CLNREVSTAT="_conflicting_interpretations"' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" && CLNREVSTAT="_conflicting_interpretations"' /tmp/vabHikq0lF/query.string.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.string.vcf.gz | /build/bcftools-1.16/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" && CLNREVSTAT="_conflicting_interpretations"' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' /tmp/vabHikq0lF/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.vcf.gz | /build/bcftools-1.16/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f '%RSX\t%VKX\n' /tmp/vabHikq0lF/query.variantkey.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.variantkey.vcf.gz | /build/bcftools-1.16/bcftools query -f '%RSX\t%VKX\n' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%XRI\n' -i'XRI[*]>1111' /tmp/vabHikq0lF/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/view.filter.vcf.gz | /build/bcftools-1.16/bcftools query -f'%XRI\n' -i'XRI[*]>1111' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' /tmp/vabHikq0lF/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/view.filter.vcf.gz | /build/bcftools-1.16/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' /tmp/vabHikq0lF/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/view.filter.vcf.gz | /build/bcftools-1.16/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' /tmp/vabHikq0lF/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/view.filter.vcf.gz | /build/bcftools-1.16/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' /tmp/vabHikq0lF/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/view.filter.vcf.gz | /build/bcftools-1.16/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' /tmp/vabHikq0lF/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/view.filter.vcf.gz | /build/bcftools-1.16/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' /tmp/vabHikq0lF/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/view.filter.vcf.gz | /build/bcftools-1.16/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' /tmp/vabHikq0lF/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' /tmp/vabHikq0lF/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' /tmp/vabHikq0lF/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' /tmp/vabHikq0lF/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' /tmp/vabHikq0lF/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/view.filter.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' /tmp/vabHikq0lF/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' /tmp/vabHikq0lF/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' /tmp/vabHikq0lF/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' /tmp/vabHikq0lF/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' .. ok test_vcf_query: /build/bcftools-1.16/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/vabHikq0lF/view.vectors.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/view.vectors.vcf.gz | /build/bcftools-1.16/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/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' /tmp/vabHikq0lF/query.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.filter.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' /tmp/vabHikq0lF/query.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.filter.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' /tmp/vabHikq0lF/query.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.filter.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' /tmp/vabHikq0lF/query.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.filter.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' /tmp/vabHikq0lF/query.2.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.2.vcf.gz | /build/bcftools-1.16/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -i'IINT="."' -f'%POS %IINT\n' /tmp/vabHikq0lF/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/missing.vcf.gz | /build/bcftools-1.16/bcftools query -i'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -i'IINT!="."' -f'%POS %IINT\n' /tmp/vabHikq0lF/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/missing.vcf.gz | /build/bcftools-1.16/bcftools query -i'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -e'IINT!="."' -f'%POS %IINT\n' /tmp/vabHikq0lF/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/missing.vcf.gz | /build/bcftools-1.16/bcftools query -e'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -e'IINT="."' -f'%POS %IINT\n' /tmp/vabHikq0lF/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/missing.vcf.gz | /build/bcftools-1.16/bcftools query -e'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' /tmp/vabHikq0lF/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/missing.vcf.gz | /build/bcftools-1.16/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' /tmp/vabHikq0lF/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/missing.vcf.gz | /build/bcftools-1.16/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' /tmp/vabHikq0lF/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/missing.vcf.gz | /build/bcftools-1.16/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' /tmp/vabHikq0lF/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/missing.vcf.gz | /build/bcftools-1.16/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' /tmp/vabHikq0lF/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/missing.vcf.gz | /build/bcftools-1.16/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' /tmp/vabHikq0lF/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/missing.vcf.gz | /build/bcftools-1.16/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' /tmp/vabHikq0lF/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/missing.vcf.gz | /build/bcftools-1.16/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' /tmp/vabHikq0lF/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/missing.vcf.gz | /build/bcftools-1.16/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' /tmp/vabHikq0lF/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/missing.vcf.gz | /build/bcftools-1.16/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -i'FILTER="A"' -f'%POS %FILTER\n' /tmp/vabHikq0lF/filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/filter.11.vcf.gz | /build/bcftools-1.16/bcftools query -i'FILTER="A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -i'FILTER!="A"' -f'%POS %FILTER\n' /tmp/vabHikq0lF/filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/filter.11.vcf.gz | /build/bcftools-1.16/bcftools query -i'FILTER!="A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -i'FILTER~"A"' -f'%POS %FILTER\n' /tmp/vabHikq0lF/filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/filter.11.vcf.gz | /build/bcftools-1.16/bcftools query -i'FILTER~"A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n' /tmp/vabHikq0lF/filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/filter.11.vcf.gz | /build/bcftools-1.16/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%LINE' /tmp/vabHikq0lF/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.vcf.gz | /build/bcftools-1.16/bcftools query -f'%LINE' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' /tmp/vabHikq0lF/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.filter-type.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' /tmp/vabHikq0lF/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.filter-type.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' /tmp/vabHikq0lF/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.filter-type.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' /tmp/vabHikq0lF/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.filter-type.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\n' -i'INFO/TYPE="xxx"' /tmp/vabHikq0lF/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.filter-type.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\n' -i'INFO/TYPE="xxx"' .. ok test_vcf_query: /build/bcftools-1.16/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/vabHikq0lF/filter-missing-floats.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/filter-missing-floats.vcf.gz | /build/bcftools-1.16/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/bcftools-1.16/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/vabHikq0lF/filter-missing-floats.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/filter-missing-floats.vcf.gz | /build/bcftools-1.16/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/bcftools-1.16/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' /tmp/vabHikq0lF/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/missing.vcf.gz | /build/bcftools-1.16/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' /tmp/vabHikq0lF/query.filter.2.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.filter.2.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' /tmp/vabHikq0lF/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/view.filter.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' /tmp/vabHikq0lF/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/view.filter.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' /tmp/vabHikq0lF/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/view.filter.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' /tmp/vabHikq0lF/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/view.filter.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' /tmp/vabHikq0lF/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/view.filter.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' /tmp/vabHikq0lF/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/view.filter.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' /tmp/vabHikq0lF/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/view.filter.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' /tmp/vabHikq0lF/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/view.filter.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' /tmp/vabHikq0lF/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/view.filter.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' /tmp/vabHikq0lF/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/view.filter.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' /tmp/vabHikq0lF/filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/filter.5.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' /tmp/vabHikq0lF/filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/filter.5.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' /tmp/vabHikq0lF/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/view.filter.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' /tmp/vabHikq0lF/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/view.filter.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' /tmp/vabHikq0lF/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/view.filter.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' /tmp/vabHikq0lF/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/view.filter.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' /tmp/vabHikq0lF/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/view.filter.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 & FMT/GQ=589' /tmp/vabHikq0lF/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/view.filter.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 & FMT/GQ=589' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' /tmp/vabHikq0lF/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/view.filter.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' /tmp/vabHikq0lF/query.filter.3.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.filter.3.vcf.gz | /build/bcftools-1.16/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"' /tmp/vabHikq0lF/query.filter.3.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.filter.3.vcf.gz | /build/bcftools-1.16/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' /tmp/vabHikq0lF/query.filter.3.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.filter.3.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %AD\n]\n' -i'AD[:0]+AD[:1] > 12' /tmp/vabHikq0lF/filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/filter.5.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %AD\n]\n' -i'AD[:0]+AD[:1] > 12' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' /tmp/vabHikq0lF/query.filter.4.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.filter.4.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%ID\n' -i 'ID=@/build/bcftools-1.16/test/query.56.out' /tmp/vabHikq0lF/view.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/view.vcf.gz | /build/bcftools-1.16/bcftools query -f'%ID\n' -i 'ID=@/build/bcftools-1.16/test/query.56.out' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD)>0.01' /tmp/vabHikq0lF/query.filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.filter.5.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD)>0.01' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD[:0],FMT/AD[:1])>0.01' /tmp/vabHikq0lF/query.filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.filter.5.vcf.gz | /build/bcftools-1.16/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/bcftools-1.16/bcftools query -f'%POS\t%AD\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01' /tmp/vabHikq0lF/query.filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.filter.5.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS\t%AD\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%CHROM %POS\n' -i'CHROM="4"' /tmp/vabHikq0lF/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.vcf.gz | /build/bcftools-1.16/bcftools query -f'%CHROM %POS\n' -i'CHROM="4"' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS\t%TAG1\n' -i'(TAG1>=-129 && TAG1<=-120) || (TAG1>=-32769 && TAG1<=-32760)' /tmp/vabHikq0lF/query.negative.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.negative.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS\t%TAG1\n' -i'(TAG1>=-129 && TAG1<=-120) || (TAG1>=-32769 && TAG1<=-32760)' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS\t%TAGV1\n' -i'(TAGV1>=-129 && TAGV1<=-120) || (TAGV1>=-32769 && TAGV1<=-32760)' /tmp/vabHikq0lF/query.negative.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.negative.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS\t%TAGV1\n' -i'(TAGV1>=-129 && TAGV1<=-120) || (TAGV1>=-32769 && TAGV1<=-32760)' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS\t%TAG2\n' -i'(TAG2>=-129 && TAG2<=-120) || (TAG2>=-32769 && TAG2<=-32760)' /tmp/vabHikq0lF/query.negative.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.negative.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS\t%TAG2\n' -i'(TAG2>=-129 && TAG2<=-120) || (TAG2>=-32769 && TAG2<=-32760)' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS\t%TAGV2\n' -i'(TAGV2>=-129 && TAGV2<=-120) || (TAGV2>=-32769 && TAGV2<=-32760)' /tmp/vabHikq0lF/query.negative.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.negative.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS\t%TAGV2\n' -i'(TAGV2>=-129 && TAGV2<=-120) || (TAGV2>=-32769 && TAGV2<=-32760)' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%POS\t%SAMPLE\t%GQ\n]' -i'N_PASS(GQ<20)==1' /tmp/vabHikq0lF/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%POS\t%SAMPLE\t%GQ\n]' -i'N_PASS(GQ<20)==1' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")==1' /tmp/vabHikq0lF/query.filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.filter.11.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")==1' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")!=1' /tmp/vabHikq0lF/query.filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.filter.11.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")!=1' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")==1' /tmp/vabHikq0lF/query.filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.filter.11.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")==1' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")!=1' /tmp/vabHikq0lF/query.filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.filter.11.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")!=1' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%CHROM\t%POS\t%INFO\t%FORMAT\n' -s D,C /tmp/vabHikq0lF/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.vcf.gz | /build/bcftools-1.16/bcftools query -f'%CHROM\t%POS\t%INFO\t%FORMAT\n' -s D,C .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS\n' -i'POS==16777217 || POS==33554432 || POS=118673904' /tmp/vabHikq0lF/query.filter.6.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.filter.6.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS\n' -i'POS==16777217 || POS==33554432 || POS=118673904' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(II)==6' /tmp/vabHikq0lF/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.filter.7.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(II)==6' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(FORMAT/FI)==7' /tmp/vabHikq0lF/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.filter.7.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(FORMAT/FI)==7' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(II)==2' /tmp/vabHikq0lF/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.filter.7.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(II)==2' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(FORMAT/FI)==1.75' /tmp/vabHikq0lF/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.filter.7.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(FORMAT/FI)==1.75' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(II)==2' /tmp/vabHikq0lF/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.filter.7.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(II)==2' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(FORMAT/FI)==1.75' /tmp/vabHikq0lF/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.filter.7.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(FORMAT/FI)==1.75' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(II)==2' /tmp/vabHikq0lF/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.filter.7.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(II)==2' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(FORMAT/FI)==1.5' /tmp/vabHikq0lF/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.filter.7.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(FORMAT/FI)==1.5' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'%ILEN==1' /tmp/vabHikq0lF/query.filter.8.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.filter.8.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'%ILEN==1' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'ILEN==1' /tmp/vabHikq0lF/query.filter.8.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.filter.8.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'ILEN==1' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] < FMT/AD[:1]' /tmp/vabHikq0lF/query.filter.9.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.filter.9.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] < FMT/AD[:1]' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] > FMT/AD[:1]' /tmp/vabHikq0lF/query.filter.9.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.filter.9.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] > FMT/AD[:1]' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[ %AD\n]' -i'AD[:1] / sum(AD[*]) > 0.5' /tmp/vabHikq0lF/query.filter.13.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.filter.13.vcf.gz | /build/bcftools-1.16/bcftools query -f'[ %AD\n]' -i'AD[:1] / sum(AD[*]) > 0.5' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS %NUM_TAG\n' -i'COUNT(INFO/NUM_TAG)=2' /tmp/vabHikq0lF/query.filter.10.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.filter.10.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS %NUM_TAG\n' -i'COUNT(INFO/NUM_TAG)=2' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2' /tmp/vabHikq0lF/query.filter.10.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.filter.10.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f '%CHROM:%POS\t%N_PASS(GT="alt" & GQ>110)\t[\t%GT]\t[\t%GQ]\n' /tmp/vabHikq0lF/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.vcf.gz | /build/bcftools-1.16/bcftools query -f '%CHROM:%POS\t%N_PASS(GT="alt" & GQ>110)\t[\t%GT]\t[\t%GQ]\n' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 1,3,0 /tmp/vabHikq0lF/query.filter.12.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.filter.12.vcf.gz | /build/bcftools-1.16/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 1,3,0 .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 0,1,3 /tmp/vabHikq0lF/query.filter.12.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.filter.12.vcf.gz | /build/bcftools-1.16/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 0,1,3 .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f "[%SAMPLE %GT\n]" -S /build/bcftools-1.16/test/query.smpl.11.txt /tmp/vabHikq0lF/query.smpl.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.smpl.vcf.gz | /build/bcftools-1.16/bcftools query -f "[%SAMPLE %GT\n]" -S /build/bcftools-1.16/test/query.smpl.11.txt .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -l -S /build/bcftools-1.16/test/query.smpl.11.txt /tmp/vabHikq0lF/query.smpl.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.smpl.vcf.gz | /build/bcftools-1.16/bcftools query -l -S /build/bcftools-1.16/test/query.smpl.11.txt .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f "[%SAMPLE %GT\n]" -S ^/build/bcftools-1.16/test/query.smpl.11.txt /tmp/vabHikq0lF/query.smpl.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.smpl.vcf.gz | /build/bcftools-1.16/bcftools query -f "[%SAMPLE %GT\n]" -S ^/build/bcftools-1.16/test/query.smpl.11.txt .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -l -S ^/build/bcftools-1.16/test/query.smpl.11.txt /tmp/vabHikq0lF/query.smpl.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.smpl.vcf.gz | /build/bcftools-1.16/bcftools query -l -S ^/build/bcftools-1.16/test/query.smpl.11.txt .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f "[%SAMPLE %GT\n]" -S /build/bcftools-1.16/test/query.smpl.txt /tmp/vabHikq0lF/query.smpl.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.smpl.vcf.gz | /build/bcftools-1.16/bcftools query -f "[%SAMPLE %GT\n]" -S /build/bcftools-1.16/test/query.smpl.txt .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -l -S /build/bcftools-1.16/test/query.smpl.txt /tmp/vabHikq0lF/query.smpl.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.smpl.vcf.gz | /build/bcftools-1.16/bcftools query -l -S /build/bcftools-1.16/test/query.smpl.txt .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%ID\n' -i'ID~"s12"' /tmp/vabHikq0lF/query.filter.id.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.filter.id.vcf.gz | /build/bcftools-1.16/bcftools query -f'%ID\n' -i'ID~"s12"' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%ID\n' -i'ID="rs123"' /tmp/vabHikq0lF/query.filter.id.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/query.filter.id.vcf.gz | /build/bcftools-1.16/bcftools query -f'%ID\n' -i'ID="rs123"' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -i'FILTER="A"' -f'%FILTER\n' /tmp/vabHikq0lF/filter.12.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/filter.12.vcf.gz | /build/bcftools-1.16/bcftools query -i'FILTER="A"' -f'%FILTER\n' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -i'FILTER~"A"' -f'%FILTER\n' /tmp/vabHikq0lF/filter.12.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/filter.12.vcf.gz | /build/bcftools-1.16/bcftools query -i'FILTER~"A"' -f'%FILTER\n' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -i'FILTER="A;B"' -f'%FILTER\n' /tmp/vabHikq0lF/filter.12.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/filter.12.vcf.gz | /build/bcftools-1.16/bcftools query -i'FILTER="A;B"' -f'%FILTER\n' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -i'FILTER!="A;B"' -f'%FILTER\n' /tmp/vabHikq0lF/filter.12.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/filter.12.vcf.gz | /build/bcftools-1.16/bcftools query -i'FILTER!="A;B"' -f'%FILTER\n' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -i'FILTER~"A;B"' -f'%FILTER\n' /tmp/vabHikq0lF/filter.12.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/filter.12.vcf.gz | /build/bcftools-1.16/bcftools query -i'FILTER~"A;B"' -f'%FILTER\n' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -i'FILTER!~"A;B"' -f'%FILTER\n' /tmp/vabHikq0lF/filter.12.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/filter.12.vcf.gz | /build/bcftools-1.16/bcftools query -i'FILTER!~"A;B"' -f'%FILTER\n' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -i'DP%10==2' -f'[ %DP]\n' /tmp/vabHikq0lF/filter.10.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/filter.10.vcf.gz | /build/bcftools-1.16/bcftools query -i'DP%10==2' -f'[ %DP]\n' .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version -cx -f /build/bcftools-1.16/test/norm.fa /tmp/vabHikq0lF/norm.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -cx -f /build/bcftools-1.16/test/norm.fa /tmp/vabHikq0lF/norm.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version -m- /tmp/vabHikq0lF/norm.split.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -m- /tmp/vabHikq0lF/norm.split.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version -m- /tmp/vabHikq0lF/norm.split.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -m- /tmp/vabHikq0lF/norm.split.2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version -m- --force /tmp/vabHikq0lF/norm.split.3.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -m- --force /tmp/vabHikq0lF/norm.split.3.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version -m- /tmp/vabHikq0lF/norm.split.4.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -m- /tmp/vabHikq0lF/norm.split.4.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version -m- --keep-sum AD /tmp/vabHikq0lF/norm.split.4.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -m- --keep-sum AD /tmp/vabHikq0lF/norm.split.4.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version -m- -f /build/bcftools-1.16/test/norm.fa /tmp/vabHikq0lF/norm.split.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -m- -f /build/bcftools-1.16/test/norm.fa /tmp/vabHikq0lF/norm.split.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version -m+ /tmp/vabHikq0lF/norm.merge.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -m+ /tmp/vabHikq0lF/norm.merge.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version -m+ /tmp/vabHikq0lF/norm.merge.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -m+ /tmp/vabHikq0lF/norm.merge.2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version -m+ /tmp/vabHikq0lF/norm.merge.3.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -m+ /tmp/vabHikq0lF/norm.merge.3.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version -m+ -s /tmp/vabHikq0lF/norm.merge.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -m+ -s /tmp/vabHikq0lF/norm.merge.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version -Nc s -f /build/bcftools-1.16/test/norm.fa /tmp/vabHikq0lF/norm.setref.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -Nc s -f /build/bcftools-1.16/test/norm.fa /tmp/vabHikq0lF/norm.setref.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version -f /build/bcftools-1.16/test/norm.fa /tmp/vabHikq0lF/norm.telomere.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -f /build/bcftools-1.16/test/norm.fa /tmp/vabHikq0lF/norm.telomere.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version -d snps /tmp/vabHikq0lF/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -d snps /tmp/vabHikq0lF/norm.rmdup.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version -d indels /tmp/vabHikq0lF/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -d indels /tmp/vabHikq0lF/norm.rmdup.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version -d both /tmp/vabHikq0lF/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -d both /tmp/vabHikq0lF/norm.rmdup.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version -d all /tmp/vabHikq0lF/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -d all /tmp/vabHikq0lF/norm.rmdup.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version -d none /tmp/vabHikq0lF/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -d none /tmp/vabHikq0lF/norm.rmdup.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version -d exact /tmp/vabHikq0lF/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -d exact /tmp/vabHikq0lF/norm.rmdup.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version -d none /tmp/vabHikq0lF/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -d none /tmp/vabHikq0lF/norm.rmdup.2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version -d exact /tmp/vabHikq0lF/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -d exact /tmp/vabHikq0lF/norm.rmdup.2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version -d indels /tmp/vabHikq0lF/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -d indels /tmp/vabHikq0lF/norm.rmdup.2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version -d any /tmp/vabHikq0lF/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -d any /tmp/vabHikq0lF/norm.rmdup.2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version -d both /tmp/vabHikq0lF/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -d both /tmp/vabHikq0lF/norm.rmdup.2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version -d snps /tmp/vabHikq0lF/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -d snps /tmp/vabHikq0lF/norm.rmdup.2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version -c s -a -f /build/bcftools-1.16/test/norm.2.fa /tmp/vabHikq0lF/norm.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -c s -a -f /build/bcftools-1.16/test/norm.2.fa /tmp/vabHikq0lF/norm.2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version -c s -f /build/bcftools-1.16/test/norm.iupac.fa /tmp/vabHikq0lF/norm.iupac.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -c s -f /build/bcftools-1.16/test/norm.iupac.fa /tmp/vabHikq0lF/norm.iupac.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version -c s -f /build/bcftools-1.16/test/norm.3.fa /tmp/vabHikq0lF/norm.3.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -c s -f /build/bcftools-1.16/test/norm.3.fa /tmp/vabHikq0lF/norm.3.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/vabHikq0lF/atomize.split.1.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob --atomize --old-rec-tag OLD_REC /tmp/vabHikq0lF/atomize.split.1.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/vabHikq0lF/atomize.split.1.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/vabHikq0lF/atomize.split.1.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/vabHikq0lF/atomize.split.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob --atomize --old-rec-tag OLD_REC /tmp/vabHikq0lF/atomize.split.2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/vabHikq0lF/atomize.split.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/vabHikq0lF/atomize.split.2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version --atomize --atom-overlaps . /tmp/vabHikq0lF/atomize.split.3.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob --atomize --atom-overlaps . /tmp/vabHikq0lF/atomize.split.3.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version -m +both /tmp/vabHikq0lF/norm.4.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -m +both /tmp/vabHikq0lF/norm.4.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version -m +any /tmp/vabHikq0lF/norm.4.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -m +any /tmp/vabHikq0lF/norm.4.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -aUc1 -C1 -s NA00002 -v snps /tmp/vabHikq0lF/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/vabHikq0lF/view.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -f PASS -Xks NA00003 /tmp/vabHikq0lF/view.vcf.gz -r20,Y .. ok test_vcf_view: /build/bcftools-1.16/bcftools view -Ob -f PASS -Xks NA00003 /tmp/vabHikq0lF/view.vcf.gz -r20,Y | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -xs NA00003 /tmp/vabHikq0lF/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view -Ob -xs NA00003 /tmp/vabHikq0lF/view.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/vabHikq0lF/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view -Ob -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/vabHikq0lF/view.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -p /tmp/vabHikq0lF/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view -Ob -p /tmp/vabHikq0lF/view.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -P /tmp/vabHikq0lF/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view -Ob -P /tmp/vabHikq0lF/view.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -hm2 -M2 -q0.3 -Q0.7 /tmp/vabHikq0lF/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/vabHikq0lF/view.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -Hu /tmp/vabHikq0lF/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -GVsnps /tmp/vabHikq0lF/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view -Ob -GVsnps /tmp/vabHikq0lF/view.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -ne 'INDEL=1 || PV4[0]<0.006' /tmp/vabHikq0lF/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/vabHikq0lF/view.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -s ^NA00003 /tmp/vabHikq0lF/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view -Ob -s ^NA00003 /tmp/vabHikq0lF/view.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version /tmp/vabHikq0lF/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/view.omitgenotypes.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -G /tmp/vabHikq0lF/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view -Ob -G /tmp/vabHikq0lF/view.omitgenotypes.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -HG /tmp/vabHikq0lF/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -a /tmp/vabHikq0lF/many.alleles.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view -Ob -a /tmp/vabHikq0lF/many.alleles.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -asA /tmp/vabHikq0lF/view.vectors.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view -Ob -asA /tmp/vabHikq0lF/view.vectors.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -asB /tmp/vabHikq0lF/view.vectors.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view -Ob -asB /tmp/vabHikq0lF/view.vectors.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -asA /tmp/vabHikq0lF/view.vectors.2.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view -Ob -asA /tmp/vabHikq0lF/view.vectors.2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -i'FMT/FGS[*:0]="AAAAAA"' /tmp/vabHikq0lF/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -i'FMT/FGS[*:2]="C"' /tmp/vabHikq0lF/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -i'FMT/FGS[*:4]="EE"' /tmp/vabHikq0lF/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -i'FMT/FRS[*:1]="BB"' /tmp/vabHikq0lF/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -i'TXT0="text"' /tmp/vabHikq0lF/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -T /build/bcftools-1.16/test/view.chrs.tab /tmp/vabHikq0lF/view.chrs.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view -Ob -T /build/bcftools-1.16/test/view.chrs.tab /tmp/vabHikq0lF/view.chrs.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -i 'POS>=3062917' /tmp/vabHikq0lF/filter.2.vcf.gz 1:3062917-3157410 .. ok test_vcf_view: /build/bcftools-1.16/bcftools view -Ob -i 'POS>=3062917' /tmp/vabHikq0lF/filter.2.vcf.gz 1:3062917-3157410 | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -r 1:10,1:12,1:10 /tmp/vabHikq0lF/idx.1.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -r 1:1172777-1172804,1:1172806-1172808 /tmp/vabHikq0lF/idx.2.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -R /build/bcftools-1.16/test/idx.2.bed /tmp/vabHikq0lF/idx.2.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -R /build/bcftools-1.16/test/idx.3.bed /tmp/vabHikq0lF/idx.3.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -R /build/bcftools-1.16/test/idx.4.bed /tmp/vabHikq0lF/idx.4.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -Ht 2 /tmp/vabHikq0lF/view-t.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -Ht 3 /tmp/vabHikq0lF/view-t.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 0 /tmp/vabHikq0lF/overlap.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 1 /tmp/vabHikq0lF/overlap.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 2 /tmp/vabHikq0lF/overlap.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 0 /tmp/vabHikq0lF/overlap.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 1 /tmp/vabHikq0lF/overlap.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 2 /tmp/vabHikq0lF/overlap.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 0 /tmp/vabHikq0lF/overlap.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 1 /tmp/vabHikq0lF/overlap.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 2 /tmp/vabHikq0lF/overlap.vcf.gz .. ok test_vcf_64bit: /build/bcftools-1.16/bcftools view /build/bcftools-1.16/test/view64bit.1.vcf -H .. ok test_vcf_64bit: /build/bcftools-1.16/bcftools view /build/bcftools-1.16/test/view64bit.1.vcf | /build/bcftools-1.16/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-1.16/bcftools view /build/bcftools-1.16/test/view64bit.1.vcf -Ou | /build/bcftools-1.16/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-1.16/bcftools view /build/bcftools-1.16/test/view64bit.2.vcf -H .. ok test_vcf_64bit: /build/bcftools-1.16/bcftools view /build/bcftools-1.16/test/view64bit.2.vcf | /build/bcftools-1.16/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-1.16/bcftools view /build/bcftools-1.16/test/view64bit.2.vcf -Ou | /build/bcftools-1.16/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-1.16/bcftools view /build/bcftools-1.16/test/view64bit.3.vcf -H .. ok test_vcf_64bit: /build/bcftools-1.16/bcftools view /build/bcftools-1.16/test/view64bit.3.vcf | /build/bcftools-1.16/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-1.16/bcftools view /build/bcftools-1.16/test/view64bit.4.vcf -H .. ok test_vcf_64bit: /build/bcftools-1.16/bcftools view /build/bcftools-1.16/test/view64bit.4.vcf | /build/bcftools-1.16/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-1.16/bcftools view /build/bcftools-1.16/test/view64bit.4.vcf -Ou | /build/bcftools-1.16/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-1.16/bcftools view /build/bcftools-1.16/test/view64bit.5.vcf -H .. ok test_vcf_64bit: /build/bcftools-1.16/bcftools view /build/bcftools-1.16/test/view64bit.5.vcf | /build/bcftools-1.16/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-1.16/bcftools view /build/bcftools-1.16/test/view64bit.5.vcf -Ou | /build/bcftools-1.16/bcftools view -H .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -C5:nonmajor /tmp/vabHikq0lF/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -c6:nonmajor /tmp/vabHikq0lF/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -q0.3:major /tmp/vabHikq0lF/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/vabHikq0lF/view.filter.annovar.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -i 'Gene.refGene~"NOD"' /tmp/vabHikq0lF/view.filter.annovar.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -i 'LJB2_MutationTaster=="0.291000"' /tmp/vabHikq0lF/view.filter.annovar.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -a /tmp/vabHikq0lF/view-a.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -T /build/bcftools-1.16/test/view.sites.txt /tmp/vabHikq0lF/view.sites.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view -Ob -T /build/bcftools-1.16/test/view.sites.txt /tmp/vabHikq0lF/view.sites.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -T /build/bcftools-1.16/test/view.sites.txt.gz /tmp/vabHikq0lF/view.sites.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view -Ob -T /build/bcftools-1.16/test/view.sites.txt.gz /tmp/vabHikq0lF/view.sites.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_head: /build/bcftools-1.16/bcftools head /build/bcftools-1.16/test/mpileup.2.vcf .. ok test_vcf_head: /build/bcftools-1.16/bcftools head -h 0 /build/bcftools-1.16/test/mpileup.2.vcf .. ok test_vcf_head: /build/bcftools-1.16/bcftools head -h 1 /build/bcftools-1.16/test/mpileup.2.vcf .. ok test_vcf_head: /build/bcftools-1.16/bcftools head -h 5 /build/bcftools-1.16/test/mpileup.2.vcf .. ok test_vcf_head: /build/bcftools-1.16/bcftools head -h 22 /build/bcftools-1.16/test/mpileup.2.vcf .. ok test_vcf_head: /build/bcftools-1.16/bcftools head -h 23 /build/bcftools-1.16/test/mpileup.2.vcf .. ok test_vcf_head: /build/bcftools-1.16/bcftools head -n 0 /build/bcftools-1.16/test/mpileup.2.vcf .. ok test_vcf_head: /build/bcftools-1.16/bcftools head -n 1 /build/bcftools-1.16/test/mpileup.2.vcf .. ok test_vcf_head: /build/bcftools-1.16/bcftools head -n 5 /build/bcftools-1.16/test/mpileup.2.vcf .. ok test_vcf_head: /build/bcftools-1.16/bcftools head -h 5 -n 5 < /build/bcftools-1.16/test/mpileup.2.vcf .. ok test_vcf_call: /build/bcftools-1.16/bcftools call --no-version -mv /build/bcftools-1.16/test/mpileup.vcf .. ok test_vcf_call: /build/bcftools-1.16/bcftools call -Ob -mv /build/bcftools-1.16/test/mpileup.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.16/bcftools call --no-version -mg0 /build/bcftools-1.16/test/mpileup.vcf .. ok test_vcf_call: /build/bcftools-1.16/bcftools call -Ob -mg0 /build/bcftools-1.16/test/mpileup.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.16/bcftools call --no-version -mv -S /build/bcftools-1.16/test/mpileup.3.samples /build/bcftools-1.16/test/mpileup.vcf .. ok test_vcf_call: /build/bcftools-1.16/bcftools call -Ob -mv -S /build/bcftools-1.16/test/mpileup.3.samples /build/bcftools-1.16/test/mpileup.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.16/bcftools call --no-version -mv -S /build/bcftools-1.16/test/mpileup.4.samples /build/bcftools-1.16/test/mpileup.vcf .. ok test_vcf_call: /build/bcftools-1.16/bcftools call -Ob -mv -S /build/bcftools-1.16/test/mpileup.4.samples /build/bcftools-1.16/test/mpileup.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.16/bcftools call --no-version -mv -S /build/bcftools-1.16/test/mpileup.5.samples /build/bcftools-1.16/test/mpileup.vcf .. ok test_vcf_call: /build/bcftools-1.16/bcftools call -Ob -mv -S /build/bcftools-1.16/test/mpileup.5.samples /build/bcftools-1.16/test/mpileup.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.16/bcftools call --no-version -mv --ploidy-file /build/bcftools-1.16/test/mpileup.ploidy -S /build/bcftools-1.16/test/mpileup.samples /build/bcftools-1.16/test/mpileup.X.vcf .. ok test_vcf_call: /build/bcftools-1.16/bcftools call -Ob -mv --ploidy-file /build/bcftools-1.16/test/mpileup.ploidy -S /build/bcftools-1.16/test/mpileup.samples /build/bcftools-1.16/test/mpileup.X.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.16/bcftools call --no-version -mv --ploidy-file /build/bcftools-1.16/test/mpileup.ploidy -S /build/bcftools-1.16/test/mpileup.ped /build/bcftools-1.16/test/mpileup.X.vcf .. ok test_vcf_call: /build/bcftools-1.16/bcftools call -Ob -mv --ploidy-file /build/bcftools-1.16/test/mpileup.ploidy -S /build/bcftools-1.16/test/mpileup.ped /build/bcftools-1.16/test/mpileup.X.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.16/bcftools call --no-version -mv --ploidy-file /build/bcftools-1.16/test/mpileup.ploidy -S /build/bcftools-1.16/test/mpileup.2.samples /build/bcftools-1.16/test/mpileup.X.vcf .. ok test_vcf_call: /build/bcftools-1.16/bcftools call -Ob -mv --ploidy-file /build/bcftools-1.16/test/mpileup.ploidy -S /build/bcftools-1.16/test/mpileup.2.samples /build/bcftools-1.16/test/mpileup.X.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.16/bcftools call --no-version -mv /build/bcftools-1.16/test/mpileup.NA19213.NA19129.vcf .. ok test_vcf_call: /build/bcftools-1.16/bcftools call -Ob -mv /build/bcftools-1.16/test/mpileup.NA19213.NA19129.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.16/bcftools call --no-version -mv -G - --group-samples-tag AD /build/bcftools-1.16/test/mpileup.NA19213.NA19129.vcf .. ok test_vcf_call: /build/bcftools-1.16/bcftools call -Ob -mv -G - --group-samples-tag AD /build/bcftools-1.16/test/mpileup.NA19213.NA19129.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.16/bcftools call --no-version -mv /build/bcftools-1.16/test/mpileup.hwe.vcf .. ok test_vcf_call: /build/bcftools-1.16/bcftools call -Ob -mv /build/bcftools-1.16/test/mpileup.hwe.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.16/bcftools call --no-version -mv -G - --group-samples-tag AD /build/bcftools-1.16/test/mpileup.hwe.vcf .. ok test_vcf_call: /build/bcftools-1.16/bcftools call -Ob -mv -G - --group-samples-tag AD /build/bcftools-1.16/test/mpileup.hwe.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.16/bcftools call --no-version -mv -G /build/bcftools-1.16/test/mpileup.hwe.samples --group-samples-tag AD /build/bcftools-1.16/test/mpileup.hwe.vcf .. ok test_vcf_call: /build/bcftools-1.16/bcftools call -Ob -mv -G /build/bcftools-1.16/test/mpileup.hwe.samples --group-samples-tag AD /build/bcftools-1.16/test/mpileup.hwe.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-1.16/bcftools call --no-version -mA -C alleles -T /tmp/vabHikq0lF/mpileup.tab.gz /build/bcftools-1.16/test/mpileup.vcf .. ok test_vcf_call_cAls: /build/bcftools-1.16/bcftools call -Ob -mA -C alleles -T /tmp/vabHikq0lF/mpileup.tab.gz /build/bcftools-1.16/test/mpileup.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-1.16/bcftools call --no-version -mA -C alleles -T /tmp/vabHikq0lF/mpileup.2.tab.gz /build/bcftools-1.16/test/mpileup.2.vcf .. ok test_vcf_call_cAls: /build/bcftools-1.16/bcftools call -Ob -mA -C alleles -T /tmp/vabHikq0lF/mpileup.2.tab.gz /build/bcftools-1.16/test/mpileup.2.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-1.16/bcftools call --no-version -mA -C alleles -T /tmp/vabHikq0lF/mpileup.3.tab.gz -i /build/bcftools-1.16/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /build/bcftools-1.16/bcftools call -Ob -mA -C alleles -T /tmp/vabHikq0lF/mpileup.3.tab.gz -i /build/bcftools-1.16/test/mpileup.3.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-1.16/bcftools call --no-version -mA -C alleles -T /tmp/vabHikq0lF/mpileup.4.tab.gz -i /build/bcftools-1.16/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /build/bcftools-1.16/bcftools call -Ob -mA -C alleles -T /tmp/vabHikq0lF/mpileup.4.tab.gz -i /build/bcftools-1.16/test/mpileup.3.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-1.16/bcftools call --no-version -mA -C alleles -T /tmp/vabHikq0lF/mpileup.5.tab.gz -i /build/bcftools-1.16/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /build/bcftools-1.16/bcftools call -Ob -mA -C alleles -T /tmp/vabHikq0lF/mpileup.5.tab.gz -i /build/bcftools-1.16/test/mpileup.3.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-1.16/bcftools call --no-version -mA -C alleles -T /tmp/vabHikq0lF/mpileup.6.tab.gz -i /build/bcftools-1.16/test/mpileup.4.vcf .. ok test_vcf_call_cAls: /build/bcftools-1.16/bcftools call -Ob -mA -C alleles -T /tmp/vabHikq0lF/mpileup.6.tab.gz -i /build/bcftools-1.16/test/mpileup.4.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-1.16/bcftools call --no-version -mA -C alleles -T /tmp/vabHikq0lF/mpileup.7.tab.gz -i /build/bcftools-1.16/test/mpileup.5.vcf .. ok test_vcf_call_cAls: /build/bcftools-1.16/bcftools call -Ob -mA -C alleles -T /tmp/vabHikq0lF/mpileup.7.tab.gz -i /build/bcftools-1.16/test/mpileup.5.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-1.16/bcftools call --no-version -mA -C alleles -T /tmp/vabHikq0lF/mpileup.cals.1.tab.gz /build/bcftools-1.16/test/mpileup.cals.1.vcf .. ok test_vcf_call_cAls: /build/bcftools-1.16/bcftools call -Ob -mA -C alleles -T /tmp/vabHikq0lF/mpileup.cals.1.tab.gz /build/bcftools-1.16/test/mpileup.cals.1.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-1.16/bcftools call --no-version -mA -C alleles -T /tmp/vabHikq0lF/mpileup.cals.2.tab.gz /build/bcftools-1.16/test/mpileup.cals.2.vcf .. ok test_vcf_call_cAls: /build/bcftools-1.16/bcftools call -Ob -mA -C alleles -T /tmp/vabHikq0lF/mpileup.cals.2.tab.gz /build/bcftools-1.16/test/mpileup.cals.2.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.16/bcftools call --no-version -cv /build/bcftools-1.16/test/mpileup.c.vcf .. ok test_vcf_call: /build/bcftools-1.16/bcftools call -Ob -cv /build/bcftools-1.16/test/mpileup.c.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.16/bcftools call --no-version -cv --ploidy-file /build/bcftools-1.16/test/mpileup.ploidy -S /build/bcftools-1.16/test/mpileup.samples /build/bcftools-1.16/test/mpileup.c.X.vcf .. ok test_vcf_call: /build/bcftools-1.16/bcftools call -Ob -cv --ploidy-file /build/bcftools-1.16/test/mpileup.ploidy -S /build/bcftools-1.16/test/mpileup.samples /build/bcftools-1.16/test/mpileup.c.X.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.16/bcftools call --no-version -cv --ploidy-file /build/bcftools-1.16/test/mpileup.ploidy -S /build/bcftools-1.16/test/mpileup.ped /build/bcftools-1.16/test/mpileup.c.X.vcf .. ok test_vcf_call: /build/bcftools-1.16/bcftools call -Ob -cv --ploidy-file /build/bcftools-1.16/test/mpileup.ploidy -S /build/bcftools-1.16/test/mpileup.ped /build/bcftools-1.16/test/mpileup.c.X.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.16/bcftools call --no-version -cv --ploidy-file /build/bcftools-1.16/test/mpileup.ploidy -S /build/bcftools-1.16/test/mpileup.2.samples /build/bcftools-1.16/test/mpileup.c.X.vcf .. ok test_vcf_call: /build/bcftools-1.16/bcftools call -Ob -cv --ploidy-file /build/bcftools-1.16/test/mpileup.ploidy -S /build/bcftools-1.16/test/mpileup.2.samples /build/bcftools-1.16/test/mpileup.c.X.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.16/bcftools call --no-version -mv /build/bcftools-1.16/test/call-G.vcf .. ok test_vcf_call: /build/bcftools-1.16/bcftools call -Ob -mv /build/bcftools-1.16/test/call-G.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.16/bcftools call --no-version -mv -G - --group-samples-tag AD /build/bcftools-1.16/test/call-G.vcf .. ok test_vcf_call: /build/bcftools-1.16/bcftools call -Ob -mv -G - --group-samples-tag AD /build/bcftools-1.16/test/call-G.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.16/bcftools call --no-version -mv -F AN_POP,AC_POP /build/bcftools-1.16/test/call-G.2.vcf .. ok test_vcf_call: /build/bcftools-1.16/bcftools call -Ob -mv -F AN_POP,AC_POP /build/bcftools-1.16/test/call-G.2.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.16/bcftools call --no-version -m /build/bcftools-1.16/test/call.af-fixation.vcf .. ok test_vcf_call: /build/bcftools-1.16/bcftools call -Ob -m /build/bcftools-1.16/test/call.af-fixation.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.16/bcftools call --no-version -m -G /build/bcftools-1.16/test/call.af-fixation.txt /build/bcftools-1.16/test/call.af-fixation.vcf .. ok test_vcf_call: /build/bcftools-1.16/bcftools call -Ob -m -G /build/bcftools-1.16/test/call.af-fixation.txt /build/bcftools-1.16/test/call.af-fixation.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.16/bcftools call --no-version -m -G /build/bcftools-1.16/test/call.af-fixation.txt -a GP,GQ /build/bcftools-1.16/test/call.af-fixation.vcf .. ok test_vcf_call: /build/bcftools-1.16/bcftools call -Ob -m -G /build/bcftools-1.16/test/call.af-fixation.txt -a GP,GQ /build/bcftools-1.16/test/call.af-fixation.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -S. -e'TXT0="text"' /build/bcftools-1.16/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -S. -e'TXT0="text"' /build/bcftools-1.16/test/view.filter.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -S. -e'FMT/FRS[*:1]="BB"' /build/bcftools-1.16/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -S. -e'FMT/FRS[*:1]="BB"' /build/bcftools-1.16/test/view.filter.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -S. -e'FMT/FGS[*:0]="AAAAAA"' /build/bcftools-1.16/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -S. -e'FMT/FGS[*:0]="AAAAAA"' /build/bcftools-1.16/test/view.filter.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -S. -e'FMT/FGS[*:1]="BBB"' /build/bcftools-1.16/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -S. -e'FMT/FGS[*:1]="BBB"' /build/bcftools-1.16/test/view.filter.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -S. -e'FMT/FGS[*:4]="EE"' /build/bcftools-1.16/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -S. -e'FMT/FGS[*:4]="EE"' /build/bcftools-1.16/test/view.filter.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -S. -e'FMT/STR="XX"' /build/bcftools-1.16/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -S. -e'FMT/STR="XX"' /build/bcftools-1.16/test/view.filter.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -S. -e'FMT/FILTER="aaa"' /build/bcftools-1.16/test/view.filter.2.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -S. -e'FMT/FILTER="aaa"' /build/bcftools-1.16/test/view.filter.2.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -mx -g2 -G2 /build/bcftools-1.16/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -mx -g2 -G2 /build/bcftools-1.16/test/filter.1.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /build/bcftools-1.16/test/filter.2.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /build/bcftools-1.16/test/filter.2.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -e'INFO/DP=19' /build/bcftools-1.16/test/filter.3.vcf | /build/bcftools-1.16/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -e'INFO/DP=19' /build/bcftools-1.16/test/filter.3.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -e'INFO/DP=19' -s XX /build/bcftools-1.16/test/filter.3.vcf | /build/bcftools-1.16/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -e'INFO/DP=19' -s XX /build/bcftools-1.16/test/filter.3.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -e'INFO/DP=19' -s XX -m+ /build/bcftools-1.16/test/filter.3.vcf | /build/bcftools-1.16/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+ /build/bcftools-1.16/test/filter.3.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -e'INFO/DP=19' -s XX -mx /build/bcftools-1.16/test/filter.3.vcf | /build/bcftools-1.16/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -e'INFO/DP=19' -s XX -mx /build/bcftools-1.16/test/filter.3.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -e'INFO/DP=19' -s XX -m+x /build/bcftools-1.16/test/filter.3.vcf | /build/bcftools-1.16/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+x /build/bcftools-1.16/test/filter.3.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -e'FMT/GT="0/2"' /build/bcftools-1.16/test/filter.3.vcf | /build/bcftools-1.16/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -e'FMT/GT="0/2"' /build/bcftools-1.16/test/filter.3.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -e'FMT/GT="0/2"' -s XX /build/bcftools-1.16/test/filter.3.vcf | /build/bcftools-1.16/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX /build/bcftools-1.16/test/filter.3.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -e'FMT/GT="0/2"' -s XX -m+ /build/bcftools-1.16/test/filter.3.vcf | /build/bcftools-1.16/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+ /build/bcftools-1.16/test/filter.3.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -e'FMT/GT="0/2"' -s XX -mx /build/bcftools-1.16/test/filter.3.vcf | /build/bcftools-1.16/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -mx /build/bcftools-1.16/test/filter.3.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -e'FMT/GT="0/2"' -s XX -m+x /build/bcftools-1.16/test/filter.3.vcf | /build/bcftools-1.16/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+x /build/bcftools-1.16/test/filter.3.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -i'FMT/GT="0/0" && AC[*]=2' /build/bcftools-1.16/test/filter.2.vcf | /build/bcftools-1.16/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -i'FMT/GT="0/0" && AC[*]=2' /build/bcftools-1.16/test/filter.2.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -i'AC[*]=2 && FMT/GT="0/0"' /build/bcftools-1.16/test/filter.2.vcf | /build/bcftools-1.16/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -i'AC[*]=2 && FMT/GT="0/0"' /build/bcftools-1.16/test/filter.2.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -i'ALT="."' /build/bcftools-1.16/test/filter.2.vcf | /build/bcftools-1.16/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -i'ALT="."' /build/bcftools-1.16/test/filter.2.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -S . -i 'FORMAT/TEST3<25' /build/bcftools-1.16/test/filter.4.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -S . -i 'FORMAT/TEST3<25' /build/bcftools-1.16/test/filter.4.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -S . -i 'FORMAT/TEST4<25' /build/bcftools-1.16/test/filter.4.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -S . -i 'FORMAT/TEST4<25' /build/bcftools-1.16/test/filter.4.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -i'GT="A"' /build/bcftools-1.16/test/filter.2.vcf | /build/bcftools-1.16/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -i'GT="A"' /build/bcftools-1.16/test/filter.2.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -i'GT="RR"' /build/bcftools-1.16/test/filter.2.vcf | /build/bcftools-1.16/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -i'GT="RR"' /build/bcftools-1.16/test/filter.2.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -i'GT="RA"' /build/bcftools-1.16/test/filter.2.vcf | /build/bcftools-1.16/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -i'GT="RA"' /build/bcftools-1.16/test/filter.2.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -i'GT="AR"' /build/bcftools-1.16/test/filter.2.vcf | /build/bcftools-1.16/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -i'GT="AR"' /build/bcftools-1.16/test/filter.2.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -i'GT="AA"' /build/bcftools-1.16/test/filter.2.vcf | /build/bcftools-1.16/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -i'GT="AA"' /build/bcftools-1.16/test/filter.2.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -i'GT="aA"' /build/bcftools-1.16/test/filter.2.vcf | /build/bcftools-1.16/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -i'GT="aA"' /build/bcftools-1.16/test/filter.2.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -i'GT="Aa"' /build/bcftools-1.16/test/filter.2.vcf | /build/bcftools-1.16/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -i'GT="Aa"' /build/bcftools-1.16/test/filter.2.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -i'GT="HOM"' /build/bcftools-1.16/test/filter.2.vcf | /build/bcftools-1.16/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -i'GT="HOM"' /build/bcftools-1.16/test/filter.2.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -i'GT="HET"' /build/bcftools-1.16/test/filter.2.vcf | /build/bcftools-1.16/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -i'GT="HET"' /build/bcftools-1.16/test/filter.2.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -i'GT="HAP"' /build/bcftools-1.16/test/filter.2.vcf | /build/bcftools-1.16/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -i'GT="HAP"' /build/bcftools-1.16/test/filter.2.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -i'AD[:1]=11' /build/bcftools-1.16/test/filter.5.vcf | /build/bcftools-1.16/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -i'AD[:1]=11' /build/bcftools-1.16/test/filter.5.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -i'AD[1:]=11' /build/bcftools-1.16/test/filter.5.vcf | /build/bcftools-1.16/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -i'AD[1:]=11' /build/bcftools-1.16/test/filter.5.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -i'FR[0:1]=11' /build/bcftools-1.16/test/filter.5.vcf | /build/bcftools-1.16/bcftools query -f '%POS[\t%FR]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -i'FR[0:1]=11' /build/bcftools-1.16/test/filter.5.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS[\t%FR]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -i'AD[*]="."' /build/bcftools-1.16/test/filter.5.vcf | /build/bcftools-1.16/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -i'AD[*]="."' /build/bcftools-1.16/test/filter.5.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -i'AD[0:0]=="."' /build/bcftools-1.16/test/filter.5.vcf | /build/bcftools-1.16/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -i'AD[0:0]=="."' /build/bcftools-1.16/test/filter.5.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -i'AD[0:0]!="."' /build/bcftools-1.16/test/filter.5.vcf | /build/bcftools-1.16/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -i'AD[0:0]!="."' /build/bcftools-1.16/test/filter.5.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -i'QUAL=="."' /build/bcftools-1.16/test/filter.5.vcf | /build/bcftools-1.16/bcftools query -f '%POS\t%QUAL\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -i'QUAL=="."' /build/bcftools-1.16/test/filter.5.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS\t%QUAL\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -i'N_PASS(DP>32)=1' /build/bcftools-1.16/test/filter.2.vcf | /build/bcftools-1.16/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -i'N_PASS(DP>32)=1' /build/bcftools-1.16/test/filter.2.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -i'F_PASS(DP>32)=0.5' /build/bcftools-1.16/test/filter.2.vcf | /build/bcftools-1.16/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -i'F_PASS(DP>32)=0.5' /build/bcftools-1.16/test/filter.2.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -i'F_MISSING>=1/5' /build/bcftools-1.16/test/filter.6.vcf | /build/bcftools-1.16/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -i'F_MISSING>=1/5' /build/bcftools-1.16/test/filter.6.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -i'F_MISSING>=0.2' /build/bcftools-1.16/test/filter.6.vcf | /build/bcftools-1.16/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -i'F_MISSING>=0.2' /build/bcftools-1.16/test/filter.6.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -i'F_PASS(GT=="mis")>=1/5' /build/bcftools-1.16/test/filter.6.vcf | /build/bcftools-1.16/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -i'F_PASS(GT=="mis")>=1/5' /build/bcftools-1.16/test/filter.6.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -i'F_PASS(GT=="mis")>=0.2' /build/bcftools-1.16/test/filter.6.vcf | /build/bcftools-1.16/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -i'F_PASS(GT=="mis")>=0.2' /build/bcftools-1.16/test/filter.6.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -mx -s + -g2:mnp,indel,other /build/bcftools-1.16/test/filter.7.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -mx -s + -g2:mnp,indel,other /build/bcftools-1.16/test/filter.7.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -S . -e 'FORMAT/AO==4' /build/bcftools-1.16/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -S . -e 'FORMAT/AO==4' /build/bcftools-1.16/test/filter.8.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -S . -e 'MAX(FORMAT/AO[0:])==4' /build/bcftools-1.16/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -S . -e 'MAX(FORMAT/AO[0:])==4' /build/bcftools-1.16/test/filter.8.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -S . -e 'MAX(FORMAT/AO)==4' /build/bcftools-1.16/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -S . -e 'MAX(FORMAT/AO)==4' /build/bcftools-1.16/test/filter.8.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -S . -e 'MIN(FORMAT/AO[0:])==3' /build/bcftools-1.16/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO[0:])==3' /build/bcftools-1.16/test/filter.8.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -S . -e 'MIN(FORMAT/AO)==2' /build/bcftools-1.16/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO)==2' /build/bcftools-1.16/test/filter.8.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -S . -e 'MIN(FORMAT/AO[0:])==3' /build/bcftools-1.16/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO[0:])==3' /build/bcftools-1.16/test/filter.8.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -S . -e 'AVG(FORMAT/AO[2:])==4' /build/bcftools-1.16/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -S . -e 'AVG(FORMAT/AO[2:])==4' /build/bcftools-1.16/test/filter.8.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -S . -e 'MEDIAN(FORMAT/AO[2:])==4' /build/bcftools-1.16/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -S . -e 'MEDIAN(FORMAT/AO[2:])==4' /build/bcftools-1.16/test/filter.8.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -S . -e 'STDEV(FORMAT/AO[0:])=0.5' /build/bcftools-1.16/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -S . -e 'STDEV(FORMAT/AO[0:])=0.5' /build/bcftools-1.16/test/filter.8.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -S . -e 'SUM(FORMAT/AO[0:])=7' /build/bcftools-1.16/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -S . -e 'SUM(FORMAT/AO[0:])=7' /build/bcftools-1.16/test/filter.8.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -S . -e 'SMPL_MAX(FORMAT/AO)==4' /build/bcftools-1.16/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -S . -e 'SMPL_MAX(FORMAT/AO)==4' /build/bcftools-1.16/test/filter.8.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -S . -e 'sMIN(FORMAT/AO)==2' /build/bcftools-1.16/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -S . -e 'sMIN(FORMAT/AO)==2' /build/bcftools-1.16/test/filter.8.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -S . -e 'ABS(sAVG(FORMAT/AO)-3.66666)<1e-5' /build/bcftools-1.16/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -S . -e 'ABS(sAVG(FORMAT/AO)-3.66666)<1e-5' /build/bcftools-1.16/test/filter.8.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -S . -e 'sMEDIAN(FORMAT/AO)==4' /build/bcftools-1.16/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -S . -e 'sMEDIAN(FORMAT/AO)==4' /build/bcftools-1.16/test/filter.8.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -S . -e 'ABS(sSTDEV(FORMAT/AO)-1.2472191)<1e-5' /build/bcftools-1.16/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -S . -e 'ABS(sSTDEV(FORMAT/AO)-1.2472191)<1e-5' /build/bcftools-1.16/test/filter.8.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -S . -e 'sSUM(FORMAT/AO)==11' /build/bcftools-1.16/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -S . -e 'sSUM(FORMAT/AO)==11' /build/bcftools-1.16/test/filter.8.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -i 'QUAL/FMT/AD==55' /build/bcftools-1.16/test/filter.9.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -i 'QUAL/FMT/AD==55' /build/bcftools-1.16/test/filter.9.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -i 'QUAL/INFO/AD==10' /build/bcftools-1.16/test/filter.9.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -i 'QUAL/INFO/AD==10' /build/bcftools-1.16/test/filter.9.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -S . -e 'ABS(SMPL_MAX(FORMAT/AO))=5' /build/bcftools-1.16/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -S . -e 'ABS(SMPL_MAX(FORMAT/AO))=5' /build/bcftools-1.16/test/filter.8.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -S . -e 'PHRED(AO[1:])>-4' /build/bcftools-1.16/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -S . -e 'PHRED(AO[1:])>-4' /build/bcftools-1.16/test/filter.8.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -S . -e 'ABS(AO[1:])==2' /build/bcftools-1.16/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -S . -e 'ABS(AO[1:])==2' /build/bcftools-1.16/test/filter.8.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -i 'sum(AD[*]) > FORMAT/DP' /build/bcftools-1.16/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -i 'sum(AD[*]) > FORMAT/DP' /build/bcftools-1.16/test/filter.10.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -i 'FORMAT/DP < sum(AD[*])' /build/bcftools-1.16/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -i 'FORMAT/DP < sum(AD[*])' /build/bcftools-1.16/test/filter.10.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -i 'sum(AD[*]) < FORMAT/DP' /build/bcftools-1.16/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -i 'sum(AD[*]) < FORMAT/DP' /build/bcftools-1.16/test/filter.10.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -i 'FORMAT/DP > sum(AD[*])' /build/bcftools-1.16/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -i 'FORMAT/DP > sum(AD[*])' /build/bcftools-1.16/test/filter.10.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 0 /build/bcftools-1.16/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 0 /build/bcftools-1.16/test/filter.1.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 1 /build/bcftools-1.16/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 1 /build/bcftools-1.16/test/filter.1.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 2 /build/bcftools-1.16/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 2 /build/bcftools-1.16/test/filter.1.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter --soft-filter xxx --mask ^2:1005-1008 /build/bcftools-1.16/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob --soft-filter xxx --mask ^2:1005-1008 /build/bcftools-1.16/test/filter.1.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_sort: /build/bcftools-1.16/bcftools sort -m 0 /build/bcftools-1.16/test/sort.vcf | /build/bcftools-1.16/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /build/bcftools-1.16/bcftools sort -Ob -m 0 /build/bcftools-1.16/test/sort.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /build/bcftools-1.16/bcftools sort -m 1000 /build/bcftools-1.16/test/sort.vcf | /build/bcftools-1.16/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /build/bcftools-1.16/bcftools sort -Ob -m 1000 /build/bcftools-1.16/test/sort.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_regions: /build/bcftools-1.16/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /build/bcftools-1.16/test/regions.tab /tmp/vabHikq0lF/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/regions.vcf.gz | /build/bcftools-1.16/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /build/bcftools-1.16/test/regions.tab .. ok test_vcf_regions: /build/bcftools-1.16/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /build/bcftools-1.16/test/regions.tab /tmp/vabHikq0lF/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-1.16/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/vabHikq0lF/regions.tab.gz /tmp/vabHikq0lF/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/regions.vcf.gz | /build/bcftools-1.16/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/vabHikq0lF/regions.tab.gz .. ok test_vcf_regions: /build/bcftools-1.16/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/vabHikq0lF/regions.tab.gz /tmp/vabHikq0lF/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-1.16/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/vabHikq0lF/regions.bed /tmp/vabHikq0lF/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/regions.vcf.gz | /build/bcftools-1.16/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/vabHikq0lF/regions.bed .. ok test_vcf_regions: /build/bcftools-1.16/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/vabHikq0lF/regions.bed /tmp/vabHikq0lF/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-1.16/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/vabHikq0lF/regions.bed.gz /tmp/vabHikq0lF/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/regions.vcf.gz | /build/bcftools-1.16/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/vabHikq0lF/regions.bed.gz .. ok test_vcf_regions: /build/bcftools-1.16/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/vabHikq0lF/regions.bed.gz /tmp/vabHikq0lF/regions.vcf.gz .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/vabHikq0lF/annotate.tab.gz -h /build/bcftools-1.16/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /build/bcftools-1.16/test/annotate.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/vabHikq0lF/annotate.tab.gz -h /build/bcftools-1.16/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /build/bcftools-1.16/test/annotate.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/vabHikq0lF/annotate2.tab.gz -h /build/bcftools-1.16/test/annotate.hdr -c CHROM,POS,-,T_STR /build/bcftools-1.16/test/annotate.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/vabHikq0lF/annotate2.tab.gz -h /build/bcftools-1.16/test/annotate.hdr -c CHROM,POS,-,T_STR /build/bcftools-1.16/test/annotate.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/vabHikq0lF/annotate2.tab.gz -h /build/bcftools-1.16/test/annotate.hdr -c CHROM,FROM,TO,T_STR /build/bcftools-1.16/test/annotate.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/vabHikq0lF/annotate2.tab.gz -h /build/bcftools-1.16/test/annotate.hdr -c CHROM,FROM,TO,T_STR /build/bcftools-1.16/test/annotate.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/vabHikq0lF/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/vabHikq0lF/annotate.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/vabHikq0lF/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/vabHikq0lF/annotate.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/vabHikq0lF/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/vabHikq0lF/annotate2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/vabHikq0lF/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/vabHikq0lF/annotate2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/vabHikq0lF/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/vabHikq0lF/annotate2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/vabHikq0lF/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/vabHikq0lF/annotate2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/vabHikq0lF/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/vabHikq0lF/annotate2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/vabHikq0lF/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/vabHikq0lF/annotate2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/vabHikq0lF/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/vabHikq0lF/annotate2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/vabHikq0lF/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/vabHikq0lF/annotate2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/vabHikq0lF/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/vabHikq0lF/annotate2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/vabHikq0lF/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/vabHikq0lF/annotate2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /build/bcftools-1.16/test/annotate3.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /build/bcftools-1.16/test/annotate3.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -x FORMAT /build/bcftools-1.16/test/annotate3.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -x FORMAT /build/bcftools-1.16/test/annotate3.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/vabHikq0lF/annots4.vcf.gz -c +INFO /tmp/vabHikq0lF/annotate4.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/vabHikq0lF/annots4.vcf.gz -c +INFO /tmp/vabHikq0lF/annotate4.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/vabHikq0lF/annots4.tab.gz -h /build/bcftools-1.16/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /build/bcftools-1.16/test/annotate4.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/vabHikq0lF/annots4.tab.gz -h /build/bcftools-1.16/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /build/bcftools-1.16/test/annotate4.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/vabHikq0lF/annots10.tab.gz -h /build/bcftools-1.16/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /build/bcftools-1.16/test/annotate10.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/vabHikq0lF/annots10.tab.gz -h /build/bcftools-1.16/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /build/bcftools-1.16/test/annotate10.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/vabHikq0lF/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/vabHikq0lF/annotate2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/vabHikq0lF/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/vabHikq0lF/annotate2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/vabHikq0lF/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /build/bcftools-1.16/test/annotate2.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/vabHikq0lF/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /build/bcftools-1.16/test/annotate2.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/vabHikq0lF/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/vabHikq0lF/annotate2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/vabHikq0lF/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/vabHikq0lF/annotate2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/vabHikq0lF/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/vabHikq0lF/annotate2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/vabHikq0lF/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/vabHikq0lF/annotate2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/vabHikq0lF/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/vabHikq0lF/annotate2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/vabHikq0lF/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/vabHikq0lF/annotate2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/vabHikq0lF/annots11.vcf.gz -c FMT /tmp/vabHikq0lF/annotate11.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/vabHikq0lF/annots11.vcf.gz -c FMT /tmp/vabHikq0lF/annotate11.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/vabHikq0lF/annots2.vcf.gz -c FMT/newGT:=GT /tmp/vabHikq0lF/annotate2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/vabHikq0lF/annots2.vcf.gz -c FMT/newGT:=GT /tmp/vabHikq0lF/annotate2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/vabHikq0lF/annots12.vcf.gz -c FMT/GT:=newGT /tmp/vabHikq0lF/annotate2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/vabHikq0lF/annots12.vcf.gz -c FMT/GT:=newGT /tmp/vabHikq0lF/annotate2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/vabHikq0lF/annots13.tab.gz -h /build/bcftools-1.16/test/annotate13.hdr -c CHROM,BEG,END,ABC /build/bcftools-1.16/test/annotate13.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/vabHikq0lF/annots13.tab.gz -h /build/bcftools-1.16/test/annotate13.hdr -c CHROM,BEG,END,ABC /build/bcftools-1.16/test/annotate13.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/vabHikq0lF/annots13.tab.gz -h /build/bcftools-1.16/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:append /build/bcftools-1.16/test/annotate13.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/vabHikq0lF/annots13.tab.gz -h /build/bcftools-1.16/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:append /build/bcftools-1.16/test/annotate13.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/vabHikq0lF/annots13.tab.gz -h /build/bcftools-1.16/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:unique /build/bcftools-1.16/test/annotate13.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/vabHikq0lF/annots13.tab.gz -h /build/bcftools-1.16/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:unique /build/bcftools-1.16/test/annotate13.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -x FILTER/XX,INFO/XX --force /build/bcftools-1.16/test/annotate14.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -x FILTER/XX,INFO/XX --force /build/bcftools-1.16/test/annotate14.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/vabHikq0lF/annotate15.tab.gz -h /build/bcftools-1.16/test/annotate15.hdr -s SAMPLE1 -c CHROM,FROM,TO,FMT/FOO,BAR /build/bcftools-1.16/test/annotate15.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/vabHikq0lF/annotate15.tab.gz -h /build/bcftools-1.16/test/annotate15.hdr -s SAMPLE1 -c CHROM,FROM,TO,FMT/FOO,BAR /build/bcftools-1.16/test/annotate15.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/vabHikq0lF/annotate15.tab.gz -h /build/bcftools-1.16/test/annotate15.hdr -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR /build/bcftools-1.16/test/annotate15.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/vabHikq0lF/annotate15.tab.gz -h /build/bcftools-1.16/test/annotate15.hdr -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR /build/bcftools-1.16/test/annotate15.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/vabHikq0lF/annotate15.tab.gz -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR -H '##FORMAT=' -H '##INFO=' /build/bcftools-1.16/test/annotate15.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/vabHikq0lF/annotate15.tab.gz -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR -H '##FORMAT=' -H '##INFO=' /build/bcftools-1.16/test/annotate15.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -x FILTER /build/bcftools-1.16/test/annotate16.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -x FILTER /build/bcftools-1.16/test/annotate16.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/vabHikq0lF/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/bcftools-1.16/test/annotate17.1.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/vabHikq0lF/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/bcftools-1.16/test/annotate17.1.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/vabHikq0lF/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/bcftools-1.16/test/annotate17.2.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/vabHikq0lF/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/bcftools-1.16/test/annotate17.2.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/vabHikq0lF/annotate17.3.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/bcftools-1.16/test/annotate17.3.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/vabHikq0lF/annotate17.3.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/bcftools-1.16/test/annotate17.3.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/vabHikq0lF/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/bcftools-1.16/test/annotate18.1.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/vabHikq0lF/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/bcftools-1.16/test/annotate18.1.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/vabHikq0lF/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/bcftools-1.16/test/annotate18.2.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/vabHikq0lF/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/bcftools-1.16/test/annotate18.2.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/vabHikq0lF/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/vabHikq0lF/annotate19.dst.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/vabHikq0lF/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/vabHikq0lF/annotate19.dst.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/vabHikq0lF/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/vabHikq0lF/annotate19.dst.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/vabHikq0lF/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/vabHikq0lF/annotate19.dst.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/vabHikq0lF/annotate20.src.vcf.gz -c FMT/GT /tmp/vabHikq0lF/annotate20.dst.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/vabHikq0lF/annotate20.src.vcf.gz -c FMT/GT /tmp/vabHikq0lF/annotate20.dst.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/vabHikq0lF/annotate20.src.vcf.gz -c +FMT/GT /tmp/vabHikq0lF/annotate20.dst.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/vabHikq0lF/annotate20.src.vcf.gz -c +FMT/GT /tmp/vabHikq0lF/annotate20.dst.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/vabHikq0lF/annotate20.src.vcf.gz -c -FMT/GT /tmp/vabHikq0lF/annotate20.dst.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/vabHikq0lF/annotate20.src.vcf.gz -c -FMT/GT /tmp/vabHikq0lF/annotate20.dst.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/vabHikq0lF/annotate.multi.tab.gz -c CHROM,POS,REF,ALT,ANN -l ANN:append /build/bcftools-1.16/test/annotate.multi.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/vabHikq0lF/annotate.multi.tab.gz -c CHROM,POS,REF,ALT,ANN -l ANN:append /build/bcftools-1.16/test/annotate.multi.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/vabHikq0lF/annotate.missing-append.tab.gz -c CHROM,POS,REF,ALT,STR,INT,FLT -l STR:append-missing,INT:append-missing,FLT:append-missing /build/bcftools-1.16/test/annotate.missing-append.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/vabHikq0lF/annotate.missing-append.tab.gz -c CHROM,POS,REF,ALT,STR,INT,FLT -l STR:append-missing,INT:append-missing,FLT:append-missing /build/bcftools-1.16/test/annotate.missing-append.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/vabHikq0lF/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /build/bcftools-1.16/test/annotate9.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/vabHikq0lF/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /build/bcftools-1.16/test/annotate9.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate --rename-annots /build/bcftools-1.16/test/annotate21.txt /build/bcftools-1.16/test/annotate21.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob --rename-annots /build/bcftools-1.16/test/annotate21.txt /build/bcftools-1.16/test/annotate21.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/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/bcftools-1.16/test/annotate21.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/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/bcftools-1.16/test/annotate21.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/vabHikq0lF/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/vabHikq0lF/annotate22.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/vabHikq0lF/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/vabHikq0lF/annotate22.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/vabHikq0lF/annotate23.tab.gz -c CHROM,POS,~ID,REF,ALT,INFO/END /build/bcftools-1.16/test/annotate23.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/vabHikq0lF/annotate23.tab.gz -c CHROM,POS,~ID,REF,ALT,INFO/END /build/bcftools-1.16/test/annotate23.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/vabHikq0lF/annotate24.src.vcf.gz -c XX /tmp/vabHikq0lF/annotate24.dst.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/vabHikq0lF/annotate24.src.vcf.gz -c XX /tmp/vabHikq0lF/annotate24.dst.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/vabHikq0lF/annotate25.tab.gz -c CHROM,POS,ID,REF,ALT,~INFO/END /build/bcftools-1.16/test/annotate25.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/vabHikq0lF/annotate25.tab.gz -c CHROM,POS,ID,REF,ALT,~INFO/END /build/bcftools-1.16/test/annotate25.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/vabHikq0lF/annotate26.tab.gz -c CHROM,POS,~POS /build/bcftools-1.16/test/annotate26.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/vabHikq0lF/annotate26.tab.gz -c CHROM,POS,~POS /build/bcftools-1.16/test/annotate26.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/vabHikq0lF/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,TSTR,TFLT,TINT /build/bcftools-1.16/test/annotate.missing.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/vabHikq0lF/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,TSTR,TFLT,TINT /build/bcftools-1.16/test/annotate.missing.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/vabHikq0lF/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.TSTR,.TFLT,.TINT /build/bcftools-1.16/test/annotate.missing.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/vabHikq0lF/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.TSTR,.TFLT,.TINT /build/bcftools-1.16/test/annotate.missing.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/vabHikq0lF/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.+TSTR,.+TFLT,.+TINT /build/bcftools-1.16/test/annotate.missing.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/vabHikq0lF/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.+TSTR,.+TFLT,.+TINT /build/bcftools-1.16/test/annotate.missing.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/vabHikq0lF/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,+TSTR,+TFLT,+TINT /build/bcftools-1.16/test/annotate.missing.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/vabHikq0lF/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,+TSTR,+TFLT,+TINT /build/bcftools-1.16/test/annotate.missing.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/vabHikq0lF/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.=TSTR,.=TFLT,.=TINT /build/bcftools-1.16/test/annotate.missing.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/vabHikq0lF/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.=TSTR,.=TFLT,.=TINT /build/bcftools-1.16/test/annotate.missing.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/vabHikq0lF/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,=TSTR,=TFLT,=TINT /build/bcftools-1.16/test/annotate.missing.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/vabHikq0lF/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,=TSTR,=TFLT,=TINT /build/bcftools-1.16/test/annotate.missing.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/vabHikq0lF/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique /build/bcftools-1.16/test/annotate.olap.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/vabHikq0lF/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique /build/bcftools-1.16/test/annotate.olap.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/vabHikq0lF/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique --min-overlap 0.4:0.5 /build/bcftools-1.16/test/annotate.olap.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/vabHikq0lF/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique --min-overlap 0.4:0.5 /build/bcftools-1.16/test/annotate.olap.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/vabHikq0lF/annots.id.vcf.gz -c ALT /tmp/vabHikq0lF/annotate.id.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/vabHikq0lF/annots.id.vcf.gz -c ALT /tmp/vabHikq0lF/annotate.id.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/vabHikq0lF/annots.id.vcf.gz -c +ALT /tmp/vabHikq0lF/annotate.id.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/vabHikq0lF/annots.id.vcf.gz -c +ALT /tmp/vabHikq0lF/annotate.id.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/vabHikq0lF/annotate27.tab.gz -c CHROM,POS,REF,ALT,EVIDENCE /build/bcftools-1.16/test/annotate27.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/vabHikq0lF/annotate27.tab.gz -c CHROM,POS,REF,ALT,EVIDENCE /build/bcftools-1.16/test/annotate27.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-1.16/bcftools concat --no-version /tmp/vabHikq0lF/concat.1.a.vcf.gz /tmp/vabHikq0lF/concat.1.b.vcf.gz .. ok test_vcf_concat: /build/bcftools-1.16/bcftools concat -Ob /tmp/vabHikq0lF/concat.1.a.vcf.gz /tmp/vabHikq0lF/concat.1.b.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-1.16/bcftools concat --no-version /tmp/vabHikq0lF/concat.1.a.bcf /tmp/vabHikq0lF/concat.1.b.bcf .. ok test_vcf_concat: /build/bcftools-1.16/bcftools concat -Ob /tmp/vabHikq0lF/concat.1.a.bcf /tmp/vabHikq0lF/concat.1.b.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-1.16/bcftools concat --no-version -a /tmp/vabHikq0lF/concat.2.a.vcf.gz /tmp/vabHikq0lF/concat.2.b.vcf.gz .. ok test_vcf_concat: /build/bcftools-1.16/bcftools concat -Ob -a /tmp/vabHikq0lF/concat.2.a.vcf.gz /tmp/vabHikq0lF/concat.2.b.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-1.16/bcftools concat --no-version -a /tmp/vabHikq0lF/concat.2.a.bcf /tmp/vabHikq0lF/concat.2.b.bcf .. ok test_vcf_concat: /build/bcftools-1.16/bcftools concat -Ob -a /tmp/vabHikq0lF/concat.2.a.bcf /tmp/vabHikq0lF/concat.2.b.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-1.16/bcftools concat --no-version -aD /tmp/vabHikq0lF/concat.2.a.vcf.gz /tmp/vabHikq0lF/concat.2.b.vcf.gz .. ok test_vcf_concat: /build/bcftools-1.16/bcftools concat -Ob -aD /tmp/vabHikq0lF/concat.2.a.vcf.gz /tmp/vabHikq0lF/concat.2.b.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-1.16/bcftools concat --no-version -aD /tmp/vabHikq0lF/concat.2.a.bcf /tmp/vabHikq0lF/concat.2.b.bcf .. ok test_vcf_concat: /build/bcftools-1.16/bcftools concat -Ob -aD /tmp/vabHikq0lF/concat.2.a.bcf /tmp/vabHikq0lF/concat.2.b.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-1.16/bcftools concat --no-version -l --ligate-warn /tmp/vabHikq0lF/concat.3.a.vcf.gz /tmp/vabHikq0lF/concat.3.b.vcf.gz /tmp/vabHikq0lF/concat.3.0.vcf.gz /tmp/vabHikq0lF/concat.3.c.vcf.gz /tmp/vabHikq0lF/concat.3.d.vcf.gz /tmp/vabHikq0lF/concat.3.e.vcf.gz /tmp/vabHikq0lF/concat.3.f.vcf.gz .. ok test_vcf_concat: /build/bcftools-1.16/bcftools concat -Ob -l --ligate-warn /tmp/vabHikq0lF/concat.3.a.vcf.gz /tmp/vabHikq0lF/concat.3.b.vcf.gz /tmp/vabHikq0lF/concat.3.0.vcf.gz /tmp/vabHikq0lF/concat.3.c.vcf.gz /tmp/vabHikq0lF/concat.3.d.vcf.gz /tmp/vabHikq0lF/concat.3.e.vcf.gz /tmp/vabHikq0lF/concat.3.f.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-1.16/bcftools concat --no-version -l --ligate-warn /tmp/vabHikq0lF/concat.3.a.bcf /tmp/vabHikq0lF/concat.3.b.bcf /tmp/vabHikq0lF/concat.3.0.bcf /tmp/vabHikq0lF/concat.3.c.bcf /tmp/vabHikq0lF/concat.3.d.bcf /tmp/vabHikq0lF/concat.3.e.bcf /tmp/vabHikq0lF/concat.3.f.bcf .. ok test_vcf_concat: /build/bcftools-1.16/bcftools concat -Ob -l --ligate-warn /tmp/vabHikq0lF/concat.3.a.bcf /tmp/vabHikq0lF/concat.3.b.bcf /tmp/vabHikq0lF/concat.3.0.bcf /tmp/vabHikq0lF/concat.3.c.bcf /tmp/vabHikq0lF/concat.3.d.bcf /tmp/vabHikq0lF/concat.3.e.bcf /tmp/vabHikq0lF/concat.3.f.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ Random seed for test_naive_concat: 3567539537 .. ok test_naive_concat: /build/bcftools-1.16/bcftools concat --naive-force /tmp/vabHikq0lF/naive_concat.0.bcf /tmp/vabHikq0lF/naive_concat.1.bcf /tmp/vabHikq0lF/naive_concat.2.bcf /tmp/vabHikq0lF/naive_concat.3.bcf /tmp/vabHikq0lF/naive_concat.4.bcf /tmp/vabHikq0lF/naive_concat.5.bcf /tmp/vabHikq0lF/naive_concat.6.bcf /tmp/vabHikq0lF/naive_concat.7.bcf /tmp/vabHikq0lF/naive_concat.8.bcf /tmp/vabHikq0lF/naive_concat.9.bcf | /build/bcftools-1.16/bcftools view -H .. ok test_naive_concat: /build/bcftools-1.16/bcftools concat --naive /tmp/vabHikq0lF/naive_concat.0.vcf.gz /tmp/vabHikq0lF/naive_concat.1.vcf.gz /tmp/vabHikq0lF/naive_concat.2.vcf.gz /tmp/vabHikq0lF/naive_concat.3.vcf.gz /tmp/vabHikq0lF/naive_concat.4.vcf.gz /tmp/vabHikq0lF/naive_concat.5.vcf.gz /tmp/vabHikq0lF/naive_concat.6.vcf.gz /tmp/vabHikq0lF/naive_concat.7.vcf.gz /tmp/vabHikq0lF/naive_concat.8.vcf.gz /tmp/vabHikq0lF/naive_concat.9.vcf.gz | /build/bcftools-1.16/bcftools view -H .. ok test_vcf_concat: /build/bcftools-1.16/bcftools concat --no-version -l /tmp/vabHikq0lF/concat.4.a.vcf.gz /tmp/vabHikq0lF/concat.4.b.vcf.gz .. ok test_vcf_concat: /build/bcftools-1.16/bcftools concat -Ob -l /tmp/vabHikq0lF/concat.4.a.vcf.gz /tmp/vabHikq0lF/concat.4.b.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-1.16/bcftools concat --no-version -l /tmp/vabHikq0lF/concat.4.a.bcf /tmp/vabHikq0lF/concat.4.b.bcf .. ok test_vcf_concat: /build/bcftools-1.16/bcftools concat -Ob -l /tmp/vabHikq0lF/concat.4.a.bcf /tmp/vabHikq0lF/concat.4.b.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-1.16/bcftools concat --no-version -l --ligate-warn /tmp/vabHikq0lF/concat.5.a.vcf.gz /tmp/vabHikq0lF/concat.5.b.vcf.gz /tmp/vabHikq0lF/concat.5.c.vcf.gz .. ok test_vcf_concat: /build/bcftools-1.16/bcftools concat -Ob -l --ligate-warn /tmp/vabHikq0lF/concat.5.a.vcf.gz /tmp/vabHikq0lF/concat.5.b.vcf.gz /tmp/vabHikq0lF/concat.5.c.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-1.16/bcftools concat --no-version -l --ligate-warn /tmp/vabHikq0lF/concat.5.a.bcf /tmp/vabHikq0lF/concat.5.b.bcf /tmp/vabHikq0lF/concat.5.c.bcf .. ok test_vcf_concat: /build/bcftools-1.16/bcftools concat -Ob -l --ligate-warn /tmp/vabHikq0lF/concat.5.a.bcf /tmp/vabHikq0lF/concat.5.b.bcf /tmp/vabHikq0lF/concat.5.c.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-1.16/bcftools concat --no-version -l --ligate-force /tmp/vabHikq0lF/concat.5.a.bcf /tmp/vabHikq0lF/concat.5.b.bcf /tmp/vabHikq0lF/concat.5.c.bcf .. ok test_vcf_concat: /build/bcftools-1.16/bcftools concat -Ob -l --ligate-force /tmp/vabHikq0lF/concat.5.a.bcf /tmp/vabHikq0lF/concat.5.b.bcf /tmp/vabHikq0lF/concat.5.c.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_reheader: /build/bcftools-1.16/bcftools reheader -h /build/bcftools-1.16/test/reheader.hdr /build/bcftools-1.16/test/reheader.vcf | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-1.16/test/reheader.vcf | /build/bcftools-1.16/bcftools reheader -h /build/bcftools-1.16/test/reheader.hdr | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.16/bcftools reheader -h /build/bcftools-1.16/test/reheader.hdr /tmp/vabHikq0lF/reheader.bcf | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/vabHikq0lF/reheader.bcf | /build/bcftools-1.16/bcftools reheader -h /build/bcftools-1.16/test/reheader.hdr | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.16/bcftools reheader -h /build/bcftools-1.16/test/reheader.hdr /tmp/vabHikq0lF/reheader.vcf.gz | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/vabHikq0lF/reheader.vcf.gz | /build/bcftools-1.16/bcftools reheader -h /build/bcftools-1.16/test/reheader.hdr | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.16/bcftools reheader -s /build/bcftools-1.16/test/reheader.samples /build/bcftools-1.16/test/reheader.vcf | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-1.16/test/reheader.vcf | /build/bcftools-1.16/bcftools reheader -s /build/bcftools-1.16/test/reheader.samples | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.16/bcftools reheader -s /build/bcftools-1.16/test/reheader.samples /tmp/vabHikq0lF/reheader.bcf | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/vabHikq0lF/reheader.bcf | /build/bcftools-1.16/bcftools reheader -s /build/bcftools-1.16/test/reheader.samples | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.16/bcftools reheader -s /build/bcftools-1.16/test/reheader.samples /tmp/vabHikq0lF/reheader.vcf.gz | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/vabHikq0lF/reheader.vcf.gz | /build/bcftools-1.16/bcftools reheader -s /build/bcftools-1.16/test/reheader.samples | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.16/bcftools reheader -s /build/bcftools-1.16/test/reheader.samples2 /build/bcftools-1.16/test/reheader.vcf | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-1.16/test/reheader.vcf | /build/bcftools-1.16/bcftools reheader -s /build/bcftools-1.16/test/reheader.samples2 | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.16/bcftools reheader -s /build/bcftools-1.16/test/reheader.samples2 /tmp/vabHikq0lF/reheader.bcf | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/vabHikq0lF/reheader.bcf | /build/bcftools-1.16/bcftools reheader -s /build/bcftools-1.16/test/reheader.samples2 | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.16/bcftools reheader -s /build/bcftools-1.16/test/reheader.samples2 /tmp/vabHikq0lF/reheader.vcf.gz | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/vabHikq0lF/reheader.vcf.gz | /build/bcftools-1.16/bcftools reheader -s /build/bcftools-1.16/test/reheader.samples2 | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.16/bcftools reheader -s /build/bcftools-1.16/test/reheader.samples3 /build/bcftools-1.16/test/reheader.vcf | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-1.16/test/reheader.vcf | /build/bcftools-1.16/bcftools reheader -s /build/bcftools-1.16/test/reheader.samples3 | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.16/bcftools reheader -s /build/bcftools-1.16/test/reheader.samples3 /tmp/vabHikq0lF/reheader.bcf | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/vabHikq0lF/reheader.bcf | /build/bcftools-1.16/bcftools reheader -s /build/bcftools-1.16/test/reheader.samples3 | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.16/bcftools reheader -s /build/bcftools-1.16/test/reheader.samples3 /tmp/vabHikq0lF/reheader.vcf.gz | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/vabHikq0lF/reheader.vcf.gz | /build/bcftools-1.16/bcftools reheader -s /build/bcftools-1.16/test/reheader.samples3 | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.16/bcftools reheader -s /build/bcftools-1.16/test/reheader.samples4 /build/bcftools-1.16/test/reheader.vcf | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-1.16/test/reheader.vcf | /build/bcftools-1.16/bcftools reheader -s /build/bcftools-1.16/test/reheader.samples4 | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.16/bcftools reheader -s /build/bcftools-1.16/test/reheader.samples4 /tmp/vabHikq0lF/reheader.bcf | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/vabHikq0lF/reheader.bcf | /build/bcftools-1.16/bcftools reheader -s /build/bcftools-1.16/test/reheader.samples4 | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.16/bcftools reheader -s /build/bcftools-1.16/test/reheader.samples4 /tmp/vabHikq0lF/reheader.vcf.gz | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/vabHikq0lF/reheader.vcf.gz | /build/bcftools-1.16/bcftools reheader -s /build/bcftools-1.16/test/reheader.samples4 | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.16/bcftools reheader -h /build/bcftools-1.16/test/reheader.empty.hdr /build/bcftools-1.16/test/empty.vcf | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-1.16/test/empty.vcf | /build/bcftools-1.16/bcftools reheader -h /build/bcftools-1.16/test/reheader.empty.hdr | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.16/bcftools reheader -h /build/bcftools-1.16/test/reheader.empty.hdr /tmp/vabHikq0lF/empty.bcf | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/vabHikq0lF/empty.bcf | /build/bcftools-1.16/bcftools reheader -h /build/bcftools-1.16/test/reheader.empty.hdr | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.16/bcftools reheader -h /build/bcftools-1.16/test/reheader.empty.hdr /tmp/vabHikq0lF/empty.vcf.gz | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/vabHikq0lF/empty.vcf.gz | /build/bcftools-1.16/bcftools reheader -h /build/bcftools-1.16/test/reheader.empty.hdr | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.16/bcftools reheader -f /build/bcftools-1.16/test/reheader.fai /build/bcftools-1.16/test/reheader.2.vcf | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.16/bcftools reheader -f /build/bcftools-1.16/test/reheader.fai /tmp/vabHikq0lF/reheader.2.bcf | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.16/bcftools reheader -f /build/bcftools-1.16/test/reheader.fai /tmp/vabHikq0lF/reheader.2.vcf.gz | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.16/bcftools reheader -h /build/bcftools-1.16/test/reheader.2.hdr -f /build/bcftools-1.16/test/reheader.fai /build/bcftools-1.16/test/reheader.2.vcf | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.16/bcftools reheader -h /build/bcftools-1.16/test/reheader.2.hdr -f /build/bcftools-1.16/test/reheader.fai /tmp/vabHikq0lF/reheader.2.bcf | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.16/bcftools reheader -h /build/bcftools-1.16/test/reheader.2.hdr -f /build/bcftools-1.16/test/reheader.fai /tmp/vabHikq0lF/reheader.2.vcf.gz | /build/bcftools-1.16/bcftools view --no-version .. ok test_rename_chrs: /build/bcftools-1.16/bcftools annotate --rename-chrs /tmp/vabHikq0lF/rename.map -Ov /tmp/vabHikq0lF/annotate.bcf | /build/bcftools-1.16/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /build/bcftools-1.16/bcftools annotate --rename-chrs /tmp/vabHikq0lF/rename.map -Ob /tmp/vabHikq0lF/annotate.bcf | /build/bcftools-1.16/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /build/bcftools-1.16/bcftools annotate --rename-chrs /tmp/vabHikq0lF/rename.map -Ov /build/bcftools-1.16/test/annotate.vcf | /build/bcftools-1.16/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /build/bcftools-1.16/bcftools annotate --rename-chrs /tmp/vabHikq0lF/rename.map -Ob /build/bcftools-1.16/test/annotate.vcf | /build/bcftools-1.16/bcftools query -f'%CHROM\t%POS\n' .. ok test_vcf_convert: /build/bcftools-1.16/bcftools convert -g -,. /tmp/vabHikq0lF/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/convert.vcf.gz | /build/bcftools-1.16/bcftools convert -g -,. .. ok test_vcf_convert: /build/bcftools-1.16/bcftools convert -g -,. --vcf-ids /tmp/vabHikq0lF/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/convert.vcf.gz | /build/bcftools-1.16/bcftools convert -g -,. --vcf-ids .. ok test_vcf_convert: /build/bcftools-1.16/bcftools convert -g -,. --vcf-ids --3N6 /tmp/vabHikq0lF/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/convert.vcf.gz | /build/bcftools-1.16/bcftools convert -g -,. --vcf-ids --3N6 .. ok test_vcf_convert: /build/bcftools-1.16/bcftools convert -g .,- /tmp/vabHikq0lF/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/convert.vcf.gz | /build/bcftools-1.16/bcftools convert -g .,- .. ok test_vcf_convert_hs2vcf: /build/bcftools-1.16/bcftools convert --vcf-ids -G /build/bcftools-1.16/test/convert.gs.gt.ids.gen,/build/bcftools-1.16/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-1.16/bcftools convert --vcf-ids -G /build/bcftools-1.16/test/convert.gs.gt.ids.gen,/build/bcftools-1.16/test/convert.gs.gt.samples -Ou | /build/bcftools-1.16/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-1.16/bcftools convert -G /build/bcftools-1.16/test/convert.gs.gt.ids.gen,/build/bcftools-1.16/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-1.16/bcftools convert -G /build/bcftools-1.16/test/convert.gs.gt.ids.gen,/build/bcftools-1.16/test/convert.gs.gt.samples -Ou | /build/bcftools-1.16/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-1.16/bcftools convert --3N6 -G /build/bcftools-1.16/test/convert.gs.gt.ids.3N6.gen,/build/bcftools-1.16/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-1.16/bcftools convert --3N6 -G /build/bcftools-1.16/test/convert.gs.gt.ids.3N6.gen,/build/bcftools-1.16/test/convert.gs.gt.samples -Ou | /build/bcftools-1.16/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-1.16/bcftools convert --vcf-ids -G /build/bcftools-1.16/test/convert.gs.gt.ids.gen.rev,/build/bcftools-1.16/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-1.16/bcftools convert --vcf-ids -G /build/bcftools-1.16/test/convert.gs.gt.ids.gen.rev,/build/bcftools-1.16/test/convert.gs.gt.samples -Ou | /build/bcftools-1.16/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-1.16/bcftools convert -G /build/bcftools-1.16/test/convert.gs.gt.ids.gen.rev,/build/bcftools-1.16/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-1.16/bcftools convert -G /build/bcftools-1.16/test/convert.gs.gt.ids.gen.rev,/build/bcftools-1.16/test/convert.gs.gt.samples -Ou | /build/bcftools-1.16/bcftools view | grep -v ^## .. ok test_vcf_convert: /build/bcftools-1.16/bcftools convert -g -,. --tag PL /tmp/vabHikq0lF/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/convert.vcf.gz | /build/bcftools-1.16/bcftools convert -g -,. --tag PL .. ok test_vcf_convert: /build/bcftools-1.16/bcftools convert -g .,- --tag PL /tmp/vabHikq0lF/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/convert.vcf.gz | /build/bcftools-1.16/bcftools convert -g .,- --tag PL .. ok test_vcf_convert: /build/bcftools-1.16/bcftools convert -g -,. --vcf-ids /tmp/vabHikq0lF/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/check.vcf.gz | /build/bcftools-1.16/bcftools convert -g -,. --vcf-ids .. ok test_vcf_convert: /build/bcftools-1.16/bcftools convert -g .,- --vcf-ids /tmp/vabHikq0lF/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/check.vcf.gz | /build/bcftools-1.16/bcftools convert -g .,- --vcf-ids .. ok test_vcf_convert: /build/bcftools-1.16/bcftools convert -g -,. --3N6 /tmp/vabHikq0lF/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/check.vcf.gz | /build/bcftools-1.16/bcftools convert -g -,. --3N6 .. ok test_vcf_convert: /build/bcftools-1.16/bcftools convert -g .,- --3N6 /tmp/vabHikq0lF/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/check.vcf.gz | /build/bcftools-1.16/bcftools convert -g .,- --3N6 .. ok test_vcf_convert: /build/bcftools-1.16/bcftools convert -g -,. --3N6 --vcf-ids /tmp/vabHikq0lF/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/check.vcf.gz | /build/bcftools-1.16/bcftools convert -g -,. --3N6 --vcf-ids .. ok test_vcf_convert: /build/bcftools-1.16/bcftools convert -g .,- --3N6 --vcf-ids /tmp/vabHikq0lF/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/check.vcf.gz | /build/bcftools-1.16/bcftools convert -g .,- --3N6 --vcf-ids .. ok test_vcf_convert: /build/bcftools-1.16/bcftools convert -h -,.,. /tmp/vabHikq0lF/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/convert.vcf.gz | /build/bcftools-1.16/bcftools convert -h -,.,. .. ok test_vcf_convert: /build/bcftools-1.16/bcftools convert -h .,-,. /tmp/vabHikq0lF/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/convert.vcf.gz | /build/bcftools-1.16/bcftools convert -h .,-,. .. ok test_vcf_convert: /build/bcftools-1.16/bcftools convert -h .,-,. --vcf-ids /tmp/vabHikq0lF/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/convert.vcf.gz | /build/bcftools-1.16/bcftools convert -h .,-,. --vcf-ids .. ok test_vcf_convert: /build/bcftools-1.16/bcftools convert -h .,.,- /tmp/vabHikq0lF/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/convert.vcf.gz | /build/bcftools-1.16/bcftools convert -h .,.,- .. ok test_vcf_convert_hls2vcf: /build/bcftools-1.16/bcftools convert -H /build/bcftools-1.16/test/convert.hls.gt.hap,/build/bcftools-1.16/test/convert.hls.gt.legend,/build/bcftools-1.16/test/convert.hls.gt.samples | grep -v ^## .. ok test_vcf_convert_hls2vcf: /build/bcftools-1.16/bcftools convert -H /build/bcftools-1.16/test/convert.hls.gt.hap,/build/bcftools-1.16/test/convert.hls.gt.legend,/build/bcftools-1.16/test/convert.hls.gt.samples -Ou | /build/bcftools-1.16/bcftools view | grep -v ^## .. ok test_vcf_convert: /build/bcftools-1.16/bcftools convert --haplegendsample -,.,. /tmp/vabHikq0lF/convert.hap-missing.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/convert.hap-missing.vcf.gz | /build/bcftools-1.16/bcftools convert --haplegendsample -,.,. .. ok test_vcf_convert: /build/bcftools-1.16/bcftools convert --hapsample -,. /tmp/vabHikq0lF/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/convert.vcf.gz | /build/bcftools-1.16/bcftools convert --hapsample -,. .. ok test_vcf_convert: /build/bcftools-1.16/bcftools convert --hapsample -,. --vcf-ids /tmp/vabHikq0lF/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/convert.vcf.gz | /build/bcftools-1.16/bcftools convert --hapsample -,. --vcf-ids .. ok test_vcf_convert: /build/bcftools-1.16/bcftools convert --hapsample .,- /tmp/vabHikq0lF/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/convert.vcf.gz | /build/bcftools-1.16/bcftools convert --hapsample .,- .. ok test_vcf_convert_hs2vcf: /build/bcftools-1.16/bcftools convert --hapsample2vcf /build/bcftools-1.16/test/convert.hs.gt.hap,/build/bcftools-1.16/test/convert.hs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-1.16/bcftools convert --hapsample2vcf /build/bcftools-1.16/test/convert.hs.gt.hap,/build/bcftools-1.16/test/convert.hs.gt.samples -Ou | /build/bcftools-1.16/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-1.16/bcftools convert --vcf-ids --hapsample2vcf /build/bcftools-1.16/test/convert.hs.gt.ids.hap,/build/bcftools-1.16/test/convert.hs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-1.16/bcftools convert --vcf-ids --hapsample2vcf /build/bcftools-1.16/test/convert.hs.gt.ids.hap,/build/bcftools-1.16/test/convert.hs.gt.samples -Ou | /build/bcftools-1.16/bcftools view | grep -v ^## .. ok test_vcf_convert_gvcf: /build/bcftools-1.16/bcftools convert --no-version --gvcf2vcf -i'FILTER="PASS"' -f /build/bcftools-1.16/test/gvcf.fa /tmp/vabHikq0lF/convert.gvcf.vcf.gz .. ok test_vcf_convert_gvcf: /build/bcftools-1.16/bcftools view -Ob /tmp/vabHikq0lF/convert.gvcf.vcf.gz | /build/bcftools-1.16/bcftools convert --gvcf2vcf -i'FILTER="PASS"' -f /build/bcftools-1.16/test/gvcf.fa | grep -v ^##bcftools .. ok test_vcf_convert_tsv2vcf: /build/bcftools-1.16/bcftools convert --no-version -c ID,CHROM,POS,AA -s SAMPLE1 -f /build/bcftools-1.16/test/23andme.fa --tsv2vcf /build/bcftools-1.16/test/convert.23andme .. ok test_vcf_convert_tsv2vcf: /build/bcftools-1.16/bcftools convert -Ou -c ID,CHROM,POS,AA -s SAMPLE1 -f /build/bcftools-1.16/test/23andme.fa --tsv2vcf /build/bcftools-1.16/test/convert.23andme | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/vabHikq0lF/consensus.vcf.gz -f /build/bcftools-1.16/test/consensus.fa -m /build/bcftools-1.16/test/consensus.tab .. ok test_vcf_consensus_chain: /build/bcftools-1.16/bcftools consensus /tmp/vabHikq0lF/consensus.vcf.gz -f /build/bcftools-1.16/test/consensus.fa -m /build/bcftools-1.16/test/consensus.tab -c /tmp/vabHikq0lF/consensus.1.chain.new >/dev/null; cat /tmp/vabHikq0lF/consensus.1.chain.new .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/vabHikq0lF/consensus.vcf.gz -f /build/bcftools-1.16/test/consensus.fa -H 1 -m /build/bcftools-1.16/test/consensus.tab .. ok test_vcf_consensus_chain: /build/bcftools-1.16/bcftools consensus /tmp/vabHikq0lF/consensus.vcf.gz -f /build/bcftools-1.16/test/consensus.fa -H 1 -m /build/bcftools-1.16/test/consensus.tab -c /tmp/vabHikq0lF/consensus.2.chain.new >/dev/null; cat /tmp/vabHikq0lF/consensus.2.chain.new .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/vabHikq0lF/consensus.vcf.gz -f /build/bcftools-1.16/test/consensus.fa -I -m /build/bcftools-1.16/test/consensus.tab .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/vabHikq0lF/consensus.vcf.gz -f /build/bcftools-1.16/test/consensus.fa -I -m /build/bcftools-1.16/test/consensus.tab --mask-with X -m /build/bcftools-1.16/test/consensus.tab --mask-with lc .. ok test_vcf_consensus_chain: /build/bcftools-1.16/bcftools consensus /tmp/vabHikq0lF/consensus.vcf.gz -f /build/bcftools-1.16/test/consensus.fa -I -m /build/bcftools-1.16/test/consensus.tab -c /tmp/vabHikq0lF/consensus.3.chain.new >/dev/null; cat /tmp/vabHikq0lF/consensus.3.chain.new .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/vabHikq0lF/consensus.vcf.gz -f /build/bcftools-1.16/test/consensus.fa -H 1 .. ok test_vcf_consensus_chain: /build/bcftools-1.16/bcftools consensus /tmp/vabHikq0lF/consensus.vcf.gz -f /build/bcftools-1.16/test/consensus.fa -H 1 -c /tmp/vabHikq0lF/consensus.4.chain.new >/dev/null; cat /tmp/vabHikq0lF/consensus.4.chain.new .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/vabHikq0lF/consensus2.vcf.gz -f /build/bcftools-1.16/test/consensus2.fa -H 1 .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/vabHikq0lF/consensus2.vcf.gz -f /build/bcftools-1.16/test/consensus2.fa -H 2 .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/vabHikq0lF/empty.vcf.gz -f /build/bcftools-1.16/test/consensus.fa .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/vabHikq0lF/consensus3.vcf.gz -f /build/bcftools-1.16/test/consensus2.fa -H 2 -M "?" .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/vabHikq0lF/consensus3.vcf.gz -f /build/bcftools-1.16/test/consensus2.fa -H 2 -M "?" -p xx_ .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/vabHikq0lF/consensus4.vcf.gz -f /build/bcftools-1.16/test/consensus2.fa .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/vabHikq0lF/consensus5.vcf.gz -f /build/bcftools-1.16/test/consensus5.fa --haplotype LA .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/vabHikq0lF/consensus6.vcf.gz -f /build/bcftools-1.16/test/consensus6.fa .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/vabHikq0lF/consensus7.vcf.gz -f /build/bcftools-1.16/test/consensus7.fa -H 2 .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/vabHikq0lF/consensus7.vcf.gz -f /build/bcftools-1.16/test/consensus7.fa -H 2pIu .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/vabHikq0lF/consensus7.vcf.gz -f /build/bcftools-1.16/test/consensus7.fa -H 1 .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/vabHikq0lF/consensus7.vcf.gz -f /build/bcftools-1.16/test/consensus7.fa -H 1pIu .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/vabHikq0lF/consensus8.vcf.gz -f /build/bcftools-1.16/test/consensus.fa .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/vabHikq0lF/consensus8.vcf.gz -f /build/bcftools-1.16/test/consensus.fa -a . .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/vabHikq0lF/consensus8.vcf.gz -f /build/bcftools-1.16/test/consensus.fa -a . -i 'type="snp" || type="ref"' .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/vabHikq0lF/consensus8.vcf.gz -f /build/bcftools-1.16/test/consensus.fa -a . -i 'ALT!=""' .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/vabHikq0lF/consensus8.vcf.gz -f /build/bcftools-1.16/test/consensus.fa -a . -e 'MinDP>15' .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/vabHikq0lF/consensus8.vcf.gz -f /build/bcftools-1.16/test/consensus.fa -a . -e 'MinDP<15' .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/vabHikq0lF/consensus.9.vcf.gz -f /build/bcftools-1.16/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/vabHikq0lF/consensus.9.vcf.gz -f /build/bcftools-1.16/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/vabHikq0lF/consensus.10.vcf.gz -f /build/bcftools-1.16/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/vabHikq0lF/consensus.10.vcf.gz -f /build/bcftools-1.16/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/vabHikq0lF/consensus.11.vcf.gz -f /build/bcftools-1.16/test/consensus.11.fa -s smpl .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/vabHikq0lF/consensus.11.vcf.gz -f /build/bcftools-1.16/test/consensus.11.fa -s smpl -a N .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/vabHikq0lF/consensus.12.vcf.gz -f /build/bcftools-1.16/test/consensus.12.fa .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/vabHikq0lF/consensus.13.vcf.gz -f /build/bcftools-1.16/test/consensus.13.fa .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/vabHikq0lF/consensus.14.vcf.gz -f /build/bcftools-1.16/test/consensus.14.fa .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/vabHikq0lF/consensus.12.vcf.gz -f /build/bcftools-1.16/test/consensus.12.fa --mark-del - --mark-ins uc --mark-snv uc .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/vabHikq0lF/consensus.15.vcf.gz -f /build/bcftools-1.16/test/consensus.15.fa -H I --mark-ins lc --mark-snv lc .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/vabHikq0lF/consensus.16.vcf.gz -f /build/bcftools-1.16/test/consensus.fa -I .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/vabHikq0lF/consensus.16.vcf.gz -f /build/bcftools-1.16/test/consensus.fa -H I .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/vabHikq0lF/consensus.17.vcf.gz -f /build/bcftools-1.16/test/consensus2.fa -M N -m /build/bcftools-1.16/test/consensus.17.bed .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/vabHikq0lF/consensus.18.vcf.gz -f /build/bcftools-1.16/test/consensus.18.fa .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/vabHikq0lF/consensus.19.vcf.gz -f /build/bcftools-1.16/test/consensus.19.fa .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r17:100-150 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r17:100-150 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r17:100-150 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -b /tmp/vabHikq0lF/mpileup.bam.list --no-version | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r17:100-150 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob -b /tmp/vabHikq0lF/mpileup.bam.urllist | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r17:100-150 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r17:100-150 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r17:100-150 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -b /tmp/vabHikq0lF/mpileup.cram.list --no-version | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r17:100-150 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob -b /tmp/vabHikq0lF/mpileup.cram.urllist | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a DP,DV -r17:100-600 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a DP,DV -r17:100-600 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a DP,DV -r17:100-600 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a DP,DV -r17:100-600 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r17:100-150 -S /build/bcftools-1.16/test/mplp.samples -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r17:100-150 -S /build/bcftools-1.16/test/mplp.samples -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r17:100-150 -S /build/bcftools-1.16/test/mplp.samples -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r17:100-150 -S /build/bcftools-1.16/test/mplp.samples -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r17:100-150 -S ^/build/bcftools-1.16/test/mplp.samples -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r17:100-150 -S ^/build/bcftools-1.16/test/mplp.samples -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r17:100-150 -S ^/build/bcftools-1.16/test/mplp.samples -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r17:100-150 -S ^/build/bcftools-1.16/test/mplp.samples -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -t17:100-150 -S /build/bcftools-1.16/test/mplp.9.samples -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.sam /build/bcftools-1.16/test/mpileup/mpileup.2.sam /build/bcftools-1.16/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -t17:100-150 -S /build/bcftools-1.16/test/mplp.9.samples -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.sam /build/bcftools-1.16/test/mpileup/mpileup.2.sam /build/bcftools-1.16/test/mpileup/mpileup.3.sam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -t17:100-150 -S /build/bcftools-1.16/test/mplp.9.samples -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -t17:100-150 -S /build/bcftools-1.16/test/mplp.9.samples -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -t17:100-150 -S /build/bcftools-1.16/test/mplp.9.samples -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -t17:100-150 -S /build/bcftools-1.16/test/mplp.9.samples -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -t17:100-150 -G /build/bcftools-1.16/test/mplp.10.samples -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.sam /build/bcftools-1.16/test/mpileup/mpileup.2.sam /build/bcftools-1.16/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -t17:100-150 -G /build/bcftools-1.16/test/mplp.10.samples -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.sam /build/bcftools-1.16/test/mpileup/mpileup.2.sam /build/bcftools-1.16/test/mpileup/mpileup.3.sam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -t17:100-150 -G /build/bcftools-1.16/test/mplp.10.samples -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -t17:100-150 -G /build/bcftools-1.16/test/mplp.10.samples -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -t17:100-150 -G /build/bcftools-1.16/test/mplp.10.samples -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -t17:100-150 -G /build/bcftools-1.16/test/mplp.10.samples -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.3.sam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.3.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.3.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -s HG00102 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.3.sam /build/bcftools-1.16/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -s HG00102 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.3.sam /build/bcftools-1.16/test/mpileup/mpileup.4.sam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -s HG00102 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.3.bam /build/bcftools-1.16/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -s HG00102 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.3.bam /build/bcftools-1.16/test/mpileup/mpileup.4.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -s HG00102 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.3.cram /build/bcftools-1.16/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -s HG00102 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.3.cram /build/bcftools-1.16/test/mpileup/mpileup.4.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -s ^HG99999 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.3.sam /build/bcftools-1.16/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -s ^HG99999 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.3.sam /build/bcftools-1.16/test/mpileup/mpileup.4.sam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -s ^HG99999 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.3.bam /build/bcftools-1.16/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -s ^HG99999 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.3.bam /build/bcftools-1.16/test/mpileup/mpileup.4.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -s ^HG99999 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.3.cram /build/bcftools-1.16/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -s ^HG99999 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.3.cram /build/bcftools-1.16/test/mpileup/mpileup.4.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -G /build/bcftools-1.16/test/mplp.11.rgs -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.3.sam /build/bcftools-1.16/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -G /build/bcftools-1.16/test/mplp.11.rgs -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.3.sam /build/bcftools-1.16/test/mpileup/mpileup.4.sam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -G /build/bcftools-1.16/test/mplp.11.rgs -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.3.bam /build/bcftools-1.16/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -G /build/bcftools-1.16/test/mplp.11.rgs -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.3.bam /build/bcftools-1.16/test/mpileup/mpileup.4.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -G /build/bcftools-1.16/test/mplp.11.rgs -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.3.cram /build/bcftools-1.16/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -G /build/bcftools-1.16/test/mplp.11.rgs -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.3.cram /build/bcftools-1.16/test/mpileup/mpileup.4.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -G /build/bcftools-1.16/test/mplp.11.rgs -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.3.sam /build/bcftools-1.16/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -G /build/bcftools-1.16/test/mplp.11.rgs -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.3.sam /build/bcftools-1.16/test/mpileup/mpileup.4.sam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -G /build/bcftools-1.16/test/mplp.11.rgs -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.3.bam /build/bcftools-1.16/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -G /build/bcftools-1.16/test/mplp.11.rgs -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.3.bam /build/bcftools-1.16/test/mpileup/mpileup.4.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -G /build/bcftools-1.16/test/mplp.11.rgs -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.3.cram /build/bcftools-1.16/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -G /build/bcftools-1.16/test/mplp.11.rgs -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.3.cram /build/bcftools-1.16/test/mpileup/mpileup.4.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a AD -f /build/bcftools-1.16/test/mpileup/indel-AD.1.fa /build/bcftools-1.16/test/mpileup/indel-AD.1.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a AD -f /build/bcftools-1.16/test/mpileup/indel-AD.1.fa -Ob /build/bcftools-1.16/test/mpileup/indel-AD.1.sam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a AD -f /build/bcftools-1.16/test/mpileup/indel-AD.1.fa /build/bcftools-1.16/test/mpileup/indel-AD.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a AD -f /build/bcftools-1.16/test/mpileup/indel-AD.1.fa -Ob /build/bcftools-1.16/test/mpileup/indel-AD.1.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a AD -f /build/bcftools-1.16/test/mpileup/indel-AD.1.fa /build/bcftools-1.16/test/mpileup/indel-AD.1.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a AD -f /build/bcftools-1.16/test/mpileup/indel-AD.1.fa -Ob /build/bcftools-1.16/test/mpileup/indel-AD.1.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a AD -r 11:75 -f /build/bcftools-1.16/test/mpileup/indel-AD.2.fa /build/bcftools-1.16/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a AD -r 11:75 -f /build/bcftools-1.16/test/mpileup/indel-AD.2.fa -Ob /build/bcftools-1.16/test/mpileup/indel-AD.2.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a AD -r 11:75 -f /build/bcftools-1.16/test/mpileup/indel-AD.2.fa /build/bcftools-1.16/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a AD -r 11:75 -f /build/bcftools-1.16/test/mpileup/indel-AD.2.fa -Ob /build/bcftools-1.16/test/mpileup/indel-AD.2.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /build/bcftools-1.16/test/mpileup/indel-AD.2.fa /build/bcftools-1.16/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /build/bcftools-1.16/test/mpileup/indel-AD.2.fa -Ob /build/bcftools-1.16/test/mpileup/indel-AD.2.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /build/bcftools-1.16/test/mpileup/indel-AD.2.fa /build/bcftools-1.16/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /build/bcftools-1.16/test/mpileup/indel-AD.2.fa -Ob /build/bcftools-1.16/test/mpileup/indel-AD.2.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /build/bcftools-1.16/test/mpileup/indel-AD.2.fa /build/bcftools-1.16/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /build/bcftools-1.16/test/mpileup/indel-AD.2.fa -Ob /build/bcftools-1.16/test/mpileup/indel-AD.2.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /build/bcftools-1.16/test/mpileup/indel-AD.2.fa /build/bcftools-1.16/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /build/bcftools-1.16/test/mpileup/indel-AD.2.fa -Ob /build/bcftools-1.16/test/mpileup/indel-AD.2.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a INFO/SCR,FMT/SCR -f /build/bcftools-1.16/test/mpileup/mpileup-SCR.fa /build/bcftools-1.16/test/mpileup/mpileup-SCR.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a INFO/SCR,FMT/SCR -f /build/bcftools-1.16/test/mpileup/mpileup-SCR.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup-SCR.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a INFO/SCR,FMT/SCR -f /build/bcftools-1.16/test/mpileup/mpileup-SCR.fa /build/bcftools-1.16/test/mpileup/mpileup-SCR.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a INFO/SCR,FMT/SCR -f /build/bcftools-1.16/test/mpileup/mpileup-SCR.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup-SCR.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -t 1:100 --skip-all-set PAIRED,PROPER_PAIR,MREVERSE -f /build/bcftools-1.16/test/mpileup/mpileup-SCR.fa /build/bcftools-1.16/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -t 1:100 --skip-all-set PAIRED,PROPER_PAIR,MREVERSE -f /build/bcftools-1.16/test/mpileup/mpileup-SCR.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup-filter.sam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -t 1:100 --skip-any-set READ1 -f /build/bcftools-1.16/test/mpileup/mpileup-SCR.fa /build/bcftools-1.16/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -t 1:100 --skip-any-set READ1 -f /build/bcftools-1.16/test/mpileup/mpileup-SCR.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup-filter.sam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -t 1:100 --skip-all-unset READ1 -f /build/bcftools-1.16/test/mpileup/mpileup-SCR.fa /build/bcftools-1.16/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -t 1:100 --skip-all-unset READ1 -f /build/bcftools-1.16/test/mpileup/mpileup-SCR.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup-filter.sam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -t 1:100 --skip-any-unset READ1 -f /build/bcftools-1.16/test/mpileup/mpileup-SCR.fa /build/bcftools-1.16/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -t 1:100 --skip-any-unset READ1 -f /build/bcftools-1.16/test/mpileup/mpileup-SCR.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup-filter.sam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r chr19:69-99 -f /build/bcftools-1.16/test/mpileup/annot-NMBZ.1.fa /build/bcftools-1.16/test/mpileup/annot-NMBZ.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r chr19:69-99 -f /build/bcftools-1.16/test/mpileup/annot-NMBZ.1.fa -Ob /build/bcftools-1.16/test/mpileup/annot-NMBZ.1.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r chr6:75 -f /build/bcftools-1.16/test/mpileup/annot-NMBZ.2.fa /build/bcftools-1.16/test/mpileup/annot-NMBZ.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r chr6:75 -f /build/bcftools-1.16/test/mpileup/annot-NMBZ.2.fa -Ob /build/bcftools-1.16/test/mpileup/annot-NMBZ.2.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r chr16:75 -f /build/bcftools-1.16/test/mpileup/annot-NMBZ.3.fa /build/bcftools-1.16/test/mpileup/annot-NMBZ.3.1.bam /build/bcftools-1.16/test/mpileup/annot-NMBZ.3.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r chr16:75 -f /build/bcftools-1.16/test/mpileup/annot-NMBZ.3.fa -Ob /build/bcftools-1.16/test/mpileup/annot-NMBZ.3.1.bam /build/bcftools-1.16/test/mpileup/annot-NMBZ.3.2.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_csq: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq.fa -g /build/bcftools-1.16/test/csq.gff3 /build/bcftools-1.16/test/csq.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq.fa -g /build/bcftools-1.16/test/csq.chr.gff3 /build/bcftools-1.16/test/csq.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq.fa -g /build/bcftools-1.16/test/csq.2.gff /build/bcftools-1.16/test/csq.2.vcf | /build/bcftools-1.16/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq.fa -g /build/bcftools-1.16/test/csq.2.gff --ncsq 64 /build/bcftools-1.16/test/csq.2.vcf | /build/bcftools-1.16/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000624631/ENST00000624631.fa -g /build/bcftools-1.16/test/csq/ENST00000624631/ENST00000624631.gff /build/bcftools-1.16/test/csq/ENST00000624631/ambiguous.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000593942/ENST00000593942.fa -g /build/bcftools-1.16/test/csq/ENST00000593942/ENST00000593942.gff /build/bcftools-1.16/test/csq/ENST00000593942/last-codon-deletion.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/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/bcftools-1.16/test/csq/ENST00000580206 && /build/bcftools-1.16/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.ins-snv.vcf | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-1.16/bcftools csq -f ENST00000580206.fa -g short.gff compound.ins-snv.vcf | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-1.16/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff single.ins-snv.vcf | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-1.16/bcftools csq -f ENST00000580206.fa -g short.gff single.ins-snv.vcf | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-1.16/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.del-snv.vcf | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-1.16/bcftools csq -f ENST00000580206.fa -g short.gff compound.del-snv.vcf | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-1.16/bcftools csq -f ENST00000580206.fa -g short.gff single.del-snv.vcf | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-1.16/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.del-ins.vcf | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-1.16/bcftools csq -f ENST00000580206.fa -g short.gff compound.del-ins.vcf | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-1.16/bcftools csq -f ENST00000580206.fa -g short.gff single.del-ins.vcf | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000573314/ENST00000573314.fa -g /build/bcftools-1.16/test/csq/ENST00000573314/ENST00000573314.gff /build/bcftools-1.16/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000573314/ENST00000573314.fa -g /build/bcftools-1.16/test/csq/ENST00000573314/ENST00000573314.gff /build/bcftools-1.16/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000557788/ENST00000557788.fa -g /build/bcftools-1.16/test/csq/ENST00000557788/ENST00000557788.gff /build/bcftools-1.16/test/csq/ENST00000557788/long-overlap-del.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000545279/ENST00000545279.fa -g /build/bcftools-1.16/test/csq/ENST00000545279/ENST00000545279.gff /build/bcftools-1.16/test/csq/ENST00000545279/splice-region-insert.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000543077/ENST00000543077.fa -g /build/bcftools-1.16/test/csq/ENST00000543077/ENST00000543077.gff /build/bcftools-1.16/test/csq/ENST00000543077/not-a-start-lost.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000543077/ENST00000543077.fa -g /build/bcftools-1.16/test/csq/ENST00000543077/ENST00000543077.gff /build/bcftools-1.16/test/csq/ENST00000543077/not-a-start-lost.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000542803/ENST00000542803.fa -g /build/bcftools-1.16/test/csq/ENST00000542803/ENST00000542803.gff /build/bcftools-1.16/test/csq/ENST00000542803/splice-region.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000542803/ENST00000542803.fa -g /build/bcftools-1.16/test/csq/ENST00000542803/ENST00000542803.gff /build/bcftools-1.16/test/csq/ENST00000542803/splice-region.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000536784/ENST00000536784.fa -g /build/bcftools-1.16/test/csq/ENST00000536784/ENST00000536784.gff /build/bcftools-1.16/test/csq/ENST00000536784/not-a-start-lost.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000536784/ENST00000536784.fa -g /build/bcftools-1.16/test/csq/ENST00000536784/ENST00000536784.gff /build/bcftools-1.16/test/csq/ENST00000536784/not-a-start-lost.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000528237/ENST00000528237.fa -g /build/bcftools-1.16/test/csq/ENST00000528237/ENST00000528237.gff /build/bcftools-1.16/test/csq/ENST00000528237/retained-stop-incomplete-cds.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000520868/ENST00000520868.fa -g /build/bcftools-1.16/test/csq/ENST00000520868/ENST00000520868.gff /build/bcftools-1.16/test/csq/ENST00000520868/long-deletion.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000520795/ENST00000520795.fa -g /build/bcftools-1.16/test/csq/ENST00000520795/ENST00000520795.gff /build/bcftools-1.16/test/csq/ENST00000520795/long-inside-del.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000520795/ENST00000520795.fa -g /build/bcftools-1.16/test/csq/ENST00000520795/ENST00000520795.gff /build/bcftools-1.16/test/csq/ENST00000520795/long-inside-del.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000519442/ENST00000519442.fa -g /build/bcftools-1.16/test/csq/ENST00000519442/ENST00000519442.gff /build/bcftools-1.16/test/csq/ENST00000519442/synon-splice-region-del.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000518414/ENST00000518414.fa -g /build/bcftools-1.16/test/csq/ENST00000518414/ENST00000518414.gff /build/bcftools-1.16/test/csq/ENST00000518414/incorrect-inframe-del.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.fa -g /build/bcftools-1.16/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.gff /build/bcftools-1.16/test/csq/ENST00000518414-ENST00000521270/valgrind.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000479739/ENST00000479739.fa -g /build/bcftools-1.16/test/csq/ENST00000479739/ENST00000479739.gff /build/bcftools-1.16/test/csq/ENST00000479739/short-cds-start-lost.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000479739/ENST00000479739.fa -g /build/bcftools-1.16/test/csq/ENST00000479739/ENST00000479739.gff /build/bcftools-1.16/test/csq/ENST00000479739/short-cds-start-lost.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000448695/ENST00000448695.fa -g /build/bcftools-1.16/test/csq/ENST00000448695/ENST00000448695.gff /build/bcftools-1.16/test/csq/ENST00000448695/syn-and-splice-reg.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000436063/ENST00000436063.fa -g /build/bcftools-1.16/test/csq/ENST00000436063/ENST00000436063.gff /build/bcftools-1.16/test/csq/ENST00000436063/insert-before-utr.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000423372/ENST00000423372.fa -g /build/bcftools-1.16/test/csq/ENST00000423372/ENST00000423372.gff /build/bcftools-1.16/test/csq/ENST00000423372/snps.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000423372/ENST00000423372.fa -g /build/bcftools-1.16/test/csq/ENST00000423372/ENST00000423372.gff /build/bcftools-1.16/test/csq/ENST00000423372/snps.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000423372/ENST00000423372.fa -g /build/bcftools-1.16/test/csq/ENST00000423372/ENST00000423372.gff /build/bcftools-1.16/test/csq/ENST00000423372/insert3.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000423372/ENST00000423372.fa -g /build/bcftools-1.16/test/csq/ENST00000423372/ENST00000423372.gff /build/bcftools-1.16/test/csq/ENST00000423372/insert3.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/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/bcftools-1.16/test/csq/ENST00000422159 && /build/bcftools-1.16/bcftools csq -f ENST00000422159.fa -g ENST00000422159.gff multiallelic.vcf | /build/bcftools-1.16/bcftools query -f'[%POS\t%REF\t%ALT\t%GT\t%TBCSQ\n]' | ../sort-csq -q ; echo ; /build/bcftools-1.16/bcftools csq -f ENST00000422159.fa -g short.gff multiallelic.vcf | /build/bcftools-1.16/bcftools query -f'[%POS\t%REF\t%ALT\t%GT\t%TBCSQ\n]' | ../sort-csq -q .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000420670/ENST00000420670.fa -g /build/bcftools-1.16/test/csq/ENST00000420670/ENST00000420670.gff /build/bcftools-1.16/test/csq/ENST00000420670/start-stop-lost.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000420670/ENST00000420670.fa -g /build/bcftools-1.16/test/csq/ENST00000420670/ENST00000420670.gff /build/bcftools-1.16/test/csq/ENST00000420670/segfault.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000420190/ENST00000420190.fa -g /build/bcftools-1.16/test/csq/ENST00000420190/ENST00000420190.gff /build/bcftools-1.16/test/csq/ENST00000420190/abort-in-csq-push.vcf | /build/bcftools-1.16/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000413103/ENST00000413103.fa -g /build/bcftools-1.16/test/csq/ENST00000413103/ENST00000413103.gff /build/bcftools-1.16/test/csq/ENST00000413103/long-deletion.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000410009/ENST00000410009.fa -g /build/bcftools-1.16/test/csq/ENST00000410009/ENST00000410009.gff /build/bcftools-1.16/test/csq/ENST00000410009/frameshift.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/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/bcftools-1.16/test/csq/ENST00000410009 && /build/bcftools-1.16/bcftools csq -B 5 -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/bcftools-1.16/test/csq/ENST00000410009 && /build/bcftools-1.16/bcftools csq -lb -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/bcftools-1.16/test/csq/ENST00000410009 && /build/bcftools-1.16/bcftools csq -b -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000409523/ENST00000409523.fa -g /build/bcftools-1.16/test/csq/ENST00000409523/ENST00000409523.gff /build/bcftools-1.16/test/csq/ENST00000409523/long-overlapping-del.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000400151/ENST00000400151.fa -g /build/bcftools-1.16/test/csq/ENST00000400151/ENST00000400151.gff /build/bcftools-1.16/test/csq/ENST00000400151/long-del.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000390520/ENST00000390520.fa -g /build/bcftools-1.16/test/csq/ENST00000390520/ENST00000390520.gff /build/bcftools-1.16/test/csq/ENST00000390520/deletion-overlap.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000382647/ENST00000382647.fa -g /build/bcftools-1.16/test/csq/ENST00000382647/ENST00000382647.gff /build/bcftools-1.16/test/csq/ENST00000382647/synon-splice-region-insert.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000381157/ENST00000381157.fa -g /build/bcftools-1.16/test/csq/ENST00000381157/ENST00000381157.gff /build/bcftools-1.16/test/csq/ENST00000381157/haploid-diploid.vcf | /build/bcftools-1.16/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n' .. ok test_csq_real: cd /build/bcftools-1.16/test/csq/ENST00000379416 && /build/bcftools-1.16/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.del-snp.vcf | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-1.16/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-del.vcf | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-1.16/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-ins.vcf | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-1.16/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-snp.vcf | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-1.16/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff single.vcf | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000378322/ENST00000378322.fa -g /build/bcftools-1.16/test/csq/ENST00000378322/ENST00000378322.gff /build/bcftools-1.16/test/csq/ENST00000378322/end-overlap-tscript.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000378322/ENST00000378322.fa -g /build/bcftools-1.16/test/csq/ENST00000378322/ENST00000378322.gff /build/bcftools-1.16/test/csq/ENST00000378322/end-overlap-tscript.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000375992/ENST00000375992.fa -g /build/bcftools-1.16/test/csq/ENST00000375992/ENST00000375992.gff /build/bcftools-1.16/test/csq/ENST00000375992/incorrect-synon-del-not-start-lost.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000373833/ENST00000373833.fa -g /build/bcftools-1.16/test/csq/ENST00000373833/ENST00000373833.gff /build/bcftools-1.16/test/csq/ENST00000373833/boundary-insertion.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000373833/ENST00000373833.fa -g /build/bcftools-1.16/test/csq/ENST00000373833/ENST00000373833.gff /build/bcftools-1.16/test/csq/ENST00000373833/boundary-insertion.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000368801/ENST00000368801.fa -g /build/bcftools-1.16/test/csq/ENST00000368801/ENST00000368801.gff /build/bcftools-1.16/test/csq/ENST00000368801/compound-lost.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000368801.2/ENST00000368801.2.fa -g /build/bcftools-1.16/test/csq/ENST00000368801.2/ENST00000368801.2.gff /build/bcftools-1.16/test/csq/ENST00000368801.2/start-lost.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000357367/ENST00000357367.fa -g /build/bcftools-1.16/test/csq/ENST00000357367/ENST00000357367.gff /build/bcftools-1.16/test/csq/ENST00000357367/stop-retained.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/not-a-start-lost.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/not-a-start-lost.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/frame3.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/frame3.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/frame2.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/frame2.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/frame1.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/frame1.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000329454/ENST00000329454.fa -g /build/bcftools-1.16/test/csq/ENST00000329454/ENST00000329454.gff /build/bcftools-1.16/test/csq/ENST00000329454/boundary-deletion.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000329454/ENST00000329454.fa -g /build/bcftools-1.16/test/csq/ENST00000329454/ENST00000329454.gff /build/bcftools-1.16/test/csq/ENST00000329454/boundary-deletion.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000318249/ENST00000318249.fa -g /build/bcftools-1.16/test/csq/ENST00000318249/ENST00000318249.gff /build/bcftools-1.16/test/csq/ENST00000318249/start-lost.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000318249/ENST00000318249.fa -g /build/bcftools-1.16/test/csq/ENST00000318249/ENST00000318249.gff /build/bcftools-1.16/test/csq/ENST00000318249/start-lost.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000318249.2/ENST00000318249.2.fa -g /build/bcftools-1.16/test/csq/ENST00000318249.2/ENST00000318249.2.gff /build/bcftools-1.16/test/csq/ENST00000318249.2/synonymous-start-lost.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000303039/ENST00000303039.fa -g /build/bcftools-1.16/test/csq/ENST00000303039/ENST00000303039.gff /build/bcftools-1.16/test/csq/ENST00000303039/not-a-stop.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000303039/ENST00000303039.fa -g /build/bcftools-1.16/test/csq/ENST00000303039/ENST00000303039.gff /build/bcftools-1.16/test/csq/ENST00000303039/not-a-stop.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000301246/ENST00000301246.fa -g /build/bcftools-1.16/test/csq/ENST00000301246/ENST00000301246.gff /build/bcftools-1.16/test/csq/ENST00000301246/15bp-insert.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000295641/ENST00000295641.fa -g /build/bcftools-1.16/test/csq/ENST00000295641/ENST00000295641.gff /build/bcftools-1.16/test/csq/ENST00000295641/not-a-start-lost.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000295641/ENST00000295641.fa -g /build/bcftools-1.16/test/csq/ENST00000295641/ENST00000295641.gff /build/bcftools-1.16/test/csq/ENST00000295641/not-a-start-lost.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000294661/ENST00000294661.fa -g /build/bcftools-1.16/test/csq/ENST00000294661/ENST00000294661.gff /build/bcftools-1.16/test/csq/ENST00000294661/non-coding-boundary.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000294661/ENST00000294661.fa -g /build/bcftools-1.16/test/csq/ENST00000294661/ENST00000294661.gff /build/bcftools-1.16/test/csq/ENST00000294661/non-coding-boundary.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000285021/ENST00000285021.fa -g /build/bcftools-1.16/test/csq/ENST00000285021/ENST00000285021.gff /build/bcftools-1.16/test/csq/ENST00000285021/stop-gained-inframe-indel.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000271583/ENST00000271583.fa -g /build/bcftools-1.16/test/csq/ENST00000271583/ENST00000271583.gff /build/bcftools-1.16/test/csq/ENST00000271583/splice-acceptor.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000269081/ENST00000269081.fa -g /build/bcftools-1.16/test/csq/ENST00000269081/ENST00000269081.gff /build/bcftools-1.16/test/csq/ENST00000269081/stop-gained-not-inframe-insertion.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000263103-INS/ENST00000263103-INS.fa -g /build/bcftools-1.16/test/csq/ENST00000263103-INS/ENST00000263103-INS.gff /build/bcftools-1.16/test/csq/ENST00000263103-INS/insertions.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000256452/ENST00000256452.fa -g /build/bcftools-1.16/test/csq/ENST00000256452/ENST00000256452.gff /build/bcftools-1.16/test/csq/ENST00000256452/intron.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000230048/ENST00000230048.fa -g /build/bcftools-1.16/test/csq/ENST00000230048/ENST00000230048.gff /build/bcftools-1.16/test/csq/ENST00000230048/start-del.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000227471/ENST00000227471.fa -g /build/bcftools-1.16/test/csq/ENST00000227471/ENST00000227471.gff /build/bcftools-1.16/test/csq/ENST00000227471/insert-splice-vs-frameshift.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000218032/ENST00000218032.fa -g /build/bcftools-1.16/test/csq/ENST00000218032/ENST00000218032.gff /build/bcftools-1.16/test/csq/ENST00000218032/start-lost.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000218032/ENST00000218032.fa -g /build/bcftools-1.16/test/csq/ENST00000218032/ENST00000218032.gff /build/bcftools-1.16/test/csq/ENST00000218032/start-lost.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000218032/ENST00000218032.fa -g /build/bcftools-1.16/test/csq/ENST00000218032/ENST00000218032.gff /build/bcftools-1.16/test/csq/ENST00000218032/start-lost-del.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/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/bcftools-1.16/test/csq/ENST00000000000 && /build/bcftools-1.16/bcftools csq -p a -f ENST00000000000.fa -g ENST00000000000.gff upstream-stop.vcf | /build/bcftools-1.16/bcftools query -f'[%POS\t%REF\t%ALT\t%SAMPLE\t%GT\t%TBCSQ\n]' | ../sort-csq -q .. ok test_csq_real: cd /build/bcftools-1.16/test/csq/ENSMUST00000133836 && /build/bcftools-1.16/bcftools csq -f ENSMUST00000133836.fa -g ENSMUST00000133836.gff filter-problem.vcf -i 'FILTER="PASS"' --phase m | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/bcftools-1.16/test/csq/ENSMUST00000121418 && /build/bcftools-1.16/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25500' --phase m | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/bcftools-1.16/test/csq/ENSMUST00000121418 && /build/bcftools-1.16/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25496' --phase m | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/bcftools-1.16/test/csq/ENSMUST00000121418 && /build/bcftools-1.16/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25105' --phase m | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENSG00000173376/ENSG00000173376.fa -g /build/bcftools-1.16/test/csq/ENSG00000173376/ENSG00000173376.gff /build/bcftools-1.16/test/csq/ENSG00000173376/synon.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/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/bcftools-1.16/test/csq/EMN908947 && /build/bcftools-1.16/bcftools csq -f EMN908947.fa -g simple.gff simple.vcf | ../sort-csq | /build/bcftools-1.16/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/bcftools-1.16/test/csq/EMN908947 && /build/bcftools-1.16/bcftools csq -f EMN908947.fa -g ribosomal-slippage.gff ribosomal-slippage.vcf --force | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/EDUMMY0003/EDUMMY0003.fa -g /build/bcftools-1.16/test/csq/EDUMMY0003/EDUMMY0003.gff /build/bcftools-1.16/test/csq/EDUMMY0003/long-del.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/EDUMMY0002/EDUMMY0002.fa -g /build/bcftools-1.16/test/csq/EDUMMY0002/EDUMMY0002.gff /build/bcftools-1.16/test/csq/EDUMMY0002/boundaries.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/EDUMMY0001/EDUMMY0001.fa -g /build/bcftools-1.16/test/csq/EDUMMY0001/EDUMMY0001.gff /build/bcftools-1.16/test/csq/EDUMMY0001/starts-with-1.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/EDUMMY0001/EDUMMY0001.fa -g /build/bcftools-1.16/test/csq/EDUMMY0001/EDUMMY0001.gff /build/bcftools-1.16/test/csq/EDUMMY0001/starts-with-1.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_roh: /build/bcftools-1.16/bcftools roh /build/bcftools-1.16/test/roh.1.vcf.gz -Or -G30 --AF-dflt 0.4| grep -v ^# .. ok test_roh: /build/bcftools-1.16/bcftools roh /build/bcftools-1.16/test/roh.1.vcf.gz -Or -G30 --AF-file /build/bcftools-1.16/test/roh.1.tab.gz| grep -v ^# .. ok test_roh: /build/bcftools-1.16/bcftools roh /build/bcftools-1.16/test/roh.1.vcf.gz -Or -G30 --AF-file /build/bcftools-1.16/test/roh.1.tab.gz --ignore-homref| grep -v ^# .. ok test_roh: /build/bcftools-1.16/bcftools roh /build/bcftools-1.16/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245| grep -v ^# .. ok test_roh: /build/bcftools-1.16/bcftools roh /build/bcftools-1.16/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --ignore-homref| grep -v ^# .. ok test_roh: /build/bcftools-1.16/bcftools roh /build/bcftools-1.16/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --ignore-homref --include-noalt| grep -v ^# .. ok test_roh: /build/bcftools-1.16/bcftools roh /build/bcftools-1.16/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --include-noalt| grep -v ^# .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck -e 0 /tmp/vabHikq0lF/gtcheck.1.vcf.gz -g /tmp/vabHikq0lF/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck -e 0 -u GT,GT /tmp/vabHikq0lF/gtcheck.1.vcf.gz -g /tmp/vabHikq0lF/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck -e 0 -u GT,PL /tmp/vabHikq0lF/gtcheck.1.vcf.gz -g /tmp/vabHikq0lF/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck -e 0 -u PL,GT /tmp/vabHikq0lF/gtcheck.1.vcf.gz -g /tmp/vabHikq0lF/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck -e 0 -u PL,PL /tmp/vabHikq0lF/gtcheck.1.vcf.gz -g /tmp/vabHikq0lF/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck -e 0 -p s1,s1 /tmp/vabHikq0lF/gtcheck.1.vcf.gz -g /tmp/vabHikq0lF/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck -e 0 /tmp/vabHikq0lF/gtcheck.2.vcf.gz -g /tmp/vabHikq0lF/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck -e 0 /tmp/vabHikq0lF/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/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/vabHikq0lF/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck -e 0 -P /build/bcftools-1.16/test/gtcheck.3.pairs /tmp/vabHikq0lF/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck -e 0 -u PL /tmp/vabHikq0lF/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck -e 0 --n-matches 4 /tmp/vabHikq0lF/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO | sort .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck -e 0 -s qry:E,D,C /tmp/vabHikq0lF/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck -e 0 -s qry:E,D,C -u PL /tmp/vabHikq0lF/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck -e 0 -s qry:B -s gt:D /tmp/vabHikq0lF/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck -e 0 -s qry:B -s gt:D -u PL /tmp/vabHikq0lF/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck -e 0 -s qry:B -s gt:D,C /tmp/vabHikq0lF/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck -e 0 -p B,C,B,D /tmp/vabHikq0lF/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck -e 0 -u GT,GT -H /tmp/vabHikq0lF/gtcheck.1.vcf.gz -g /tmp/vabHikq0lF/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck -e 0 -u GT,PL -H /tmp/vabHikq0lF/gtcheck.1.vcf.gz -g /tmp/vabHikq0lF/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck -e 0 -u PL,GT -H /tmp/vabHikq0lF/gtcheck.1.vcf.gz -g /tmp/vabHikq0lF/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck -e 0 -u PL,PL -H /tmp/vabHikq0lF/gtcheck.1.vcf.gz -g /tmp/vabHikq0lF/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck -e 0 -P /build/bcftools-1.16/test/gtcheck.4.pairs --distinctive-sites 3 /tmp/vabHikq0lF/gtcheck.4.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck -e 0 -P /build/bcftools-1.16/test/gtcheck.4.pairs --distinctive-sites 3,1 /tmp/vabHikq0lF/gtcheck.4.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck -u GT -e 30 /tmp/vabHikq0lF/gtcheck.1.vcf.gz -g /tmp/vabHikq0lF/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck -u GT -e 30 -p s1,s1 /tmp/vabHikq0lF/gtcheck.1.vcf.gz -g /tmp/vabHikq0lF/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck -u GT -e 300 /tmp/vabHikq0lF/gtcheck.1.vcf.gz -g /tmp/vabHikq0lF/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck -u PL -e 30 /tmp/vabHikq0lF/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck /tmp/vabHikq0lF/gtcheck.ntop.vcf.gz -g /tmp/vabHikq0lF/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck --n-matches 2 /tmp/vabHikq0lF/gtcheck.ntop.vcf.gz -g /tmp/vabHikq0lF/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck /tmp/vabHikq0lF/gtcheck.5.vcf.gz -g /tmp/vabHikq0lF/gtcheck.5.gts.vcf.gz | grep -v ^# | grep -v Time .. ok Number of tests: total .. 1477 passed .. 1477 failed .. 0 make[2]: Leaving directory '/build/bcftools-1.16' make[1]: Leaving directory '/build/bcftools-1.16' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/bcftools/ make -j16 install DESTDIR=/build/bcftools-1.16/debian/bcftools AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/bcftools-1.16' mkdir -p -m 755 /build/bcftools-1.16/debian/bcftools/usr/bin /build/bcftools-1.16/debian/bcftools/usr/share/man/man1 /build/bcftools-1.16/debian/bcftools/usr/lib/x86_64-linux-gnu/bcftools install -p bcftools /build/bcftools-1.16/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/bcftools-1.16/debian/bcftools/usr/bin install -p -m 644 doc/bcftools.1 /build/bcftools-1.16/debian/bcftools/usr/share/man/man1 install -p plugins/*.so /build/bcftools-1.16/debian/bcftools/usr/lib/x86_64-linux-gnu/bcftools make[1]: Leaving directory '/build/bcftools-1.16' debian/rules override_dh_install make[1]: Entering directory '/build/bcftools-1.16' 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/bcftools-1.16' dh_installdocs dh_installchangelogs debian/rules override_dh_installman make[1]: Entering directory '/build/bcftools-1.16' dh_installman --language=C make[1]: Leaving directory '/build/bcftools-1.16' 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_1.16-1_amd64.deb'. dpkg-deb: building package 'bcftools-dbgsym' in '../bcftools-dbgsym_1.16-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../bcftools_1.16-1_amd64.buildinfo dpkg-genchanges --build=binary -O../bcftools_1.16-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1489716 and its subdirectories I: Current time: Wed Jul 10 03:34:52 -12 2024 I: pbuilder-time-stamp: 1720625692