I: pbuilder: network access will be disabled during build I: Current time: Wed Jul 28 13:54:09 +14 2021 I: pbuilder-time-stamp: 1627430049 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration 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_1.11-1.dsc] I: copying [./bcftools_1.11.orig.tar.gz] I: copying [./bcftools_1.11-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.pkgiB7uW/trustedkeys.kbx': General error gpgv: Signature made Fri Oct 2 03:48:11 2020 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./bcftools_1.11-1.dsc dpkg-source: info: extracting bcftools in bcftools-1.11 dpkg-source: info: unpacking bcftools_1.11.orig.tar.gz dpkg-source: info: unpacking bcftools_1.11-1.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/5168/tmp/hooks/D01_modify_environment starting debug: Running on codethink12-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/5168/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/5168/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.1.4(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=8' DIRSTACK=() DISTRIBUTION= EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/var/lib/jenkins HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=5168 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.wrmUl1lcEW/pbuilderrc_VLmU --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.wrmUl1lcEW/b2 --logfile b2/build.log --extrapackages usrmerge bcftools_1.11-1.dsc' SUDO_GID=117 SUDO_UID=110 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root USERNAME=root _='I: set' http_proxy=http://192.168.101.16:3128 I: uname -a Linux i-capture-the-hostname 4.15.0-151-generic #157-Ubuntu SMP Fri Jul 9 21:03:48 UTC 2021 aarch64 GNU/Linux I: ls -l /bin total 5252 -rwxr-xr-x 1 root root 1282512 Jun 22 16:26 bash -rwxr-xr-x 3 root root 34808 Jul 21 2020 bunzip2 -rwxr-xr-x 3 root root 34808 Jul 21 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep -rwxr-xr-x 3 root root 34808 Jul 21 2020 bzip2 -rwxr-xr-x 1 root root 14264 Jul 21 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore -rwxr-xr-x 1 root root 39832 Sep 23 2020 cat -rwxr-xr-x 1 root root 64512 Sep 23 2020 chgrp -rwxr-xr-x 1 root root 60368 Sep 23 2020 chmod -rwxr-xr-x 1 root root 64528 Sep 23 2020 chown -rwxr-xr-x 1 root root 138896 Sep 23 2020 cp -rwxr-xr-x 1 root root 129544 Dec 11 2020 dash -rwxr-xr-x 1 root root 101384 Sep 23 2020 date -rwxr-xr-x 1 root root 80984 Sep 23 2020 dd -rwxr-xr-x 1 root root 89824 Sep 23 2020 df -rwxr-xr-x 1 root root 143088 Sep 23 2020 dir -rwxr-xr-x 1 root root 76152 Feb 8 04:38 dmesg lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname -rwxr-xr-x 1 root root 35632 Sep 23 2020 echo -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep -rwxr-xr-x 1 root root 31512 Sep 23 2020 false -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep -rwxr-xr-x 1 root root 64856 Feb 8 04:38 findmnt -rwsr-xr-x 1 root root 34824 Feb 27 06:12 fusermount -rwxr-xr-x 1 root root 178400 Nov 10 2020 grep -rwxr-xr-x 2 root root 2346 Mar 3 13:30 gunzip -rwxr-xr-x 1 root root 6376 Mar 3 13:30 gzexe -rwxr-xr-x 1 root root 93744 Mar 3 13:30 gzip -rwxr-xr-x 1 root root 18440 Nov 8 2019 hostname -rwxr-xr-x 1 root root 68720 Sep 23 2020 ln -rwxr-xr-x 1 root root 52720 Feb 8 2020 login -rwxr-xr-x 1 root root 143088 Sep 23 2020 ls -rwxr-xr-x 1 root root 161960 Feb 8 04:38 lsblk -rwxr-xr-x 1 root root 85200 Sep 23 2020 mkdir -rwxr-xr-x 1 root root 68744 Sep 23 2020 mknod -rwxr-xr-x 1 root root 43976 Sep 23 2020 mktemp -rwxr-xr-x 1 root root 51368 Feb 8 04:38 more -rwsr-xr-x 1 root root 51360 Feb 8 04:38 mount -rwxr-xr-x 1 root root 14496 Feb 8 04:38 mountpoint -rwxr-xr-x 1 root root 134808 Sep 23 2020 mv lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 19 05:38 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 35720 Sep 23 2020 pwd lrwxrwxrwx 1 root root 4 Jun 22 16:26 rbash -> bash -rwxr-xr-x 1 root root 43872 Sep 23 2020 readlink -rwxr-xr-x 1 root root 68592 Sep 23 2020 rm -rwxr-xr-x 1 root root 43880 Sep 23 2020 rmdir -rwxr-xr-x 1 root root 19208 Sep 28 2020 run-parts -rwxr-xr-x 1 root root 114016 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 Jul 28 13:54 sh -> bash lrwxrwxrwx 1 root root 4 Jul 27 23:25 sh.distrib -> dash -rwxr-xr-x 1 root root 35656 Sep 23 2020 sleep -rwxr-xr-x 1 root root 72640 Sep 23 2020 stty -rwsr-xr-x 1 root root 67776 Feb 8 04:38 su -rwxr-xr-x 1 root root 35672 Sep 23 2020 sync -rwxr-xr-x 1 root root 535768 Feb 17 23:55 tar -rwxr-xr-x 1 root root 10568 Sep 28 2020 tempfile -rwxr-xr-x 1 root root 89120 Sep 23 2020 touch -rwxr-xr-x 1 root root 31512 Sep 23 2020 true -rwxr-xr-x 1 root root 14264 Feb 27 06:12 ulockmgr_server -rwsr-xr-x 1 root root 30880 Feb 8 04:38 umount -rwxr-xr-x 1 root root 35640 Sep 23 2020 uname -rwxr-xr-x 2 root root 2346 Mar 3 13:30 uncompress -rwxr-xr-x 1 root root 143088 Sep 23 2020 vdir -rwxr-xr-x 1 root root 59584 Feb 8 04:38 wdctl lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 3 13:30 zcat -rwxr-xr-x 1 root root 1678 Mar 3 13:30 zcmp -rwxr-xr-x 1 root root 5880 Mar 3 13:30 zdiff -rwxr-xr-x 1 root root 29 Mar 3 13:30 zegrep -rwxr-xr-x 1 root root 29 Mar 3 13:30 zfgrep -rwxr-xr-x 1 root root 2081 Mar 3 13:30 zforce -rwxr-xr-x 1 root root 7585 Mar 3 13:30 zgrep -rwxr-xr-x 1 root root 2206 Mar 3 13:30 zless -rwxr-xr-x 1 root root 1842 Mar 3 13:30 zmore -rwxr-xr-x 1 root root 4553 Mar 3 13:30 znew I: user script /srv/workspace/pbuilder/5168/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), zlib1g-dev, libbz2-dev, liblzma-dev, libhts-dev (>= 1.11), 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 ... 19646 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 (>= 1.11); 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} libgsl25{a} libgslcblas0{a} libhts-dev{a} libhts3{a} libicu67{a} libio-pty-perl{a} libldap-2.4-2{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} libsigsegv2{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 26.7 MB of archives. After unpacking 91.0 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main arm64 bsdextrautils arm64 2.36.1-7 [141 kB] Get: 2 http://deb.debian.org/debian bullseye/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 3 http://deb.debian.org/debian bullseye/main arm64 groff-base arm64 1.22.4-6 [883 kB] Get: 4 http://deb.debian.org/debian bullseye/main arm64 libpipeline1 arm64 1.5.3-1 [33.0 kB] Get: 5 http://deb.debian.org/debian bullseye/main arm64 man-db arm64 2.9.4-2 [1336 kB] Get: 6 http://deb.debian.org/debian bullseye/main arm64 sensible-utils all 0.0.14 [14.8 kB] Get: 7 http://deb.debian.org/debian bullseye/main arm64 libmagic-mgc arm64 1:5.39-3 [273 kB] Get: 8 http://deb.debian.org/debian bullseye/main arm64 libmagic1 arm64 1:5.39-3 [121 kB] Get: 9 http://deb.debian.org/debian bullseye/main arm64 file arm64 1:5.39-3 [69.1 kB] Get: 10 http://deb.debian.org/debian bullseye/main arm64 gettext-base arm64 0.21-4 [173 kB] Get: 11 http://deb.debian.org/debian bullseye/main arm64 libsigsegv2 arm64 2.13-1 [34.7 kB] Get: 12 http://deb.debian.org/debian bullseye/main arm64 m4 arm64 1.4.18-5 [199 kB] Get: 13 http://deb.debian.org/debian bullseye/main arm64 autoconf all 2.69-14 [313 kB] Get: 14 http://deb.debian.org/debian bullseye/main arm64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 15 http://deb.debian.org/debian bullseye/main arm64 automake all 1:1.16.3-2 [814 kB] Get: 16 http://deb.debian.org/debian bullseye/main arm64 autopoint all 0.21-4 [510 kB] Get: 17 http://deb.debian.org/debian bullseye/main arm64 libdebhelper-perl all 13.3.4 [189 kB] Get: 18 http://deb.debian.org/debian bullseye/main arm64 libtool all 2.4.6-15 [513 kB] Get: 19 http://deb.debian.org/debian bullseye/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian bullseye/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian bullseye/main arm64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 22 http://deb.debian.org/debian bullseye/main arm64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 23 http://deb.debian.org/debian bullseye/main arm64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 24 http://deb.debian.org/debian bullseye/main arm64 libelf1 arm64 0.183-1 [164 kB] Get: 25 http://deb.debian.org/debian bullseye/main arm64 dwz arm64 0.13+20210201-1 [155 kB] Get: 26 http://deb.debian.org/debian bullseye/main arm64 libicu67 arm64 67.1-7 [8467 kB] Get: 27 http://deb.debian.org/debian bullseye/main arm64 libxml2 arm64 2.9.10+dfsg-6.7 [629 kB] Get: 28 http://deb.debian.org/debian bullseye/main arm64 gettext arm64 0.21-4 [1261 kB] Get: 29 http://deb.debian.org/debian bullseye/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 30 http://deb.debian.org/debian bullseye/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian bullseye/main arm64 debhelper all 13.3.4 [1049 kB] Get: 32 http://deb.debian.org/debian bullseye/main arm64 libbrotli1 arm64 1.0.9-2+b2 [267 kB] Get: 33 http://deb.debian.org/debian bullseye/main arm64 libbz2-dev arm64 1.0.8-4 [31.5 kB] Get: 34 http://deb.debian.org/debian bullseye/main arm64 libsasl2-modules-db arm64 2.1.27+dfsg-2.1 [69.3 kB] Get: 35 http://deb.debian.org/debian bullseye/main arm64 libsasl2-2 arm64 2.1.27+dfsg-2.1 [105 kB] Get: 36 http://deb.debian.org/debian bullseye/main arm64 libldap-2.4-2 arm64 2.4.57+dfsg-3 [222 kB] Get: 37 http://deb.debian.org/debian bullseye/main arm64 libnghttp2-14 arm64 1.43.0-1 [73.8 kB] Get: 38 http://deb.debian.org/debian bullseye/main arm64 libpsl5 arm64 0.21.0-1.2 [57.1 kB] Get: 39 http://deb.debian.org/debian bullseye/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b2 [59.4 kB] Get: 40 http://deb.debian.org/debian bullseye/main arm64 libssh2-1 arm64 1.9.0-2 [150 kB] Get: 41 http://deb.debian.org/debian bullseye/main arm64 libcurl3-gnutls arm64 7.74.0-1.3+b1 [318 kB] Get: 42 http://deb.debian.org/debian bullseye/main arm64 libcurl4-gnutls-dev arm64 7.74.0-1.3+b1 [419 kB] Get: 43 http://deb.debian.org/debian bullseye/main arm64 libdeflate0 arm64 1.7-1 [47.7 kB] Get: 44 http://deb.debian.org/debian bullseye/main arm64 libdeflate-dev arm64 1.7-1 [44.5 kB] Get: 45 http://deb.debian.org/debian bullseye/main arm64 libgslcblas0 arm64 2.6+dfsg-2 [73.4 kB] Get: 46 http://deb.debian.org/debian bullseye/main arm64 libgsl25 arm64 2.6+dfsg-2 [812 kB] Get: 47 http://deb.debian.org/debian bullseye/main arm64 libgsl-dev arm64 2.6+dfsg-2 [1006 kB] Get: 48 http://deb.debian.org/debian bullseye/main arm64 libhts3 arm64 1.11-4 [346 kB] Get: 49 http://deb.debian.org/debian bullseye/main arm64 liblzma-dev arm64 5.2.5-2 [227 kB] Get: 50 http://deb.debian.org/debian bullseye/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-2 [189 kB] Get: 51 http://deb.debian.org/debian bullseye/main arm64 libhts-dev arm64 1.11-4 [3856 kB] Get: 52 http://deb.debian.org/debian bullseye/main arm64 libio-pty-perl arm64 1:1.15-2 [36.0 kB] Get: 53 http://deb.debian.org/debian bullseye/main arm64 tabix arm64 1.11-4 [316 kB] Fetched 26.7 MB in 1s (43.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19646 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-7_arm64.deb ... Unpacking bsdextrautils (2.36.1-7) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../01-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-6_arm64.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../03-libpipeline1_1.5.3-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.4-2_arm64.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../05-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../06-libmagic-mgc_1%3a5.39-3_arm64.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../07-libmagic1_1%3a5.39-3_arm64.deb ... Unpacking libmagic1:arm64 (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../08-file_1%3a5.39-3_arm64.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../09-gettext-base_0.21-4_arm64.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package libsigsegv2:arm64. Preparing to unpack .../10-libsigsegv2_2.13-1_arm64.deb ... Unpacking libsigsegv2:arm64 (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.18-5_arm64.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.69-14_all.deb ... Unpacking autoconf (2.69-14) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../13-autotools-dev_20180224.1+nmu1_all.deb ... Unpacking autotools-dev (20180224.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../14-automake_1%3a1.16.3-2_all.deb ... Unpacking automake (1:1.16.3-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../15-autopoint_0.21-4_all.deb ... Unpacking autopoint (0.21-4) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../16-libdebhelper-perl_13.3.4_all.deb ... Unpacking libdebhelper-perl (13.3.4) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.4.6-15_all.deb ... Unpacking libtool (2.4.6-15) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../19-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 .../20-libsub-override-perl_0.09-2_all.deb ... Unpacking libsub-override-perl (0.09-2) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../21-libfile-stripnondeterminism-perl_1.12.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.12.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../22-dh-strip-nondeterminism_1.12.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.12.0-1) ... Selecting previously unselected package libelf1:arm64. Preparing to unpack .../23-libelf1_0.183-1_arm64.deb ... Unpacking libelf1:arm64 (0.183-1) ... Selecting previously unselected package dwz. Preparing to unpack .../24-dwz_0.13+20210201-1_arm64.deb ... Unpacking dwz (0.13+20210201-1) ... Selecting previously unselected package libicu67:arm64. Preparing to unpack .../25-libicu67_67.1-7_arm64.deb ... Unpacking libicu67:arm64 (67.1-7) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../26-libxml2_2.9.10+dfsg-6.7_arm64.deb ... Unpacking libxml2:arm64 (2.9.10+dfsg-6.7) ... Selecting previously unselected package gettext. Preparing to unpack .../27-gettext_0.21-4_arm64.deb ... Unpacking gettext (0.21-4) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../28-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../29-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../30-debhelper_13.3.4_all.deb ... Unpacking debhelper (13.3.4) ... Selecting previously unselected package libbrotli1:arm64. Preparing to unpack .../31-libbrotli1_1.0.9-2+b2_arm64.deb ... Unpacking libbrotli1:arm64 (1.0.9-2+b2) ... Selecting previously unselected package libbz2-dev:arm64. Preparing to unpack .../32-libbz2-dev_1.0.8-4_arm64.deb ... Unpacking libbz2-dev:arm64 (1.0.8-4) ... Selecting previously unselected package libsasl2-modules-db:arm64. Preparing to unpack .../33-libsasl2-modules-db_2.1.27+dfsg-2.1_arm64.deb ... Unpacking libsasl2-modules-db:arm64 (2.1.27+dfsg-2.1) ... 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Unpacking libssh2-1:arm64 (1.9.0-2) ... Selecting previously unselected package libcurl3-gnutls:arm64. Preparing to unpack .../40-libcurl3-gnutls_7.74.0-1.3+b1_arm64.deb ... Unpacking libcurl3-gnutls:arm64 (7.74.0-1.3+b1) ... Selecting previously unselected package libcurl4-gnutls-dev:arm64. Preparing to unpack .../41-libcurl4-gnutls-dev_7.74.0-1.3+b1_arm64.deb ... Unpacking libcurl4-gnutls-dev:arm64 (7.74.0-1.3+b1) ... Selecting previously unselected package libdeflate0:arm64. Preparing to unpack .../42-libdeflate0_1.7-1_arm64.deb ... Unpacking libdeflate0:arm64 (1.7-1) ... Selecting previously unselected package libdeflate-dev:arm64. Preparing to unpack .../43-libdeflate-dev_1.7-1_arm64.deb ... Unpacking libdeflate-dev:arm64 (1.7-1) ... Selecting previously unselected package libgslcblas0:arm64. Preparing to unpack .../44-libgslcblas0_2.6+dfsg-2_arm64.deb ... Unpacking libgslcblas0:arm64 (2.6+dfsg-2) ... Selecting previously unselected package libgsl25:arm64. 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Setting up libsasl2-modules-db:arm64 (2.1.27+dfsg-2.1) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libsigsegv2:arm64 (2.13-1) ... Setting up autopoint (0.21-4) ... Setting up libsasl2-2:arm64 (2.1.27+dfsg-2.1) ... Setting up liblzma-dev:arm64 (5.2.5-2) ... Setting up zlib1g-dev:arm64 (1:1.2.11.dfsg-2) ... Setting up sensible-utils (0.0.14) ... Setting up libuchardet0:arm64 (0.0.7-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libssh2-1:arm64 (1.9.0-2) ... Setting up libdeflate-dev:arm64 (1.7-1) ... Setting up tabix (1.11-4) ... Setting up libelf1:arm64 (0.183-1) ... Setting up libxml2:arm64 (2.9.10+dfsg-6.7) ... Setting up libbz2-dev:arm64 (1.0.8-4) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up gettext (0.21-4) ... Setting up libgsl-dev (2.6+dfsg-2) ... Setting up libtool (2.4.6-15) ... Setting up libldap-2.4-2:arm64 (2.4.57+dfsg-3) ... Setting up m4 (1.4.18-5) ... Setting up libcurl3-gnutls:arm64 (7.74.0-1.3+b1) ... Setting up libcurl4-gnutls-dev:arm64 (7.74.0-1.3+b1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.12.0-1) ... Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libhts3:arm64 (1.11-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhts-dev:arm64 (1.11-4) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up dh-autoreconf (20) ... Setting up debhelper (13.3.4) ... Processing triggers for libc-bin (2.31-13) ... 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 Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl The following NEW packages will be installed: libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl usrmerge 0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. Need to get 59.5 kB of archives. After this operation, 157 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian bullseye/main arm64 libnumber-compare-perl all 0.03-1.1 [6956 B] Get:2 http://deb.debian.org/debian bullseye/main arm64 libtext-glob-perl all 0.11-1 [8888 B] Get:3 http://deb.debian.org/debian bullseye/main arm64 libfile-find-rule-perl all 0.34-1 [30.6 kB] Get:4 http://deb.debian.org/debian bullseye/main arm64 usrmerge all 25 [13.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 59.5 kB in 0s (1147 kB/s) Selecting previously unselected package libnumber-compare-perl. (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 ... 22088 files and directories currently installed.) Preparing to unpack .../libnumber-compare-perl_0.03-1.1_all.deb ... Unpacking libnumber-compare-perl (0.03-1.1) ... Selecting previously unselected package libtext-glob-perl. Preparing to unpack .../libtext-glob-perl_0.11-1_all.deb ... Unpacking libtext-glob-perl (0.11-1) ... Selecting previously unselected package libfile-find-rule-perl. Preparing to unpack .../libfile-find-rule-perl_0.34-1_all.deb ... Unpacking libfile-find-rule-perl (0.34-1) ... Selecting previously unselected package usrmerge. Preparing to unpack .../archives/usrmerge_25_all.deb ... Unpacking usrmerge (25) ... Setting up libtext-glob-perl (0.11-1) ... Setting up libnumber-compare-perl (0.03-1.1) ... Setting up libfile-find-rule-perl (0.34-1) ... Setting up usrmerge (25) ... The system has been successfully converted. Processing triggers for man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. I: Building the package hostname: Temporary failure in name resolution I: Running cd /build/bcftools-1.11/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../bcftools_1.11-1_source.changes dpkg-buildpackage: info: source package bcftools dpkg-buildpackage: info: source version 1.11-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean rm -f config.mk && touch config.mk dh clean dh_auto_clean make -j8 distclean make[1]: Entering directory '/build/bcftools-1.11' rm -f test/*.o test/*~ test/test-rbuf test/test-regidx rm -f plugins/*.so plugins/*.P rm -f test/*.hex 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[1]: Leaving directory '/build/bcftools-1.11' dh_clean debian/rules binary dh binary dh_update_autotools_config debian/rules override_dh_autoreconf make[1]: Entering directory '/build/bcftools-1.11' 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.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:94: the top level configure.ac:94: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:94: the top level configure.ac:94: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:94: the top level configure.ac:94: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: 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-1.11' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/bcftools-1.11' dh_auto_configure -- \ --with-htslib=system \ --enable-gsl \ --with-cblas=gslcblas \ --with-bcf-plugin-dir=/usr/lib/aarch64-linux-gnu/bcftools ./configure --build=aarch64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/aarch64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system --enable-gsl --with-cblas=gslcblas --with-bcf-plugin-dir=/usr/lib/aarch64-linux-gnu/bcftools checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for htslib/sam.h... yes checking for hts_version in -lhts... yes checking shared library type... plain .so checking for library containing dlopen... -ldl 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-1.11' dh_auto_build make -j8 make[1]: Entering directory '/build/bcftools-1.11' echo '#define BCFTOOLS_VERSION "1.11"' > version.h gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfindex.o vcfindex.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tabix.o tabix.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfstats.o vcfstats.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfisec.o vcfisec.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfmerge.o vcfmerge.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfquery.o vcfquery.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcffilter.o vcffilter.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o filter.o filter.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfsom.o vcfsom.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfnorm.o vcfnorm.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfgtcheck.o vcfgtcheck.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfview.o vcfview.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfannotate.o vcfannotate.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfroh.o vcfroh.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfconcat.o vcfconcat.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcall.o vcfcall.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mcall.o mcall.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcmp.o vcmp.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gvcf.o gvcf.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o reheader.o reheader.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o convert.o convert.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfconvert.o vcfconvert.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tsv2vcf.o tsv2vcf.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcnv.o vcfcnv.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o HMM.o HMM.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o consensus.o consensus.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ploidy.o ploidy.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bin.o bin.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hclust.o hclust.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o version.o version.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o regidx.o regidx.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -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 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o csq.o csq.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfbuf.o vcfbuf.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mpileup.o mpileup.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -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 -fdebug-prefix-map=/build/bcftools-1.11=. -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 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfsort.o vcfsort.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cols.o cols.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o extsort.o extsort.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ccall.o ccall.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o em.o em.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o prob1.o prob1.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kmin.o kmin.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DPLUGINPATH='"/usr/lib/aarch64-linux-gnu/bcftools"' -c -o vcfplugin.o vcfplugin.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -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 -fdebug-prefix-map=/build/bcftools-1.11=. -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 -fdebug-prefix-map=/build/bcftools-1.11=. -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 -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -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 -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -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 -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -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 -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -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 -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -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 -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -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 -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -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 -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -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 -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -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 -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -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 -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -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 -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -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 -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -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 -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -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 -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -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 -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -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 -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -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 -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -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 -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -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 -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -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 -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -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 -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -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 -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -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 -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -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 -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -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 -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -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 -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -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 -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -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 -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -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 -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -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 -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -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 -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -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 -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -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 -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/trio-dnm.so version.c plugins/trio-dnm.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -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 -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -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 -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -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 -ldl gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -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 -ldl gcc -Wl,-z,relro -o test/test-regidx test/test-regidx.o regidx.o -lhts -lpthread -lz -ldl 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 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 ccall.o em.o prob1.o kmin.o vcfplugin.o -lhts -lm -lz -ldl -lpthread make[1]: Leaving directory '/build/bcftools-1.11' debian/rules override_dh_auto_test make[1]: Entering directory '/build/bcftools-1.11' make test-no-plugins VERBOSE=1 make[2]: Entering directory '/build/bcftools-1.11' ./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 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/YesswOGw3Q/merge.a.vcf.gz 2:3199812-3199812 .. ok test_tabix: /build/bcftools-1.11/bcftools view -H /tmp/YesswOGw3Q/merge.a.bcf 2:3199812-3199812 .. ok test_tabix: tabix /tmp/YesswOGw3Q/merge.a.vcf.gz 1:3000151-3000151 .. ok test_tabix: /build/bcftools-1.11/bcftools view -H /tmp/YesswOGw3Q/merge.a.bcf 1:3000151-3000151 .. ok test_index: /build/bcftools-1.11/bcftools view -H /tmp/YesswOGw3Q/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /build/bcftools-1.11/bcftools view -H /tmp/YesswOGw3Q/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/bcftools-1.11/bcftools view -H /tmp/YesswOGw3Q/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/bcftools-1.11/bcftools view -H /tmp/YesswOGw3Q/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /build/bcftools-1.11/bcftools view -H /tmp/YesswOGw3Q/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/bcftools-1.11/bcftools view -H /tmp/YesswOGw3Q/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /build/bcftools-1.11/bcftools view -H /tmp/YesswOGw3Q/large_chrom_csi_limit.bcf chr20 .. ok test_index: /build/bcftools-1.11/bcftools view -H /tmp/YesswOGw3Q/large_chrom_csi_limit.bcf chr20 .. ok test_index: /build/bcftools-1.11/bcftools view -H /tmp/YesswOGw3Q/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /build/bcftools-1.11/bcftools view -H /tmp/YesswOGw3Q/large_chrom_csi_limit.bcf chr20 .. ok test_vcf_idxstats: /build/bcftools-1.11/bcftools index -s /tmp/YesswOGw3Q/idx.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.11/bcftools index -s /tmp/YesswOGw3Q/idx.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.11/bcftools index -s /tmp/YesswOGw3Q/idx.bcf .. ok test_vcf_idxstats: /build/bcftools-1.11/bcftools index -n /tmp/YesswOGw3Q/idx.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.11/bcftools index -n /tmp/YesswOGw3Q/idx.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.11/bcftools index -n /tmp/YesswOGw3Q/idx.bcf .. ok test_vcf_idxstats: /build/bcftools-1.11/bcftools index -s /tmp/YesswOGw3Q/empty.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.11/bcftools index -s /tmp/YesswOGw3Q/empty.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.11/bcftools index -s /tmp/YesswOGw3Q/empty.bcf .. ok test_vcf_idxstats: /build/bcftools-1.11/bcftools index -n /tmp/YesswOGw3Q/empty.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.11/bcftools index -n /tmp/YesswOGw3Q/empty.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.11/bcftools index -n /tmp/YesswOGw3Q/empty.bcf .. ok test_vcf_check: /build/bcftools-1.11/bcftools stats -s - /tmp/YesswOGw3Q/check.vcf.gz | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/check.vcf.gz | /build/bcftools-1.11/bcftools stats -s - | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check_merge: /build/bcftools-1.11/misc/plot-vcfstats -m /tmp/YesswOGw3Q/check.1.chk /tmp/YesswOGw3Q/check.2.chk /tmp/YesswOGw3Q/check.3.chk /tmp/YesswOGw3Q/check.4.chk | grep -v 'plot-vcfstats' | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_stats: /build/bcftools-1.11/bcftools stats -s - /tmp/YesswOGw3Q/stats.a.vcf.gz /tmp/YesswOGw3Q/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/bcftools-1.11/bcftools stats -s B /tmp/YesswOGw3Q/stats.a.vcf.gz /tmp/YesswOGw3Q/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/bcftools-1.11/bcftools stats -s - /tmp/YesswOGw3Q/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_isec: /build/bcftools-1.11/bcftools isec -n =2 /tmp/YesswOGw3Q/isec.a.vcf.gz /tmp/YesswOGw3Q/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.11/bcftools isec -Ob -n =2 /tmp/YesswOGw3Q/isec.a.vcf.gz /tmp/YesswOGw3Q/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.11/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/YesswOGw3Q/isec.a.vcf.gz /tmp/YesswOGw3Q/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.11/bcftools isec -Ob -n =2 -i"STRLEN(REF)==2" /tmp/YesswOGw3Q/isec.a.vcf.gz /tmp/YesswOGw3Q/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.11/bcftools isec -n =2 -c both /tmp/YesswOGw3Q/isec.a.vcf.gz /tmp/YesswOGw3Q/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.11/bcftools isec -Ob -n =2 -c both /tmp/YesswOGw3Q/isec.a.vcf.gz /tmp/YesswOGw3Q/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.11/bcftools isec -n =2 -c any /tmp/YesswOGw3Q/isec.a.vcf.gz /tmp/YesswOGw3Q/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.11/bcftools isec -Ob -n =2 -c any /tmp/YesswOGw3Q/isec.a.vcf.gz /tmp/YesswOGw3Q/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.11/bcftools isec -C -c any /tmp/YesswOGw3Q/isec.a.vcf.gz /tmp/YesswOGw3Q/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.11/bcftools isec -Ob -C -c any /tmp/YesswOGw3Q/isec.a.vcf.gz /tmp/YesswOGw3Q/isec.b.vcf.gz .. ok test_vcf_isec2: /build/bcftools-1.11/bcftools isec --no-version -T /tmp/YesswOGw3Q/isec.tab.gz /tmp/YesswOGw3Q/isec.a.vcf.gz .. ok test_vcf_isec2: /build/bcftools-1.11/bcftools isec -Ob -T /tmp/YesswOGw3Q/isec.tab.gz /tmp/YesswOGw3Q/isec.a.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_isec: /build/bcftools-1.11/bcftools isec -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/YesswOGw3Q/isec-miss.1.1.vcf.gz /tmp/YesswOGw3Q/isec-miss.1.2.vcf.gz /tmp/YesswOGw3Q/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.11/bcftools isec -Ob -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/YesswOGw3Q/isec-miss.1.1.vcf.gz /tmp/YesswOGw3Q/isec-miss.1.2.vcf.gz /tmp/YesswOGw3Q/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.11/bcftools isec -R /build/bcftools-1.11/test/isec-miss.1.regs.txt -n +1 /tmp/YesswOGw3Q/isec-miss.1.1.vcf.gz /tmp/YesswOGw3Q/isec-miss.1.2.vcf.gz /tmp/YesswOGw3Q/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.11/bcftools isec -Ob -R /build/bcftools-1.11/test/isec-miss.1.regs.txt -n +1 /tmp/YesswOGw3Q/isec-miss.1.1.vcf.gz /tmp/YesswOGw3Q/isec-miss.1.2.vcf.gz /tmp/YesswOGw3Q/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.11/bcftools isec -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/YesswOGw3Q/isec-miss.2.1.vcf.gz /tmp/YesswOGw3Q/isec-miss.2.2.vcf.gz /tmp/YesswOGw3Q/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.11/bcftools isec -Ob -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/YesswOGw3Q/isec-miss.2.1.vcf.gz /tmp/YesswOGw3Q/isec-miss.2.2.vcf.gz /tmp/YesswOGw3Q/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.11/bcftools isec -R /build/bcftools-1.11/test/isec-miss.1.regs.txt -n +1 /tmp/YesswOGw3Q/isec-miss.2.1.vcf.gz /tmp/YesswOGw3Q/isec-miss.2.2.vcf.gz /tmp/YesswOGw3Q/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.11/bcftools isec -Ob -R /build/bcftools-1.11/test/isec-miss.1.regs.txt -n +1 /tmp/YesswOGw3Q/isec-miss.2.1.vcf.gz /tmp/YesswOGw3Q/isec-miss.2.2.vcf.gz /tmp/YesswOGw3Q/isec-miss.2.3.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version -i AF:join /tmp/YesswOGw3Q/merge.join.a.vcf.gz /tmp/YesswOGw3Q/merge.join.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob -i AF:join /tmp/YesswOGw3Q/merge.join.a.vcf.gz /tmp/YesswOGw3Q/merge.join.b.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version -i AF:join /tmp/YesswOGw3Q/merge.join.a.bcf /tmp/YesswOGw3Q/merge.join.b.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob -i AF:join /tmp/YesswOGw3Q/merge.join.a.bcf /tmp/YesswOGw3Q/merge.join.b.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --force-samples /tmp/YesswOGw3Q/merge.LPL.a.vcf.gz /tmp/YesswOGw3Q/merge.LPL.b.vcf.gz /tmp/YesswOGw3Q/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples /tmp/YesswOGw3Q/merge.LPL.a.vcf.gz /tmp/YesswOGw3Q/merge.LPL.b.vcf.gz /tmp/YesswOGw3Q/merge.LPL.c.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --force-samples /tmp/YesswOGw3Q/merge.LPL.a.bcf /tmp/YesswOGw3Q/merge.LPL.b.bcf /tmp/YesswOGw3Q/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples /tmp/YesswOGw3Q/merge.LPL.a.bcf /tmp/YesswOGw3Q/merge.LPL.b.bcf /tmp/YesswOGw3Q/merge.LPL.c.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --force-samples -L 1 /tmp/YesswOGw3Q/merge.LPL.a.vcf.gz /tmp/YesswOGw3Q/merge.LPL.b.vcf.gz /tmp/YesswOGw3Q/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -L 1 /tmp/YesswOGw3Q/merge.LPL.a.vcf.gz /tmp/YesswOGw3Q/merge.LPL.b.vcf.gz /tmp/YesswOGw3Q/merge.LPL.c.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --force-samples -L 1 /tmp/YesswOGw3Q/merge.LPL.a.bcf /tmp/YesswOGw3Q/merge.LPL.b.bcf /tmp/YesswOGw3Q/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -L 1 /tmp/YesswOGw3Q/merge.LPL.a.bcf /tmp/YesswOGw3Q/merge.LPL.b.bcf /tmp/YesswOGw3Q/merge.LPL.c.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --force-samples -L 2 /tmp/YesswOGw3Q/merge.LPL.a.vcf.gz /tmp/YesswOGw3Q/merge.LPL.b.vcf.gz /tmp/YesswOGw3Q/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -L 2 /tmp/YesswOGw3Q/merge.LPL.a.vcf.gz /tmp/YesswOGw3Q/merge.LPL.b.vcf.gz /tmp/YesswOGw3Q/merge.LPL.c.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --force-samples -L 2 /tmp/YesswOGw3Q/merge.LPL.a.bcf /tmp/YesswOGw3Q/merge.LPL.b.bcf /tmp/YesswOGw3Q/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -L 2 /tmp/YesswOGw3Q/merge.LPL.a.bcf /tmp/YesswOGw3Q/merge.LPL.b.bcf /tmp/YesswOGw3Q/merge.LPL.c.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --force-samples -L 3 /tmp/YesswOGw3Q/merge.LPL.a.vcf.gz /tmp/YesswOGw3Q/merge.LPL.b.vcf.gz /tmp/YesswOGw3Q/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -L 3 /tmp/YesswOGw3Q/merge.LPL.a.vcf.gz /tmp/YesswOGw3Q/merge.LPL.b.vcf.gz /tmp/YesswOGw3Q/merge.LPL.c.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --force-samples -L 3 /tmp/YesswOGw3Q/merge.LPL.a.bcf /tmp/YesswOGw3Q/merge.LPL.b.bcf /tmp/YesswOGw3Q/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -L 3 /tmp/YesswOGw3Q/merge.LPL.a.bcf /tmp/YesswOGw3Q/merge.LPL.b.bcf /tmp/YesswOGw3Q/merge.LPL.c.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --force-samples -L 4 /tmp/YesswOGw3Q/merge.LPL.a.vcf.gz /tmp/YesswOGw3Q/merge.LPL.b.vcf.gz /tmp/YesswOGw3Q/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -L 4 /tmp/YesswOGw3Q/merge.LPL.a.vcf.gz /tmp/YesswOGw3Q/merge.LPL.b.vcf.gz /tmp/YesswOGw3Q/merge.LPL.c.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --force-samples -L 4 /tmp/YesswOGw3Q/merge.LPL.a.bcf /tmp/YesswOGw3Q/merge.LPL.b.bcf /tmp/YesswOGw3Q/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -L 4 /tmp/YesswOGw3Q/merge.LPL.a.bcf /tmp/YesswOGw3Q/merge.LPL.b.bcf /tmp/YesswOGw3Q/merge.LPL.c.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --force-samples -L 5 /tmp/YesswOGw3Q/merge.LPL.a.vcf.gz /tmp/YesswOGw3Q/merge.LPL.b.vcf.gz /tmp/YesswOGw3Q/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -L 5 /tmp/YesswOGw3Q/merge.LPL.a.vcf.gz /tmp/YesswOGw3Q/merge.LPL.b.vcf.gz /tmp/YesswOGw3Q/merge.LPL.c.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --force-samples -L 5 /tmp/YesswOGw3Q/merge.LPL.a.bcf /tmp/YesswOGw3Q/merge.LPL.b.bcf /tmp/YesswOGw3Q/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -L 5 /tmp/YesswOGw3Q/merge.LPL.a.bcf /tmp/YesswOGw3Q/merge.LPL.b.bcf /tmp/YesswOGw3Q/merge.LPL.c.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --force-samples /tmp/YesswOGw3Q/merge.a.vcf.gz /tmp/YesswOGw3Q/merge.b.vcf.gz /tmp/YesswOGw3Q/merge.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples /tmp/YesswOGw3Q/merge.a.vcf.gz /tmp/YesswOGw3Q/merge.b.vcf.gz /tmp/YesswOGw3Q/merge.c.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --force-samples /tmp/YesswOGw3Q/merge.a.bcf /tmp/YesswOGw3Q/merge.b.bcf /tmp/YesswOGw3Q/merge.c.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples /tmp/YesswOGw3Q/merge.a.bcf /tmp/YesswOGw3Q/merge.b.bcf /tmp/YesswOGw3Q/merge.c.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --force-samples -Fx /tmp/YesswOGw3Q/merge.a.vcf.gz /tmp/YesswOGw3Q/merge.b.vcf.gz /tmp/YesswOGw3Q/merge.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -Fx /tmp/YesswOGw3Q/merge.a.vcf.gz /tmp/YesswOGw3Q/merge.b.vcf.gz /tmp/YesswOGw3Q/merge.c.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --force-samples -Fx /tmp/YesswOGw3Q/merge.a.bcf /tmp/YesswOGw3Q/merge.b.bcf /tmp/YesswOGw3Q/merge.c.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -Fx /tmp/YesswOGw3Q/merge.a.bcf /tmp/YesswOGw3Q/merge.b.bcf /tmp/YesswOGw3Q/merge.c.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --force-samples -0 /tmp/YesswOGw3Q/merge.a.vcf.gz /tmp/YesswOGw3Q/merge.b.vcf.gz /tmp/YesswOGw3Q/merge.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -0 /tmp/YesswOGw3Q/merge.a.vcf.gz /tmp/YesswOGw3Q/merge.b.vcf.gz /tmp/YesswOGw3Q/merge.c.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --force-samples -0 /tmp/YesswOGw3Q/merge.a.bcf /tmp/YesswOGw3Q/merge.b.bcf /tmp/YesswOGw3Q/merge.c.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -0 /tmp/YesswOGw3Q/merge.a.bcf /tmp/YesswOGw3Q/merge.b.bcf /tmp/YesswOGw3Q/merge.c.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --force-samples -m none /tmp/YesswOGw3Q/merge.2.a.vcf.gz /tmp/YesswOGw3Q/merge.2.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -m none /tmp/YesswOGw3Q/merge.2.a.vcf.gz /tmp/YesswOGw3Q/merge.2.b.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --force-samples -m none /tmp/YesswOGw3Q/merge.2.a.bcf /tmp/YesswOGw3Q/merge.2.b.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -m none /tmp/YesswOGw3Q/merge.2.a.bcf /tmp/YesswOGw3Q/merge.2.b.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --force-samples -m both /tmp/YesswOGw3Q/merge.2.a.vcf.gz /tmp/YesswOGw3Q/merge.2.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -m both /tmp/YesswOGw3Q/merge.2.a.vcf.gz /tmp/YesswOGw3Q/merge.2.b.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --force-samples -m both /tmp/YesswOGw3Q/merge.2.a.bcf /tmp/YesswOGw3Q/merge.2.b.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -m both /tmp/YesswOGw3Q/merge.2.a.bcf /tmp/YesswOGw3Q/merge.2.b.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --force-samples -m all /tmp/YesswOGw3Q/merge.2.a.vcf.gz /tmp/YesswOGw3Q/merge.2.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -m all /tmp/YesswOGw3Q/merge.2.a.vcf.gz /tmp/YesswOGw3Q/merge.2.b.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --force-samples -m all /tmp/YesswOGw3Q/merge.2.a.bcf /tmp/YesswOGw3Q/merge.2.b.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -m all /tmp/YesswOGw3Q/merge.2.a.bcf /tmp/YesswOGw3Q/merge.2.b.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/YesswOGw3Q/merge.3.a.vcf.gz /tmp/YesswOGw3Q/merge.3.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/YesswOGw3Q/merge.3.a.vcf.gz /tmp/YesswOGw3Q/merge.3.b.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/YesswOGw3Q/merge.3.a.bcf /tmp/YesswOGw3Q/merge.3.b.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/YesswOGw3Q/merge.3.a.bcf /tmp/YesswOGw3Q/merge.3.b.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --force-samples -m id /tmp/YesswOGw3Q/merge.4.a.vcf.gz /tmp/YesswOGw3Q/merge.4.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -m id /tmp/YesswOGw3Q/merge.4.a.vcf.gz /tmp/YesswOGw3Q/merge.4.b.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --force-samples -m id /tmp/YesswOGw3Q/merge.4.a.bcf /tmp/YesswOGw3Q/merge.4.b.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -m id /tmp/YesswOGw3Q/merge.4.a.bcf /tmp/YesswOGw3Q/merge.4.b.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --gvcf - /tmp/YesswOGw3Q/gvcf.merge.1.vcf.gz /tmp/YesswOGw3Q/gvcf.merge.2.vcf.gz /tmp/YesswOGw3Q/gvcf.merge.3.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --gvcf - /tmp/YesswOGw3Q/gvcf.merge.1.vcf.gz /tmp/YesswOGw3Q/gvcf.merge.2.vcf.gz /tmp/YesswOGw3Q/gvcf.merge.3.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --gvcf - /tmp/YesswOGw3Q/gvcf.merge.1.bcf /tmp/YesswOGw3Q/gvcf.merge.2.bcf /tmp/YesswOGw3Q/gvcf.merge.3.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --gvcf - /tmp/YesswOGw3Q/gvcf.merge.1.bcf /tmp/YesswOGw3Q/gvcf.merge.2.bcf /tmp/YesswOGw3Q/gvcf.merge.3.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --gvcf - /tmp/YesswOGw3Q/merge.gvcf.2.a.vcf.gz /tmp/YesswOGw3Q/merge.gvcf.2.b.vcf.gz /tmp/YesswOGw3Q/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --gvcf - /tmp/YesswOGw3Q/merge.gvcf.2.a.vcf.gz /tmp/YesswOGw3Q/merge.gvcf.2.b.vcf.gz /tmp/YesswOGw3Q/merge.gvcf.2.c.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --gvcf - -i SRC:join /tmp/YesswOGw3Q/merge.gvcf.3.a.vcf.gz /tmp/YesswOGw3Q/merge.gvcf.3.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --gvcf - -i SRC:join /tmp/YesswOGw3Q/merge.gvcf.3.a.vcf.gz /tmp/YesswOGw3Q/merge.gvcf.3.b.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --gvcf - /tmp/YesswOGw3Q/merge.gvcf.4.a.vcf.gz /tmp/YesswOGw3Q/merge.gvcf.4.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --gvcf - /tmp/YesswOGw3Q/merge.gvcf.4.a.vcf.gz /tmp/YesswOGw3Q/merge.gvcf.4.b.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --gvcf - /tmp/YesswOGw3Q/merge.gvcf.4.a.bcf /tmp/YesswOGw3Q/merge.gvcf.4.b.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --gvcf - /tmp/YesswOGw3Q/merge.gvcf.4.a.bcf /tmp/YesswOGw3Q/merge.gvcf.4.b.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version /tmp/YesswOGw3Q/merge.5.a.vcf.gz /tmp/YesswOGw3Q/merge.5.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob /tmp/YesswOGw3Q/merge.5.a.vcf.gz /tmp/YesswOGw3Q/merge.5.b.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version /tmp/YesswOGw3Q/merge.5.a.bcf /tmp/YesswOGw3Q/merge.5.b.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob /tmp/YesswOGw3Q/merge.5.a.bcf /tmp/YesswOGw3Q/merge.5.b.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version /tmp/YesswOGw3Q/merge.6.a.vcf.gz /tmp/YesswOGw3Q/merge.6.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob /tmp/YesswOGw3Q/merge.6.a.vcf.gz /tmp/YesswOGw3Q/merge.6.b.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version /tmp/YesswOGw3Q/merge.6.a.bcf /tmp/YesswOGw3Q/merge.6.b.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob /tmp/YesswOGw3Q/merge.6.a.bcf /tmp/YesswOGw3Q/merge.6.b.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --gvcf - /tmp/YesswOGw3Q/merge.gvcf.7.a.vcf.gz /tmp/YesswOGw3Q/merge.gvcf.7.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --gvcf - /tmp/YesswOGw3Q/merge.gvcf.7.a.vcf.gz /tmp/YesswOGw3Q/merge.gvcf.7.b.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --gvcf - /tmp/YesswOGw3Q/merge.gvcf.7.a.bcf /tmp/YesswOGw3Q/merge.gvcf.7.b.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --gvcf - /tmp/YesswOGw3Q/merge.gvcf.7.a.bcf /tmp/YesswOGw3Q/merge.gvcf.7.b.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --gvcf - /tmp/YesswOGw3Q/merge.gvcf.8.a.vcf.gz /tmp/YesswOGw3Q/merge.gvcf.8.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --gvcf - /tmp/YesswOGw3Q/merge.gvcf.8.a.vcf.gz /tmp/YesswOGw3Q/merge.gvcf.8.b.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --gvcf - /tmp/YesswOGw3Q/merge.gvcf.8.a.bcf /tmp/YesswOGw3Q/merge.gvcf.8.b.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --gvcf - /tmp/YesswOGw3Q/merge.gvcf.8.a.bcf /tmp/YesswOGw3Q/merge.gvcf.8.b.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --force-samples /tmp/YesswOGw3Q/merge.7.a.vcf.gz /tmp/YesswOGw3Q/merge.7.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples /tmp/YesswOGw3Q/merge.7.a.vcf.gz /tmp/YesswOGw3Q/merge.7.b.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --force-samples /tmp/YesswOGw3Q/merge.7.a.bcf /tmp/YesswOGw3Q/merge.7.b.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples /tmp/YesswOGw3Q/merge.7.a.bcf /tmp/YesswOGw3Q/merge.7.b.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --gvcf /build/bcftools-1.11/test/gvcf.fa /tmp/YesswOGw3Q/merge.gvcf.9a.vcf.gz /tmp/YesswOGw3Q/merge.gvcf.9b.vcf.gz /tmp/YesswOGw3Q/merge.gvcf.9c.vcf.gz /tmp/YesswOGw3Q/merge.gvcf.9d.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --gvcf /build/bcftools-1.11/test/gvcf.fa /tmp/YesswOGw3Q/merge.gvcf.9a.vcf.gz /tmp/YesswOGw3Q/merge.gvcf.9b.vcf.gz /tmp/YesswOGw3Q/merge.gvcf.9c.vcf.gz /tmp/YesswOGw3Q/merge.gvcf.9d.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --gvcf /build/bcftools-1.11/test/gvcf.fa /tmp/YesswOGw3Q/merge.gvcf.9a.bcf /tmp/YesswOGw3Q/merge.gvcf.9b.bcf /tmp/YesswOGw3Q/merge.gvcf.9c.bcf /tmp/YesswOGw3Q/merge.gvcf.9d.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --gvcf /build/bcftools-1.11/test/gvcf.fa /tmp/YesswOGw3Q/merge.gvcf.9a.bcf /tmp/YesswOGw3Q/merge.gvcf.9b.bcf /tmp/YesswOGw3Q/merge.gvcf.9c.bcf /tmp/YesswOGw3Q/merge.gvcf.9d.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --gvcf /build/bcftools-1.11/test/gvcf.fa -r 22:21-23 /tmp/YesswOGw3Q/merge.gvcf.9a.vcf.gz /tmp/YesswOGw3Q/merge.gvcf.9b.vcf.gz /tmp/YesswOGw3Q/merge.gvcf.9c.vcf.gz /tmp/YesswOGw3Q/merge.gvcf.9d.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --gvcf /build/bcftools-1.11/test/gvcf.fa -r 22:21-23 /tmp/YesswOGw3Q/merge.gvcf.9a.vcf.gz /tmp/YesswOGw3Q/merge.gvcf.9b.vcf.gz /tmp/YesswOGw3Q/merge.gvcf.9c.vcf.gz /tmp/YesswOGw3Q/merge.gvcf.9d.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --gvcf /build/bcftools-1.11/test/gvcf.fa -r 22:21-23 /tmp/YesswOGw3Q/merge.gvcf.9a.bcf /tmp/YesswOGw3Q/merge.gvcf.9b.bcf /tmp/YesswOGw3Q/merge.gvcf.9c.bcf /tmp/YesswOGw3Q/merge.gvcf.9d.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --gvcf /build/bcftools-1.11/test/gvcf.fa -r 22:21-23 /tmp/YesswOGw3Q/merge.gvcf.9a.bcf /tmp/YesswOGw3Q/merge.gvcf.9b.bcf /tmp/YesswOGw3Q/merge.gvcf.9c.bcf /tmp/YesswOGw3Q/merge.gvcf.9d.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --gvcf /build/bcftools-1.11/test/gvcf.fa /tmp/YesswOGw3Q/merge.gvcf.9a.vcf.gz /tmp/YesswOGw3Q/merge.gvcf.9b.vcf.gz /tmp/YesswOGw3Q/merge.gvcf.9c.vcf.gz /tmp/YesswOGw3Q/merge.gvcf.9d.vcf.gz /tmp/YesswOGw3Q/merge.gvcf.9e.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --gvcf /build/bcftools-1.11/test/gvcf.fa /tmp/YesswOGw3Q/merge.gvcf.9a.vcf.gz /tmp/YesswOGw3Q/merge.gvcf.9b.vcf.gz /tmp/YesswOGw3Q/merge.gvcf.9c.vcf.gz /tmp/YesswOGw3Q/merge.gvcf.9d.vcf.gz /tmp/YesswOGw3Q/merge.gvcf.9e.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --gvcf /build/bcftools-1.11/test/gvcf.fa /tmp/YesswOGw3Q/merge.gvcf.9a.bcf /tmp/YesswOGw3Q/merge.gvcf.9b.bcf /tmp/YesswOGw3Q/merge.gvcf.9c.bcf /tmp/YesswOGw3Q/merge.gvcf.9d.bcf /tmp/YesswOGw3Q/merge.gvcf.9e.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --gvcf /build/bcftools-1.11/test/gvcf.fa /tmp/YesswOGw3Q/merge.gvcf.9a.bcf /tmp/YesswOGw3Q/merge.gvcf.9b.bcf /tmp/YesswOGw3Q/merge.gvcf.9c.bcf /tmp/YesswOGw3Q/merge.gvcf.9d.bcf /tmp/YesswOGw3Q/merge.gvcf.9e.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --gvcf /build/bcftools-1.11/test/gvcf.fa -r 22:21-23 /tmp/YesswOGw3Q/merge.gvcf.9a.vcf.gz /tmp/YesswOGw3Q/merge.gvcf.9b.vcf.gz /tmp/YesswOGw3Q/merge.gvcf.9c.vcf.gz /tmp/YesswOGw3Q/merge.gvcf.9d.vcf.gz /tmp/YesswOGw3Q/merge.gvcf.9e.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --gvcf /build/bcftools-1.11/test/gvcf.fa -r 22:21-23 /tmp/YesswOGw3Q/merge.gvcf.9a.vcf.gz /tmp/YesswOGw3Q/merge.gvcf.9b.vcf.gz /tmp/YesswOGw3Q/merge.gvcf.9c.vcf.gz /tmp/YesswOGw3Q/merge.gvcf.9d.vcf.gz /tmp/YesswOGw3Q/merge.gvcf.9e.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --gvcf /build/bcftools-1.11/test/gvcf.fa -r 22:21-23 /tmp/YesswOGw3Q/merge.gvcf.9a.bcf /tmp/YesswOGw3Q/merge.gvcf.9b.bcf /tmp/YesswOGw3Q/merge.gvcf.9c.bcf /tmp/YesswOGw3Q/merge.gvcf.9d.bcf /tmp/YesswOGw3Q/merge.gvcf.9e.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --gvcf /build/bcftools-1.11/test/gvcf.fa -r 22:21-23 /tmp/YesswOGw3Q/merge.gvcf.9a.bcf /tmp/YesswOGw3Q/merge.gvcf.9b.bcf /tmp/YesswOGw3Q/merge.gvcf.9c.bcf /tmp/YesswOGw3Q/merge.gvcf.9d.bcf /tmp/YesswOGw3Q/merge.gvcf.9e.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version /tmp/YesswOGw3Q/merge.gvcf.10.a.vcf.gz /tmp/YesswOGw3Q/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob /tmp/YesswOGw3Q/merge.gvcf.10.a.vcf.gz /tmp/YesswOGw3Q/merge.gvcf.10.b.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version /tmp/YesswOGw3Q/merge.gvcf.10.a.bcf /tmp/YesswOGw3Q/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob /tmp/YesswOGw3Q/merge.gvcf.10.a.bcf /tmp/YesswOGw3Q/merge.gvcf.10.b.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version -m none /tmp/YesswOGw3Q/merge.gvcf.10.a.vcf.gz /tmp/YesswOGw3Q/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob -m none /tmp/YesswOGw3Q/merge.gvcf.10.a.vcf.gz /tmp/YesswOGw3Q/merge.gvcf.10.b.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version -m none /tmp/YesswOGw3Q/merge.gvcf.10.a.bcf /tmp/YesswOGw3Q/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob -m none /tmp/YesswOGw3Q/merge.gvcf.10.a.bcf /tmp/YesswOGw3Q/merge.gvcf.10.b.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version -g /build/bcftools-1.11/test/merge.gvcf.10.fa /tmp/YesswOGw3Q/merge.gvcf.10.a.vcf.gz /tmp/YesswOGw3Q/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob -g /build/bcftools-1.11/test/merge.gvcf.10.fa /tmp/YesswOGw3Q/merge.gvcf.10.a.vcf.gz /tmp/YesswOGw3Q/merge.gvcf.10.b.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version -g /build/bcftools-1.11/test/merge.gvcf.10.fa /tmp/YesswOGw3Q/merge.gvcf.10.a.bcf /tmp/YesswOGw3Q/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob -g /build/bcftools-1.11/test/merge.gvcf.10.fa /tmp/YesswOGw3Q/merge.gvcf.10.a.bcf /tmp/YesswOGw3Q/merge.gvcf.10.b.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version -g /build/bcftools-1.11/test/merge.gvcf.10.fa -m none /tmp/YesswOGw3Q/merge.gvcf.10.a.vcf.gz /tmp/YesswOGw3Q/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob -g /build/bcftools-1.11/test/merge.gvcf.10.fa -m none /tmp/YesswOGw3Q/merge.gvcf.10.a.vcf.gz /tmp/YesswOGw3Q/merge.gvcf.10.b.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version -g /build/bcftools-1.11/test/merge.gvcf.10.fa -m none /tmp/YesswOGw3Q/merge.gvcf.10.a.bcf /tmp/YesswOGw3Q/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob -g /build/bcftools-1.11/test/merge.gvcf.10.fa -m none /tmp/YesswOGw3Q/merge.gvcf.10.a.bcf /tmp/YesswOGw3Q/merge.gvcf.10.b.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version -g /build/bcftools-1.11/test/merge.gvcf.10.fa /tmp/YesswOGw3Q/merge.gvcf.10.b.vcf.gz /tmp/YesswOGw3Q/merge.gvcf.10.a.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob -g /build/bcftools-1.11/test/merge.gvcf.10.fa /tmp/YesswOGw3Q/merge.gvcf.10.b.vcf.gz /tmp/YesswOGw3Q/merge.gvcf.10.a.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version -g /build/bcftools-1.11/test/merge.gvcf.10.fa /tmp/YesswOGw3Q/merge.gvcf.10.b.bcf /tmp/YesswOGw3Q/merge.gvcf.10.a.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob -g /build/bcftools-1.11/test/merge.gvcf.10.fa /tmp/YesswOGw3Q/merge.gvcf.10.b.bcf /tmp/YesswOGw3Q/merge.gvcf.10.a.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version -g /build/bcftools-1.11/test/merge.gvcf.10.fa -m none /tmp/YesswOGw3Q/merge.gvcf.10.b.vcf.gz /tmp/YesswOGw3Q/merge.gvcf.10.a.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob -g /build/bcftools-1.11/test/merge.gvcf.10.fa -m none /tmp/YesswOGw3Q/merge.gvcf.10.b.vcf.gz /tmp/YesswOGw3Q/merge.gvcf.10.a.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version -g /build/bcftools-1.11/test/merge.gvcf.10.fa -m none /tmp/YesswOGw3Q/merge.gvcf.10.b.bcf /tmp/YesswOGw3Q/merge.gvcf.10.a.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob -g /build/bcftools-1.11/test/merge.gvcf.10.fa -m none /tmp/YesswOGw3Q/merge.gvcf.10.b.bcf /tmp/YesswOGw3Q/merge.gvcf.10.a.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version /tmp/YesswOGw3Q/merge.noidx.a.vcf.gz /tmp/YesswOGw3Q/merge.noidx.b.vcf.gz /tmp/YesswOGw3Q/merge.noidx.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob /tmp/YesswOGw3Q/merge.noidx.a.vcf.gz /tmp/YesswOGw3Q/merge.noidx.b.vcf.gz /tmp/YesswOGw3Q/merge.noidx.c.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version /tmp/YesswOGw3Q/merge.noidx.a.bcf /tmp/YesswOGw3Q/merge.noidx.b.bcf /tmp/YesswOGw3Q/merge.noidx.c.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob /tmp/YesswOGw3Q/merge.noidx.a.bcf /tmp/YesswOGw3Q/merge.noidx.b.bcf /tmp/YesswOGw3Q/merge.noidx.c.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --no-index /build/bcftools-1.11/test/merge.noidx.a.vcf /build/bcftools-1.11/test/merge.noidx.b.vcf /build/bcftools-1.11/test/merge.noidx.c.vcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --no-index /build/bcftools-1.11/test/merge.noidx.a.vcf /build/bcftools-1.11/test/merge.noidx.b.vcf /build/bcftools-1.11/test/merge.noidx.c.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --no-index /tmp/YesswOGw3Q/merge.noidx.a.bcf /tmp/YesswOGw3Q/merge.noidx.b.bcf /tmp/YesswOGw3Q/merge.noidx.c.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --no-index /tmp/YesswOGw3Q/merge.noidx.a.bcf /tmp/YesswOGw3Q/merge.noidx.b.bcf /tmp/YesswOGw3Q/merge.noidx.c.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided,_conflicting_interpretations"' /tmp/YesswOGw3Q/query.string.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/query.string.vcf.gz | /build/bcftools-1.11/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided,_conflicting_interpretations"' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" || CLNREVSTAT="_conflicting_interpretations"' /tmp/YesswOGw3Q/query.string.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/query.string.vcf.gz | /build/bcftools-1.11/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" || CLNREVSTAT="_conflicting_interpretations"' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" && CLNREVSTAT="_conflicting_interpretations"' /tmp/YesswOGw3Q/query.string.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/query.string.vcf.gz | /build/bcftools-1.11/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" && CLNREVSTAT="_conflicting_interpretations"' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' /tmp/YesswOGw3Q/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/query.vcf.gz | /build/bcftools-1.11/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-1.11/bcftools query -f '%RSX\t%VKX\n' /tmp/YesswOGw3Q/query.variantkey.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/query.variantkey.vcf.gz | /build/bcftools-1.11/bcftools query -f '%RSX\t%VKX\n' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%XRI\n' -i'XRI[*]>1111' /tmp/YesswOGw3Q/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/view.filter.vcf.gz | /build/bcftools-1.11/bcftools query -f'%XRI\n' -i'XRI[*]>1111' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' /tmp/YesswOGw3Q/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/view.filter.vcf.gz | /build/bcftools-1.11/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' /tmp/YesswOGw3Q/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/view.filter.vcf.gz | /build/bcftools-1.11/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' /tmp/YesswOGw3Q/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/view.filter.vcf.gz | /build/bcftools-1.11/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' /tmp/YesswOGw3Q/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/view.filter.vcf.gz | /build/bcftools-1.11/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' /tmp/YesswOGw3Q/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/view.filter.vcf.gz | /build/bcftools-1.11/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' /tmp/YesswOGw3Q/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/view.filter.vcf.gz | /build/bcftools-1.11/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' /tmp/YesswOGw3Q/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/query.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' /tmp/YesswOGw3Q/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/query.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' /tmp/YesswOGw3Q/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/query.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' /tmp/YesswOGw3Q/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/query.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' /tmp/YesswOGw3Q/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/view.filter.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' /tmp/YesswOGw3Q/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/query.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' /tmp/YesswOGw3Q/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/query.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' /tmp/YesswOGw3Q/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/query.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' /tmp/YesswOGw3Q/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/query.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' .. ok test_vcf_query: /build/bcftools-1.11/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/YesswOGw3Q/view.vectors.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/view.vectors.vcf.gz | /build/bcftools-1.11/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-1.11/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' /tmp/YesswOGw3Q/query.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/query.filter.vcf.gz | /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' /tmp/YesswOGw3Q/query.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/query.filter.vcf.gz | /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' /tmp/YesswOGw3Q/query.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/query.filter.vcf.gz | /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' /tmp/YesswOGw3Q/query.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/query.filter.vcf.gz | /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' /tmp/YesswOGw3Q/query.2.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/query.2.vcf.gz | /build/bcftools-1.11/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -i'IINT="."' -f'%POS %IINT\n' /tmp/YesswOGw3Q/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/missing.vcf.gz | /build/bcftools-1.11/bcftools query -i'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -i'IINT!="."' -f'%POS %IINT\n' /tmp/YesswOGw3Q/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/missing.vcf.gz | /build/bcftools-1.11/bcftools query -i'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -e'IINT!="."' -f'%POS %IINT\n' /tmp/YesswOGw3Q/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/missing.vcf.gz | /build/bcftools-1.11/bcftools query -e'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -e'IINT="."' -f'%POS %IINT\n' /tmp/YesswOGw3Q/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/missing.vcf.gz | /build/bcftools-1.11/bcftools query -e'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' /tmp/YesswOGw3Q/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/missing.vcf.gz | /build/bcftools-1.11/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' /tmp/YesswOGw3Q/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/missing.vcf.gz | /build/bcftools-1.11/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' /tmp/YesswOGw3Q/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/missing.vcf.gz | /build/bcftools-1.11/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' /tmp/YesswOGw3Q/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/missing.vcf.gz | /build/bcftools-1.11/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' /tmp/YesswOGw3Q/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/missing.vcf.gz | /build/bcftools-1.11/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' /tmp/YesswOGw3Q/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/missing.vcf.gz | /build/bcftools-1.11/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' /tmp/YesswOGw3Q/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/missing.vcf.gz | /build/bcftools-1.11/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' /tmp/YesswOGw3Q/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/missing.vcf.gz | /build/bcftools-1.11/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' /tmp/YesswOGw3Q/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/missing.vcf.gz | /build/bcftools-1.11/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -i'FILTER="A"' -f'%POS %FILTER\n' /tmp/YesswOGw3Q/filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/filter.11.vcf.gz | /build/bcftools-1.11/bcftools query -i'FILTER="A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -i'FILTER!="A"' -f'%POS %FILTER\n' /tmp/YesswOGw3Q/filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/filter.11.vcf.gz | /build/bcftools-1.11/bcftools query -i'FILTER!="A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -i'FILTER~"A"' -f'%POS %FILTER\n' /tmp/YesswOGw3Q/filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/filter.11.vcf.gz | /build/bcftools-1.11/bcftools query -i'FILTER~"A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n' /tmp/YesswOGw3Q/filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/filter.11.vcf.gz | /build/bcftools-1.11/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%LINE' /tmp/YesswOGw3Q/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/query.vcf.gz | /build/bcftools-1.11/bcftools query -f'%LINE' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' /tmp/YesswOGw3Q/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/query.filter-type.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' /tmp/YesswOGw3Q/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/query.filter-type.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' /tmp/YesswOGw3Q/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/query.filter-type.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' /tmp/YesswOGw3Q/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/query.filter-type.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\n' -i'INFO/TYPE="xxx"' /tmp/YesswOGw3Q/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/query.filter-type.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\n' -i'INFO/TYPE="xxx"' .. ok test_vcf_query: /build/bcftools-1.11/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/YesswOGw3Q/filter-missing-floats.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/filter-missing-floats.vcf.gz | /build/bcftools-1.11/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-1.11/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/YesswOGw3Q/filter-missing-floats.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/filter-missing-floats.vcf.gz | /build/bcftools-1.11/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-1.11/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' /tmp/YesswOGw3Q/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/missing.vcf.gz | /build/bcftools-1.11/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' /tmp/YesswOGw3Q/query.filter.2.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/query.filter.2.vcf.gz | /build/bcftools-1.11/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' /tmp/YesswOGw3Q/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/view.filter.vcf.gz | /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' /tmp/YesswOGw3Q/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/view.filter.vcf.gz | /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' /tmp/YesswOGw3Q/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/view.filter.vcf.gz | /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' /tmp/YesswOGw3Q/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/view.filter.vcf.gz | /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' /tmp/YesswOGw3Q/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/view.filter.vcf.gz | /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' /tmp/YesswOGw3Q/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/view.filter.vcf.gz | /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' /tmp/YesswOGw3Q/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/view.filter.vcf.gz | /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' /tmp/YesswOGw3Q/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/view.filter.vcf.gz | /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' /tmp/YesswOGw3Q/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/view.filter.vcf.gz | /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' /tmp/YesswOGw3Q/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/view.filter.vcf.gz | /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' /tmp/YesswOGw3Q/filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/filter.5.vcf.gz | /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' /tmp/YesswOGw3Q/filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/filter.5.vcf.gz | /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' /tmp/YesswOGw3Q/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/view.filter.vcf.gz | /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' /tmp/YesswOGw3Q/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/view.filter.vcf.gz | /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' /tmp/YesswOGw3Q/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/view.filter.vcf.gz | /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' /tmp/YesswOGw3Q/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/view.filter.vcf.gz | /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' /tmp/YesswOGw3Q/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/view.filter.vcf.gz | /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 & FMT/GQ=589' /tmp/YesswOGw3Q/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/view.filter.vcf.gz | /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 & FMT/GQ=589' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' /tmp/YesswOGw3Q/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/view.filter.vcf.gz | /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' /tmp/YesswOGw3Q/query.filter.3.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/query.filter.3.vcf.gz | /build/bcftools-1.11/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"' /tmp/YesswOGw3Q/query.filter.3.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/query.filter.3.vcf.gz | /build/bcftools-1.11/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' /tmp/YesswOGw3Q/query.filter.3.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/query.filter.3.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %AD\n]\n' -i'AD[:0]+AD[:1] > 12' /tmp/YesswOGw3Q/filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/filter.5.vcf.gz | /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %AD\n]\n' -i'AD[:0]+AD[:1] > 12' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' /tmp/YesswOGw3Q/query.filter.4.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/query.filter.4.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%ID\n' -i 'ID=@/build/bcftools-1.11/test/query.56.out' /tmp/YesswOGw3Q/view.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/view.vcf.gz | /build/bcftools-1.11/bcftools query -f'%ID\n' -i 'ID=@/build/bcftools-1.11/test/query.56.out' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD)>0.01' /tmp/YesswOGw3Q/query.filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/query.filter.5.vcf.gz | /build/bcftools-1.11/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-1.11/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD[:0],FMT/AD[:1])>0.01' /tmp/YesswOGw3Q/query.filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/query.filter.5.vcf.gz | /build/bcftools-1.11/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-1.11/bcftools query -f'%POS\t%AD\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01' /tmp/YesswOGw3Q/query.filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/query.filter.5.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS\t%AD\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%CHROM %POS\n' -i'CHROM="4"' /tmp/YesswOGw3Q/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/query.vcf.gz | /build/bcftools-1.11/bcftools query -f'%CHROM %POS\n' -i'CHROM="4"' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS\t%TAG1\n' -i'(TAG1>=-129 && TAG1<=-120) || (TAG1>=-32769 && TAG1<=-32760)' /tmp/YesswOGw3Q/query.negative.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/query.negative.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS\t%TAG1\n' -i'(TAG1>=-129 && TAG1<=-120) || (TAG1>=-32769 && TAG1<=-32760)' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS\t%TAGV1\n' -i'(TAGV1>=-129 && TAGV1<=-120) || (TAGV1>=-32769 && TAGV1<=-32760)' /tmp/YesswOGw3Q/query.negative.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/query.negative.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS\t%TAGV1\n' -i'(TAGV1>=-129 && TAGV1<=-120) || (TAGV1>=-32769 && TAGV1<=-32760)' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS\t%TAG2\n' -i'(TAG2>=-129 && TAG2<=-120) || (TAG2>=-32769 && TAG2<=-32760)' /tmp/YesswOGw3Q/query.negative.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/query.negative.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS\t%TAG2\n' -i'(TAG2>=-129 && TAG2<=-120) || (TAG2>=-32769 && TAG2<=-32760)' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS\t%TAGV2\n' -i'(TAGV2>=-129 && TAGV2<=-120) || (TAGV2>=-32769 && TAGV2<=-32760)' /tmp/YesswOGw3Q/query.negative.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/query.negative.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS\t%TAGV2\n' -i'(TAGV2>=-129 && TAGV2<=-120) || (TAGV2>=-32769 && TAGV2<=-32760)' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'[%POS\t%SAMPLE\t%GQ\n]' -i'N_PASS(GQ<20)==1' /tmp/YesswOGw3Q/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/query.vcf.gz | /build/bcftools-1.11/bcftools query -f'[%POS\t%SAMPLE\t%GQ\n]' -i'N_PASS(GQ<20)==1' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%CHROM\t%POS\t%INFO\t%FORMAT\n' -s D,C /tmp/YesswOGw3Q/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/query.vcf.gz | /build/bcftools-1.11/bcftools query -f'%CHROM\t%POS\t%INFO\t%FORMAT\n' -s D,C .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS\n' -i'POS==16777217 || POS==33554432 || POS=118673904' /tmp/YesswOGw3Q/query.filter.6.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/query.filter.6.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS\n' -i'POS==16777217 || POS==33554432 || POS=118673904' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(II)==6' /tmp/YesswOGw3Q/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/query.filter.7.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(II)==6' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(FORMAT/FI)==7' /tmp/YesswOGw3Q/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/query.filter.7.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(FORMAT/FI)==7' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(II)==2' /tmp/YesswOGw3Q/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/query.filter.7.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(II)==2' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(FORMAT/FI)==1.75' /tmp/YesswOGw3Q/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/query.filter.7.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(FORMAT/FI)==1.75' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(II)==2' /tmp/YesswOGw3Q/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/query.filter.7.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(II)==2' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(FORMAT/FI)==1.75' /tmp/YesswOGw3Q/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/query.filter.7.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(FORMAT/FI)==1.75' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(II)==2' /tmp/YesswOGw3Q/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/query.filter.7.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(II)==2' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(FORMAT/FI)==1.5' /tmp/YesswOGw3Q/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/query.filter.7.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(FORMAT/FI)==1.5' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'%ILEN==1' /tmp/YesswOGw3Q/query.filter.8.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/query.filter.8.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'%ILEN==1' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'ILEN==1' /tmp/YesswOGw3Q/query.filter.8.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/query.filter.8.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'ILEN==1' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] < FMT/AD[:1]' /tmp/YesswOGw3Q/query.filter.9.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/query.filter.9.vcf.gz | /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] < FMT/AD[:1]' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] > FMT/AD[:1]' /tmp/YesswOGw3Q/query.filter.9.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/query.filter.9.vcf.gz | /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] > FMT/AD[:1]' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS %NUM_TAG\n' -i'COUNT(INFO/NUM_TAG)=2' /tmp/YesswOGw3Q/query.filter.10.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/query.filter.10.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS %NUM_TAG\n' -i'COUNT(INFO/NUM_TAG)=2' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2' /tmp/YesswOGw3Q/query.filter.10.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/query.filter.10.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f '%CHROM:%POS\t%N_PASS(GT="alt" & GQ>110)\t[\t%GT]\t[\t%GQ]\n' /tmp/YesswOGw3Q/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/query.vcf.gz | /build/bcftools-1.11/bcftools query -f '%CHROM:%POS\t%N_PASS(GT="alt" & GQ>110)\t[\t%GT]\t[\t%GQ]\n' .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm --no-version -cx -f /build/bcftools-1.11/test/norm.fa /tmp/YesswOGw3Q/norm.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -cx -f /build/bcftools-1.11/test/norm.fa /tmp/YesswOGw3Q/norm.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm --no-version -m- /tmp/YesswOGw3Q/norm.split.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -m- /tmp/YesswOGw3Q/norm.split.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm --no-version -m- /tmp/YesswOGw3Q/norm.split.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -m- /tmp/YesswOGw3Q/norm.split.2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm --no-version -m- --force /tmp/YesswOGw3Q/norm.split.3.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -m- --force /tmp/YesswOGw3Q/norm.split.3.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm --no-version -m- /tmp/YesswOGw3Q/norm.split.4.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -m- /tmp/YesswOGw3Q/norm.split.4.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm --no-version -m- --keep-sum AD /tmp/YesswOGw3Q/norm.split.4.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -m- --keep-sum AD /tmp/YesswOGw3Q/norm.split.4.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm --no-version -m- -f /build/bcftools-1.11/test/norm.fa /tmp/YesswOGw3Q/norm.split.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -m- -f /build/bcftools-1.11/test/norm.fa /tmp/YesswOGw3Q/norm.split.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm --no-version -m+ /tmp/YesswOGw3Q/norm.merge.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -m+ /tmp/YesswOGw3Q/norm.merge.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm --no-version -m+ /tmp/YesswOGw3Q/norm.merge.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -m+ /tmp/YesswOGw3Q/norm.merge.2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm --no-version -m+ /tmp/YesswOGw3Q/norm.merge.3.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -m+ /tmp/YesswOGw3Q/norm.merge.3.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm --no-version -m+ -s /tmp/YesswOGw3Q/norm.merge.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -m+ -s /tmp/YesswOGw3Q/norm.merge.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm --no-version -Nc s -f /build/bcftools-1.11/test/norm.fa /tmp/YesswOGw3Q/norm.setref.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -Nc s -f /build/bcftools-1.11/test/norm.fa /tmp/YesswOGw3Q/norm.setref.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm --no-version -f /build/bcftools-1.11/test/norm.fa /tmp/YesswOGw3Q/norm.telomere.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -f /build/bcftools-1.11/test/norm.fa /tmp/YesswOGw3Q/norm.telomere.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm --no-version -d snps /tmp/YesswOGw3Q/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -d snps /tmp/YesswOGw3Q/norm.rmdup.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm --no-version -d indels /tmp/YesswOGw3Q/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -d indels /tmp/YesswOGw3Q/norm.rmdup.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm --no-version -d both /tmp/YesswOGw3Q/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -d both /tmp/YesswOGw3Q/norm.rmdup.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm --no-version -d all /tmp/YesswOGw3Q/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -d all /tmp/YesswOGw3Q/norm.rmdup.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm --no-version -d none /tmp/YesswOGw3Q/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -d none /tmp/YesswOGw3Q/norm.rmdup.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm --no-version -d exact /tmp/YesswOGw3Q/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -d exact /tmp/YesswOGw3Q/norm.rmdup.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm --no-version -d none /tmp/YesswOGw3Q/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -d none /tmp/YesswOGw3Q/norm.rmdup.2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm --no-version -d exact /tmp/YesswOGw3Q/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -d exact /tmp/YesswOGw3Q/norm.rmdup.2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm --no-version -d indels /tmp/YesswOGw3Q/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -d indels /tmp/YesswOGw3Q/norm.rmdup.2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm --no-version -d any /tmp/YesswOGw3Q/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -d any /tmp/YesswOGw3Q/norm.rmdup.2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm --no-version -d both /tmp/YesswOGw3Q/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -d both /tmp/YesswOGw3Q/norm.rmdup.2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm --no-version -d snps /tmp/YesswOGw3Q/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -d snps /tmp/YesswOGw3Q/norm.rmdup.2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm --no-version -f /build/bcftools-1.11/test/norm.2.fa /tmp/YesswOGw3Q/norm.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -f /build/bcftools-1.11/test/norm.2.fa /tmp/YesswOGw3Q/norm.2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm --no-version -c s -f /build/bcftools-1.11/test/norm.iupac.fa /tmp/YesswOGw3Q/norm.iupac.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -c s -f /build/bcftools-1.11/test/norm.iupac.fa /tmp/YesswOGw3Q/norm.iupac.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm --no-version -c s -f /build/bcftools-1.11/test/norm.3.fa /tmp/YesswOGw3Q/norm.3.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -c s -f /build/bcftools-1.11/test/norm.3.fa /tmp/YesswOGw3Q/norm.3.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -aUc1 -C1 -s NA00002 -v snps /tmp/YesswOGw3Q/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/YesswOGw3Q/view.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -f PASS -Xks NA00003 /tmp/YesswOGw3Q/view.vcf.gz -r20,Y .. ok test_vcf_view: /build/bcftools-1.11/bcftools view -Ob -f PASS -Xks NA00003 /tmp/YesswOGw3Q/view.vcf.gz -r20,Y | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -xs NA00003 /tmp/YesswOGw3Q/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view -Ob -xs NA00003 /tmp/YesswOGw3Q/view.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/YesswOGw3Q/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view -Ob -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/YesswOGw3Q/view.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -p /tmp/YesswOGw3Q/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view -Ob -p /tmp/YesswOGw3Q/view.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -P /tmp/YesswOGw3Q/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view -Ob -P /tmp/YesswOGw3Q/view.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -hm2 -M2 -q0.3 -Q0.7 /tmp/YesswOGw3Q/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/YesswOGw3Q/view.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -Hu /tmp/YesswOGw3Q/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -GVsnps /tmp/YesswOGw3Q/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view -Ob -GVsnps /tmp/YesswOGw3Q/view.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -ne 'INDEL=1 || PV4[0]<0.006' /tmp/YesswOGw3Q/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/YesswOGw3Q/view.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -s ^NA00003 /tmp/YesswOGw3Q/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view -Ob -s ^NA00003 /tmp/YesswOGw3Q/view.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version /tmp/YesswOGw3Q/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/view.omitgenotypes.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -G /tmp/YesswOGw3Q/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view -Ob -G /tmp/YesswOGw3Q/view.omitgenotypes.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -HG /tmp/YesswOGw3Q/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -a /tmp/YesswOGw3Q/many.alleles.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view -Ob -a /tmp/YesswOGw3Q/many.alleles.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -asA /tmp/YesswOGw3Q/view.vectors.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view -Ob -asA /tmp/YesswOGw3Q/view.vectors.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -asB /tmp/YesswOGw3Q/view.vectors.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view -Ob -asB /tmp/YesswOGw3Q/view.vectors.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -asA /tmp/YesswOGw3Q/view.vectors.2.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view -Ob -asA /tmp/YesswOGw3Q/view.vectors.2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -H -i'FMT/FGS[*:0]="AAAAAA"' /tmp/YesswOGw3Q/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -H -i'FMT/FGS[*:2]="C"' /tmp/YesswOGw3Q/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -H -i'FMT/FGS[*:4]="EE"' /tmp/YesswOGw3Q/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -H -i'FMT/FRS[*:1]="BB"' /tmp/YesswOGw3Q/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -H -i'TXT0="text"' /tmp/YesswOGw3Q/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -T /build/bcftools-1.11/test/view.chrs.tab /tmp/YesswOGw3Q/view.chrs.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view -Ob -T /build/bcftools-1.11/test/view.chrs.tab /tmp/YesswOGw3Q/view.chrs.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -i 'POS>=3062917' /tmp/YesswOGw3Q/filter.2.vcf.gz 1:3062917-3157410 .. ok test_vcf_view: /build/bcftools-1.11/bcftools view -Ob -i 'POS>=3062917' /tmp/YesswOGw3Q/filter.2.vcf.gz 1:3062917-3157410 | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -H -r 1:10,1:12,1:10 /tmp/YesswOGw3Q/idx.1.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -H -r 1:1172777-1172804,1:1172806-1172808 /tmp/YesswOGw3Q/idx.2.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -H -R /build/bcftools-1.11/test/idx.2.bed /tmp/YesswOGw3Q/idx.2.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -H -R /build/bcftools-1.11/test/idx.3.bed /tmp/YesswOGw3Q/idx.3.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -H -R /build/bcftools-1.11/test/idx.4.bed /tmp/YesswOGw3Q/idx.4.vcf.gz .. ok test_vcf_64bit: /build/bcftools-1.11/bcftools view /build/bcftools-1.11/test/view64bit.1.vcf -H .. ok test_vcf_64bit: /build/bcftools-1.11/bcftools view /build/bcftools-1.11/test/view64bit.1.vcf | /build/bcftools-1.11/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-1.11/bcftools view /build/bcftools-1.11/test/view64bit.1.vcf -Ou | /build/bcftools-1.11/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-1.11/bcftools view /build/bcftools-1.11/test/view64bit.2.vcf -H .. ok test_vcf_64bit: /build/bcftools-1.11/bcftools view /build/bcftools-1.11/test/view64bit.2.vcf | /build/bcftools-1.11/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-1.11/bcftools view /build/bcftools-1.11/test/view64bit.2.vcf -Ou | /build/bcftools-1.11/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-1.11/bcftools view /build/bcftools-1.11/test/view64bit.3.vcf -H .. ok test_vcf_64bit: /build/bcftools-1.11/bcftools view /build/bcftools-1.11/test/view64bit.3.vcf | /build/bcftools-1.11/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-1.11/bcftools view /build/bcftools-1.11/test/view64bit.4.vcf -H .. ok test_vcf_64bit: /build/bcftools-1.11/bcftools view /build/bcftools-1.11/test/view64bit.4.vcf | /build/bcftools-1.11/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-1.11/bcftools view /build/bcftools-1.11/test/view64bit.4.vcf -Ou | /build/bcftools-1.11/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-1.11/bcftools view /build/bcftools-1.11/test/view64bit.5.vcf -H .. ok test_vcf_64bit: /build/bcftools-1.11/bcftools view /build/bcftools-1.11/test/view64bit.5.vcf | /build/bcftools-1.11/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-1.11/bcftools view /build/bcftools-1.11/test/view64bit.5.vcf -Ou | /build/bcftools-1.11/bcftools view -H .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -H -C5:nonmajor /tmp/YesswOGw3Q/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -H -c6:nonmajor /tmp/YesswOGw3Q/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -H -q0.3:major /tmp/YesswOGw3Q/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/YesswOGw3Q/view.filter.annovar.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -H -i 'Gene.refGene~"NOD"' /tmp/YesswOGw3Q/view.filter.annovar.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -H -i 'LJB2_MutationTaster=="0.291000"' /tmp/YesswOGw3Q/view.filter.annovar.vcf.gz .. ok test_vcf_call: /build/bcftools-1.11/bcftools call --no-version -mv /build/bcftools-1.11/test/mpileup.vcf .. ok test_vcf_call: /build/bcftools-1.11/bcftools call -Ob -mv /build/bcftools-1.11/test/mpileup.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.11/bcftools call --no-version -mg0 /build/bcftools-1.11/test/mpileup.vcf .. ok test_vcf_call: /build/bcftools-1.11/bcftools call -Ob -mg0 /build/bcftools-1.11/test/mpileup.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.11/bcftools call --no-version -mv -S /build/bcftools-1.11/test/mpileup.3.samples /build/bcftools-1.11/test/mpileup.vcf .. ok test_vcf_call: /build/bcftools-1.11/bcftools call -Ob -mv -S /build/bcftools-1.11/test/mpileup.3.samples /build/bcftools-1.11/test/mpileup.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.11/bcftools call --no-version -mv -S /build/bcftools-1.11/test/mpileup.4.samples /build/bcftools-1.11/test/mpileup.vcf .. ok test_vcf_call: /build/bcftools-1.11/bcftools call -Ob -mv -S /build/bcftools-1.11/test/mpileup.4.samples /build/bcftools-1.11/test/mpileup.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.11/bcftools call --no-version -mv -S /build/bcftools-1.11/test/mpileup.5.samples /build/bcftools-1.11/test/mpileup.vcf .. ok test_vcf_call: /build/bcftools-1.11/bcftools call -Ob -mv -S /build/bcftools-1.11/test/mpileup.5.samples /build/bcftools-1.11/test/mpileup.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.11/bcftools call --no-version -mv --ploidy-file /build/bcftools-1.11/test/mpileup.ploidy -S /build/bcftools-1.11/test/mpileup.samples /build/bcftools-1.11/test/mpileup.X.vcf .. ok test_vcf_call: /build/bcftools-1.11/bcftools call -Ob -mv --ploidy-file /build/bcftools-1.11/test/mpileup.ploidy -S /build/bcftools-1.11/test/mpileup.samples /build/bcftools-1.11/test/mpileup.X.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.11/bcftools call --no-version -mv --ploidy-file /build/bcftools-1.11/test/mpileup.ploidy -S /build/bcftools-1.11/test/mpileup.ped /build/bcftools-1.11/test/mpileup.X.vcf .. ok test_vcf_call: /build/bcftools-1.11/bcftools call -Ob -mv --ploidy-file /build/bcftools-1.11/test/mpileup.ploidy -S /build/bcftools-1.11/test/mpileup.ped /build/bcftools-1.11/test/mpileup.X.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.11/bcftools call --no-version -mv --ploidy-file /build/bcftools-1.11/test/mpileup.ploidy -S /build/bcftools-1.11/test/mpileup.2.samples /build/bcftools-1.11/test/mpileup.X.vcf .. ok test_vcf_call: /build/bcftools-1.11/bcftools call -Ob -mv --ploidy-file /build/bcftools-1.11/test/mpileup.ploidy -S /build/bcftools-1.11/test/mpileup.2.samples /build/bcftools-1.11/test/mpileup.X.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.11/bcftools call --no-version -mv /build/bcftools-1.11/test/mpileup.NA19213.NA19129.vcf .. ok test_vcf_call: /build/bcftools-1.11/bcftools call -Ob -mv /build/bcftools-1.11/test/mpileup.NA19213.NA19129.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.11/bcftools call --no-version -mv -G - /build/bcftools-1.11/test/mpileup.NA19213.NA19129.vcf .. ok test_vcf_call: /build/bcftools-1.11/bcftools call -Ob -mv -G - /build/bcftools-1.11/test/mpileup.NA19213.NA19129.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.11/bcftools call --no-version -mv /build/bcftools-1.11/test/mpileup.hwe.vcf .. ok test_vcf_call: /build/bcftools-1.11/bcftools call -Ob -mv /build/bcftools-1.11/test/mpileup.hwe.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.11/bcftools call --no-version -mv -G - /build/bcftools-1.11/test/mpileup.hwe.vcf .. ok test_vcf_call: /build/bcftools-1.11/bcftools call -Ob -mv -G - /build/bcftools-1.11/test/mpileup.hwe.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.11/bcftools call --no-version -mv -G /build/bcftools-1.11/test/mpileup.hwe.samples /build/bcftools-1.11/test/mpileup.hwe.vcf .. ok test_vcf_call: /build/bcftools-1.11/bcftools call -Ob -mv -G /build/bcftools-1.11/test/mpileup.hwe.samples /build/bcftools-1.11/test/mpileup.hwe.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-1.11/bcftools call --no-version -mA -C alleles -T /tmp/YesswOGw3Q/mpileup.tab.gz /build/bcftools-1.11/test/mpileup.vcf .. ok test_vcf_call_cAls: /build/bcftools-1.11/bcftools call -Ob -mA -C alleles -T /tmp/YesswOGw3Q/mpileup.tab.gz /build/bcftools-1.11/test/mpileup.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-1.11/bcftools call --no-version -mA -C alleles -T /tmp/YesswOGw3Q/mpileup.2.tab.gz /build/bcftools-1.11/test/mpileup.2.vcf .. ok test_vcf_call_cAls: /build/bcftools-1.11/bcftools call -Ob -mA -C alleles -T /tmp/YesswOGw3Q/mpileup.2.tab.gz /build/bcftools-1.11/test/mpileup.2.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-1.11/bcftools call --no-version -mA -C alleles -T /tmp/YesswOGw3Q/mpileup.3.tab.gz -i /build/bcftools-1.11/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /build/bcftools-1.11/bcftools call -Ob -mA -C alleles -T /tmp/YesswOGw3Q/mpileup.3.tab.gz -i /build/bcftools-1.11/test/mpileup.3.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-1.11/bcftools call --no-version -mA -C alleles -T /tmp/YesswOGw3Q/mpileup.4.tab.gz -i /build/bcftools-1.11/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /build/bcftools-1.11/bcftools call -Ob -mA -C alleles -T /tmp/YesswOGw3Q/mpileup.4.tab.gz -i /build/bcftools-1.11/test/mpileup.3.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-1.11/bcftools call --no-version -mA -C alleles -T /tmp/YesswOGw3Q/mpileup.5.tab.gz -i /build/bcftools-1.11/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /build/bcftools-1.11/bcftools call -Ob -mA -C alleles -T /tmp/YesswOGw3Q/mpileup.5.tab.gz -i /build/bcftools-1.11/test/mpileup.3.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-1.11/bcftools call --no-version -mA -C alleles -T /tmp/YesswOGw3Q/mpileup.6.tab.gz -i /build/bcftools-1.11/test/mpileup.4.vcf .. ok test_vcf_call_cAls: /build/bcftools-1.11/bcftools call -Ob -mA -C alleles -T /tmp/YesswOGw3Q/mpileup.6.tab.gz -i /build/bcftools-1.11/test/mpileup.4.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-1.11/bcftools call --no-version -mA -C alleles -T /tmp/YesswOGw3Q/mpileup.7.tab.gz -i /build/bcftools-1.11/test/mpileup.5.vcf .. ok test_vcf_call_cAls: /build/bcftools-1.11/bcftools call -Ob -mA -C alleles -T /tmp/YesswOGw3Q/mpileup.7.tab.gz -i /build/bcftools-1.11/test/mpileup.5.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-1.11/bcftools call --no-version -mA -C alleles -T /tmp/YesswOGw3Q/mpileup.cals.1.tab.gz /build/bcftools-1.11/test/mpileup.cals.1.vcf .. ok test_vcf_call_cAls: /build/bcftools-1.11/bcftools call -Ob -mA -C alleles -T /tmp/YesswOGw3Q/mpileup.cals.1.tab.gz /build/bcftools-1.11/test/mpileup.cals.1.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-1.11/bcftools call --no-version -mA -C alleles -T /tmp/YesswOGw3Q/mpileup.cals.2.tab.gz /build/bcftools-1.11/test/mpileup.cals.2.vcf .. ok test_vcf_call_cAls: /build/bcftools-1.11/bcftools call -Ob -mA -C alleles -T /tmp/YesswOGw3Q/mpileup.cals.2.tab.gz /build/bcftools-1.11/test/mpileup.cals.2.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.11/bcftools call --no-version -cv /build/bcftools-1.11/test/mpileup.c.vcf .. ok test_vcf_call: /build/bcftools-1.11/bcftools call -Ob -cv /build/bcftools-1.11/test/mpileup.c.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.11/bcftools call --no-version -cv --ploidy-file /build/bcftools-1.11/test/mpileup.ploidy -S /build/bcftools-1.11/test/mpileup.samples /build/bcftools-1.11/test/mpileup.c.X.vcf .. ok test_vcf_call: /build/bcftools-1.11/bcftools call -Ob -cv --ploidy-file /build/bcftools-1.11/test/mpileup.ploidy -S /build/bcftools-1.11/test/mpileup.samples /build/bcftools-1.11/test/mpileup.c.X.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.11/bcftools call --no-version -cv --ploidy-file /build/bcftools-1.11/test/mpileup.ploidy -S /build/bcftools-1.11/test/mpileup.ped /build/bcftools-1.11/test/mpileup.c.X.vcf .. ok test_vcf_call: /build/bcftools-1.11/bcftools call -Ob -cv --ploidy-file /build/bcftools-1.11/test/mpileup.ploidy -S /build/bcftools-1.11/test/mpileup.ped /build/bcftools-1.11/test/mpileup.c.X.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.11/bcftools call --no-version -cv --ploidy-file /build/bcftools-1.11/test/mpileup.ploidy -S /build/bcftools-1.11/test/mpileup.2.samples /build/bcftools-1.11/test/mpileup.c.X.vcf .. ok test_vcf_call: /build/bcftools-1.11/bcftools call -Ob -cv --ploidy-file /build/bcftools-1.11/test/mpileup.ploidy -S /build/bcftools-1.11/test/mpileup.2.samples /build/bcftools-1.11/test/mpileup.c.X.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -S. -e'TXT0="text"' /build/bcftools-1.11/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -S. -e'TXT0="text"' /build/bcftools-1.11/test/view.filter.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -S. -e'FMT/FRS[*:1]="BB"' /build/bcftools-1.11/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -S. -e'FMT/FRS[*:1]="BB"' /build/bcftools-1.11/test/view.filter.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -S. -e'FMT/FGS[*:0]="AAAAAA"' /build/bcftools-1.11/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -S. -e'FMT/FGS[*:0]="AAAAAA"' /build/bcftools-1.11/test/view.filter.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -S. -e'FMT/FGS[*:1]="BBB"' /build/bcftools-1.11/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -S. -e'FMT/FGS[*:1]="BBB"' /build/bcftools-1.11/test/view.filter.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -S. -e'FMT/FGS[*:4]="EE"' /build/bcftools-1.11/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -S. -e'FMT/FGS[*:4]="EE"' /build/bcftools-1.11/test/view.filter.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -S. -e'FMT/STR="XX"' /build/bcftools-1.11/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -S. -e'FMT/STR="XX"' /build/bcftools-1.11/test/view.filter.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -S. -e'FMT/FILTER="aaa"' /build/bcftools-1.11/test/view.filter.2.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -S. -e'FMT/FILTER="aaa"' /build/bcftools-1.11/test/view.filter.2.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -mx -g2 -G2 /build/bcftools-1.11/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -mx -g2 -G2 /build/bcftools-1.11/test/filter.1.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /build/bcftools-1.11/test/filter.2.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /build/bcftools-1.11/test/filter.2.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -e'INFO/DP=19' /build/bcftools-1.11/test/filter.3.vcf | /build/bcftools-1.11/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -e'INFO/DP=19' /build/bcftools-1.11/test/filter.3.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -e'INFO/DP=19' -s XX /build/bcftools-1.11/test/filter.3.vcf | /build/bcftools-1.11/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -e'INFO/DP=19' -s XX /build/bcftools-1.11/test/filter.3.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -e'INFO/DP=19' -s XX -m+ /build/bcftools-1.11/test/filter.3.vcf | /build/bcftools-1.11/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+ /build/bcftools-1.11/test/filter.3.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -e'INFO/DP=19' -s XX -mx /build/bcftools-1.11/test/filter.3.vcf | /build/bcftools-1.11/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -e'INFO/DP=19' -s XX -mx /build/bcftools-1.11/test/filter.3.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -e'INFO/DP=19' -s XX -m+x /build/bcftools-1.11/test/filter.3.vcf | /build/bcftools-1.11/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+x /build/bcftools-1.11/test/filter.3.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -e'FMT/GT="0/2"' /build/bcftools-1.11/test/filter.3.vcf | /build/bcftools-1.11/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -e'FMT/GT="0/2"' /build/bcftools-1.11/test/filter.3.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -e'FMT/GT="0/2"' -s XX /build/bcftools-1.11/test/filter.3.vcf | /build/bcftools-1.11/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX /build/bcftools-1.11/test/filter.3.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -e'FMT/GT="0/2"' -s XX -m+ /build/bcftools-1.11/test/filter.3.vcf | /build/bcftools-1.11/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+ /build/bcftools-1.11/test/filter.3.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -e'FMT/GT="0/2"' -s XX -mx /build/bcftools-1.11/test/filter.3.vcf | /build/bcftools-1.11/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -mx /build/bcftools-1.11/test/filter.3.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -e'FMT/GT="0/2"' -s XX -m+x /build/bcftools-1.11/test/filter.3.vcf | /build/bcftools-1.11/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+x /build/bcftools-1.11/test/filter.3.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -i'FMT/GT="0/0" && AC[*]=2' /build/bcftools-1.11/test/filter.2.vcf | /build/bcftools-1.11/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -i'FMT/GT="0/0" && AC[*]=2' /build/bcftools-1.11/test/filter.2.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -i'AC[*]=2 && FMT/GT="0/0"' /build/bcftools-1.11/test/filter.2.vcf | /build/bcftools-1.11/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -i'AC[*]=2 && FMT/GT="0/0"' /build/bcftools-1.11/test/filter.2.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -i'ALT="."' /build/bcftools-1.11/test/filter.2.vcf | /build/bcftools-1.11/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -i'ALT="."' /build/bcftools-1.11/test/filter.2.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -S . -i 'FORMAT/TEST3<25' /build/bcftools-1.11/test/filter.4.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -S . -i 'FORMAT/TEST3<25' /build/bcftools-1.11/test/filter.4.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -S . -i 'FORMAT/TEST4<25' /build/bcftools-1.11/test/filter.4.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -S . -i 'FORMAT/TEST4<25' /build/bcftools-1.11/test/filter.4.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -i'GT="A"' /build/bcftools-1.11/test/filter.2.vcf | /build/bcftools-1.11/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -i'GT="A"' /build/bcftools-1.11/test/filter.2.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -i'GT="RR"' /build/bcftools-1.11/test/filter.2.vcf | /build/bcftools-1.11/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -i'GT="RR"' /build/bcftools-1.11/test/filter.2.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -i'GT="RA"' /build/bcftools-1.11/test/filter.2.vcf | /build/bcftools-1.11/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -i'GT="RA"' /build/bcftools-1.11/test/filter.2.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -i'GT="AR"' /build/bcftools-1.11/test/filter.2.vcf | /build/bcftools-1.11/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -i'GT="AR"' /build/bcftools-1.11/test/filter.2.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -i'GT="AA"' /build/bcftools-1.11/test/filter.2.vcf | /build/bcftools-1.11/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -i'GT="AA"' /build/bcftools-1.11/test/filter.2.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -i'GT="aA"' /build/bcftools-1.11/test/filter.2.vcf | /build/bcftools-1.11/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -i'GT="aA"' /build/bcftools-1.11/test/filter.2.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -i'GT="Aa"' /build/bcftools-1.11/test/filter.2.vcf | /build/bcftools-1.11/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -i'GT="Aa"' /build/bcftools-1.11/test/filter.2.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -i'GT="HOM"' /build/bcftools-1.11/test/filter.2.vcf | /build/bcftools-1.11/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -i'GT="HOM"' /build/bcftools-1.11/test/filter.2.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -i'GT="HET"' /build/bcftools-1.11/test/filter.2.vcf | /build/bcftools-1.11/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -i'GT="HET"' /build/bcftools-1.11/test/filter.2.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -i'GT="HAP"' /build/bcftools-1.11/test/filter.2.vcf | /build/bcftools-1.11/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -i'GT="HAP"' /build/bcftools-1.11/test/filter.2.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -i'AD[:1]=11' /build/bcftools-1.11/test/filter.5.vcf | /build/bcftools-1.11/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -i'AD[:1]=11' /build/bcftools-1.11/test/filter.5.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -i'AD[1:]=11' /build/bcftools-1.11/test/filter.5.vcf | /build/bcftools-1.11/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -i'AD[1:]=11' /build/bcftools-1.11/test/filter.5.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -i'FR[0:1]=11' /build/bcftools-1.11/test/filter.5.vcf | /build/bcftools-1.11/bcftools query -f '%POS[\t%FR]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -i'FR[0:1]=11' /build/bcftools-1.11/test/filter.5.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS[\t%FR]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -i'AD[*]="."' /build/bcftools-1.11/test/filter.5.vcf | /build/bcftools-1.11/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -i'AD[*]="."' /build/bcftools-1.11/test/filter.5.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -i'AD[0:0]=="."' /build/bcftools-1.11/test/filter.5.vcf | /build/bcftools-1.11/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -i'AD[0:0]=="."' /build/bcftools-1.11/test/filter.5.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -i'AD[0:0]!="."' /build/bcftools-1.11/test/filter.5.vcf | /build/bcftools-1.11/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -i'AD[0:0]!="."' /build/bcftools-1.11/test/filter.5.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -i'QUAL=="."' /build/bcftools-1.11/test/filter.5.vcf | /build/bcftools-1.11/bcftools query -f '%POS\t%QUAL\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -i'QUAL=="."' /build/bcftools-1.11/test/filter.5.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS\t%QUAL\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -i'N_PASS(DP>32)=1' /build/bcftools-1.11/test/filter.2.vcf | /build/bcftools-1.11/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -i'N_PASS(DP>32)=1' /build/bcftools-1.11/test/filter.2.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -i'F_PASS(DP>32)=0.5' /build/bcftools-1.11/test/filter.2.vcf | /build/bcftools-1.11/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -i'F_PASS(DP>32)=0.5' /build/bcftools-1.11/test/filter.2.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -i'F_MISSING>=1/5' /build/bcftools-1.11/test/filter.6.vcf | /build/bcftools-1.11/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -i'F_MISSING>=1/5' /build/bcftools-1.11/test/filter.6.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -i'F_MISSING>=0.2' /build/bcftools-1.11/test/filter.6.vcf | /build/bcftools-1.11/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -i'F_MISSING>=0.2' /build/bcftools-1.11/test/filter.6.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -i'F_PASS(GT=="mis")>=1/5' /build/bcftools-1.11/test/filter.6.vcf | /build/bcftools-1.11/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -i'F_PASS(GT=="mis")>=1/5' /build/bcftools-1.11/test/filter.6.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -i'F_PASS(GT=="mis")>=0.2' /build/bcftools-1.11/test/filter.6.vcf | /build/bcftools-1.11/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -i'F_PASS(GT=="mis")>=0.2' /build/bcftools-1.11/test/filter.6.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -mx -s + -g2:mnp,indel,other /build/bcftools-1.11/test/filter.7.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -mx -s + -g2:mnp,indel,other /build/bcftools-1.11/test/filter.7.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -S . -e 'FORMAT/AO==4' /build/bcftools-1.11/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -S . -e 'FORMAT/AO==4' /build/bcftools-1.11/test/filter.8.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -S . -e 'MAX(FORMAT/AO[0:])==4' /build/bcftools-1.11/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -S . -e 'MAX(FORMAT/AO[0:])==4' /build/bcftools-1.11/test/filter.8.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -S . -e 'MAX(FORMAT/AO)==4' /build/bcftools-1.11/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -S . -e 'MAX(FORMAT/AO)==4' /build/bcftools-1.11/test/filter.8.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -S . -e 'MIN(FORMAT/AO[0:])==3' /build/bcftools-1.11/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO[0:])==3' /build/bcftools-1.11/test/filter.8.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -S . -e 'MIN(FORMAT/AO)==2' /build/bcftools-1.11/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO)==2' /build/bcftools-1.11/test/filter.8.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -S . -e 'MIN(FORMAT/AO[0:])==3' /build/bcftools-1.11/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO[0:])==3' /build/bcftools-1.11/test/filter.8.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -S . -e 'AVG(FORMAT/AO[2:])==4' /build/bcftools-1.11/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -S . -e 'AVG(FORMAT/AO[2:])==4' /build/bcftools-1.11/test/filter.8.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -S . -e 'MEDIAN(FORMAT/AO[2:])==4' /build/bcftools-1.11/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -S . -e 'MEDIAN(FORMAT/AO[2:])==4' /build/bcftools-1.11/test/filter.8.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -S . -e 'STDEV(FORMAT/AO[0:])=0.5' /build/bcftools-1.11/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -S . -e 'STDEV(FORMAT/AO[0:])=0.5' /build/bcftools-1.11/test/filter.8.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -S . -e 'SUM(FORMAT/AO[0:])=7' /build/bcftools-1.11/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -S . -e 'SUM(FORMAT/AO[0:])=7' /build/bcftools-1.11/test/filter.8.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -S . -e 'SMPL_MAX(FORMAT/AO)==4' /build/bcftools-1.11/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -S . -e 'SMPL_MAX(FORMAT/AO)==4' /build/bcftools-1.11/test/filter.8.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -S . -e 'sMIN(FORMAT/AO)==2' /build/bcftools-1.11/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -S . -e 'sMIN(FORMAT/AO)==2' /build/bcftools-1.11/test/filter.8.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -S . -e 'ABS(sAVG(FORMAT/AO)-3.66666)<1e-5' /build/bcftools-1.11/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -S . -e 'ABS(sAVG(FORMAT/AO)-3.66666)<1e-5' /build/bcftools-1.11/test/filter.8.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -S . -e 'sMEDIAN(FORMAT/AO)==4' /build/bcftools-1.11/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -S . -e 'sMEDIAN(FORMAT/AO)==4' /build/bcftools-1.11/test/filter.8.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -S . -e 'ABS(sSTDEV(FORMAT/AO)-1.2472191)<1e-5' /build/bcftools-1.11/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -S . -e 'ABS(sSTDEV(FORMAT/AO)-1.2472191)<1e-5' /build/bcftools-1.11/test/filter.8.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -S . -e 'sSUM(FORMAT/AO)==11' /build/bcftools-1.11/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -S . -e 'sSUM(FORMAT/AO)==11' /build/bcftools-1.11/test/filter.8.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -i 'QUAL/FMT/AD==55' /build/bcftools-1.11/test/filter.9.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -i 'QUAL/FMT/AD==55' /build/bcftools-1.11/test/filter.9.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -i 'QUAL/INFO/AD==10' /build/bcftools-1.11/test/filter.9.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -i 'QUAL/INFO/AD==10' /build/bcftools-1.11/test/filter.9.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -S . -e 'ABS(SMPL_MAX(FORMAT/AO))=5' /build/bcftools-1.11/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -S . -e 'ABS(SMPL_MAX(FORMAT/AO))=5' /build/bcftools-1.11/test/filter.8.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -S . -e 'PHRED(AO[1:])>-4' /build/bcftools-1.11/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -S . -e 'PHRED(AO[1:])>-4' /build/bcftools-1.11/test/filter.8.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -S . -e 'ABS(AO[1:])==2' /build/bcftools-1.11/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -S . -e 'ABS(AO[1:])==2' /build/bcftools-1.11/test/filter.8.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -i 'sum(AD[*]) > FORMAT/DP' /build/bcftools-1.11/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -i 'sum(AD[*]) > FORMAT/DP' /build/bcftools-1.11/test/filter.10.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -i 'FORMAT/DP < sum(AD[*])' /build/bcftools-1.11/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -i 'FORMAT/DP < sum(AD[*])' /build/bcftools-1.11/test/filter.10.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -i 'sum(AD[*]) < FORMAT/DP' /build/bcftools-1.11/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -i 'sum(AD[*]) < FORMAT/DP' /build/bcftools-1.11/test/filter.10.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -i 'FORMAT/DP > sum(AD[*])' /build/bcftools-1.11/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -i 'FORMAT/DP > sum(AD[*])' /build/bcftools-1.11/test/filter.10.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_sort: /build/bcftools-1.11/bcftools sort -m 0 /build/bcftools-1.11/test/sort.vcf | /build/bcftools-1.11/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /build/bcftools-1.11/bcftools sort -Ob -m 0 /build/bcftools-1.11/test/sort.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /build/bcftools-1.11/bcftools sort -m 1000 /build/bcftools-1.11/test/sort.vcf | /build/bcftools-1.11/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /build/bcftools-1.11/bcftools sort -Ob -m 1000 /build/bcftools-1.11/test/sort.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_regions: /build/bcftools-1.11/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /build/bcftools-1.11/test/regions.tab /tmp/YesswOGw3Q/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/regions.vcf.gz | /build/bcftools-1.11/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /build/bcftools-1.11/test/regions.tab .. ok test_vcf_regions: /build/bcftools-1.11/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /build/bcftools-1.11/test/regions.tab /tmp/YesswOGw3Q/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-1.11/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/YesswOGw3Q/regions.tab.gz /tmp/YesswOGw3Q/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/regions.vcf.gz | /build/bcftools-1.11/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/YesswOGw3Q/regions.tab.gz .. ok test_vcf_regions: /build/bcftools-1.11/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/YesswOGw3Q/regions.tab.gz /tmp/YesswOGw3Q/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-1.11/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/YesswOGw3Q/regions.bed /tmp/YesswOGw3Q/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/regions.vcf.gz | /build/bcftools-1.11/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/YesswOGw3Q/regions.bed .. ok test_vcf_regions: /build/bcftools-1.11/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/YesswOGw3Q/regions.bed /tmp/YesswOGw3Q/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-1.11/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/YesswOGw3Q/regions.bed.gz /tmp/YesswOGw3Q/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/regions.vcf.gz | /build/bcftools-1.11/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/YesswOGw3Q/regions.bed.gz .. ok test_vcf_regions: /build/bcftools-1.11/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/YesswOGw3Q/regions.bed.gz /tmp/YesswOGw3Q/regions.vcf.gz .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/YesswOGw3Q/annotate.tab.gz -h /build/bcftools-1.11/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /build/bcftools-1.11/test/annotate.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/YesswOGw3Q/annotate.tab.gz -h /build/bcftools-1.11/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /build/bcftools-1.11/test/annotate.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/YesswOGw3Q/annotate2.tab.gz -h /build/bcftools-1.11/test/annotate.hdr -c CHROM,POS,-,T_STR /build/bcftools-1.11/test/annotate.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/YesswOGw3Q/annotate2.tab.gz -h /build/bcftools-1.11/test/annotate.hdr -c CHROM,POS,-,T_STR /build/bcftools-1.11/test/annotate.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/YesswOGw3Q/annotate2.tab.gz -h /build/bcftools-1.11/test/annotate.hdr -c CHROM,FROM,TO,T_STR /build/bcftools-1.11/test/annotate.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/YesswOGw3Q/annotate2.tab.gz -h /build/bcftools-1.11/test/annotate.hdr -c CHROM,FROM,TO,T_STR /build/bcftools-1.11/test/annotate.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/YesswOGw3Q/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/YesswOGw3Q/annotate.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/YesswOGw3Q/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/YesswOGw3Q/annotate.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/YesswOGw3Q/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/YesswOGw3Q/annotate2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/YesswOGw3Q/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/YesswOGw3Q/annotate2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/YesswOGw3Q/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/YesswOGw3Q/annotate2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/YesswOGw3Q/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/YesswOGw3Q/annotate2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/YesswOGw3Q/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/YesswOGw3Q/annotate2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/YesswOGw3Q/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/YesswOGw3Q/annotate2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/YesswOGw3Q/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/YesswOGw3Q/annotate2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/YesswOGw3Q/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/YesswOGw3Q/annotate2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/YesswOGw3Q/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/YesswOGw3Q/annotate2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/YesswOGw3Q/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/YesswOGw3Q/annotate2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /build/bcftools-1.11/test/annotate3.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /build/bcftools-1.11/test/annotate3.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -x FORMAT /build/bcftools-1.11/test/annotate3.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -x FORMAT /build/bcftools-1.11/test/annotate3.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/YesswOGw3Q/annots4.vcf.gz -c +INFO /tmp/YesswOGw3Q/annotate4.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/YesswOGw3Q/annots4.vcf.gz -c +INFO /tmp/YesswOGw3Q/annotate4.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/YesswOGw3Q/annots4.tab.gz -h /build/bcftools-1.11/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /build/bcftools-1.11/test/annotate4.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/YesswOGw3Q/annots4.tab.gz -h /build/bcftools-1.11/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /build/bcftools-1.11/test/annotate4.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/YesswOGw3Q/annots10.tab.gz -h /build/bcftools-1.11/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /build/bcftools-1.11/test/annotate10.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/YesswOGw3Q/annots10.tab.gz -h /build/bcftools-1.11/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /build/bcftools-1.11/test/annotate10.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/YesswOGw3Q/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/YesswOGw3Q/annotate2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/YesswOGw3Q/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/YesswOGw3Q/annotate2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/YesswOGw3Q/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /build/bcftools-1.11/test/annotate2.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/YesswOGw3Q/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /build/bcftools-1.11/test/annotate2.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/YesswOGw3Q/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/YesswOGw3Q/annotate2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/YesswOGw3Q/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/YesswOGw3Q/annotate2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/YesswOGw3Q/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/YesswOGw3Q/annotate2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/YesswOGw3Q/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/YesswOGw3Q/annotate2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/YesswOGw3Q/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/YesswOGw3Q/annotate2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/YesswOGw3Q/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/YesswOGw3Q/annotate2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/YesswOGw3Q/annots11.vcf.gz -c FMT /tmp/YesswOGw3Q/annotate11.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/YesswOGw3Q/annots11.vcf.gz -c FMT /tmp/YesswOGw3Q/annotate11.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/YesswOGw3Q/annots2.vcf.gz -c FMT/newGT:=GT /tmp/YesswOGw3Q/annotate2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/YesswOGw3Q/annots2.vcf.gz -c FMT/newGT:=GT /tmp/YesswOGw3Q/annotate2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/YesswOGw3Q/annots12.vcf.gz -c FMT/GT:=newGT /tmp/YesswOGw3Q/annotate2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/YesswOGw3Q/annots12.vcf.gz -c FMT/GT:=newGT /tmp/YesswOGw3Q/annotate2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/YesswOGw3Q/annots13.tab.gz -h /build/bcftools-1.11/test/annotate13.hdr -c CHROM,BEG,END,ABC /build/bcftools-1.11/test/annotate13.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/YesswOGw3Q/annots13.tab.gz -h /build/bcftools-1.11/test/annotate13.hdr -c CHROM,BEG,END,ABC /build/bcftools-1.11/test/annotate13.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/YesswOGw3Q/annots13.tab.gz -h /build/bcftools-1.11/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:append /build/bcftools-1.11/test/annotate13.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/YesswOGw3Q/annots13.tab.gz -h /build/bcftools-1.11/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:append /build/bcftools-1.11/test/annotate13.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/YesswOGw3Q/annots13.tab.gz -h /build/bcftools-1.11/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:unique /build/bcftools-1.11/test/annotate13.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/YesswOGw3Q/annots13.tab.gz -h /build/bcftools-1.11/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:unique /build/bcftools-1.11/test/annotate13.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -x FILTER/XX,INFO/XX --force /build/bcftools-1.11/test/annotate14.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -x FILTER/XX,INFO/XX --force /build/bcftools-1.11/test/annotate14.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/YesswOGw3Q/annotate15.tab.gz -h /build/bcftools-1.11/test/annotate15.hdr -s SAMPLE1 -c CHROM,FROM,TO,FMT/FOO,BAR /build/bcftools-1.11/test/annotate15.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/YesswOGw3Q/annotate15.tab.gz -h /build/bcftools-1.11/test/annotate15.hdr -s SAMPLE1 -c CHROM,FROM,TO,FMT/FOO,BAR /build/bcftools-1.11/test/annotate15.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/YesswOGw3Q/annotate15.tab.gz -h /build/bcftools-1.11/test/annotate15.hdr -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR /build/bcftools-1.11/test/annotate15.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/YesswOGw3Q/annotate15.tab.gz -h /build/bcftools-1.11/test/annotate15.hdr -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR /build/bcftools-1.11/test/annotate15.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -x FILTER /build/bcftools-1.11/test/annotate16.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -x FILTER /build/bcftools-1.11/test/annotate16.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/YesswOGw3Q/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/bcftools-1.11/test/annotate17.1.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/YesswOGw3Q/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/bcftools-1.11/test/annotate17.1.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/YesswOGw3Q/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/bcftools-1.11/test/annotate17.2.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/YesswOGw3Q/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/bcftools-1.11/test/annotate17.2.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/YesswOGw3Q/annotate17.3.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/bcftools-1.11/test/annotate17.3.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/YesswOGw3Q/annotate17.3.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/bcftools-1.11/test/annotate17.3.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/YesswOGw3Q/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-1.11/test/annotate18.1.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/YesswOGw3Q/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-1.11/test/annotate18.1.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/YesswOGw3Q/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-1.11/test/annotate18.2.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/YesswOGw3Q/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-1.11/test/annotate18.2.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/YesswOGw3Q/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/YesswOGw3Q/annotate19.dst.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/YesswOGw3Q/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/YesswOGw3Q/annotate19.dst.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/YesswOGw3Q/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/YesswOGw3Q/annotate19.dst.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/YesswOGw3Q/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/YesswOGw3Q/annotate19.dst.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/YesswOGw3Q/annotate20.src.vcf.gz -c FMT/GT /tmp/YesswOGw3Q/annotate20.dst.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/YesswOGw3Q/annotate20.src.vcf.gz -c FMT/GT /tmp/YesswOGw3Q/annotate20.dst.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/YesswOGw3Q/annotate20.src.vcf.gz -c +FMT/GT /tmp/YesswOGw3Q/annotate20.dst.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/YesswOGw3Q/annotate20.src.vcf.gz -c +FMT/GT /tmp/YesswOGw3Q/annotate20.dst.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/YesswOGw3Q/annotate20.src.vcf.gz -c -FMT/GT /tmp/YesswOGw3Q/annotate20.dst.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/YesswOGw3Q/annotate20.src.vcf.gz -c -FMT/GT /tmp/YesswOGw3Q/annotate20.dst.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/YesswOGw3Q/annotate.multi.tab.gz -c CHROM,POS,REF,ALT,ANN -l ANN:append /build/bcftools-1.11/test/annotate.multi.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/YesswOGw3Q/annotate.multi.tab.gz -c CHROM,POS,REF,ALT,ANN -l ANN:append /build/bcftools-1.11/test/annotate.multi.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/YesswOGw3Q/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /build/bcftools-1.11/test/annotate9.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/YesswOGw3Q/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /build/bcftools-1.11/test/annotate9.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-1.11/bcftools concat --no-version /tmp/YesswOGw3Q/concat.1.a.vcf.gz /tmp/YesswOGw3Q/concat.1.b.vcf.gz .. ok test_vcf_concat: /build/bcftools-1.11/bcftools concat -Ob /tmp/YesswOGw3Q/concat.1.a.vcf.gz /tmp/YesswOGw3Q/concat.1.b.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-1.11/bcftools concat --no-version /tmp/YesswOGw3Q/concat.1.a.bcf /tmp/YesswOGw3Q/concat.1.b.bcf .. ok test_vcf_concat: /build/bcftools-1.11/bcftools concat -Ob /tmp/YesswOGw3Q/concat.1.a.bcf /tmp/YesswOGw3Q/concat.1.b.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-1.11/bcftools concat --no-version -a /tmp/YesswOGw3Q/concat.2.a.vcf.gz /tmp/YesswOGw3Q/concat.2.b.vcf.gz .. ok test_vcf_concat: /build/bcftools-1.11/bcftools concat -Ob -a /tmp/YesswOGw3Q/concat.2.a.vcf.gz /tmp/YesswOGw3Q/concat.2.b.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-1.11/bcftools concat --no-version -a /tmp/YesswOGw3Q/concat.2.a.bcf /tmp/YesswOGw3Q/concat.2.b.bcf .. ok test_vcf_concat: /build/bcftools-1.11/bcftools concat -Ob -a /tmp/YesswOGw3Q/concat.2.a.bcf /tmp/YesswOGw3Q/concat.2.b.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-1.11/bcftools concat --no-version -aD /tmp/YesswOGw3Q/concat.2.a.vcf.gz /tmp/YesswOGw3Q/concat.2.b.vcf.gz .. ok test_vcf_concat: /build/bcftools-1.11/bcftools concat -Ob -aD /tmp/YesswOGw3Q/concat.2.a.vcf.gz /tmp/YesswOGw3Q/concat.2.b.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-1.11/bcftools concat --no-version -aD /tmp/YesswOGw3Q/concat.2.a.bcf /tmp/YesswOGw3Q/concat.2.b.bcf .. ok test_vcf_concat: /build/bcftools-1.11/bcftools concat -Ob -aD /tmp/YesswOGw3Q/concat.2.a.bcf /tmp/YesswOGw3Q/concat.2.b.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-1.11/bcftools concat --no-version -l /tmp/YesswOGw3Q/concat.3.a.vcf.gz /tmp/YesswOGw3Q/concat.3.b.vcf.gz /tmp/YesswOGw3Q/concat.3.0.vcf.gz /tmp/YesswOGw3Q/concat.3.c.vcf.gz /tmp/YesswOGw3Q/concat.3.d.vcf.gz /tmp/YesswOGw3Q/concat.3.e.vcf.gz /tmp/YesswOGw3Q/concat.3.f.vcf.gz .. ok test_vcf_concat: /build/bcftools-1.11/bcftools concat -Ob -l /tmp/YesswOGw3Q/concat.3.a.vcf.gz /tmp/YesswOGw3Q/concat.3.b.vcf.gz /tmp/YesswOGw3Q/concat.3.0.vcf.gz /tmp/YesswOGw3Q/concat.3.c.vcf.gz /tmp/YesswOGw3Q/concat.3.d.vcf.gz /tmp/YesswOGw3Q/concat.3.e.vcf.gz /tmp/YesswOGw3Q/concat.3.f.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-1.11/bcftools concat --no-version -l /tmp/YesswOGw3Q/concat.3.a.bcf /tmp/YesswOGw3Q/concat.3.b.bcf /tmp/YesswOGw3Q/concat.3.0.bcf /tmp/YesswOGw3Q/concat.3.c.bcf /tmp/YesswOGw3Q/concat.3.d.bcf /tmp/YesswOGw3Q/concat.3.e.bcf /tmp/YesswOGw3Q/concat.3.f.bcf .. ok test_vcf_concat: /build/bcftools-1.11/bcftools concat -Ob -l /tmp/YesswOGw3Q/concat.3.a.bcf /tmp/YesswOGw3Q/concat.3.b.bcf /tmp/YesswOGw3Q/concat.3.0.bcf /tmp/YesswOGw3Q/concat.3.c.bcf /tmp/YesswOGw3Q/concat.3.d.bcf /tmp/YesswOGw3Q/concat.3.e.bcf /tmp/YesswOGw3Q/concat.3.f.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ Random seed for test_naive_concat: 1864856394 .. ok test_naive_concat: /build/bcftools-1.11/bcftools concat --naive-force /tmp/YesswOGw3Q/naive_concat.0.bcf /tmp/YesswOGw3Q/naive_concat.1.bcf /tmp/YesswOGw3Q/naive_concat.2.bcf /tmp/YesswOGw3Q/naive_concat.3.bcf /tmp/YesswOGw3Q/naive_concat.4.bcf /tmp/YesswOGw3Q/naive_concat.5.bcf /tmp/YesswOGw3Q/naive_concat.6.bcf /tmp/YesswOGw3Q/naive_concat.7.bcf /tmp/YesswOGw3Q/naive_concat.8.bcf /tmp/YesswOGw3Q/naive_concat.9.bcf | /build/bcftools-1.11/bcftools view -H .. ok test_naive_concat: /build/bcftools-1.11/bcftools concat --naive /tmp/YesswOGw3Q/naive_concat.0.vcf.gz /tmp/YesswOGw3Q/naive_concat.1.vcf.gz /tmp/YesswOGw3Q/naive_concat.2.vcf.gz /tmp/YesswOGw3Q/naive_concat.3.vcf.gz /tmp/YesswOGw3Q/naive_concat.4.vcf.gz /tmp/YesswOGw3Q/naive_concat.5.vcf.gz /tmp/YesswOGw3Q/naive_concat.6.vcf.gz /tmp/YesswOGw3Q/naive_concat.7.vcf.gz /tmp/YesswOGw3Q/naive_concat.8.vcf.gz /tmp/YesswOGw3Q/naive_concat.9.vcf.gz | /build/bcftools-1.11/bcftools view -H .. ok test_vcf_reheader: /build/bcftools-1.11/bcftools reheader -h /build/bcftools-1.11/test/reheader.hdr /build/bcftools-1.11/test/reheader.vcf | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-1.11/test/reheader.vcf | /build/bcftools-1.11/bcftools reheader -h /build/bcftools-1.11/test/reheader.hdr | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.11/bcftools reheader -h /build/bcftools-1.11/test/reheader.hdr /tmp/YesswOGw3Q/reheader.bcf | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/YesswOGw3Q/reheader.bcf | /build/bcftools-1.11/bcftools reheader -h /build/bcftools-1.11/test/reheader.hdr | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.11/bcftools reheader -h /build/bcftools-1.11/test/reheader.hdr /tmp/YesswOGw3Q/reheader.vcf.gz | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/YesswOGw3Q/reheader.vcf.gz | /build/bcftools-1.11/bcftools reheader -h /build/bcftools-1.11/test/reheader.hdr | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.11/bcftools reheader -s /build/bcftools-1.11/test/reheader.samples /build/bcftools-1.11/test/reheader.vcf | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-1.11/test/reheader.vcf | /build/bcftools-1.11/bcftools reheader -s /build/bcftools-1.11/test/reheader.samples | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.11/bcftools reheader -s /build/bcftools-1.11/test/reheader.samples /tmp/YesswOGw3Q/reheader.bcf | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/YesswOGw3Q/reheader.bcf | /build/bcftools-1.11/bcftools reheader -s /build/bcftools-1.11/test/reheader.samples | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.11/bcftools reheader -s /build/bcftools-1.11/test/reheader.samples /tmp/YesswOGw3Q/reheader.vcf.gz | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/YesswOGw3Q/reheader.vcf.gz | /build/bcftools-1.11/bcftools reheader -s /build/bcftools-1.11/test/reheader.samples | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.11/bcftools reheader -s /build/bcftools-1.11/test/reheader.samples2 /build/bcftools-1.11/test/reheader.vcf | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-1.11/test/reheader.vcf | /build/bcftools-1.11/bcftools reheader -s /build/bcftools-1.11/test/reheader.samples2 | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.11/bcftools reheader -s /build/bcftools-1.11/test/reheader.samples2 /tmp/YesswOGw3Q/reheader.bcf | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/YesswOGw3Q/reheader.bcf | /build/bcftools-1.11/bcftools reheader -s /build/bcftools-1.11/test/reheader.samples2 | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.11/bcftools reheader -s /build/bcftools-1.11/test/reheader.samples2 /tmp/YesswOGw3Q/reheader.vcf.gz | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/YesswOGw3Q/reheader.vcf.gz | /build/bcftools-1.11/bcftools reheader -s /build/bcftools-1.11/test/reheader.samples2 | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.11/bcftools reheader -s /build/bcftools-1.11/test/reheader.samples3 /build/bcftools-1.11/test/reheader.vcf | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-1.11/test/reheader.vcf | /build/bcftools-1.11/bcftools reheader -s /build/bcftools-1.11/test/reheader.samples3 | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.11/bcftools reheader -s /build/bcftools-1.11/test/reheader.samples3 /tmp/YesswOGw3Q/reheader.bcf | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/YesswOGw3Q/reheader.bcf | /build/bcftools-1.11/bcftools reheader -s /build/bcftools-1.11/test/reheader.samples3 | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.11/bcftools reheader -s /build/bcftools-1.11/test/reheader.samples3 /tmp/YesswOGw3Q/reheader.vcf.gz | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/YesswOGw3Q/reheader.vcf.gz | /build/bcftools-1.11/bcftools reheader -s /build/bcftools-1.11/test/reheader.samples3 | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.11/bcftools reheader -s /build/bcftools-1.11/test/reheader.samples4 /build/bcftools-1.11/test/reheader.vcf | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-1.11/test/reheader.vcf | /build/bcftools-1.11/bcftools reheader -s /build/bcftools-1.11/test/reheader.samples4 | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.11/bcftools reheader -s /build/bcftools-1.11/test/reheader.samples4 /tmp/YesswOGw3Q/reheader.bcf | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/YesswOGw3Q/reheader.bcf | /build/bcftools-1.11/bcftools reheader -s /build/bcftools-1.11/test/reheader.samples4 | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.11/bcftools reheader -s /build/bcftools-1.11/test/reheader.samples4 /tmp/YesswOGw3Q/reheader.vcf.gz | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/YesswOGw3Q/reheader.vcf.gz | /build/bcftools-1.11/bcftools reheader -s /build/bcftools-1.11/test/reheader.samples4 | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.11/bcftools reheader -h /build/bcftools-1.11/test/reheader.empty.hdr /build/bcftools-1.11/test/empty.vcf | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-1.11/test/empty.vcf | /build/bcftools-1.11/bcftools reheader -h /build/bcftools-1.11/test/reheader.empty.hdr | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.11/bcftools reheader -h /build/bcftools-1.11/test/reheader.empty.hdr /tmp/YesswOGw3Q/empty.bcf | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/YesswOGw3Q/empty.bcf | /build/bcftools-1.11/bcftools reheader -h /build/bcftools-1.11/test/reheader.empty.hdr | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.11/bcftools reheader -h /build/bcftools-1.11/test/reheader.empty.hdr /tmp/YesswOGw3Q/empty.vcf.gz | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/YesswOGw3Q/empty.vcf.gz | /build/bcftools-1.11/bcftools reheader -h /build/bcftools-1.11/test/reheader.empty.hdr | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.11/bcftools reheader -f /build/bcftools-1.11/test/reheader.fai /build/bcftools-1.11/test/reheader.2.vcf | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.11/bcftools reheader -f /build/bcftools-1.11/test/reheader.fai /tmp/YesswOGw3Q/reheader.2.bcf | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.11/bcftools reheader -f /build/bcftools-1.11/test/reheader.fai /tmp/YesswOGw3Q/reheader.2.vcf.gz | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.11/bcftools reheader -h /build/bcftools-1.11/test/reheader.2.hdr -f /build/bcftools-1.11/test/reheader.fai /build/bcftools-1.11/test/reheader.2.vcf | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.11/bcftools reheader -h /build/bcftools-1.11/test/reheader.2.hdr -f /build/bcftools-1.11/test/reheader.fai /tmp/YesswOGw3Q/reheader.2.bcf | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.11/bcftools reheader -h /build/bcftools-1.11/test/reheader.2.hdr -f /build/bcftools-1.11/test/reheader.fai /tmp/YesswOGw3Q/reheader.2.vcf.gz | /build/bcftools-1.11/bcftools view --no-version .. ok test_rename_chrs: /build/bcftools-1.11/bcftools annotate --rename-chrs /tmp/YesswOGw3Q/rename.map -Ov /tmp/YesswOGw3Q/annotate.bcf | /build/bcftools-1.11/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /build/bcftools-1.11/bcftools annotate --rename-chrs /tmp/YesswOGw3Q/rename.map -Ob /tmp/YesswOGw3Q/annotate.bcf | /build/bcftools-1.11/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /build/bcftools-1.11/bcftools annotate --rename-chrs /tmp/YesswOGw3Q/rename.map -Ov /build/bcftools-1.11/test/annotate.vcf | /build/bcftools-1.11/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /build/bcftools-1.11/bcftools annotate --rename-chrs /tmp/YesswOGw3Q/rename.map -Ob /build/bcftools-1.11/test/annotate.vcf | /build/bcftools-1.11/bcftools query -f'%CHROM\t%POS\n' .. ok test_vcf_convert: /build/bcftools-1.11/bcftools convert -g -,. /tmp/YesswOGw3Q/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/convert.vcf.gz | /build/bcftools-1.11/bcftools convert -g -,. .. ok test_vcf_convert: /build/bcftools-1.11/bcftools convert -g .,- /tmp/YesswOGw3Q/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/convert.vcf.gz | /build/bcftools-1.11/bcftools convert -g .,- .. ok test_vcf_convert: /build/bcftools-1.11/bcftools convert -g -,. --tag PL /tmp/YesswOGw3Q/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/convert.vcf.gz | /build/bcftools-1.11/bcftools convert -g -,. --tag PL .. ok test_vcf_convert: /build/bcftools-1.11/bcftools convert -g .,- --tag PL /tmp/YesswOGw3Q/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/convert.vcf.gz | /build/bcftools-1.11/bcftools convert -g .,- --tag PL .. ok test_vcf_convert: /build/bcftools-1.11/bcftools convert -g -,. --vcf-ids /tmp/YesswOGw3Q/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/check.vcf.gz | /build/bcftools-1.11/bcftools convert -g -,. --vcf-ids .. ok test_vcf_convert: /build/bcftools-1.11/bcftools convert -g .,- --vcf-ids /tmp/YesswOGw3Q/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/check.vcf.gz | /build/bcftools-1.11/bcftools convert -g .,- --vcf-ids .. ok test_vcf_convert: /build/bcftools-1.11/bcftools convert -g -,. --chrom /tmp/YesswOGw3Q/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/check.vcf.gz | /build/bcftools-1.11/bcftools convert -g -,. --chrom .. ok test_vcf_convert: /build/bcftools-1.11/bcftools convert -g .,- --chrom /tmp/YesswOGw3Q/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/check.vcf.gz | /build/bcftools-1.11/bcftools convert -g .,- --chrom .. ok test_vcf_convert: /build/bcftools-1.11/bcftools convert -g -,. --chrom --vcf-ids /tmp/YesswOGw3Q/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/check.vcf.gz | /build/bcftools-1.11/bcftools convert -g -,. --chrom --vcf-ids .. ok test_vcf_convert: /build/bcftools-1.11/bcftools convert -g .,- --chrom --vcf-ids /tmp/YesswOGw3Q/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/check.vcf.gz | /build/bcftools-1.11/bcftools convert -g .,- --chrom --vcf-ids .. ok test_vcf_convert: /build/bcftools-1.11/bcftools convert -h -,.,. /tmp/YesswOGw3Q/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/convert.vcf.gz | /build/bcftools-1.11/bcftools convert -h -,.,. .. ok test_vcf_convert: /build/bcftools-1.11/bcftools convert -h .,-,. /tmp/YesswOGw3Q/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/convert.vcf.gz | /build/bcftools-1.11/bcftools convert -h .,-,. .. ok test_vcf_convert: /build/bcftools-1.11/bcftools convert -h .,.,- /tmp/YesswOGw3Q/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/convert.vcf.gz | /build/bcftools-1.11/bcftools convert -h .,.,- .. ok test_vcf_convert_hls2vcf: /build/bcftools-1.11/bcftools convert -H /build/bcftools-1.11/test/convert.hls.gt.hap,/build/bcftools-1.11/test/convert.hls.gt.legend,/build/bcftools-1.11/test/convert.hls.gt.samples | grep -v ^## .. ok test_vcf_convert_hls2vcf: /build/bcftools-1.11/bcftools convert -H /build/bcftools-1.11/test/convert.hls.gt.hap,/build/bcftools-1.11/test/convert.hls.gt.legend,/build/bcftools-1.11/test/convert.hls.gt.samples -Ou | /build/bcftools-1.11/bcftools view | grep -v ^## .. ok test_vcf_convert_hls2vcf: /build/bcftools-1.11/bcftools convert --vcf-ids -H /build/bcftools-1.11/test/convert.hls.gt.hap,/build/bcftools-1.11/test/convert.hls.gt.legend,/build/bcftools-1.11/test/convert.hls.gt.samples | grep -v ^## .. ok test_vcf_convert_hls2vcf: /build/bcftools-1.11/bcftools convert --vcf-ids -H /build/bcftools-1.11/test/convert.hls.gt.hap,/build/bcftools-1.11/test/convert.hls.gt.legend,/build/bcftools-1.11/test/convert.hls.gt.samples -Ou | /build/bcftools-1.11/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-1.11/bcftools convert --hapsample2vcf /build/bcftools-1.11/test/convert.hs.gt.hap,/build/bcftools-1.11/test/convert.hs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-1.11/bcftools convert --hapsample2vcf /build/bcftools-1.11/test/convert.hs.gt.hap,/build/bcftools-1.11/test/convert.hs.gt.samples -Ou | /build/bcftools-1.11/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-1.11/bcftools convert --vcf-ids --hapsample2vcf /build/bcftools-1.11/test/convert.hs.gt.hap,/build/bcftools-1.11/test/convert.hs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-1.11/bcftools convert --vcf-ids --hapsample2vcf /build/bcftools-1.11/test/convert.hs.gt.hap,/build/bcftools-1.11/test/convert.hs.gt.samples -Ou | /build/bcftools-1.11/bcftools view | grep -v ^## .. ok test_vcf_convert: /build/bcftools-1.11/bcftools convert --hapsample -,. /tmp/YesswOGw3Q/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/convert.vcf.gz | /build/bcftools-1.11/bcftools convert --hapsample -,. .. ok test_vcf_convert: /build/bcftools-1.11/bcftools convert --hapsample .,- /tmp/YesswOGw3Q/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/convert.vcf.gz | /build/bcftools-1.11/bcftools convert --hapsample .,- .. ok test_vcf_convert: /build/bcftools-1.11/bcftools convert --haplegendsample -,.,. /tmp/YesswOGw3Q/convert.hap-missing.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/convert.hap-missing.vcf.gz | /build/bcftools-1.11/bcftools convert --haplegendsample -,.,. .. ok test_vcf_convert_gvcf: /build/bcftools-1.11/bcftools convert --no-version --gvcf2vcf -i'FILTER="PASS"' -f /build/bcftools-1.11/test/gvcf.fa /tmp/YesswOGw3Q/convert.gvcf.vcf.gz .. ok test_vcf_convert_gvcf: /build/bcftools-1.11/bcftools view -Ob /tmp/YesswOGw3Q/convert.gvcf.vcf.gz | /build/bcftools-1.11/bcftools convert --gvcf2vcf -i'FILTER="PASS"' -f /build/bcftools-1.11/test/gvcf.fa | grep -v ^##bcftools .. ok test_vcf_convert_tsv2vcf: /build/bcftools-1.11/bcftools convert --no-version -c ID,CHROM,POS,AA -s SAMPLE1 -f /build/bcftools-1.11/test/23andme.fa --tsv2vcf /build/bcftools-1.11/test/convert.23andme .. ok test_vcf_convert_tsv2vcf: /build/bcftools-1.11/bcftools convert -Ou -c ID,CHROM,POS,AA -s SAMPLE1 -f /build/bcftools-1.11/test/23andme.fa --tsv2vcf /build/bcftools-1.11/test/convert.23andme | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/YesswOGw3Q/consensus.vcf.gz -f /build/bcftools-1.11/test/consensus.fa -m /build/bcftools-1.11/test/consensus.tab .. ok test_vcf_consensus_chain: /build/bcftools-1.11/bcftools consensus /tmp/YesswOGw3Q/consensus.vcf.gz -f /build/bcftools-1.11/test/consensus.fa -m /build/bcftools-1.11/test/consensus.tab -c /tmp/YesswOGw3Q/consensus.1.chain.new >/dev/null; cat /tmp/YesswOGw3Q/consensus.1.chain.new .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/YesswOGw3Q/consensus.vcf.gz -f /build/bcftools-1.11/test/consensus.fa -H 1 -m /build/bcftools-1.11/test/consensus.tab .. ok test_vcf_consensus_chain: /build/bcftools-1.11/bcftools consensus /tmp/YesswOGw3Q/consensus.vcf.gz -f /build/bcftools-1.11/test/consensus.fa -H 1 -m /build/bcftools-1.11/test/consensus.tab -c /tmp/YesswOGw3Q/consensus.2.chain.new >/dev/null; cat /tmp/YesswOGw3Q/consensus.2.chain.new .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/YesswOGw3Q/consensus.vcf.gz -f /build/bcftools-1.11/test/consensus.fa -I -m /build/bcftools-1.11/test/consensus.tab .. ok test_vcf_consensus_chain: /build/bcftools-1.11/bcftools consensus /tmp/YesswOGw3Q/consensus.vcf.gz -f /build/bcftools-1.11/test/consensus.fa -I -m /build/bcftools-1.11/test/consensus.tab -c /tmp/YesswOGw3Q/consensus.3.chain.new >/dev/null; cat /tmp/YesswOGw3Q/consensus.3.chain.new .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/YesswOGw3Q/consensus.vcf.gz -f /build/bcftools-1.11/test/consensus.fa -H 1 .. ok test_vcf_consensus_chain: /build/bcftools-1.11/bcftools consensus /tmp/YesswOGw3Q/consensus.vcf.gz -f /build/bcftools-1.11/test/consensus.fa -H 1 -c /tmp/YesswOGw3Q/consensus.4.chain.new >/dev/null; cat /tmp/YesswOGw3Q/consensus.4.chain.new .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/YesswOGw3Q/consensus2.vcf.gz -f /build/bcftools-1.11/test/consensus2.fa -H 1 .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/YesswOGw3Q/consensus2.vcf.gz -f /build/bcftools-1.11/test/consensus2.fa -H 2 .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/YesswOGw3Q/empty.vcf.gz -f /build/bcftools-1.11/test/consensus.fa .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/YesswOGw3Q/consensus3.vcf.gz -f /build/bcftools-1.11/test/consensus2.fa -H 2 -M "?" .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/YesswOGw3Q/consensus3.vcf.gz -f /build/bcftools-1.11/test/consensus2.fa -H 2 -M "?" -p xx_ .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/YesswOGw3Q/consensus4.vcf.gz -f /build/bcftools-1.11/test/consensus2.fa .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/YesswOGw3Q/consensus5.vcf.gz -f /build/bcftools-1.11/test/consensus5.fa --haplotype LA .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/YesswOGw3Q/consensus6.vcf.gz -f /build/bcftools-1.11/test/consensus6.fa .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/YesswOGw3Q/consensus7.vcf.gz -f /build/bcftools-1.11/test/consensus7.fa -H 2 .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/YesswOGw3Q/consensus7.vcf.gz -f /build/bcftools-1.11/test/consensus7.fa -H 2pIu .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/YesswOGw3Q/consensus7.vcf.gz -f /build/bcftools-1.11/test/consensus7.fa -H 1 .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/YesswOGw3Q/consensus7.vcf.gz -f /build/bcftools-1.11/test/consensus7.fa -H 1pIu .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/YesswOGw3Q/consensus8.vcf.gz -f /build/bcftools-1.11/test/consensus.fa .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/YesswOGw3Q/consensus8.vcf.gz -f /build/bcftools-1.11/test/consensus.fa -a . .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/YesswOGw3Q/consensus8.vcf.gz -f /build/bcftools-1.11/test/consensus.fa -a . -i 'type="snp" || type="ref"' .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/YesswOGw3Q/consensus8.vcf.gz -f /build/bcftools-1.11/test/consensus.fa -a . -i 'ALT!=""' .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/YesswOGw3Q/consensus8.vcf.gz -f /build/bcftools-1.11/test/consensus.fa -a . -e 'MinDP>15' .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/YesswOGw3Q/consensus8.vcf.gz -f /build/bcftools-1.11/test/consensus.fa -a . -e 'MinDP<15' .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/YesswOGw3Q/consensus.9.vcf.gz -f /build/bcftools-1.11/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/YesswOGw3Q/consensus.9.vcf.gz -f /build/bcftools-1.11/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/YesswOGw3Q/consensus.10.vcf.gz -f /build/bcftools-1.11/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/YesswOGw3Q/consensus.10.vcf.gz -f /build/bcftools-1.11/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/YesswOGw3Q/consensus.11.vcf.gz -f /build/bcftools-1.11/test/consensus.11.fa -s smpl .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/YesswOGw3Q/consensus.11.vcf.gz -f /build/bcftools-1.11/test/consensus.11.fa -s smpl -a N .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/YesswOGw3Q/consensus.12.vcf.gz -f /build/bcftools-1.11/test/consensus.12.fa .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/YesswOGw3Q/consensus.13.vcf.gz -f /build/bcftools-1.11/test/consensus.13.fa .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -r17:100-150 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.1.bam /build/bcftools-1.11/test/mpileup/mpileup.2.bam /build/bcftools-1.11/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -r17:100-150 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.1.bam /build/bcftools-1.11/test/mpileup/mpileup.2.bam /build/bcftools-1.11/test/mpileup/mpileup.3.bam | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -r17:100-150 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -b /tmp/YesswOGw3Q/mpileup.bam.list --no-version | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -r17:100-150 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob -b /tmp/YesswOGw3Q/mpileup.bam.urllist | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -r17:100-150 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.1.cram /build/bcftools-1.11/test/mpileup/mpileup.2.cram /build/bcftools-1.11/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -r17:100-150 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.1.cram /build/bcftools-1.11/test/mpileup/mpileup.2.cram /build/bcftools-1.11/test/mpileup/mpileup.3.cram | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -r17:100-150 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -b /tmp/YesswOGw3Q/mpileup.cram.list --no-version | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -r17:100-150 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob -b /tmp/YesswOGw3Q/mpileup.cram.urllist | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -a DP,DV -r17:100-600 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.1.bam /build/bcftools-1.11/test/mpileup/mpileup.2.bam /build/bcftools-1.11/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -a DP,DV -r17:100-600 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.1.bam /build/bcftools-1.11/test/mpileup/mpileup.2.bam /build/bcftools-1.11/test/mpileup/mpileup.3.bam | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -a DP,DV -r17:100-600 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.1.cram /build/bcftools-1.11/test/mpileup/mpileup.2.cram /build/bcftools-1.11/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -a DP,DV -r17:100-600 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.1.cram /build/bcftools-1.11/test/mpileup/mpileup.2.cram /build/bcftools-1.11/test/mpileup/mpileup.3.cram | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.1.bam | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.1.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.1.cram | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.1.bam /build/bcftools-1.11/test/mpileup/mpileup.2.bam /build/bcftools-1.11/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.1.bam /build/bcftools-1.11/test/mpileup/mpileup.2.bam /build/bcftools-1.11/test/mpileup/mpileup.3.bam | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.1.cram /build/bcftools-1.11/test/mpileup/mpileup.2.cram /build/bcftools-1.11/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.1.cram /build/bcftools-1.11/test/mpileup/mpileup.2.cram /build/bcftools-1.11/test/mpileup/mpileup.3.cram | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.1.bam /build/bcftools-1.11/test/mpileup/mpileup.2.bam /build/bcftools-1.11/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.1.bam /build/bcftools-1.11/test/mpileup/mpileup.2.bam /build/bcftools-1.11/test/mpileup/mpileup.3.bam | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.1.cram /build/bcftools-1.11/test/mpileup/mpileup.2.cram /build/bcftools-1.11/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.1.cram /build/bcftools-1.11/test/mpileup/mpileup.2.cram /build/bcftools-1.11/test/mpileup/mpileup.3.cram | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.1.bam /build/bcftools-1.11/test/mpileup/mpileup.2.bam /build/bcftools-1.11/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.1.bam /build/bcftools-1.11/test/mpileup/mpileup.2.bam /build/bcftools-1.11/test/mpileup/mpileup.3.bam | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.1.cram /build/bcftools-1.11/test/mpileup/mpileup.2.cram /build/bcftools-1.11/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.1.cram /build/bcftools-1.11/test/mpileup/mpileup.2.cram /build/bcftools-1.11/test/mpileup/mpileup.3.cram | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/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-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.1.bam /build/bcftools-1.11/test/mpileup/mpileup.2.bam /build/bcftools-1.11/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/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-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.1.bam /build/bcftools-1.11/test/mpileup/mpileup.2.bam /build/bcftools-1.11/test/mpileup/mpileup.3.bam | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/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-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.1.cram /build/bcftools-1.11/test/mpileup/mpileup.2.cram /build/bcftools-1.11/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/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-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.1.cram /build/bcftools-1.11/test/mpileup/mpileup.2.cram /build/bcftools-1.11/test/mpileup/mpileup.3.cram | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.1.bam /build/bcftools-1.11/test/mpileup/mpileup.2.bam /build/bcftools-1.11/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.1.bam /build/bcftools-1.11/test/mpileup/mpileup.2.bam /build/bcftools-1.11/test/mpileup/mpileup.3.bam | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.1.cram /build/bcftools-1.11/test/mpileup/mpileup.2.cram /build/bcftools-1.11/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.1.cram /build/bcftools-1.11/test/mpileup/mpileup.2.cram /build/bcftools-1.11/test/mpileup/mpileup.3.cram | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -r17:100-150 -S /build/bcftools-1.11/test/mplp.samples -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.1.bam /build/bcftools-1.11/test/mpileup/mpileup.2.bam /build/bcftools-1.11/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -r17:100-150 -S /build/bcftools-1.11/test/mplp.samples -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.1.bam /build/bcftools-1.11/test/mpileup/mpileup.2.bam /build/bcftools-1.11/test/mpileup/mpileup.3.bam | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -r17:100-150 -S /build/bcftools-1.11/test/mplp.samples -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.1.cram /build/bcftools-1.11/test/mpileup/mpileup.2.cram /build/bcftools-1.11/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -r17:100-150 -S /build/bcftools-1.11/test/mplp.samples -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.1.cram /build/bcftools-1.11/test/mpileup/mpileup.2.cram /build/bcftools-1.11/test/mpileup/mpileup.3.cram | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.1.bam /build/bcftools-1.11/test/mpileup/mpileup.2.bam /build/bcftools-1.11/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.1.bam /build/bcftools-1.11/test/mpileup/mpileup.2.bam /build/bcftools-1.11/test/mpileup/mpileup.3.bam | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.1.cram /build/bcftools-1.11/test/mpileup/mpileup.2.cram /build/bcftools-1.11/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.1.cram /build/bcftools-1.11/test/mpileup/mpileup.2.cram /build/bcftools-1.11/test/mpileup/mpileup.3.cram | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -r17:100-150 -S ^/build/bcftools-1.11/test/mplp.samples -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.1.bam /build/bcftools-1.11/test/mpileup/mpileup.2.bam /build/bcftools-1.11/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -r17:100-150 -S ^/build/bcftools-1.11/test/mplp.samples -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.1.bam /build/bcftools-1.11/test/mpileup/mpileup.2.bam /build/bcftools-1.11/test/mpileup/mpileup.3.bam | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -r17:100-150 -S ^/build/bcftools-1.11/test/mplp.samples -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.1.cram /build/bcftools-1.11/test/mpileup/mpileup.2.cram /build/bcftools-1.11/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -r17:100-150 -S ^/build/bcftools-1.11/test/mplp.samples -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.1.cram /build/bcftools-1.11/test/mpileup/mpileup.2.cram /build/bcftools-1.11/test/mpileup/mpileup.3.cram | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -t17:100-150 -S /build/bcftools-1.11/test/mplp.9.samples -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.1.bam /build/bcftools-1.11/test/mpileup/mpileup.2.bam /build/bcftools-1.11/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -t17:100-150 -S /build/bcftools-1.11/test/mplp.9.samples -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.1.bam /build/bcftools-1.11/test/mpileup/mpileup.2.bam /build/bcftools-1.11/test/mpileup/mpileup.3.bam | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -t17:100-150 -S /build/bcftools-1.11/test/mplp.9.samples -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.1.cram /build/bcftools-1.11/test/mpileup/mpileup.2.cram /build/bcftools-1.11/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -t17:100-150 -S /build/bcftools-1.11/test/mplp.9.samples -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.1.cram /build/bcftools-1.11/test/mpileup/mpileup.2.cram /build/bcftools-1.11/test/mpileup/mpileup.3.cram | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -t17:100-150 -G /build/bcftools-1.11/test/mplp.10.samples -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.1.bam /build/bcftools-1.11/test/mpileup/mpileup.2.bam /build/bcftools-1.11/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -t17:100-150 -G /build/bcftools-1.11/test/mplp.10.samples -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.1.bam /build/bcftools-1.11/test/mpileup/mpileup.2.bam /build/bcftools-1.11/test/mpileup/mpileup.3.bam | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -t17:100-150 -G /build/bcftools-1.11/test/mplp.10.samples -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.1.cram /build/bcftools-1.11/test/mpileup/mpileup.2.cram /build/bcftools-1.11/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -t17:100-150 -G /build/bcftools-1.11/test/mplp.10.samples -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.1.cram /build/bcftools-1.11/test/mpileup/mpileup.2.cram /build/bcftools-1.11/test/mpileup/mpileup.3.cram | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.3.bam | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.3.cram | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -s HG00102 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.3.bam /build/bcftools-1.11/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -s HG00102 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.3.bam /build/bcftools-1.11/test/mpileup/mpileup.4.bam | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -s HG00102 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.3.cram /build/bcftools-1.11/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -s HG00102 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.3.cram /build/bcftools-1.11/test/mpileup/mpileup.4.cram | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -s ^HG99999 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.3.bam /build/bcftools-1.11/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -s ^HG99999 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.3.bam /build/bcftools-1.11/test/mpileup/mpileup.4.bam | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -s ^HG99999 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.3.cram /build/bcftools-1.11/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -s ^HG99999 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.3.cram /build/bcftools-1.11/test/mpileup/mpileup.4.cram | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -G /build/bcftools-1.11/test/mplp.11.rgs -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.3.bam /build/bcftools-1.11/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -G /build/bcftools-1.11/test/mplp.11.rgs -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.3.bam /build/bcftools-1.11/test/mpileup/mpileup.4.bam | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -G /build/bcftools-1.11/test/mplp.11.rgs -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.3.cram /build/bcftools-1.11/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -G /build/bcftools-1.11/test/mplp.11.rgs -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.3.cram /build/bcftools-1.11/test/mpileup/mpileup.4.cram | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -G /build/bcftools-1.11/test/mplp.11.rgs -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.3.bam /build/bcftools-1.11/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -G /build/bcftools-1.11/test/mplp.11.rgs -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.3.bam /build/bcftools-1.11/test/mpileup/mpileup.4.bam | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -G /build/bcftools-1.11/test/mplp.11.rgs -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.3.cram /build/bcftools-1.11/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -G /build/bcftools-1.11/test/mplp.11.rgs -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.3.cram /build/bcftools-1.11/test/mpileup/mpileup.4.cram | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -a AD -f /build/bcftools-1.11/test/mpileup/indel-AD.1.fa /build/bcftools-1.11/test/mpileup/indel-AD.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -a AD -f /build/bcftools-1.11/test/mpileup/indel-AD.1.fa -Ob /build/bcftools-1.11/test/mpileup/indel-AD.1.bam | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -a AD -f /build/bcftools-1.11/test/mpileup/indel-AD.1.fa /build/bcftools-1.11/test/mpileup/indel-AD.1.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -a AD -f /build/bcftools-1.11/test/mpileup/indel-AD.1.fa -Ob /build/bcftools-1.11/test/mpileup/indel-AD.1.cram | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -a INFO/SCR,FMT/SCR -f /build/bcftools-1.11/test/mpileup/mpileup-SCR.fa /build/bcftools-1.11/test/mpileup/mpileup-SCR.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -a INFO/SCR,FMT/SCR -f /build/bcftools-1.11/test/mpileup/mpileup-SCR.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup-SCR.bam | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -a INFO/SCR,FMT/SCR -f /build/bcftools-1.11/test/mpileup/mpileup-SCR.fa /build/bcftools-1.11/test/mpileup/mpileup-SCR.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -a INFO/SCR,FMT/SCR -f /build/bcftools-1.11/test/mpileup/mpileup-SCR.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup-SCR.cram | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_csq: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq.fa -g /build/bcftools-1.11/test/csq.gff3 /build/bcftools-1.11/test/csq.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000624631/ENST00000624631.fa -g /build/bcftools-1.11/test/csq/ENST00000624631/ENST00000624631.gff /build/bcftools-1.11/test/csq/ENST00000624631/ambiguous.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000593942/ENST00000593942.fa -g /build/bcftools-1.11/test/csq/ENST00000593942/ENST00000593942.gff /build/bcftools-1.11/test/csq/ENST00000593942/last-codon-deletion.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000573314/ENST00000573314.fa -g /build/bcftools-1.11/test/csq/ENST00000573314/ENST00000573314.gff /build/bcftools-1.11/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -l -f /build/bcftools-1.11/test/csq/ENST00000573314/ENST00000573314.fa -g /build/bcftools-1.11/test/csq/ENST00000573314/ENST00000573314.gff /build/bcftools-1.11/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000557788/ENST00000557788.fa -g /build/bcftools-1.11/test/csq/ENST00000557788/ENST00000557788.gff /build/bcftools-1.11/test/csq/ENST00000557788/long-overlap-del.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000545279/ENST00000545279.fa -g /build/bcftools-1.11/test/csq/ENST00000545279/ENST00000545279.gff /build/bcftools-1.11/test/csq/ENST00000545279/splice-region-insert.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000543077/ENST00000543077.fa -g /build/bcftools-1.11/test/csq/ENST00000543077/ENST00000543077.gff /build/bcftools-1.11/test/csq/ENST00000543077/not-a-start-lost.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -l -f /build/bcftools-1.11/test/csq/ENST00000543077/ENST00000543077.fa -g /build/bcftools-1.11/test/csq/ENST00000543077/ENST00000543077.gff /build/bcftools-1.11/test/csq/ENST00000543077/not-a-start-lost.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000542803/ENST00000542803.fa -g /build/bcftools-1.11/test/csq/ENST00000542803/ENST00000542803.gff /build/bcftools-1.11/test/csq/ENST00000542803/splice-region.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -l -f /build/bcftools-1.11/test/csq/ENST00000542803/ENST00000542803.fa -g /build/bcftools-1.11/test/csq/ENST00000542803/ENST00000542803.gff /build/bcftools-1.11/test/csq/ENST00000542803/splice-region.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000536784/ENST00000536784.fa -g /build/bcftools-1.11/test/csq/ENST00000536784/ENST00000536784.gff /build/bcftools-1.11/test/csq/ENST00000536784/not-a-start-lost.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -l -f /build/bcftools-1.11/test/csq/ENST00000536784/ENST00000536784.fa -g /build/bcftools-1.11/test/csq/ENST00000536784/ENST00000536784.gff /build/bcftools-1.11/test/csq/ENST00000536784/not-a-start-lost.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000528237/ENST00000528237.fa -g /build/bcftools-1.11/test/csq/ENST00000528237/ENST00000528237.gff /build/bcftools-1.11/test/csq/ENST00000528237/retained-stop-incomplete-cds.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000520868/ENST00000520868.fa -g /build/bcftools-1.11/test/csq/ENST00000520868/ENST00000520868.gff /build/bcftools-1.11/test/csq/ENST00000520868/long-deletion.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000520795/ENST00000520795.fa -g /build/bcftools-1.11/test/csq/ENST00000520795/ENST00000520795.gff /build/bcftools-1.11/test/csq/ENST00000520795/long-inside-del.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -l -f /build/bcftools-1.11/test/csq/ENST00000520795/ENST00000520795.fa -g /build/bcftools-1.11/test/csq/ENST00000520795/ENST00000520795.gff /build/bcftools-1.11/test/csq/ENST00000520795/long-inside-del.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000519442/ENST00000519442.fa -g /build/bcftools-1.11/test/csq/ENST00000519442/ENST00000519442.gff /build/bcftools-1.11/test/csq/ENST00000519442/synon-splice-region-del.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000518414/ENST00000518414.fa -g /build/bcftools-1.11/test/csq/ENST00000518414/ENST00000518414.gff /build/bcftools-1.11/test/csq/ENST00000518414/incorrect-inframe-del.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.fa -g /build/bcftools-1.11/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.gff /build/bcftools-1.11/test/csq/ENST00000518414-ENST00000521270/valgrind.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000479739/ENST00000479739.fa -g /build/bcftools-1.11/test/csq/ENST00000479739/ENST00000479739.gff /build/bcftools-1.11/test/csq/ENST00000479739/short-cds-start-lost.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -l -f /build/bcftools-1.11/test/csq/ENST00000479739/ENST00000479739.fa -g /build/bcftools-1.11/test/csq/ENST00000479739/ENST00000479739.gff /build/bcftools-1.11/test/csq/ENST00000479739/short-cds-start-lost.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000448695/ENST00000448695.fa -g /build/bcftools-1.11/test/csq/ENST00000448695/ENST00000448695.gff /build/bcftools-1.11/test/csq/ENST00000448695/syn-and-splice-reg.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000436063/ENST00000436063.fa -g /build/bcftools-1.11/test/csq/ENST00000436063/ENST00000436063.gff /build/bcftools-1.11/test/csq/ENST00000436063/insert-before-utr.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000423372/ENST00000423372.fa -g /build/bcftools-1.11/test/csq/ENST00000423372/ENST00000423372.gff /build/bcftools-1.11/test/csq/ENST00000423372/snps.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -l -f /build/bcftools-1.11/test/csq/ENST00000423372/ENST00000423372.fa -g /build/bcftools-1.11/test/csq/ENST00000423372/ENST00000423372.gff /build/bcftools-1.11/test/csq/ENST00000423372/snps.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000423372/ENST00000423372.fa -g /build/bcftools-1.11/test/csq/ENST00000423372/ENST00000423372.gff /build/bcftools-1.11/test/csq/ENST00000423372/insert3.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -l -f /build/bcftools-1.11/test/csq/ENST00000423372/ENST00000423372.fa -g /build/bcftools-1.11/test/csq/ENST00000423372/ENST00000423372.gff /build/bcftools-1.11/test/csq/ENST00000423372/insert3.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000420670/ENST00000420670.fa -g /build/bcftools-1.11/test/csq/ENST00000420670/ENST00000420670.gff /build/bcftools-1.11/test/csq/ENST00000420670/start-stop-lost.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000420670/ENST00000420670.fa -g /build/bcftools-1.11/test/csq/ENST00000420670/ENST00000420670.gff /build/bcftools-1.11/test/csq/ENST00000420670/segfault.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000420190/ENST00000420190.fa -g /build/bcftools-1.11/test/csq/ENST00000420190/ENST00000420190.gff /build/bcftools-1.11/test/csq/ENST00000420190/abort-in-csq-push.vcf | /build/bcftools-1.11/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000413103/ENST00000413103.fa -g /build/bcftools-1.11/test/csq/ENST00000413103/ENST00000413103.gff /build/bcftools-1.11/test/csq/ENST00000413103/long-deletion.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000410009/ENST00000410009.fa -g /build/bcftools-1.11/test/csq/ENST00000410009/ENST00000410009.gff /build/bcftools-1.11/test/csq/ENST00000410009/frameshift.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/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-1.11/test/csq/ENST00000410009 && /build/bcftools-1.11/bcftools csq -lb -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/bcftools-1.11/test/csq/ENST00000410009 && /build/bcftools-1.11/bcftools csq -b -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000409523/ENST00000409523.fa -g /build/bcftools-1.11/test/csq/ENST00000409523/ENST00000409523.gff /build/bcftools-1.11/test/csq/ENST00000409523/long-overlapping-del.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000400151/ENST00000400151.fa -g /build/bcftools-1.11/test/csq/ENST00000400151/ENST00000400151.gff /build/bcftools-1.11/test/csq/ENST00000400151/long-del.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000390520/ENST00000390520.fa -g /build/bcftools-1.11/test/csq/ENST00000390520/ENST00000390520.gff /build/bcftools-1.11/test/csq/ENST00000390520/deletion-overlap.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000382647/ENST00000382647.fa -g /build/bcftools-1.11/test/csq/ENST00000382647/ENST00000382647.gff /build/bcftools-1.11/test/csq/ENST00000382647/synon-splice-region-insert.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000381157/ENST00000381157.fa -g /build/bcftools-1.11/test/csq/ENST00000381157/ENST00000381157.gff /build/bcftools-1.11/test/csq/ENST00000381157/haploid-diploid.vcf | /build/bcftools-1.11/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000378322/ENST00000378322.fa -g /build/bcftools-1.11/test/csq/ENST00000378322/ENST00000378322.gff /build/bcftools-1.11/test/csq/ENST00000378322/end-overlap-tscript.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -l -f /build/bcftools-1.11/test/csq/ENST00000378322/ENST00000378322.fa -g /build/bcftools-1.11/test/csq/ENST00000378322/ENST00000378322.gff /build/bcftools-1.11/test/csq/ENST00000378322/end-overlap-tscript.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000375992/ENST00000375992.fa -g /build/bcftools-1.11/test/csq/ENST00000375992/ENST00000375992.gff /build/bcftools-1.11/test/csq/ENST00000375992/incorrect-synon-del-not-start-lost.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000373833/ENST00000373833.fa -g /build/bcftools-1.11/test/csq/ENST00000373833/ENST00000373833.gff /build/bcftools-1.11/test/csq/ENST00000373833/boundary-insertion.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -l -f /build/bcftools-1.11/test/csq/ENST00000373833/ENST00000373833.fa -g /build/bcftools-1.11/test/csq/ENST00000373833/ENST00000373833.gff /build/bcftools-1.11/test/csq/ENST00000373833/boundary-insertion.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000368801/ENST00000368801.fa -g /build/bcftools-1.11/test/csq/ENST00000368801/ENST00000368801.gff /build/bcftools-1.11/test/csq/ENST00000368801/compound-lost.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000368801.2/ENST00000368801.2.fa -g /build/bcftools-1.11/test/csq/ENST00000368801.2/ENST00000368801.2.gff /build/bcftools-1.11/test/csq/ENST00000368801.2/start-lost.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000357367/ENST00000357367.fa -g /build/bcftools-1.11/test/csq/ENST00000357367/ENST00000357367.gff /build/bcftools-1.11/test/csq/ENST00000357367/stop-retained.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.11/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -l -f /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.11/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.11/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -l -f /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.11/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.11/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -l -f /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.11/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.11/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -l -f /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.11/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.11/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -l -f /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.11/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.11/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -l -f /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.11/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.11/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -l -f /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.11/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.11/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -l -f /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.11/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.11/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -l -f /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.11/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.11/test/csq/ENST00000341065/not-a-start-lost.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -l -f /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.11/test/csq/ENST00000341065/not-a-start-lost.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.11/test/csq/ENST00000341065/frame3.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -l -f /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.11/test/csq/ENST00000341065/frame3.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.11/test/csq/ENST00000341065/frame2.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -l -f /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.11/test/csq/ENST00000341065/frame2.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.11/test/csq/ENST00000341065/frame1.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -l -f /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.11/test/csq/ENST00000341065/frame1.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000329454/ENST00000329454.fa -g /build/bcftools-1.11/test/csq/ENST00000329454/ENST00000329454.gff /build/bcftools-1.11/test/csq/ENST00000329454/boundary-deletion.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -l -f /build/bcftools-1.11/test/csq/ENST00000329454/ENST00000329454.fa -g /build/bcftools-1.11/test/csq/ENST00000329454/ENST00000329454.gff /build/bcftools-1.11/test/csq/ENST00000329454/boundary-deletion.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000318249/ENST00000318249.fa -g /build/bcftools-1.11/test/csq/ENST00000318249/ENST00000318249.gff /build/bcftools-1.11/test/csq/ENST00000318249/start-lost.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -l -f /build/bcftools-1.11/test/csq/ENST00000318249/ENST00000318249.fa -g /build/bcftools-1.11/test/csq/ENST00000318249/ENST00000318249.gff /build/bcftools-1.11/test/csq/ENST00000318249/start-lost.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000318249.2/ENST00000318249.2.fa -g /build/bcftools-1.11/test/csq/ENST00000318249.2/ENST00000318249.2.gff /build/bcftools-1.11/test/csq/ENST00000318249.2/synonymous-start-lost.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000303039/ENST00000303039.fa -g /build/bcftools-1.11/test/csq/ENST00000303039/ENST00000303039.gff /build/bcftools-1.11/test/csq/ENST00000303039/not-a-stop.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -l -f /build/bcftools-1.11/test/csq/ENST00000303039/ENST00000303039.fa -g /build/bcftools-1.11/test/csq/ENST00000303039/ENST00000303039.gff /build/bcftools-1.11/test/csq/ENST00000303039/not-a-stop.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000301246/ENST00000301246.fa -g /build/bcftools-1.11/test/csq/ENST00000301246/ENST00000301246.gff /build/bcftools-1.11/test/csq/ENST00000301246/15bp-insert.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000295641/ENST00000295641.fa -g /build/bcftools-1.11/test/csq/ENST00000295641/ENST00000295641.gff /build/bcftools-1.11/test/csq/ENST00000295641/not-a-start-lost.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -l -f /build/bcftools-1.11/test/csq/ENST00000295641/ENST00000295641.fa -g /build/bcftools-1.11/test/csq/ENST00000295641/ENST00000295641.gff /build/bcftools-1.11/test/csq/ENST00000295641/not-a-start-lost.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000294661/ENST00000294661.fa -g /build/bcftools-1.11/test/csq/ENST00000294661/ENST00000294661.gff /build/bcftools-1.11/test/csq/ENST00000294661/non-coding-boundary.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -l -f /build/bcftools-1.11/test/csq/ENST00000294661/ENST00000294661.fa -g /build/bcftools-1.11/test/csq/ENST00000294661/ENST00000294661.gff /build/bcftools-1.11/test/csq/ENST00000294661/non-coding-boundary.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000271583/ENST00000271583.fa -g /build/bcftools-1.11/test/csq/ENST00000271583/ENST00000271583.gff /build/bcftools-1.11/test/csq/ENST00000271583/splice-acceptor.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000263103-INS/ENST00000263103-INS.fa -g /build/bcftools-1.11/test/csq/ENST00000263103-INS/ENST00000263103-INS.gff /build/bcftools-1.11/test/csq/ENST00000263103-INS/insertions.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000256452/ENST00000256452.fa -g /build/bcftools-1.11/test/csq/ENST00000256452/ENST00000256452.gff /build/bcftools-1.11/test/csq/ENST00000256452/intron.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000230048/ENST00000230048.fa -g /build/bcftools-1.11/test/csq/ENST00000230048/ENST00000230048.gff /build/bcftools-1.11/test/csq/ENST00000230048/start-del.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000227471/ENST00000227471.fa -g /build/bcftools-1.11/test/csq/ENST00000227471/ENST00000227471.gff /build/bcftools-1.11/test/csq/ENST00000227471/insert-splice-vs-frameshift.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000218032/ENST00000218032.fa -g /build/bcftools-1.11/test/csq/ENST00000218032/ENST00000218032.gff /build/bcftools-1.11/test/csq/ENST00000218032/start-lost.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -l -f /build/bcftools-1.11/test/csq/ENST00000218032/ENST00000218032.fa -g /build/bcftools-1.11/test/csq/ENST00000218032/ENST00000218032.gff /build/bcftools-1.11/test/csq/ENST00000218032/start-lost.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000218032/ENST00000218032.fa -g /build/bcftools-1.11/test/csq/ENST00000218032/ENST00000218032.gff /build/bcftools-1.11/test/csq/ENST00000218032/start-lost-del.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/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-1.11/test/csq/ENSMUST00000133836 && /build/bcftools-1.11/bcftools csq -f ENSMUST00000133836.fa -g ENSMUST00000133836.gff filter-problem.vcf -i 'FILTER="PASS"' --phase m | ../sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/bcftools-1.11/test/csq/ENSMUST00000121418 && /build/bcftools-1.11/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25500' --phase m | ../sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/bcftools-1.11/test/csq/ENSMUST00000121418 && /build/bcftools-1.11/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25496' --phase m | ../sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/bcftools-1.11/test/csq/ENSMUST00000121418 && /build/bcftools-1.11/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25105' --phase m | ../sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENSG00000173376/ENSG00000173376.fa -g /build/bcftools-1.11/test/csq/ENSG00000173376/ENSG00000173376.gff /build/bcftools-1.11/test/csq/ENSG00000173376/synon.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/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-1.11/test/csq/EMN908947 && /build/bcftools-1.11/bcftools csq -f EMN908947.fa -g simple.gff simple.vcf | ../sort-csq | /build/bcftools-1.11/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-1.11/test/csq/EMN908947 && /build/bcftools-1.11/bcftools csq -f EMN908947.fa -g ribosomal-slippage.gff ribosomal-slippage.vcf --force | ../sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/EDUMMY0003/EDUMMY0003.fa -g /build/bcftools-1.11/test/csq/EDUMMY0003/EDUMMY0003.gff /build/bcftools-1.11/test/csq/EDUMMY0003/long-del.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/EDUMMY0002/EDUMMY0002.fa -g /build/bcftools-1.11/test/csq/EDUMMY0002/EDUMMY0002.gff /build/bcftools-1.11/test/csq/EDUMMY0002/boundaries.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/EDUMMY0001/EDUMMY0001.fa -g /build/bcftools-1.11/test/csq/EDUMMY0001/EDUMMY0001.gff /build/bcftools-1.11/test/csq/EDUMMY0001/starts-with-1.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools 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-1.11/bcftools csq -l -f /build/bcftools-1.11/test/csq/EDUMMY0001/EDUMMY0001.fa -g /build/bcftools-1.11/test/csq/EDUMMY0001/EDUMMY0001.gff /build/bcftools-1.11/test/csq/EDUMMY0001/starts-with-1.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/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-1.11/bcftools roh /build/bcftools-1.11/test/roh.1.vcf.gz -Or -G30 --AF-dflt 0.4| grep -v ^# .. ok test_roh: /build/bcftools-1.11/bcftools roh /build/bcftools-1.11/test/roh.1.vcf.gz -Or -G30 --AF-file /build/bcftools-1.11/test/roh.1.tab.gz| grep -v ^# .. ok test_roh: /build/bcftools-1.11/bcftools roh /build/bcftools-1.11/test/roh.1.vcf.gz -Or -G30 --AF-file /build/bcftools-1.11/test/roh.1.tab.gz --ignore-homref| grep -v ^# .. ok test_roh: /build/bcftools-1.11/bcftools roh /build/bcftools-1.11/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245| grep -v ^# .. ok test_roh: /build/bcftools-1.11/bcftools roh /build/bcftools-1.11/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --ignore-homref| grep -v ^# .. ok test_roh: /build/bcftools-1.11/bcftools roh /build/bcftools-1.11/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-1.11/bcftools roh /build/bcftools-1.11/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --include-noalt| grep -v ^# .. ok test_gtcheck: /build/bcftools-1.11/bcftools gtcheck -e 0 /tmp/YesswOGw3Q/gtcheck.1.vcf.gz -g /tmp/YesswOGw3Q/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.11/bcftools gtcheck -e 0 -u GT,GT /tmp/YesswOGw3Q/gtcheck.1.vcf.gz -g /tmp/YesswOGw3Q/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.11/bcftools gtcheck -e 0 -u GT,PL /tmp/YesswOGw3Q/gtcheck.1.vcf.gz -g /tmp/YesswOGw3Q/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.11/bcftools gtcheck -e 0 -u PL,GT /tmp/YesswOGw3Q/gtcheck.1.vcf.gz -g /tmp/YesswOGw3Q/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.11/bcftools gtcheck -e 0 -u PL,PL /tmp/YesswOGw3Q/gtcheck.1.vcf.gz -g /tmp/YesswOGw3Q/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.11/bcftools gtcheck -e 0 -p s1,s1 /tmp/YesswOGw3Q/gtcheck.1.vcf.gz -g /tmp/YesswOGw3Q/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.11/bcftools gtcheck -e 0 /tmp/YesswOGw3Q/gtcheck.2.vcf.gz -g /tmp/YesswOGw3Q/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.11/bcftools gtcheck -e 0 /tmp/YesswOGw3Q/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.11/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/YesswOGw3Q/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.11/bcftools gtcheck -e 0 -P /build/bcftools-1.11/test/gtcheck.3.pairs /tmp/YesswOGw3Q/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.11/bcftools gtcheck -e 0 -u PL /tmp/YesswOGw3Q/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.11/bcftools gtcheck -e 0 --n-matches 4 /tmp/YesswOGw3Q/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO | sort .. ok test_gtcheck: /build/bcftools-1.11/bcftools gtcheck -e 0 -s qry:E,D,C /tmp/YesswOGw3Q/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.11/bcftools gtcheck -e 0 -s qry:E,D,C -u PL /tmp/YesswOGw3Q/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.11/bcftools gtcheck -e 0 -s qry:B -s gt:D /tmp/YesswOGw3Q/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.11/bcftools gtcheck -e 0 -s qry:B -s gt:D -u PL /tmp/YesswOGw3Q/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.11/bcftools gtcheck -e 0 -s qry:B -s gt:D,C /tmp/YesswOGw3Q/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.11/bcftools gtcheck -e 0 -p B,C,B,D /tmp/YesswOGw3Q/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.11/bcftools gtcheck -e 0 -u GT,GT -H /tmp/YesswOGw3Q/gtcheck.1.vcf.gz -g /tmp/YesswOGw3Q/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.11/bcftools gtcheck -e 0 -u GT,PL -H /tmp/YesswOGw3Q/gtcheck.1.vcf.gz -g /tmp/YesswOGw3Q/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.11/bcftools gtcheck -e 0 -u PL,GT -H /tmp/YesswOGw3Q/gtcheck.1.vcf.gz -g /tmp/YesswOGw3Q/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.11/bcftools gtcheck -e 0 -u PL,PL -H /tmp/YesswOGw3Q/gtcheck.1.vcf.gz -g /tmp/YesswOGw3Q/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.11/bcftools gtcheck -e 0 -P /build/bcftools-1.11/test/gtcheck.4.pairs --distinctive-sites 3 /tmp/YesswOGw3Q/gtcheck.4.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.11/bcftools gtcheck -e 0 -P /build/bcftools-1.11/test/gtcheck.4.pairs --distinctive-sites 3,1 /tmp/YesswOGw3Q/gtcheck.4.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.11/bcftools gtcheck -u GT -e 30 /tmp/YesswOGw3Q/gtcheck.1.vcf.gz -g /tmp/YesswOGw3Q/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.11/bcftools gtcheck -u GT -e 30 -p s1,s1 /tmp/YesswOGw3Q/gtcheck.1.vcf.gz -g /tmp/YesswOGw3Q/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.11/bcftools gtcheck -u GT -e 300 /tmp/YesswOGw3Q/gtcheck.1.vcf.gz -g /tmp/YesswOGw3Q/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.11/bcftools gtcheck -u PL -e 30 /tmp/YesswOGw3Q/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok Number of tests: total .. 1210 passed .. 1210 failed .. 0 make[2]: Leaving directory '/build/bcftools-1.11' make[1]: Leaving directory '/build/bcftools-1.11' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install make -j8 install DESTDIR=/build/bcftools-1.11/debian/bcftools AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/bcftools-1.11' mkdir -p -m 755 /build/bcftools-1.11/debian/bcftools/usr/bin /build/bcftools-1.11/debian/bcftools/usr/share/man/man1 /build/bcftools-1.11/debian/bcftools/usr/lib/aarch64-linux-gnu/bcftools install -p bcftools /build/bcftools-1.11/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-1.11/debian/bcftools/usr/bin install -p -m 644 doc/bcftools.1 /build/bcftools-1.11/debian/bcftools/usr/share/man/man1 install -p plugins/*.so /build/bcftools-1.11/debian/bcftools/usr/lib/aarch64-linux-gnu/bcftools make[1]: Leaving directory '/build/bcftools-1.11' debian/rules override_dh_install make[1]: Entering directory '/build/bcftools-1.11' 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-1.11' dh_installdocs dh_installchangelogs debian/rules override_dh_installman make[1]: Entering directory '/build/bcftools-1.11' dh_installman --language=C make[1]: Leaving directory '/build/bcftools-1.11' 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_1.11-1_arm64.deb'. dpkg-deb: building package 'bcftools-dbgsym' in '../bcftools-dbgsym_1.11-1_arm64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../bcftools_1.11-1_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/5168/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/5168/tmp/hooks/B01_cleanup finished 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/5168 and its subdirectories I: Current time: Wed Jul 28 13:57:23 +14 2021 I: pbuilder-time-stamp: 1627430243