Tue May 23 10:30:07 UTC 2023 I: starting to build bcftools/bookworm/armhf on jenkins on '2023-05-23 10:29' Tue May 23 10:30:07 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_24/655/console.log Tue May 23 10:30:07 UTC 2023 I: Downloading source for bookworm/bcftools=1.16-1 --2023-05-23 10:30:08-- http://cdn-fastly.deb.debian.org/debian/pool/main/b/bcftools/bcftools_1.16-1.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2150 (2.1K) [text/prs.lines.tag] Saving to: ‘bcftools_1.16-1.dsc’ 0K .. 100% 138M=0s 2023-05-23 10:30:08 (138 MB/s) - ‘bcftools_1.16-1.dsc’ saved [2150/2150] Tue May 23 10:30:08 UTC 2023 I: bcftools_1.16-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: bcftools Binary: bcftools Architecture: any Version: 1.16-1 Maintainer: Debian Med Packaging Team Uploaders: Michael R. Crusoe , Étienne Mollier Homepage: https://samtools.github.io/bcftools/ Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/bcftools Vcs-Git: https://salsa.debian.org/med-team/bcftools.git Testsuite: autopkgtest Testsuite-Triggers: perl, tabix Build-Depends: debhelper-compat (= 13), zlib1g-dev, libbz2-dev, liblzma-dev, libhts-dev (>= 1.14), libgsl-dev, tabix , libio-pty-perl Package-List: bcftools deb science optional arch=any Checksums-Sha1: bd037586bb5beac3c0ee4c94c4d97c8a14f3f161 3432435 bcftools_1.16.orig.tar.gz 21d58c2e0aa06ea1759ceea0dc5d464346f42588 7320 bcftools_1.16-1.debian.tar.xz Checksums-Sha256: c44c85a04e058e1f1eceeb712106031100bbd700b8ff3f623f7ff872469a4ba3 3432435 bcftools_1.16.orig.tar.gz 227c2eb682a38fd8315b707d1867d02f8f4e01a11f15f93f86932eb42dc116a5 7320 bcftools_1.16-1.debian.tar.xz Files: 16f53096864b0376af3779ece0d65ce2 3432435 bcftools_1.16.orig.tar.gz a98e9de814dcc9c7dab2ae1543a86293 7320 bcftools_1.16-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmM2vUMRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtE5Yw/9FpYZIgOAkscQUXxckcbU3KRO8my/gyYu cLx3mdSOrhgmisPqFl0fgslCcpcqwCIBtJfBLFCTCPwEs0dwZKia+ZTTYNij5JHu YG+zPMV+tARGHjKvOGuCtD5Q0DWEOc5ghcijxo0po6J7MF2Iii3SHV/pHlZQEaIH AldUKI1UpaJ6tuPd1zsTlSq1k3dEganBefW14h21Z+901ug9X59DGZ9T95hzQwIv LZY/DmGHPp/6qY9Qks40Z5mp3JRAFFwcpcbI2v3V5nQ0sXGeBId+LNJj4ZUtwUB6 nWzYNw2BwmcvqNpDibE6Ma7cMye6DKhdPqoSXL/cdf/K/dImuTh0jY9IhjUO/BYj //EjR58+Fv5mA3TXHpAZAdE3Ea6yoX4FuYC0os1Jbb4fZBJlD2S7qLpeeRPl5m6X fmiQJvS1ewE3adMgYyHh8M+uDeXYj1YNwb1qctEeVU1WRWD7VaMBzYFI/95FjqBu nT6sPE3ojOZn9Zhvx0o+HsAkYzRLl2V+jR+8QcnTxi0absyZ7HaSMk1I7k4PesEh nNY04l00KFRJFaI7t1f/VAvXGQhZIOhUJlPWUKr6gsWusureEwwuSghI+BOXaQzO gi4jgStC8BFtZWApVNTM+HISZ6Yup4xl1kr8G3BvbFcjqVYJinGLCAGP+NSa6mJa oNFuUVLKEvY= =WwKJ -----END PGP SIGNATURE----- Tue May 23 10:30:08 UTC 2023 I: Checking whether the package is not for us Tue May 23 10:30:08 UTC 2023 I: Starting 1st build on remote node ff4a-armhf-rb.debian.net. Tue May 23 10:30:08 UTC 2023 I: Preparing to do remote build '1' on ff4a-armhf-rb.debian.net. Tue May 23 10:46:33 UTC 2023 I: Deleting $TMPDIR on ff4a-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon May 22 22:30:24 -12 2023 I: pbuilder-time-stamp: 1684837824 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [bcftools_1.16-1.dsc] I: copying [./bcftools_1.16.orig.tar.gz] I: copying [./bcftools_1.16-1.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Sep 29 21:56:19 2022 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./bcftools_1.16-1.dsc: no acceptable signature found dpkg-source: info: extracting bcftools in bcftools-1.16 dpkg-source: info: unpacking bcftools_1.16.orig.tar.gz dpkg-source: info: unpacking bcftools_1.16-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying tests-pluginpath.patch dpkg-source: info: applying skip_new_test_failing_on_32bit.patch dpkg-source: info: applying 2to3.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/7757/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='bb2a2d8a19f747dcabc0725aa051eec1' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='7757' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.p7KDElAa/pbuilderrc_qdGP --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.p7KDElAa/b1 --logfile b1/build.log bcftools_1.16-1.dsc' SUDO_GID='113' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:3142/' I: uname -a Linux ff4a 5.10.0-23-armmp-lpae #1 SMP Debian 5.10.179-1 (2023-05-12) armv7l GNU/Linux I: ls -l /bin total 5072 -rwxr-xr-x 1 root root 838488 Apr 23 09:24 bash -rwxr-xr-x 3 root root 67144 Sep 18 2022 bunzip2 -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzip2 -rwxr-xr-x 1 root root 67112 Sep 18 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore -rwxr-xr-x 1 root root 67632 Sep 20 2022 cat -rwxr-xr-x 1 root root 67676 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 67644 Sep 20 2022 chmod -rwxr-xr-x 1 root root 67684 Sep 20 2022 chown -rwxr-xr-x 1 root root 133532 Sep 20 2022 cp -rwxr-xr-x 1 root root 132868 Jan 5 01:20 dash -rwxr-xr-x 1 root root 133220 Sep 20 2022 date -rwxr-xr-x 1 root root 67732 Sep 20 2022 dd -rwxr-xr-x 1 root root 68104 Sep 20 2022 df -rwxr-xr-x 1 root root 133632 Sep 20 2022 dir -rwxr-xr-x 1 root root 59128 Mar 22 21:02 dmesg lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname -rwxr-xr-x 1 root root 67560 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep -rwxr-xr-x 1 root root 67548 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep -rwxr-xr-x 1 root root 55748 Mar 22 21:02 findmnt -rwsr-xr-x 1 root root 26208 Mar 22 20:15 fusermount -rwxr-xr-x 1 root root 128608 Jan 24 02:43 grep -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe -rwxr-xr-x 1 root root 64220 Apr 9 2022 gzip -rwxr-xr-x 1 root root 67032 Dec 19 01:33 hostname -rwxr-xr-x 1 root root 67720 Sep 20 2022 ln -rwxr-xr-x 1 root root 35132 Mar 22 21:51 login -rwxr-xr-x 1 root root 133632 Sep 20 2022 ls -rwxr-xr-x 1 root root 136808 Mar 22 21:02 lsblk -rwxr-xr-x 1 root root 67800 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 67764 Sep 20 2022 mknod -rwxr-xr-x 1 root root 67596 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 38504 Mar 22 21:02 more -rwsr-xr-x 1 root root 38496 Mar 22 21:02 mount -rwxr-xr-x 1 root root 9824 Mar 22 21:02 mountpoint -rwxr-xr-x 1 root root 133532 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 67608 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Apr 23 09:24 rbash -> bash -rwxr-xr-x 1 root root 67600 Sep 20 2022 readlink -rwxr-xr-x 1 root root 67672 Sep 20 2022 rm -rwxr-xr-x 1 root root 67600 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 67400 Nov 2 2022 run-parts -rwxr-xr-x 1 root root 133372 Jan 5 07:55 sed lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash -rwxr-xr-x 1 root root 67584 Sep 20 2022 sleep -rwxr-xr-x 1 root root 67644 Sep 20 2022 stty -rwsr-xr-x 1 root root 50800 Mar 22 21:02 su -rwxr-xr-x 1 root root 67584 Sep 20 2022 sync -rwxr-xr-x 1 root root 336764 Apr 6 02:25 tar -rwxr-xr-x 1 root root 67144 Nov 2 2022 tempfile -rwxr-xr-x 1 root root 133224 Sep 20 2022 touch -rwxr-xr-x 1 root root 67548 Sep 20 2022 true -rwxr-xr-x 1 root root 9768 Mar 22 20:15 ulockmgr_server -rwsr-xr-x 1 root root 22108 Mar 22 21:02 umount -rwxr-xr-x 1 root root 67572 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 133632 Sep 20 2022 vdir -rwxr-xr-x 1 root root 42608 Mar 22 21:02 wdctl lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew I: user script /srv/workspace/pbuilder/7757/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: armhf Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), zlib1g-dev, libbz2-dev, liblzma-dev, libhts-dev (>= 1.14), libgsl-dev, tabix, libio-pty-perl dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19329 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. pbuilder-satisfydepends-dummy depends on liblzma-dev; however: Package liblzma-dev is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev (>= 1.14); however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on libgsl-dev; however: Package libgsl-dev is not installed. pbuilder-satisfydepends-dummy depends on tabix; however: Package tabix is not installed. pbuilder-satisfydepends-dummy depends on libio-pty-perl; however: Package libio-pty-perl is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbrotli1{a} libbz2-dev{a} libcurl3-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1{a} libfile-stripnondeterminism-perl{a} libgsl-dev{a} libgsl27{a} libgslcblas0{a} libhts-dev{a} libhts3{a} libhtscodecs2{a} libicu72{a} libio-pty-perl{a} libldap-2.5-0{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libnghttp2-14{a} libpipeline1{a} libpsl5{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} tabix{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc ca-certificates curl libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix wget 0 packages upgraded, 53 newly installed, 0 to remove and 0 not upgraded. Need to get 25.2 MB of archives. After unpacking 88.2 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main armhf sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 2 http://deb.debian.org/debian bookworm/main armhf libmagic-mgc armhf 1:5.44-3 [305 kB] Get: 3 http://deb.debian.org/debian bookworm/main armhf libmagic1 armhf 1:5.44-3 [96.5 kB] Get: 4 http://deb.debian.org/debian bookworm/main armhf file armhf 1:5.44-3 [41.6 kB] Get: 5 http://deb.debian.org/debian bookworm/main armhf gettext-base armhf 0.21-12 [157 kB] Get: 6 http://deb.debian.org/debian bookworm/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB] Get: 7 http://deb.debian.org/debian bookworm/main armhf groff-base armhf 1.22.4-10 [825 kB] Get: 8 http://deb.debian.org/debian bookworm/main armhf bsdextrautils armhf 2.38.1-5+b1 [78.6 kB] Get: 9 http://deb.debian.org/debian bookworm/main armhf libpipeline1 armhf 1.5.7-1 [33.6 kB] Get: 10 http://deb.debian.org/debian bookworm/main armhf man-db armhf 2.11.2-2 [1351 kB] Get: 11 http://deb.debian.org/debian bookworm/main armhf m4 armhf 1.4.19-3 [265 kB] Get: 12 http://deb.debian.org/debian bookworm/main armhf autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian bookworm/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian bookworm/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian bookworm/main armhf autopoint all 0.21-12 [495 kB] Get: 16 http://deb.debian.org/debian bookworm/main armhf libdebhelper-perl all 13.11.4 [81.2 kB] Get: 17 http://deb.debian.org/debian bookworm/main armhf libtool all 2.4.7-5 [517 kB] Get: 18 http://deb.debian.org/debian bookworm/main armhf dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian bookworm/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian bookworm/main armhf libsub-override-perl all 0.09-4 [9304 B] Get: 21 http://deb.debian.org/debian bookworm/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 22 http://deb.debian.org/debian bookworm/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 23 http://deb.debian.org/debian bookworm/main armhf libelf1 armhf 0.188-2.1 [170 kB] Get: 24 http://deb.debian.org/debian bookworm/main armhf dwz armhf 0.15-1 [101 kB] Get: 25 http://deb.debian.org/debian bookworm/main armhf libicu72 armhf 72.1-3 [9048 kB] Get: 26 http://deb.debian.org/debian bookworm/main armhf libxml2 armhf 2.9.14+dfsg-1.2 [591 kB] Get: 27 http://deb.debian.org/debian bookworm/main armhf gettext armhf 0.21-12 [1229 kB] Get: 28 http://deb.debian.org/debian bookworm/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian bookworm/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian bookworm/main armhf debhelper all 13.11.4 [942 kB] Get: 31 http://deb.debian.org/debian bookworm/main armhf libbrotli1 armhf 1.0.9-2+b6 [271 kB] Get: 32 http://deb.debian.org/debian bookworm/main armhf libbz2-dev armhf 1.0.8-5+b1 [28.1 kB] Get: 33 http://deb.debian.org/debian bookworm/main armhf libsasl2-modules-db armhf 2.1.28+dfsg-10 [19.0 kB] Get: 34 http://deb.debian.org/debian bookworm/main armhf libsasl2-2 armhf 2.1.28+dfsg-10 [52.3 kB] Get: 35 http://deb.debian.org/debian bookworm/main armhf libldap-2.5-0 armhf 2.5.13+dfsg-5 [158 kB] Get: 36 http://deb.debian.org/debian bookworm/main armhf libnghttp2-14 armhf 1.52.0-1 [60.8 kB] Get: 37 http://deb.debian.org/debian bookworm/main armhf libpsl5 armhf 0.21.2-1 [57.5 kB] Get: 38 http://deb.debian.org/debian bookworm/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [55.2 kB] Get: 39 http://deb.debian.org/debian bookworm/main armhf libssh2-1 armhf 1.10.0-3+b1 [163 kB] Get: 40 http://deb.debian.org/debian bookworm/main armhf libcurl3-gnutls armhf 7.88.1-9 [343 kB] Get: 41 http://deb.debian.org/debian bookworm/main armhf libcurl4-gnutls-dev armhf 7.88.1-9 [448 kB] Get: 42 http://deb.debian.org/debian bookworm/main armhf libdeflate0 armhf 1.14-1 [52.2 kB] Get: 43 http://deb.debian.org/debian bookworm/main armhf libdeflate-dev armhf 1.14-1 [48.7 kB] Get: 44 http://deb.debian.org/debian bookworm/main armhf libgslcblas0 armhf 2.7.1+dfsg-3+b1 [87.7 kB] Get: 45 http://deb.debian.org/debian bookworm/main armhf libgsl27 armhf 2.7.1+dfsg-3+b1 [773 kB] Get: 46 http://deb.debian.org/debian bookworm/main armhf libgsl-dev armhf 2.7.1+dfsg-3+b1 [975 kB] Get: 47 http://deb.debian.org/debian bookworm/main armhf libhtscodecs2 armhf 1.3.0-4 [60.4 kB] Get: 48 http://deb.debian.org/debian bookworm/main armhf libhts3 armhf 1.16+ds-3 [375 kB] Get: 49 http://deb.debian.org/debian bookworm/main armhf liblzma-dev armhf 5.4.1-0.2 [248 kB] Get: 50 http://deb.debian.org/debian bookworm/main armhf zlib1g-dev armhf 1:1.2.13.dfsg-1 [902 kB] Get: 51 http://deb.debian.org/debian bookworm/main armhf libhts-dev armhf 1.16+ds-3 [1517 kB] Get: 52 http://deb.debian.org/debian bookworm/main armhf libio-pty-perl armhf 1:1.17-1 [34.5 kB] Get: 53 http://deb.debian.org/debian bookworm/main armhf tabix armhf 1.16+ds-3 [388 kB] Fetched 25.2 MB in 4s (6409 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19329 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.44-3_armhf.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:armhf. Preparing to unpack .../02-libmagic1_1%3a5.44-3_armhf.deb ... 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Setting up m4 (1.4.19-3) ... Setting up file (1:5.44-3) ... Setting up libsasl2-modules-db:armhf (2.1.28+dfsg-10) ... Setting up autotools-dev (20220109.1) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up autopoint (0.21-12) ... Setting up libsasl2-2:armhf (2.1.28+dfsg-10) ... Setting up autoconf (2.71-3) ... Setting up liblzma-dev:armhf (5.4.1-0.2) ... Setting up zlib1g-dev:armhf (1:1.2.13.dfsg-1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libuchardet0:armhf (0.0.7-1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libssh2-1:armhf (1.10.0-3+b1) ... Setting up libdeflate-dev:armhf (1.14-1) ... Setting up tabix (1.16+ds-3) ... Setting up libelf1:armhf (0.188-2.1) ... Setting up libxml2:armhf (2.9.14+dfsg-1.2) ... Setting up libbz2-dev:armhf (1.0.8-5+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up gettext (0.21-12) ... Setting up libgsl-dev (2.7.1+dfsg-3+b1) ... Setting up libtool (2.4.7-5) ... Setting up libldap-2.5-0:armhf (2.5.13+dfsg-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-10) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3-gnutls:armhf (7.88.1-9) ... Setting up libcurl4-gnutls-dev:armhf (7.88.1-9) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libhts3:armhf (1.16+ds-3) ... Setting up libhts-dev:armhf (1.16+ds-3) ... Setting up debhelper (13.11.4) ... Processing triggers for libc-bin (2.36-9) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/bcftools-1.16/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../bcftools_1.16-1_source.changes dpkg-buildpackage: info: source package bcftools dpkg-buildpackage: info: source version 1.16-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean rm -f config.mk && touch config.mk dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/bcftools-1.16' dh_auto_clean make -j3 distclean make[2]: Entering directory '/build/bcftools-1.16' rm -f test/*.o test/*.fa.fai test/*~ test/test-rbuf test/test-regidx rm -f plugins/*.so plugins/*.P rm -f test/*.unsorted.hex test/*.unsorted.tsv rm -rf plugins/*.dSYM rm -f gmon.out *.o *.a *~ bcftools version.h rm -rf *.dSYM test/*.dSYM rm -f config.cache config.h config.log config.mk config.status rm -rf autom4te.cache rm -f TAGS make[2]: Leaving directory '/build/bcftools-1.16' rm -f test/mpileup/indel-AD.1.out.new test/view-t.1.out.new test/view-t.2.out.new make[1]: Leaving directory '/build/bcftools-1.16' dh_clean debian/rules binary dh binary dh_update_autotools_config debian/rules override_dh_autoreconf make[1]: Entering directory '/build/bcftools-1.16' rm -f config.mk && touch config.mk export MAKEFLAGS="-s"; dh_autoreconf configure.ac:94: warning: _AC_CONFIG_SUBDIRS: you should use literals ./lib/autoconf/status.m4:1096: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:94: the top level make[1]: Leaving directory '/build/bcftools-1.16' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/bcftools-1.16' dh_auto_configure -- \ --with-htslib=system \ --enable-gsl \ --with-cblas=gslcblas \ --with-bcf-plugin-dir=/usr/lib/arm-linux-gnueabihf/bcftools ./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system --enable-gsl --with-cblas=gslcblas --with-bcf-plugin-dir=/usr/lib/arm-linux-gnueabihf/bcftools checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking for grep that handles long lines and -e... /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... 64 checking for htslib/sam.h... yes checking for hts_version in -lhts... yes checking shared library type... plain .so checking for library containing dlopen... none required checking if the compiler accepts -rdynamic... yes checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing regcomp... none required configure: creating ./config.status config.status: creating config.mk config.status: creating config.h make[1]: Leaving directory '/build/bcftools-1.16' dh_auto_build make -j3 make[1]: Entering directory '/build/bcftools-1.16' echo '#define BCFTOOLS_VERSION "1.16"' > version.h gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfindex.o vcfindex.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tabix.o tabix.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfstats.o vcfstats.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfisec.o vcfisec.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfmerge.o vcfmerge.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfquery.o vcfquery.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcffilter.o vcffilter.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o filter.o filter.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfsom.o vcfsom.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfnorm.o vcfnorm.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfgtcheck.o vcfgtcheck.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfview.o vcfview.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfannotate.o vcfannotate.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfroh.o vcfroh.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfconcat.o vcfconcat.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcall.o vcfcall.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mcall.o mcall.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcmp.o vcmp.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gvcf.o gvcf.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o reheader.o reheader.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o convert.o convert.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfconvert.o vcfconvert.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tsv2vcf.o tsv2vcf.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcnv.o vcfcnv.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfhead.o vcfhead.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o HMM.o HMM.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o consensus.o consensus.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ploidy.o ploidy.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bin.o bin.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hclust.o hclust.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o version.o version.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o regidx.o regidx.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o smpl_ilist.o smpl_ilist.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o csq.o csq.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfbuf.o vcfbuf.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mpileup.o mpileup.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sample.o bam_sample.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfsort.o vcfsort.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cols.o cols.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o extsort.o extsort.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dist.o dist.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o abuf.o abuf.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ccall.o ccall.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o em.o em.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o prob1.o prob1.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kmin.o kmin.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o str_finder.o str_finder.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DPLUGINPATH='"/usr/lib/arm-linux-gnueabihf/bcftools"' -c -o vcfplugin.o vcfplugin.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-rbuf.o test/test-rbuf.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-regidx.o test/test-regidx.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/GTisec.so version.c plugins/GTisec.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/GTsubset.so version.c plugins/GTsubset.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/ad-bias.so convert.c version.c plugins/ad-bias.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/add-variantkey.so version.c plugins/add-variantkey.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/af-dist.so bin.c version.c plugins/af-dist.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/allele-length.so version.c plugins/allele-length.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/check-ploidy.so version.c plugins/check-ploidy.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/check-sparsity.so version.c plugins/check-sparsity.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/color-chrs.so HMM.c version.c plugins/color-chrs.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/contrast.so version.c plugins/contrast.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/counts.so version.c plugins/counts.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/dosage.so version.c plugins/dosage.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fill-AN-AC.so version.c plugins/fill-AN-AC.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fill-from-fasta.so filter.c version.c plugins/fill-from-fasta.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fill-tags.so version.c plugins/fill-tags.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fixploidy.so ploidy.c regidx.c version.c plugins/fixploidy.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fixref.so version.c plugins/fixref.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/frameshifts.so version.c plugins/frameshifts.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/guess-ploidy.so version.c plugins/guess-ploidy.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/gvcfz.so version.c plugins/gvcfz.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/impute-info.so version.c plugins/impute-info.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/indel-stats.so version.c plugins/indel-stats.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/isecGT.so smpl_ilist.c version.c plugins/isecGT.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/mendelian.so version.c plugins/mendelian.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/missing2ref.so version.c plugins/missing2ref.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/parental-origin.so version.c plugins/parental-origin.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/prune.so version.c plugins/prune.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/remove-overlaps.so version.c plugins/remove-overlaps.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/scatter.so version.c plugins/scatter.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/setGT.so version.c plugins/setGT.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/smpl-stats.so version.c plugins/smpl-stats.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/split-vep.so version.c plugins/split-vep.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/split.so version.c plugins/split.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/tag2tag.so version.c plugins/tag2tag.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/trio-dnm2.so version.c plugins/trio-dnm2.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/trio-stats.so version.c plugins/trio-stats.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/trio-switch-rate.so version.c plugins/trio-switch-rate.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/variant-distance.so version.c plugins/variant-distance.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/variantkey-hex.so version.c plugins/variantkey-hex.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o main.o main.c gcc -Wl,-z,relro -o test/test-rbuf test/test-rbuf.o -lz gcc -Wl,-z,relro -o test/test-regidx test/test-regidx.o regidx.o -lhts -lpthread -lz gcc -rdynamic -Wl,-z,relro -o bcftools main.o vcfindex.o tabix.o vcfstats.o vcfisec.o vcfmerge.o vcfquery.o vcffilter.o filter.o vcfsom.o vcfnorm.o vcfgtcheck.o vcfview.o vcfannotate.o vcfroh.o vcfconcat.o vcfcall.o mcall.o vcmp.o gvcf.o reheader.o convert.o vcfconvert.o tsv2vcf.o vcfcnv.o vcfhead.o HMM.o consensus.o ploidy.o bin.o hclust.o version.o regidx.o smpl_ilist.o csq.o vcfbuf.o mpileup.o bam2bcf.o bam2bcf_indel.o bam_sample.o vcfsort.o cols.o extsort.o dist.o abuf.o ccall.o em.o prob1.o kmin.o str_finder.o vcfplugin.o -lhts -lm -lz -lpthread make[1]: Leaving directory '/build/bcftools-1.16' debian/rules override_dh_auto_test make[1]: Entering directory '/build/bcftools-1.16' make test-no-plugins VERBOSE=1 make[2]: Entering directory '/build/bcftools-1.16' ./test/test-rbuf Inserted 1-9 starting at offset 5: 5 6 7 8 9 0 1 2 3 1 2 3 4 5 6 7 8 9 4th is 4 Deleting 1-2: 7 8 9 0 1 2 3 3 4 5 6 7 8 9 Prepending 0-8: 8 9 0 1 2 3 4 5 6 7 8 7 6 5 4 3 2 1 0 3 Expanding: 8 9 10 11 12 13 14 15 16 17 8 7 6 5 4 3 2 1 0 3 ./test/test-regidx REF_PATH=: ./test/test.pl --exec bgzip= --exec tabix= --htsdir= ${TEST_OPTS:-} test_usage: bcftools .. ok test_usage_subcommand: bcftools index .. ok test_usage_subcommand: bcftools annotate .. ok test_usage_subcommand: bcftools concat .. ok test_usage_subcommand: bcftools convert .. ok test_usage_subcommand: bcftools head .. ok test_usage_subcommand: bcftools isec .. ok test_usage_subcommand: bcftools merge .. ok test_usage_subcommand: bcftools norm .. ok test_usage_subcommand: bcftools plugin .. ok test_usage_subcommand: bcftools query .. ok test_usage_subcommand: bcftools reheader .. ok test_usage_subcommand: bcftools sort .. ok test_usage_subcommand: bcftools view .. ok test_usage_subcommand: bcftools call .. ok test_usage_subcommand: bcftools consensus .. ok test_usage_subcommand: bcftools cnv .. ok test_usage_subcommand: bcftools csq .. ok test_usage_subcommand: bcftools filter .. ok test_usage_subcommand: bcftools gtcheck .. ok test_usage_subcommand: bcftools mpileup .. ok test_usage_subcommand: bcftools roh .. ok test_usage_subcommand: bcftools stats .. ok test_tabix: tabix /tmp/NK5uwruTra/merge.a.vcf.gz 2:3199812-3199812 .. ok test_tabix: /build/bcftools-1.16/bcftools view -H /tmp/NK5uwruTra/merge.a.bcf 2:3199812-3199812 .. ok test_tabix: tabix /tmp/NK5uwruTra/merge.a.vcf.gz 1:3000151-3000151 .. ok test_tabix: /build/bcftools-1.16/bcftools view -H /tmp/NK5uwruTra/merge.a.bcf 1:3000151-3000151 .. ok test_index: /build/bcftools-1.16/bcftools view -H /tmp/NK5uwruTra/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /build/bcftools-1.16/bcftools view -H /tmp/NK5uwruTra/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/bcftools-1.16/bcftools view -H /tmp/NK5uwruTra/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/bcftools-1.16/bcftools view -H /tmp/NK5uwruTra/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /build/bcftools-1.16/bcftools view -H /tmp/NK5uwruTra/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/bcftools-1.16/bcftools view -H /tmp/NK5uwruTra/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /build/bcftools-1.16/bcftools view -H /tmp/NK5uwruTra/large_chrom_csi_limit.bcf chr20 .. ok test_index: /build/bcftools-1.16/bcftools view -H /tmp/NK5uwruTra/large_chrom_csi_limit.bcf chr20 .. ok test_index: /build/bcftools-1.16/bcftools view -H /tmp/NK5uwruTra/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /build/bcftools-1.16/bcftools view -H /tmp/NK5uwruTra/large_chrom_csi_limit.bcf chr20 .. ok test_vcf_idxstats: /build/bcftools-1.16/bcftools index -s /tmp/NK5uwruTra/idx.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.16/bcftools index -s /tmp/NK5uwruTra/idx.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.16/bcftools index -s /tmp/NK5uwruTra/idx.bcf .. ok test_vcf_idxstats: /build/bcftools-1.16/bcftools index -n /tmp/NK5uwruTra/idx.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.16/bcftools index -n /tmp/NK5uwruTra/idx.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.16/bcftools index -n /tmp/NK5uwruTra/idx.vcf.gz.csi .. ok test_vcf_idxstats: /build/bcftools-1.16/bcftools index -n /tmp/NK5uwruTra/idx.bcf .. ok test_vcf_idxstats: /build/bcftools-1.16/bcftools index -n /tmp/NK5uwruTra/idx.bcf.csi .. ok test_vcf_idxstats: /build/bcftools-1.16/bcftools index -s /tmp/NK5uwruTra/empty.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.16/bcftools index -s /tmp/NK5uwruTra/empty.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.16/bcftools index -s /tmp/NK5uwruTra/empty.bcf .. ok test_vcf_idxstats: /build/bcftools-1.16/bcftools index -n /tmp/NK5uwruTra/empty.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.16/bcftools index -n /tmp/NK5uwruTra/empty.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.16/bcftools index -n /tmp/NK5uwruTra/empty.vcf.gz.csi .. ok test_vcf_idxstats: /build/bcftools-1.16/bcftools index -n /tmp/NK5uwruTra/empty.bcf .. ok test_vcf_idxstats: /build/bcftools-1.16/bcftools index -n /tmp/NK5uwruTra/empty.bcf.csi .. ok test_vcf_check: /build/bcftools-1.16/bcftools stats -s - /tmp/NK5uwruTra/check.vcf.gz | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/check.vcf.gz | /build/bcftools-1.16/bcftools stats -s - | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check_merge: /build/bcftools-1.16/misc/plot-vcfstats -m /tmp/NK5uwruTra/check.1.chk /tmp/NK5uwruTra/check.2.chk /tmp/NK5uwruTra/check.3.chk /tmp/NK5uwruTra/check.4.chk | grep -v 'plot-vcfstats' | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_stats: /build/bcftools-1.16/bcftools stats -s - /tmp/NK5uwruTra/stats.a.vcf.gz /tmp/NK5uwruTra/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/bcftools-1.16/bcftools stats -s B /tmp/NK5uwruTra/stats.a.vcf.gz /tmp/NK5uwruTra/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/bcftools-1.16/bcftools stats -s - /tmp/NK5uwruTra/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_isec: /build/bcftools-1.16/bcftools isec -n =2 /tmp/NK5uwruTra/isec.a.vcf.gz /tmp/NK5uwruTra/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.16/bcftools isec -Ob -n =2 /tmp/NK5uwruTra/isec.a.vcf.gz /tmp/NK5uwruTra/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.16/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/NK5uwruTra/isec.a.vcf.gz /tmp/NK5uwruTra/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.16/bcftools isec -Ob -n =2 -i"STRLEN(REF)==2" /tmp/NK5uwruTra/isec.a.vcf.gz /tmp/NK5uwruTra/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.16/bcftools isec -n =2 -c both /tmp/NK5uwruTra/isec.a.vcf.gz /tmp/NK5uwruTra/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.16/bcftools isec -Ob -n =2 -c both /tmp/NK5uwruTra/isec.a.vcf.gz /tmp/NK5uwruTra/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.16/bcftools isec -n =2 -c any /tmp/NK5uwruTra/isec.a.vcf.gz /tmp/NK5uwruTra/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.16/bcftools isec -Ob -n =2 -c any /tmp/NK5uwruTra/isec.a.vcf.gz /tmp/NK5uwruTra/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.16/bcftools isec -C -c any /tmp/NK5uwruTra/isec.a.vcf.gz /tmp/NK5uwruTra/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.16/bcftools isec -Ob -C -c any /tmp/NK5uwruTra/isec.a.vcf.gz /tmp/NK5uwruTra/isec.b.vcf.gz .. ok test_vcf_isec2: /build/bcftools-1.16/bcftools isec --no-version -T /tmp/NK5uwruTra/isec.tab.gz /tmp/NK5uwruTra/isec.a.vcf.gz .. ok test_vcf_isec2: /build/bcftools-1.16/bcftools isec -Ob -T /tmp/NK5uwruTra/isec.tab.gz /tmp/NK5uwruTra/isec.a.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_isec: /build/bcftools-1.16/bcftools isec -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/NK5uwruTra/isec-miss.1.1.vcf.gz /tmp/NK5uwruTra/isec-miss.1.2.vcf.gz /tmp/NK5uwruTra/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.16/bcftools isec -Ob -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/NK5uwruTra/isec-miss.1.1.vcf.gz /tmp/NK5uwruTra/isec-miss.1.2.vcf.gz /tmp/NK5uwruTra/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.16/bcftools isec -R /build/bcftools-1.16/test/isec-miss.1.regs.txt -n +1 /tmp/NK5uwruTra/isec-miss.1.1.vcf.gz /tmp/NK5uwruTra/isec-miss.1.2.vcf.gz /tmp/NK5uwruTra/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.16/bcftools isec -Ob -R /build/bcftools-1.16/test/isec-miss.1.regs.txt -n +1 /tmp/NK5uwruTra/isec-miss.1.1.vcf.gz /tmp/NK5uwruTra/isec-miss.1.2.vcf.gz /tmp/NK5uwruTra/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.16/bcftools isec -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/NK5uwruTra/isec-miss.2.1.vcf.gz /tmp/NK5uwruTra/isec-miss.2.2.vcf.gz /tmp/NK5uwruTra/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.16/bcftools isec -Ob -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/NK5uwruTra/isec-miss.2.1.vcf.gz /tmp/NK5uwruTra/isec-miss.2.2.vcf.gz /tmp/NK5uwruTra/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.16/bcftools isec -R /build/bcftools-1.16/test/isec-miss.1.regs.txt -n +1 /tmp/NK5uwruTra/isec-miss.2.1.vcf.gz /tmp/NK5uwruTra/isec-miss.2.2.vcf.gz /tmp/NK5uwruTra/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.16/bcftools isec -Ob -R /build/bcftools-1.16/test/isec-miss.1.regs.txt -n +1 /tmp/NK5uwruTra/isec-miss.2.1.vcf.gz /tmp/NK5uwruTra/isec-miss.2.2.vcf.gz /tmp/NK5uwruTra/isec-miss.2.3.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version -i AF:join /tmp/NK5uwruTra/merge.join.a.vcf.gz /tmp/NK5uwruTra/merge.join.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob -i AF:join /tmp/NK5uwruTra/merge.join.a.vcf.gz /tmp/NK5uwruTra/merge.join.b.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version -i AF:join /tmp/NK5uwruTra/merge.join.a.bcf /tmp/NK5uwruTra/merge.join.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob -i AF:join /tmp/NK5uwruTra/merge.join.a.bcf /tmp/NK5uwruTra/merge.join.b.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --force-samples /tmp/NK5uwruTra/merge.LPL.a.vcf.gz /tmp/NK5uwruTra/merge.LPL.b.vcf.gz /tmp/NK5uwruTra/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples /tmp/NK5uwruTra/merge.LPL.a.vcf.gz /tmp/NK5uwruTra/merge.LPL.b.vcf.gz /tmp/NK5uwruTra/merge.LPL.c.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --force-samples /tmp/NK5uwruTra/merge.LPL.a.bcf /tmp/NK5uwruTra/merge.LPL.b.bcf /tmp/NK5uwruTra/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples /tmp/NK5uwruTra/merge.LPL.a.bcf /tmp/NK5uwruTra/merge.LPL.b.bcf /tmp/NK5uwruTra/merge.LPL.c.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --force-samples -L 1 /tmp/NK5uwruTra/merge.LPL.a.vcf.gz /tmp/NK5uwruTra/merge.LPL.b.vcf.gz /tmp/NK5uwruTra/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -L 1 /tmp/NK5uwruTra/merge.LPL.a.vcf.gz /tmp/NK5uwruTra/merge.LPL.b.vcf.gz /tmp/NK5uwruTra/merge.LPL.c.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --force-samples -L 1 /tmp/NK5uwruTra/merge.LPL.a.bcf /tmp/NK5uwruTra/merge.LPL.b.bcf /tmp/NK5uwruTra/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -L 1 /tmp/NK5uwruTra/merge.LPL.a.bcf /tmp/NK5uwruTra/merge.LPL.b.bcf /tmp/NK5uwruTra/merge.LPL.c.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --force-samples -L 2 /tmp/NK5uwruTra/merge.LPL.a.vcf.gz /tmp/NK5uwruTra/merge.LPL.b.vcf.gz /tmp/NK5uwruTra/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -L 2 /tmp/NK5uwruTra/merge.LPL.a.vcf.gz /tmp/NK5uwruTra/merge.LPL.b.vcf.gz /tmp/NK5uwruTra/merge.LPL.c.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --force-samples -L 2 /tmp/NK5uwruTra/merge.LPL.a.bcf /tmp/NK5uwruTra/merge.LPL.b.bcf /tmp/NK5uwruTra/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -L 2 /tmp/NK5uwruTra/merge.LPL.a.bcf /tmp/NK5uwruTra/merge.LPL.b.bcf /tmp/NK5uwruTra/merge.LPL.c.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --force-samples -L 3 /tmp/NK5uwruTra/merge.LPL.a.vcf.gz /tmp/NK5uwruTra/merge.LPL.b.vcf.gz /tmp/NK5uwruTra/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -L 3 /tmp/NK5uwruTra/merge.LPL.a.vcf.gz /tmp/NK5uwruTra/merge.LPL.b.vcf.gz /tmp/NK5uwruTra/merge.LPL.c.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --force-samples -L 3 /tmp/NK5uwruTra/merge.LPL.a.bcf /tmp/NK5uwruTra/merge.LPL.b.bcf /tmp/NK5uwruTra/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -L 3 /tmp/NK5uwruTra/merge.LPL.a.bcf /tmp/NK5uwruTra/merge.LPL.b.bcf /tmp/NK5uwruTra/merge.LPL.c.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --force-samples -L 4 /tmp/NK5uwruTra/merge.LPL.a.vcf.gz /tmp/NK5uwruTra/merge.LPL.b.vcf.gz /tmp/NK5uwruTra/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -L 4 /tmp/NK5uwruTra/merge.LPL.a.vcf.gz /tmp/NK5uwruTra/merge.LPL.b.vcf.gz /tmp/NK5uwruTra/merge.LPL.c.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --force-samples -L 4 /tmp/NK5uwruTra/merge.LPL.a.bcf /tmp/NK5uwruTra/merge.LPL.b.bcf /tmp/NK5uwruTra/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -L 4 /tmp/NK5uwruTra/merge.LPL.a.bcf /tmp/NK5uwruTra/merge.LPL.b.bcf /tmp/NK5uwruTra/merge.LPL.c.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --force-samples -L 5 /tmp/NK5uwruTra/merge.LPL.a.vcf.gz /tmp/NK5uwruTra/merge.LPL.b.vcf.gz /tmp/NK5uwruTra/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -L 5 /tmp/NK5uwruTra/merge.LPL.a.vcf.gz /tmp/NK5uwruTra/merge.LPL.b.vcf.gz /tmp/NK5uwruTra/merge.LPL.c.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --force-samples -L 5 /tmp/NK5uwruTra/merge.LPL.a.bcf /tmp/NK5uwruTra/merge.LPL.b.bcf /tmp/NK5uwruTra/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -L 5 /tmp/NK5uwruTra/merge.LPL.a.bcf /tmp/NK5uwruTra/merge.LPL.b.bcf /tmp/NK5uwruTra/merge.LPL.c.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --force-samples /tmp/NK5uwruTra/merge.a.vcf.gz /tmp/NK5uwruTra/merge.b.vcf.gz /tmp/NK5uwruTra/merge.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples /tmp/NK5uwruTra/merge.a.vcf.gz /tmp/NK5uwruTra/merge.b.vcf.gz /tmp/NK5uwruTra/merge.c.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --force-samples /tmp/NK5uwruTra/merge.a.bcf /tmp/NK5uwruTra/merge.b.bcf /tmp/NK5uwruTra/merge.c.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples /tmp/NK5uwruTra/merge.a.bcf /tmp/NK5uwruTra/merge.b.bcf /tmp/NK5uwruTra/merge.c.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --force-samples -Fx /tmp/NK5uwruTra/merge.a.vcf.gz /tmp/NK5uwruTra/merge.b.vcf.gz /tmp/NK5uwruTra/merge.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -Fx /tmp/NK5uwruTra/merge.a.vcf.gz /tmp/NK5uwruTra/merge.b.vcf.gz /tmp/NK5uwruTra/merge.c.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --force-samples -Fx /tmp/NK5uwruTra/merge.a.bcf /tmp/NK5uwruTra/merge.b.bcf /tmp/NK5uwruTra/merge.c.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -Fx /tmp/NK5uwruTra/merge.a.bcf /tmp/NK5uwruTra/merge.b.bcf /tmp/NK5uwruTra/merge.c.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --force-samples -0 /tmp/NK5uwruTra/merge.a.vcf.gz /tmp/NK5uwruTra/merge.b.vcf.gz /tmp/NK5uwruTra/merge.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -0 /tmp/NK5uwruTra/merge.a.vcf.gz /tmp/NK5uwruTra/merge.b.vcf.gz /tmp/NK5uwruTra/merge.c.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --force-samples -0 /tmp/NK5uwruTra/merge.a.bcf /tmp/NK5uwruTra/merge.b.bcf /tmp/NK5uwruTra/merge.c.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -0 /tmp/NK5uwruTra/merge.a.bcf /tmp/NK5uwruTra/merge.b.bcf /tmp/NK5uwruTra/merge.c.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --force-samples -m none /tmp/NK5uwruTra/merge.2.a.vcf.gz /tmp/NK5uwruTra/merge.2.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -m none /tmp/NK5uwruTra/merge.2.a.vcf.gz /tmp/NK5uwruTra/merge.2.b.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --force-samples -m none /tmp/NK5uwruTra/merge.2.a.bcf /tmp/NK5uwruTra/merge.2.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -m none /tmp/NK5uwruTra/merge.2.a.bcf /tmp/NK5uwruTra/merge.2.b.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --force-samples -m both /tmp/NK5uwruTra/merge.2.a.vcf.gz /tmp/NK5uwruTra/merge.2.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -m both /tmp/NK5uwruTra/merge.2.a.vcf.gz /tmp/NK5uwruTra/merge.2.b.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --force-samples -m both /tmp/NK5uwruTra/merge.2.a.bcf /tmp/NK5uwruTra/merge.2.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -m both /tmp/NK5uwruTra/merge.2.a.bcf /tmp/NK5uwruTra/merge.2.b.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --force-samples -m all /tmp/NK5uwruTra/merge.2.a.vcf.gz /tmp/NK5uwruTra/merge.2.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -m all /tmp/NK5uwruTra/merge.2.a.vcf.gz /tmp/NK5uwruTra/merge.2.b.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --force-samples -m all /tmp/NK5uwruTra/merge.2.a.bcf /tmp/NK5uwruTra/merge.2.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -m all /tmp/NK5uwruTra/merge.2.a.bcf /tmp/NK5uwruTra/merge.2.b.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/NK5uwruTra/merge.3.a.vcf.gz /tmp/NK5uwruTra/merge.3.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/NK5uwruTra/merge.3.a.vcf.gz /tmp/NK5uwruTra/merge.3.b.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/NK5uwruTra/merge.3.a.bcf /tmp/NK5uwruTra/merge.3.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/NK5uwruTra/merge.3.a.bcf /tmp/NK5uwruTra/merge.3.b.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --force-samples -m id /tmp/NK5uwruTra/merge.4.a.vcf.gz /tmp/NK5uwruTra/merge.4.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -m id /tmp/NK5uwruTra/merge.4.a.vcf.gz /tmp/NK5uwruTra/merge.4.b.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --force-samples -m id /tmp/NK5uwruTra/merge.4.a.bcf /tmp/NK5uwruTra/merge.4.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -m id /tmp/NK5uwruTra/merge.4.a.bcf /tmp/NK5uwruTra/merge.4.b.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --gvcf - /tmp/NK5uwruTra/gvcf.merge.1.vcf.gz /tmp/NK5uwruTra/gvcf.merge.2.vcf.gz /tmp/NK5uwruTra/gvcf.merge.3.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --gvcf - /tmp/NK5uwruTra/gvcf.merge.1.vcf.gz /tmp/NK5uwruTra/gvcf.merge.2.vcf.gz /tmp/NK5uwruTra/gvcf.merge.3.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --gvcf - /tmp/NK5uwruTra/gvcf.merge.1.bcf /tmp/NK5uwruTra/gvcf.merge.2.bcf /tmp/NK5uwruTra/gvcf.merge.3.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --gvcf - /tmp/NK5uwruTra/gvcf.merge.1.bcf /tmp/NK5uwruTra/gvcf.merge.2.bcf /tmp/NK5uwruTra/gvcf.merge.3.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --gvcf - /tmp/NK5uwruTra/merge.gvcf.2.a.vcf.gz /tmp/NK5uwruTra/merge.gvcf.2.b.vcf.gz /tmp/NK5uwruTra/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --gvcf - /tmp/NK5uwruTra/merge.gvcf.2.a.vcf.gz /tmp/NK5uwruTra/merge.gvcf.2.b.vcf.gz /tmp/NK5uwruTra/merge.gvcf.2.c.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --gvcf - -i SRC:join /tmp/NK5uwruTra/merge.gvcf.3.a.vcf.gz /tmp/NK5uwruTra/merge.gvcf.3.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --gvcf - -i SRC:join /tmp/NK5uwruTra/merge.gvcf.3.a.vcf.gz /tmp/NK5uwruTra/merge.gvcf.3.b.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --gvcf - /tmp/NK5uwruTra/merge.gvcf.4.a.vcf.gz /tmp/NK5uwruTra/merge.gvcf.4.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --gvcf - /tmp/NK5uwruTra/merge.gvcf.4.a.vcf.gz /tmp/NK5uwruTra/merge.gvcf.4.b.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --gvcf - /tmp/NK5uwruTra/merge.gvcf.4.a.bcf /tmp/NK5uwruTra/merge.gvcf.4.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --gvcf - /tmp/NK5uwruTra/merge.gvcf.4.a.bcf /tmp/NK5uwruTra/merge.gvcf.4.b.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version /tmp/NK5uwruTra/merge.5.a.vcf.gz /tmp/NK5uwruTra/merge.5.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob /tmp/NK5uwruTra/merge.5.a.vcf.gz /tmp/NK5uwruTra/merge.5.b.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version /tmp/NK5uwruTra/merge.5.a.bcf /tmp/NK5uwruTra/merge.5.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob /tmp/NK5uwruTra/merge.5.a.bcf /tmp/NK5uwruTra/merge.5.b.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version /tmp/NK5uwruTra/merge.6.a.vcf.gz /tmp/NK5uwruTra/merge.6.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob /tmp/NK5uwruTra/merge.6.a.vcf.gz /tmp/NK5uwruTra/merge.6.b.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version /tmp/NK5uwruTra/merge.6.a.bcf /tmp/NK5uwruTra/merge.6.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob /tmp/NK5uwruTra/merge.6.a.bcf /tmp/NK5uwruTra/merge.6.b.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --gvcf - /tmp/NK5uwruTra/merge.gvcf.7.a.vcf.gz /tmp/NK5uwruTra/merge.gvcf.7.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --gvcf - /tmp/NK5uwruTra/merge.gvcf.7.a.vcf.gz /tmp/NK5uwruTra/merge.gvcf.7.b.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --gvcf - /tmp/NK5uwruTra/merge.gvcf.7.a.bcf /tmp/NK5uwruTra/merge.gvcf.7.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --gvcf - /tmp/NK5uwruTra/merge.gvcf.7.a.bcf /tmp/NK5uwruTra/merge.gvcf.7.b.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --gvcf - /tmp/NK5uwruTra/merge.gvcf.8.a.vcf.gz /tmp/NK5uwruTra/merge.gvcf.8.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --gvcf - /tmp/NK5uwruTra/merge.gvcf.8.a.vcf.gz /tmp/NK5uwruTra/merge.gvcf.8.b.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --gvcf - /tmp/NK5uwruTra/merge.gvcf.8.a.bcf /tmp/NK5uwruTra/merge.gvcf.8.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --gvcf - /tmp/NK5uwruTra/merge.gvcf.8.a.bcf /tmp/NK5uwruTra/merge.gvcf.8.b.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --force-samples /tmp/NK5uwruTra/merge.7.a.vcf.gz /tmp/NK5uwruTra/merge.7.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples /tmp/NK5uwruTra/merge.7.a.vcf.gz /tmp/NK5uwruTra/merge.7.b.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --force-samples /tmp/NK5uwruTra/merge.7.a.bcf /tmp/NK5uwruTra/merge.7.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples /tmp/NK5uwruTra/merge.7.a.bcf /tmp/NK5uwruTra/merge.7.b.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --gvcf /build/bcftools-1.16/test/gvcf.fa /tmp/NK5uwruTra/merge.gvcf.9a.vcf.gz /tmp/NK5uwruTra/merge.gvcf.9b.vcf.gz /tmp/NK5uwruTra/merge.gvcf.9c.vcf.gz /tmp/NK5uwruTra/merge.gvcf.9d.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --gvcf /build/bcftools-1.16/test/gvcf.fa /tmp/NK5uwruTra/merge.gvcf.9a.vcf.gz /tmp/NK5uwruTra/merge.gvcf.9b.vcf.gz /tmp/NK5uwruTra/merge.gvcf.9c.vcf.gz /tmp/NK5uwruTra/merge.gvcf.9d.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --gvcf /build/bcftools-1.16/test/gvcf.fa /tmp/NK5uwruTra/merge.gvcf.9a.bcf /tmp/NK5uwruTra/merge.gvcf.9b.bcf /tmp/NK5uwruTra/merge.gvcf.9c.bcf /tmp/NK5uwruTra/merge.gvcf.9d.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --gvcf /build/bcftools-1.16/test/gvcf.fa /tmp/NK5uwruTra/merge.gvcf.9a.bcf /tmp/NK5uwruTra/merge.gvcf.9b.bcf /tmp/NK5uwruTra/merge.gvcf.9c.bcf /tmp/NK5uwruTra/merge.gvcf.9d.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --gvcf /build/bcftools-1.16/test/gvcf.fa -r 22:21-23 /tmp/NK5uwruTra/merge.gvcf.9a.vcf.gz /tmp/NK5uwruTra/merge.gvcf.9b.vcf.gz /tmp/NK5uwruTra/merge.gvcf.9c.vcf.gz /tmp/NK5uwruTra/merge.gvcf.9d.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --gvcf /build/bcftools-1.16/test/gvcf.fa -r 22:21-23 /tmp/NK5uwruTra/merge.gvcf.9a.vcf.gz /tmp/NK5uwruTra/merge.gvcf.9b.vcf.gz /tmp/NK5uwruTra/merge.gvcf.9c.vcf.gz /tmp/NK5uwruTra/merge.gvcf.9d.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --gvcf /build/bcftools-1.16/test/gvcf.fa -r 22:21-23 /tmp/NK5uwruTra/merge.gvcf.9a.bcf /tmp/NK5uwruTra/merge.gvcf.9b.bcf /tmp/NK5uwruTra/merge.gvcf.9c.bcf /tmp/NK5uwruTra/merge.gvcf.9d.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --gvcf /build/bcftools-1.16/test/gvcf.fa -r 22:21-23 /tmp/NK5uwruTra/merge.gvcf.9a.bcf /tmp/NK5uwruTra/merge.gvcf.9b.bcf /tmp/NK5uwruTra/merge.gvcf.9c.bcf /tmp/NK5uwruTra/merge.gvcf.9d.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --gvcf /build/bcftools-1.16/test/gvcf.fa /tmp/NK5uwruTra/merge.gvcf.9a.vcf.gz /tmp/NK5uwruTra/merge.gvcf.9b.vcf.gz /tmp/NK5uwruTra/merge.gvcf.9c.vcf.gz /tmp/NK5uwruTra/merge.gvcf.9d.vcf.gz /tmp/NK5uwruTra/merge.gvcf.9e.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --gvcf /build/bcftools-1.16/test/gvcf.fa /tmp/NK5uwruTra/merge.gvcf.9a.vcf.gz /tmp/NK5uwruTra/merge.gvcf.9b.vcf.gz /tmp/NK5uwruTra/merge.gvcf.9c.vcf.gz /tmp/NK5uwruTra/merge.gvcf.9d.vcf.gz /tmp/NK5uwruTra/merge.gvcf.9e.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --gvcf /build/bcftools-1.16/test/gvcf.fa /tmp/NK5uwruTra/merge.gvcf.9a.bcf /tmp/NK5uwruTra/merge.gvcf.9b.bcf /tmp/NK5uwruTra/merge.gvcf.9c.bcf /tmp/NK5uwruTra/merge.gvcf.9d.bcf /tmp/NK5uwruTra/merge.gvcf.9e.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --gvcf /build/bcftools-1.16/test/gvcf.fa /tmp/NK5uwruTra/merge.gvcf.9a.bcf /tmp/NK5uwruTra/merge.gvcf.9b.bcf /tmp/NK5uwruTra/merge.gvcf.9c.bcf /tmp/NK5uwruTra/merge.gvcf.9d.bcf /tmp/NK5uwruTra/merge.gvcf.9e.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --gvcf /build/bcftools-1.16/test/gvcf.fa -r 22:21-23 /tmp/NK5uwruTra/merge.gvcf.9a.vcf.gz /tmp/NK5uwruTra/merge.gvcf.9b.vcf.gz /tmp/NK5uwruTra/merge.gvcf.9c.vcf.gz /tmp/NK5uwruTra/merge.gvcf.9d.vcf.gz /tmp/NK5uwruTra/merge.gvcf.9e.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --gvcf /build/bcftools-1.16/test/gvcf.fa -r 22:21-23 /tmp/NK5uwruTra/merge.gvcf.9a.vcf.gz /tmp/NK5uwruTra/merge.gvcf.9b.vcf.gz /tmp/NK5uwruTra/merge.gvcf.9c.vcf.gz /tmp/NK5uwruTra/merge.gvcf.9d.vcf.gz /tmp/NK5uwruTra/merge.gvcf.9e.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --gvcf /build/bcftools-1.16/test/gvcf.fa -r 22:21-23 /tmp/NK5uwruTra/merge.gvcf.9a.bcf /tmp/NK5uwruTra/merge.gvcf.9b.bcf /tmp/NK5uwruTra/merge.gvcf.9c.bcf /tmp/NK5uwruTra/merge.gvcf.9d.bcf /tmp/NK5uwruTra/merge.gvcf.9e.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --gvcf /build/bcftools-1.16/test/gvcf.fa -r 22:21-23 /tmp/NK5uwruTra/merge.gvcf.9a.bcf /tmp/NK5uwruTra/merge.gvcf.9b.bcf /tmp/NK5uwruTra/merge.gvcf.9c.bcf /tmp/NK5uwruTra/merge.gvcf.9d.bcf /tmp/NK5uwruTra/merge.gvcf.9e.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version /tmp/NK5uwruTra/merge.gvcf.10.a.vcf.gz /tmp/NK5uwruTra/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob /tmp/NK5uwruTra/merge.gvcf.10.a.vcf.gz /tmp/NK5uwruTra/merge.gvcf.10.b.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version /tmp/NK5uwruTra/merge.gvcf.10.a.bcf /tmp/NK5uwruTra/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob /tmp/NK5uwruTra/merge.gvcf.10.a.bcf /tmp/NK5uwruTra/merge.gvcf.10.b.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version -m none /tmp/NK5uwruTra/merge.gvcf.10.a.vcf.gz /tmp/NK5uwruTra/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob -m none /tmp/NK5uwruTra/merge.gvcf.10.a.vcf.gz /tmp/NK5uwruTra/merge.gvcf.10.b.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version -m none /tmp/NK5uwruTra/merge.gvcf.10.a.bcf /tmp/NK5uwruTra/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob -m none /tmp/NK5uwruTra/merge.gvcf.10.a.bcf /tmp/NK5uwruTra/merge.gvcf.10.b.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version -g /build/bcftools-1.16/test/merge.gvcf.10.fa /tmp/NK5uwruTra/merge.gvcf.10.a.vcf.gz /tmp/NK5uwruTra/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob -g /build/bcftools-1.16/test/merge.gvcf.10.fa /tmp/NK5uwruTra/merge.gvcf.10.a.vcf.gz /tmp/NK5uwruTra/merge.gvcf.10.b.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version -g /build/bcftools-1.16/test/merge.gvcf.10.fa /tmp/NK5uwruTra/merge.gvcf.10.a.bcf /tmp/NK5uwruTra/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob -g /build/bcftools-1.16/test/merge.gvcf.10.fa /tmp/NK5uwruTra/merge.gvcf.10.a.bcf /tmp/NK5uwruTra/merge.gvcf.10.b.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version -g /build/bcftools-1.16/test/merge.gvcf.10.fa -m none /tmp/NK5uwruTra/merge.gvcf.10.a.vcf.gz /tmp/NK5uwruTra/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob -g /build/bcftools-1.16/test/merge.gvcf.10.fa -m none /tmp/NK5uwruTra/merge.gvcf.10.a.vcf.gz /tmp/NK5uwruTra/merge.gvcf.10.b.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version -g /build/bcftools-1.16/test/merge.gvcf.10.fa -m none /tmp/NK5uwruTra/merge.gvcf.10.a.bcf /tmp/NK5uwruTra/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob -g /build/bcftools-1.16/test/merge.gvcf.10.fa -m none /tmp/NK5uwruTra/merge.gvcf.10.a.bcf /tmp/NK5uwruTra/merge.gvcf.10.b.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version -g /build/bcftools-1.16/test/merge.gvcf.10.fa /tmp/NK5uwruTra/merge.gvcf.10.b.vcf.gz /tmp/NK5uwruTra/merge.gvcf.10.a.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob -g /build/bcftools-1.16/test/merge.gvcf.10.fa /tmp/NK5uwruTra/merge.gvcf.10.b.vcf.gz /tmp/NK5uwruTra/merge.gvcf.10.a.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version -g /build/bcftools-1.16/test/merge.gvcf.10.fa /tmp/NK5uwruTra/merge.gvcf.10.b.bcf /tmp/NK5uwruTra/merge.gvcf.10.a.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob -g /build/bcftools-1.16/test/merge.gvcf.10.fa /tmp/NK5uwruTra/merge.gvcf.10.b.bcf /tmp/NK5uwruTra/merge.gvcf.10.a.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version -g /build/bcftools-1.16/test/merge.gvcf.10.fa -m none /tmp/NK5uwruTra/merge.gvcf.10.b.vcf.gz /tmp/NK5uwruTra/merge.gvcf.10.a.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob -g /build/bcftools-1.16/test/merge.gvcf.10.fa -m none /tmp/NK5uwruTra/merge.gvcf.10.b.vcf.gz /tmp/NK5uwruTra/merge.gvcf.10.a.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version -g /build/bcftools-1.16/test/merge.gvcf.10.fa -m none /tmp/NK5uwruTra/merge.gvcf.10.b.bcf /tmp/NK5uwruTra/merge.gvcf.10.a.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob -g /build/bcftools-1.16/test/merge.gvcf.10.fa -m none /tmp/NK5uwruTra/merge.gvcf.10.b.bcf /tmp/NK5uwruTra/merge.gvcf.10.a.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version /tmp/NK5uwruTra/merge.noidx.a.vcf.gz /tmp/NK5uwruTra/merge.noidx.b.vcf.gz /tmp/NK5uwruTra/merge.noidx.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob /tmp/NK5uwruTra/merge.noidx.a.vcf.gz /tmp/NK5uwruTra/merge.noidx.b.vcf.gz /tmp/NK5uwruTra/merge.noidx.c.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version /tmp/NK5uwruTra/merge.noidx.a.bcf /tmp/NK5uwruTra/merge.noidx.b.bcf /tmp/NK5uwruTra/merge.noidx.c.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob /tmp/NK5uwruTra/merge.noidx.a.bcf /tmp/NK5uwruTra/merge.noidx.b.bcf /tmp/NK5uwruTra/merge.noidx.c.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --no-index /build/bcftools-1.16/test/merge.noidx.a.vcf /build/bcftools-1.16/test/merge.noidx.b.vcf /build/bcftools-1.16/test/merge.noidx.c.vcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --no-index /build/bcftools-1.16/test/merge.noidx.a.vcf /build/bcftools-1.16/test/merge.noidx.b.vcf /build/bcftools-1.16/test/merge.noidx.c.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version --no-index /tmp/NK5uwruTra/merge.noidx.a.bcf /tmp/NK5uwruTra/merge.noidx.b.bcf /tmp/NK5uwruTra/merge.noidx.c.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --no-index /tmp/NK5uwruTra/merge.noidx.a.bcf /tmp/NK5uwruTra/merge.noidx.b.bcf /tmp/NK5uwruTra/merge.noidx.c.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version /tmp/NK5uwruTra/merge.8.a.vcf.gz /tmp/NK5uwruTra/merge.8.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob /tmp/NK5uwruTra/merge.8.a.vcf.gz /tmp/NK5uwruTra/merge.8.b.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version /tmp/NK5uwruTra/merge.8.a.bcf /tmp/NK5uwruTra/merge.8.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob /tmp/NK5uwruTra/merge.8.a.bcf /tmp/NK5uwruTra/merge.8.b.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version -i AN:sum,AC:sum /tmp/NK5uwruTra/merge.8.a.vcf.gz /tmp/NK5uwruTra/merge.8.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob -i AN:sum,AC:sum /tmp/NK5uwruTra/merge.8.a.vcf.gz /tmp/NK5uwruTra/merge.8.b.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version -i AN:sum,AC:sum /tmp/NK5uwruTra/merge.8.a.bcf /tmp/NK5uwruTra/merge.8.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob -i AN:sum,AC:sum /tmp/NK5uwruTra/merge.8.a.bcf /tmp/NK5uwruTra/merge.8.b.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version /tmp/NK5uwruTra/merge.9.a.vcf.gz /tmp/NK5uwruTra/merge.9.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob /tmp/NK5uwruTra/merge.9.a.vcf.gz /tmp/NK5uwruTra/merge.9.b.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version /tmp/NK5uwruTra/merge.9.a.bcf /tmp/NK5uwruTra/merge.9.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob /tmp/NK5uwruTra/merge.9.a.bcf /tmp/NK5uwruTra/merge.9.b.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version -i AN:sum,AC:sum /tmp/NK5uwruTra/merge.9.a.vcf.gz /tmp/NK5uwruTra/merge.9.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob -i AN:sum,AC:sum /tmp/NK5uwruTra/merge.9.a.vcf.gz /tmp/NK5uwruTra/merge.9.b.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version -i AN:sum,AC:sum /tmp/NK5uwruTra/merge.9.a.bcf /tmp/NK5uwruTra/merge.9.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob -i AN:sum,AC:sum /tmp/NK5uwruTra/merge.9.a.bcf /tmp/NK5uwruTra/merge.9.b.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version -m none /tmp/NK5uwruTra/merge.10.a.vcf.gz /tmp/NK5uwruTra/merge.10.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob -m none /tmp/NK5uwruTra/merge.10.a.vcf.gz /tmp/NK5uwruTra/merge.10.b.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version -m none /tmp/NK5uwruTra/merge.10.a.bcf /tmp/NK5uwruTra/merge.10.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob -m none /tmp/NK5uwruTra/merge.10.a.bcf /tmp/NK5uwruTra/merge.10.b.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version -m both /tmp/NK5uwruTra/merge.10.a.vcf.gz /tmp/NK5uwruTra/merge.10.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob -m both /tmp/NK5uwruTra/merge.10.a.vcf.gz /tmp/NK5uwruTra/merge.10.b.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version -m both /tmp/NK5uwruTra/merge.10.a.bcf /tmp/NK5uwruTra/merge.10.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob -m both /tmp/NK5uwruTra/merge.10.a.bcf /tmp/NK5uwruTra/merge.10.b.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version -m snp-ins-del /tmp/NK5uwruTra/merge.10.a.vcf.gz /tmp/NK5uwruTra/merge.10.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob -m snp-ins-del /tmp/NK5uwruTra/merge.10.a.vcf.gz /tmp/NK5uwruTra/merge.10.b.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version -m snp-ins-del /tmp/NK5uwruTra/merge.10.a.bcf /tmp/NK5uwruTra/merge.10.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob -m snp-ins-del /tmp/NK5uwruTra/merge.10.a.bcf /tmp/NK5uwruTra/merge.10.b.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided,_conflicting_interpretations"' /tmp/NK5uwruTra/query.string.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.string.vcf.gz | /build/bcftools-1.16/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided,_conflicting_interpretations"' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" || CLNREVSTAT="_conflicting_interpretations"' /tmp/NK5uwruTra/query.string.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.string.vcf.gz | /build/bcftools-1.16/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" || CLNREVSTAT="_conflicting_interpretations"' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" && CLNREVSTAT="_conflicting_interpretations"' /tmp/NK5uwruTra/query.string.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.string.vcf.gz | /build/bcftools-1.16/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" && CLNREVSTAT="_conflicting_interpretations"' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' /tmp/NK5uwruTra/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.vcf.gz | /build/bcftools-1.16/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f '%RSX\t%VKX\n' /tmp/NK5uwruTra/query.variantkey.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.variantkey.vcf.gz | /build/bcftools-1.16/bcftools query -f '%RSX\t%VKX\n' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%XRI\n' -i'XRI[*]>1111' /tmp/NK5uwruTra/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/view.filter.vcf.gz | /build/bcftools-1.16/bcftools query -f'%XRI\n' -i'XRI[*]>1111' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' /tmp/NK5uwruTra/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/view.filter.vcf.gz | /build/bcftools-1.16/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' /tmp/NK5uwruTra/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/view.filter.vcf.gz | /build/bcftools-1.16/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' /tmp/NK5uwruTra/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/view.filter.vcf.gz | /build/bcftools-1.16/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' /tmp/NK5uwruTra/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/view.filter.vcf.gz | /build/bcftools-1.16/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' /tmp/NK5uwruTra/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/view.filter.vcf.gz | /build/bcftools-1.16/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' /tmp/NK5uwruTra/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/view.filter.vcf.gz | /build/bcftools-1.16/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' /tmp/NK5uwruTra/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' /tmp/NK5uwruTra/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' /tmp/NK5uwruTra/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' /tmp/NK5uwruTra/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' /tmp/NK5uwruTra/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/view.filter.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' /tmp/NK5uwruTra/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' /tmp/NK5uwruTra/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' /tmp/NK5uwruTra/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' /tmp/NK5uwruTra/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'I8=%I8 I16=%I16 I32=%I32 IF=%IF IA8=%IA8 IA16=%IA16 IA32=%IA32 IAF=%IAF IA8=%IA8{1} IA16=%IA16{1} IA32=%IA32{1} IAF=%IAF{1} [ %F8:%F16:%F32:%FF]\n' /tmp/NK5uwruTra/view.vectors.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/view.vectors.vcf.gz | /build/bcftools-1.16/bcftools query -f'I8=%I8 I16=%I16 I32=%I32 IF=%IF IA8=%IA8 IA16=%IA16 IA32=%IA32 IAF=%IAF IA8=%IA8{1} IA16=%IA16{1} IA32=%IA32{1} IAF=%IAF{1} [ %F8:%F16:%F32:%FF]\n' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' /tmp/NK5uwruTra/query.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.filter.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' /tmp/NK5uwruTra/query.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.filter.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' /tmp/NK5uwruTra/query.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.filter.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' /tmp/NK5uwruTra/query.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.filter.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' /tmp/NK5uwruTra/query.2.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.2.vcf.gz | /build/bcftools-1.16/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -i'IINT="."' -f'%POS %IINT\n' /tmp/NK5uwruTra/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/missing.vcf.gz | /build/bcftools-1.16/bcftools query -i'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -i'IINT!="."' -f'%POS %IINT\n' /tmp/NK5uwruTra/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/missing.vcf.gz | /build/bcftools-1.16/bcftools query -i'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -e'IINT!="."' -f'%POS %IINT\n' /tmp/NK5uwruTra/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/missing.vcf.gz | /build/bcftools-1.16/bcftools query -e'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -e'IINT="."' -f'%POS %IINT\n' /tmp/NK5uwruTra/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/missing.vcf.gz | /build/bcftools-1.16/bcftools query -e'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' /tmp/NK5uwruTra/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/missing.vcf.gz | /build/bcftools-1.16/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' /tmp/NK5uwruTra/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/missing.vcf.gz | /build/bcftools-1.16/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' /tmp/NK5uwruTra/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/missing.vcf.gz | /build/bcftools-1.16/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' /tmp/NK5uwruTra/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/missing.vcf.gz | /build/bcftools-1.16/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' /tmp/NK5uwruTra/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/missing.vcf.gz | /build/bcftools-1.16/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' /tmp/NK5uwruTra/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/missing.vcf.gz | /build/bcftools-1.16/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' /tmp/NK5uwruTra/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/missing.vcf.gz | /build/bcftools-1.16/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' /tmp/NK5uwruTra/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/missing.vcf.gz | /build/bcftools-1.16/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' /tmp/NK5uwruTra/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/missing.vcf.gz | /build/bcftools-1.16/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -i'FILTER="A"' -f'%POS %FILTER\n' /tmp/NK5uwruTra/filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/filter.11.vcf.gz | /build/bcftools-1.16/bcftools query -i'FILTER="A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -i'FILTER!="A"' -f'%POS %FILTER\n' /tmp/NK5uwruTra/filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/filter.11.vcf.gz | /build/bcftools-1.16/bcftools query -i'FILTER!="A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -i'FILTER~"A"' -f'%POS %FILTER\n' /tmp/NK5uwruTra/filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/filter.11.vcf.gz | /build/bcftools-1.16/bcftools query -i'FILTER~"A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n' /tmp/NK5uwruTra/filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/filter.11.vcf.gz | /build/bcftools-1.16/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%LINE' /tmp/NK5uwruTra/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.vcf.gz | /build/bcftools-1.16/bcftools query -f'%LINE' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' /tmp/NK5uwruTra/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.filter-type.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' /tmp/NK5uwruTra/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.filter-type.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' /tmp/NK5uwruTra/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.filter-type.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' /tmp/NK5uwruTra/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.filter-type.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\n' -i'INFO/TYPE="xxx"' /tmp/NK5uwruTra/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.filter-type.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\n' -i'INFO/TYPE="xxx"' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -i'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001' /tmp/NK5uwruTra/filter-missing-floats.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/filter-missing-floats.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -i'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -e'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001' /tmp/NK5uwruTra/filter-missing-floats.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/filter-missing-floats.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -e'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' /tmp/NK5uwruTra/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/missing.vcf.gz | /build/bcftools-1.16/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' /tmp/NK5uwruTra/query.filter.2.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.filter.2.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' /tmp/NK5uwruTra/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/view.filter.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' /tmp/NK5uwruTra/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/view.filter.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' /tmp/NK5uwruTra/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/view.filter.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' /tmp/NK5uwruTra/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/view.filter.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' /tmp/NK5uwruTra/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/view.filter.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' /tmp/NK5uwruTra/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/view.filter.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' /tmp/NK5uwruTra/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/view.filter.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' /tmp/NK5uwruTra/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/view.filter.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' /tmp/NK5uwruTra/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/view.filter.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' /tmp/NK5uwruTra/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/view.filter.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' /tmp/NK5uwruTra/filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/filter.5.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' /tmp/NK5uwruTra/filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/filter.5.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' /tmp/NK5uwruTra/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/view.filter.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' /tmp/NK5uwruTra/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/view.filter.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' /tmp/NK5uwruTra/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/view.filter.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' /tmp/NK5uwruTra/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/view.filter.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' /tmp/NK5uwruTra/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/view.filter.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 & FMT/GQ=589' /tmp/NK5uwruTra/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/view.filter.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 & FMT/GQ=589' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' /tmp/NK5uwruTra/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/view.filter.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' /tmp/NK5uwruTra/query.filter.3.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.filter.3.vcf.gz | /build/bcftools-1.16/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"' /tmp/NK5uwruTra/query.filter.3.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.filter.3.vcf.gz | /build/bcftools-1.16/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' /tmp/NK5uwruTra/query.filter.3.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.filter.3.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %AD\n]\n' -i'AD[:0]+AD[:1] > 12' /tmp/NK5uwruTra/filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/filter.5.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %AD\n]\n' -i'AD[:0]+AD[:1] > 12' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' /tmp/NK5uwruTra/query.filter.4.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.filter.4.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%ID\n' -i 'ID=@/build/bcftools-1.16/test/query.56.out' /tmp/NK5uwruTra/view.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/view.vcf.gz | /build/bcftools-1.16/bcftools query -f'%ID\n' -i 'ID=@/build/bcftools-1.16/test/query.56.out' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD)>0.01' /tmp/NK5uwruTra/query.filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.filter.5.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD)>0.01' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD[:0],FMT/AD[:1])>0.01' /tmp/NK5uwruTra/query.filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.filter.5.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD[:0],FMT/AD[:1])>0.01' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS\t%AD\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01' /tmp/NK5uwruTra/query.filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.filter.5.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS\t%AD\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%CHROM %POS\n' -i'CHROM="4"' /tmp/NK5uwruTra/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.vcf.gz | /build/bcftools-1.16/bcftools query -f'%CHROM %POS\n' -i'CHROM="4"' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS\t%TAG1\n' -i'(TAG1>=-129 && TAG1<=-120) || (TAG1>=-32769 && TAG1<=-32760)' /tmp/NK5uwruTra/query.negative.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.negative.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS\t%TAG1\n' -i'(TAG1>=-129 && TAG1<=-120) || (TAG1>=-32769 && TAG1<=-32760)' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS\t%TAGV1\n' -i'(TAGV1>=-129 && TAGV1<=-120) || (TAGV1>=-32769 && TAGV1<=-32760)' /tmp/NK5uwruTra/query.negative.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.negative.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS\t%TAGV1\n' -i'(TAGV1>=-129 && TAGV1<=-120) || (TAGV1>=-32769 && TAGV1<=-32760)' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS\t%TAG2\n' -i'(TAG2>=-129 && TAG2<=-120) || (TAG2>=-32769 && TAG2<=-32760)' /tmp/NK5uwruTra/query.negative.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.negative.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS\t%TAG2\n' -i'(TAG2>=-129 && TAG2<=-120) || (TAG2>=-32769 && TAG2<=-32760)' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS\t%TAGV2\n' -i'(TAGV2>=-129 && TAGV2<=-120) || (TAGV2>=-32769 && TAGV2<=-32760)' /tmp/NK5uwruTra/query.negative.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.negative.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS\t%TAGV2\n' -i'(TAGV2>=-129 && TAGV2<=-120) || (TAGV2>=-32769 && TAGV2<=-32760)' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%POS\t%SAMPLE\t%GQ\n]' -i'N_PASS(GQ<20)==1' /tmp/NK5uwruTra/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%POS\t%SAMPLE\t%GQ\n]' -i'N_PASS(GQ<20)==1' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")==1' /tmp/NK5uwruTra/query.filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.filter.11.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")==1' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")!=1' /tmp/NK5uwruTra/query.filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.filter.11.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")!=1' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")==1' /tmp/NK5uwruTra/query.filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.filter.11.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")==1' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")!=1' /tmp/NK5uwruTra/query.filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.filter.11.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")!=1' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%CHROM\t%POS\t%INFO\t%FORMAT\n' -s D,C /tmp/NK5uwruTra/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.vcf.gz | /build/bcftools-1.16/bcftools query -f'%CHROM\t%POS\t%INFO\t%FORMAT\n' -s D,C .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS\n' -i'POS==16777217 || POS==33554432 || POS=118673904' /tmp/NK5uwruTra/query.filter.6.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.filter.6.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS\n' -i'POS==16777217 || POS==33554432 || POS=118673904' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(II)==6' /tmp/NK5uwruTra/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.filter.7.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(II)==6' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(FORMAT/FI)==7' /tmp/NK5uwruTra/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.filter.7.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(FORMAT/FI)==7' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(II)==2' /tmp/NK5uwruTra/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.filter.7.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(II)==2' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(FORMAT/FI)==1.75' /tmp/NK5uwruTra/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.filter.7.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(FORMAT/FI)==1.75' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(II)==2' /tmp/NK5uwruTra/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.filter.7.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(II)==2' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(FORMAT/FI)==1.75' /tmp/NK5uwruTra/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.filter.7.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(FORMAT/FI)==1.75' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(II)==2' /tmp/NK5uwruTra/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.filter.7.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(II)==2' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(FORMAT/FI)==1.5' /tmp/NK5uwruTra/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.filter.7.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(FORMAT/FI)==1.5' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'%ILEN==1' /tmp/NK5uwruTra/query.filter.8.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.filter.8.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'%ILEN==1' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'ILEN==1' /tmp/NK5uwruTra/query.filter.8.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.filter.8.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'ILEN==1' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] < FMT/AD[:1]' /tmp/NK5uwruTra/query.filter.9.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.filter.9.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] < FMT/AD[:1]' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] > FMT/AD[:1]' /tmp/NK5uwruTra/query.filter.9.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.filter.9.vcf.gz | /build/bcftools-1.16/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] > FMT/AD[:1]' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'[ %AD\n]' -i'AD[:1] / sum(AD[*]) > 0.5' /tmp/NK5uwruTra/query.filter.13.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.filter.13.vcf.gz | /build/bcftools-1.16/bcftools query -f'[ %AD\n]' -i'AD[:1] / sum(AD[*]) > 0.5' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS %NUM_TAG\n' -i'COUNT(INFO/NUM_TAG)=2' /tmp/NK5uwruTra/query.filter.10.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.filter.10.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS %NUM_TAG\n' -i'COUNT(INFO/NUM_TAG)=2' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%POS %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2' /tmp/NK5uwruTra/query.filter.10.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.filter.10.vcf.gz | /build/bcftools-1.16/bcftools query -f'%POS %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f '%CHROM:%POS\t%N_PASS(GT="alt" & GQ>110)\t[\t%GT]\t[\t%GQ]\n' /tmp/NK5uwruTra/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.vcf.gz | /build/bcftools-1.16/bcftools query -f '%CHROM:%POS\t%N_PASS(GT="alt" & GQ>110)\t[\t%GT]\t[\t%GQ]\n' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 1,3,0 /tmp/NK5uwruTra/query.filter.12.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.filter.12.vcf.gz | /build/bcftools-1.16/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 1,3,0 .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 0,1,3 /tmp/NK5uwruTra/query.filter.12.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.filter.12.vcf.gz | /build/bcftools-1.16/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 0,1,3 .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f "[%SAMPLE %GT\n]" -S /build/bcftools-1.16/test/query.smpl.11.txt /tmp/NK5uwruTra/query.smpl.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.smpl.vcf.gz | /build/bcftools-1.16/bcftools query -f "[%SAMPLE %GT\n]" -S /build/bcftools-1.16/test/query.smpl.11.txt .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -l -S /build/bcftools-1.16/test/query.smpl.11.txt /tmp/NK5uwruTra/query.smpl.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.smpl.vcf.gz | /build/bcftools-1.16/bcftools query -l -S /build/bcftools-1.16/test/query.smpl.11.txt .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f "[%SAMPLE %GT\n]" -S ^/build/bcftools-1.16/test/query.smpl.11.txt /tmp/NK5uwruTra/query.smpl.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.smpl.vcf.gz | /build/bcftools-1.16/bcftools query -f "[%SAMPLE %GT\n]" -S ^/build/bcftools-1.16/test/query.smpl.11.txt .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -l -S ^/build/bcftools-1.16/test/query.smpl.11.txt /tmp/NK5uwruTra/query.smpl.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.smpl.vcf.gz | /build/bcftools-1.16/bcftools query -l -S ^/build/bcftools-1.16/test/query.smpl.11.txt .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f "[%SAMPLE %GT\n]" -S /build/bcftools-1.16/test/query.smpl.txt /tmp/NK5uwruTra/query.smpl.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.smpl.vcf.gz | /build/bcftools-1.16/bcftools query -f "[%SAMPLE %GT\n]" -S /build/bcftools-1.16/test/query.smpl.txt .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -l -S /build/bcftools-1.16/test/query.smpl.txt /tmp/NK5uwruTra/query.smpl.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.smpl.vcf.gz | /build/bcftools-1.16/bcftools query -l -S /build/bcftools-1.16/test/query.smpl.txt .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%ID\n' -i'ID~"s12"' /tmp/NK5uwruTra/query.filter.id.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.filter.id.vcf.gz | /build/bcftools-1.16/bcftools query -f'%ID\n' -i'ID~"s12"' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -f'%ID\n' -i'ID="rs123"' /tmp/NK5uwruTra/query.filter.id.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/query.filter.id.vcf.gz | /build/bcftools-1.16/bcftools query -f'%ID\n' -i'ID="rs123"' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -i'FILTER="A"' -f'%FILTER\n' /tmp/NK5uwruTra/filter.12.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/filter.12.vcf.gz | /build/bcftools-1.16/bcftools query -i'FILTER="A"' -f'%FILTER\n' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -i'FILTER~"A"' -f'%FILTER\n' /tmp/NK5uwruTra/filter.12.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/filter.12.vcf.gz | /build/bcftools-1.16/bcftools query -i'FILTER~"A"' -f'%FILTER\n' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -i'FILTER="A;B"' -f'%FILTER\n' /tmp/NK5uwruTra/filter.12.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/filter.12.vcf.gz | /build/bcftools-1.16/bcftools query -i'FILTER="A;B"' -f'%FILTER\n' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -i'FILTER!="A;B"' -f'%FILTER\n' /tmp/NK5uwruTra/filter.12.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/filter.12.vcf.gz | /build/bcftools-1.16/bcftools query -i'FILTER!="A;B"' -f'%FILTER\n' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -i'FILTER~"A;B"' -f'%FILTER\n' /tmp/NK5uwruTra/filter.12.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/filter.12.vcf.gz | /build/bcftools-1.16/bcftools query -i'FILTER~"A;B"' -f'%FILTER\n' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -i'FILTER!~"A;B"' -f'%FILTER\n' /tmp/NK5uwruTra/filter.12.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/filter.12.vcf.gz | /build/bcftools-1.16/bcftools query -i'FILTER!~"A;B"' -f'%FILTER\n' .. ok test_vcf_query: /build/bcftools-1.16/bcftools query -i'DP%10==2' -f'[ %DP]\n' /tmp/NK5uwruTra/filter.10.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/filter.10.vcf.gz | /build/bcftools-1.16/bcftools query -i'DP%10==2' -f'[ %DP]\n' .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version -cx -f /build/bcftools-1.16/test/norm.fa /tmp/NK5uwruTra/norm.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -cx -f /build/bcftools-1.16/test/norm.fa /tmp/NK5uwruTra/norm.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version -m- /tmp/NK5uwruTra/norm.split.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -m- /tmp/NK5uwruTra/norm.split.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version -m- /tmp/NK5uwruTra/norm.split.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -m- /tmp/NK5uwruTra/norm.split.2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version -m- --force /tmp/NK5uwruTra/norm.split.3.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -m- --force /tmp/NK5uwruTra/norm.split.3.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version -m- /tmp/NK5uwruTra/norm.split.4.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -m- /tmp/NK5uwruTra/norm.split.4.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version -m- --keep-sum AD /tmp/NK5uwruTra/norm.split.4.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -m- --keep-sum AD /tmp/NK5uwruTra/norm.split.4.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version -m- -f /build/bcftools-1.16/test/norm.fa /tmp/NK5uwruTra/norm.split.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -m- -f /build/bcftools-1.16/test/norm.fa /tmp/NK5uwruTra/norm.split.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version -m+ /tmp/NK5uwruTra/norm.merge.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -m+ /tmp/NK5uwruTra/norm.merge.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version -m+ /tmp/NK5uwruTra/norm.merge.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -m+ /tmp/NK5uwruTra/norm.merge.2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version -m+ /tmp/NK5uwruTra/norm.merge.3.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -m+ /tmp/NK5uwruTra/norm.merge.3.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version -m+ -s /tmp/NK5uwruTra/norm.merge.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -m+ -s /tmp/NK5uwruTra/norm.merge.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version -Nc s -f /build/bcftools-1.16/test/norm.fa /tmp/NK5uwruTra/norm.setref.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -Nc s -f /build/bcftools-1.16/test/norm.fa /tmp/NK5uwruTra/norm.setref.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version -f /build/bcftools-1.16/test/norm.fa /tmp/NK5uwruTra/norm.telomere.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -f /build/bcftools-1.16/test/norm.fa /tmp/NK5uwruTra/norm.telomere.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version -d snps /tmp/NK5uwruTra/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -d snps /tmp/NK5uwruTra/norm.rmdup.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version -d indels /tmp/NK5uwruTra/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -d indels /tmp/NK5uwruTra/norm.rmdup.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version -d both /tmp/NK5uwruTra/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -d both /tmp/NK5uwruTra/norm.rmdup.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version -d all /tmp/NK5uwruTra/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -d all /tmp/NK5uwruTra/norm.rmdup.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version -d none /tmp/NK5uwruTra/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -d none /tmp/NK5uwruTra/norm.rmdup.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version -d exact /tmp/NK5uwruTra/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -d exact /tmp/NK5uwruTra/norm.rmdup.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version -d none /tmp/NK5uwruTra/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -d none /tmp/NK5uwruTra/norm.rmdup.2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version -d exact /tmp/NK5uwruTra/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -d exact /tmp/NK5uwruTra/norm.rmdup.2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version -d indels /tmp/NK5uwruTra/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -d indels /tmp/NK5uwruTra/norm.rmdup.2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version -d any /tmp/NK5uwruTra/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -d any /tmp/NK5uwruTra/norm.rmdup.2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version -d both /tmp/NK5uwruTra/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -d both /tmp/NK5uwruTra/norm.rmdup.2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version -d snps /tmp/NK5uwruTra/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -d snps /tmp/NK5uwruTra/norm.rmdup.2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version -c s -a -f /build/bcftools-1.16/test/norm.2.fa /tmp/NK5uwruTra/norm.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -c s -a -f /build/bcftools-1.16/test/norm.2.fa /tmp/NK5uwruTra/norm.2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version -c s -f /build/bcftools-1.16/test/norm.iupac.fa /tmp/NK5uwruTra/norm.iupac.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -c s -f /build/bcftools-1.16/test/norm.iupac.fa /tmp/NK5uwruTra/norm.iupac.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version -c s -f /build/bcftools-1.16/test/norm.3.fa /tmp/NK5uwruTra/norm.3.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -c s -f /build/bcftools-1.16/test/norm.3.fa /tmp/NK5uwruTra/norm.3.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/NK5uwruTra/atomize.split.1.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob --atomize --old-rec-tag OLD_REC /tmp/NK5uwruTra/atomize.split.1.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/NK5uwruTra/atomize.split.1.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/NK5uwruTra/atomize.split.1.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/NK5uwruTra/atomize.split.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob --atomize --old-rec-tag OLD_REC /tmp/NK5uwruTra/atomize.split.2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/NK5uwruTra/atomize.split.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/NK5uwruTra/atomize.split.2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version --atomize --atom-overlaps . /tmp/NK5uwruTra/atomize.split.3.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob --atomize --atom-overlaps . /tmp/NK5uwruTra/atomize.split.3.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version -m +both /tmp/NK5uwruTra/norm.4.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -m +both /tmp/NK5uwruTra/norm.4.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm --no-version -m +any /tmp/NK5uwruTra/norm.4.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -m +any /tmp/NK5uwruTra/norm.4.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -aUc1 -C1 -s NA00002 -v snps /tmp/NK5uwruTra/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/NK5uwruTra/view.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -f PASS -Xks NA00003 /tmp/NK5uwruTra/view.vcf.gz -r20,Y .. ok test_vcf_view: /build/bcftools-1.16/bcftools view -Ob -f PASS -Xks NA00003 /tmp/NK5uwruTra/view.vcf.gz -r20,Y | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -xs NA00003 /tmp/NK5uwruTra/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view -Ob -xs NA00003 /tmp/NK5uwruTra/view.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/NK5uwruTra/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view -Ob -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/NK5uwruTra/view.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -p /tmp/NK5uwruTra/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view -Ob -p /tmp/NK5uwruTra/view.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -P /tmp/NK5uwruTra/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view -Ob -P /tmp/NK5uwruTra/view.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -hm2 -M2 -q0.3 -Q0.7 /tmp/NK5uwruTra/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/NK5uwruTra/view.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -Hu /tmp/NK5uwruTra/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -GVsnps /tmp/NK5uwruTra/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view -Ob -GVsnps /tmp/NK5uwruTra/view.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -ne 'INDEL=1 || PV4[0]<0.006' /tmp/NK5uwruTra/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/NK5uwruTra/view.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -s ^NA00003 /tmp/NK5uwruTra/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view -Ob -s ^NA00003 /tmp/NK5uwruTra/view.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version /tmp/NK5uwruTra/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/view.omitgenotypes.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -G /tmp/NK5uwruTra/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view -Ob -G /tmp/NK5uwruTra/view.omitgenotypes.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -HG /tmp/NK5uwruTra/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -a /tmp/NK5uwruTra/many.alleles.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view -Ob -a /tmp/NK5uwruTra/many.alleles.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -asA /tmp/NK5uwruTra/view.vectors.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view -Ob -asA /tmp/NK5uwruTra/view.vectors.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -asB /tmp/NK5uwruTra/view.vectors.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view -Ob -asB /tmp/NK5uwruTra/view.vectors.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -asA /tmp/NK5uwruTra/view.vectors.2.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view -Ob -asA /tmp/NK5uwruTra/view.vectors.2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -i'FMT/FGS[*:0]="AAAAAA"' /tmp/NK5uwruTra/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -i'FMT/FGS[*:2]="C"' /tmp/NK5uwruTra/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -i'FMT/FGS[*:4]="EE"' /tmp/NK5uwruTra/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -i'FMT/FRS[*:1]="BB"' /tmp/NK5uwruTra/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -i'TXT0="text"' /tmp/NK5uwruTra/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -T /build/bcftools-1.16/test/view.chrs.tab /tmp/NK5uwruTra/view.chrs.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view -Ob -T /build/bcftools-1.16/test/view.chrs.tab /tmp/NK5uwruTra/view.chrs.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -i 'POS>=3062917' /tmp/NK5uwruTra/filter.2.vcf.gz 1:3062917-3157410 .. ok test_vcf_view: /build/bcftools-1.16/bcftools view -Ob -i 'POS>=3062917' /tmp/NK5uwruTra/filter.2.vcf.gz 1:3062917-3157410 | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -r 1:10,1:12,1:10 /tmp/NK5uwruTra/idx.1.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -r 1:1172777-1172804,1:1172806-1172808 /tmp/NK5uwruTra/idx.2.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -R /build/bcftools-1.16/test/idx.2.bed /tmp/NK5uwruTra/idx.2.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -R /build/bcftools-1.16/test/idx.3.bed /tmp/NK5uwruTra/idx.3.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -R /build/bcftools-1.16/test/idx.4.bed /tmp/NK5uwruTra/idx.4.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -Ht 2 /tmp/NK5uwruTra/view-t.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -Ht 3 /tmp/NK5uwruTra/view-t.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 0 /tmp/NK5uwruTra/overlap.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 1 /tmp/NK5uwruTra/overlap.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 2 /tmp/NK5uwruTra/overlap.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 0 /tmp/NK5uwruTra/overlap.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 1 /tmp/NK5uwruTra/overlap.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 2 /tmp/NK5uwruTra/overlap.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 0 /tmp/NK5uwruTra/overlap.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 1 /tmp/NK5uwruTra/overlap.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 2 /tmp/NK5uwruTra/overlap.vcf.gz .. ok test_vcf_64bit: /build/bcftools-1.16/bcftools view /build/bcftools-1.16/test/view64bit.1.vcf -H .. ok test_vcf_64bit: /build/bcftools-1.16/bcftools view /build/bcftools-1.16/test/view64bit.1.vcf | /build/bcftools-1.16/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-1.16/bcftools view /build/bcftools-1.16/test/view64bit.1.vcf -Ou | /build/bcftools-1.16/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-1.16/bcftools view /build/bcftools-1.16/test/view64bit.2.vcf -H .. ok test_vcf_64bit: /build/bcftools-1.16/bcftools view /build/bcftools-1.16/test/view64bit.2.vcf | /build/bcftools-1.16/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-1.16/bcftools view /build/bcftools-1.16/test/view64bit.2.vcf -Ou | /build/bcftools-1.16/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-1.16/bcftools view /build/bcftools-1.16/test/view64bit.3.vcf -H .. ok test_vcf_64bit: /build/bcftools-1.16/bcftools view /build/bcftools-1.16/test/view64bit.3.vcf | /build/bcftools-1.16/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-1.16/bcftools view /build/bcftools-1.16/test/view64bit.4.vcf -H .. ok test_vcf_64bit: /build/bcftools-1.16/bcftools view /build/bcftools-1.16/test/view64bit.4.vcf | /build/bcftools-1.16/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-1.16/bcftools view /build/bcftools-1.16/test/view64bit.4.vcf -Ou | /build/bcftools-1.16/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-1.16/bcftools view /build/bcftools-1.16/test/view64bit.5.vcf -H .. ok test_vcf_64bit: /build/bcftools-1.16/bcftools view /build/bcftools-1.16/test/view64bit.5.vcf | /build/bcftools-1.16/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-1.16/bcftools view /build/bcftools-1.16/test/view64bit.5.vcf -Ou | /build/bcftools-1.16/bcftools view -H .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -C5:nonmajor /tmp/NK5uwruTra/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -c6:nonmajor /tmp/NK5uwruTra/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -q0.3:major /tmp/NK5uwruTra/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/NK5uwruTra/view.filter.annovar.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -i 'Gene.refGene~"NOD"' /tmp/NK5uwruTra/view.filter.annovar.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -i 'LJB2_MutationTaster=="0.291000"' /tmp/NK5uwruTra/view.filter.annovar.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -a /tmp/NK5uwruTra/view-a.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -T /build/bcftools-1.16/test/view.sites.txt /tmp/NK5uwruTra/view.sites.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view -Ob -T /build/bcftools-1.16/test/view.sites.txt /tmp/NK5uwruTra/view.sites.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -T /build/bcftools-1.16/test/view.sites.txt.gz /tmp/NK5uwruTra/view.sites.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view -Ob -T /build/bcftools-1.16/test/view.sites.txt.gz /tmp/NK5uwruTra/view.sites.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_head: /build/bcftools-1.16/bcftools head /build/bcftools-1.16/test/mpileup.2.vcf .. ok test_vcf_head: /build/bcftools-1.16/bcftools head -h 0 /build/bcftools-1.16/test/mpileup.2.vcf .. ok test_vcf_head: /build/bcftools-1.16/bcftools head -h 1 /build/bcftools-1.16/test/mpileup.2.vcf .. ok test_vcf_head: /build/bcftools-1.16/bcftools head -h 5 /build/bcftools-1.16/test/mpileup.2.vcf .. ok test_vcf_head: /build/bcftools-1.16/bcftools head -h 22 /build/bcftools-1.16/test/mpileup.2.vcf .. ok test_vcf_head: /build/bcftools-1.16/bcftools head -h 23 /build/bcftools-1.16/test/mpileup.2.vcf .. ok test_vcf_head: /build/bcftools-1.16/bcftools head -n 0 /build/bcftools-1.16/test/mpileup.2.vcf .. ok test_vcf_head: /build/bcftools-1.16/bcftools head -n 1 /build/bcftools-1.16/test/mpileup.2.vcf .. ok test_vcf_head: /build/bcftools-1.16/bcftools head -n 5 /build/bcftools-1.16/test/mpileup.2.vcf .. ok test_vcf_head: /build/bcftools-1.16/bcftools head -h 5 -n 5 < /build/bcftools-1.16/test/mpileup.2.vcf .. ok test_vcf_call: /build/bcftools-1.16/bcftools call --no-version -mv /build/bcftools-1.16/test/mpileup.vcf .. ok test_vcf_call: /build/bcftools-1.16/bcftools call -Ob -mv /build/bcftools-1.16/test/mpileup.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.16/bcftools call --no-version -mg0 /build/bcftools-1.16/test/mpileup.vcf .. ok test_vcf_call: /build/bcftools-1.16/bcftools call -Ob -mg0 /build/bcftools-1.16/test/mpileup.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.16/bcftools call --no-version -mv -S /build/bcftools-1.16/test/mpileup.3.samples /build/bcftools-1.16/test/mpileup.vcf .. ok test_vcf_call: /build/bcftools-1.16/bcftools call -Ob -mv -S /build/bcftools-1.16/test/mpileup.3.samples /build/bcftools-1.16/test/mpileup.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.16/bcftools call --no-version -mv -S /build/bcftools-1.16/test/mpileup.4.samples /build/bcftools-1.16/test/mpileup.vcf .. ok test_vcf_call: /build/bcftools-1.16/bcftools call -Ob -mv -S /build/bcftools-1.16/test/mpileup.4.samples /build/bcftools-1.16/test/mpileup.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.16/bcftools call --no-version -mv -S /build/bcftools-1.16/test/mpileup.5.samples /build/bcftools-1.16/test/mpileup.vcf .. ok test_vcf_call: /build/bcftools-1.16/bcftools call -Ob -mv -S /build/bcftools-1.16/test/mpileup.5.samples /build/bcftools-1.16/test/mpileup.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.16/bcftools call --no-version -mv --ploidy-file /build/bcftools-1.16/test/mpileup.ploidy -S /build/bcftools-1.16/test/mpileup.samples /build/bcftools-1.16/test/mpileup.X.vcf .. ok test_vcf_call: /build/bcftools-1.16/bcftools call -Ob -mv --ploidy-file /build/bcftools-1.16/test/mpileup.ploidy -S /build/bcftools-1.16/test/mpileup.samples /build/bcftools-1.16/test/mpileup.X.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.16/bcftools call --no-version -mv --ploidy-file /build/bcftools-1.16/test/mpileup.ploidy -S /build/bcftools-1.16/test/mpileup.ped /build/bcftools-1.16/test/mpileup.X.vcf .. ok test_vcf_call: /build/bcftools-1.16/bcftools call -Ob -mv --ploidy-file /build/bcftools-1.16/test/mpileup.ploidy -S /build/bcftools-1.16/test/mpileup.ped /build/bcftools-1.16/test/mpileup.X.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.16/bcftools call --no-version -mv --ploidy-file /build/bcftools-1.16/test/mpileup.ploidy -S /build/bcftools-1.16/test/mpileup.2.samples /build/bcftools-1.16/test/mpileup.X.vcf .. ok test_vcf_call: /build/bcftools-1.16/bcftools call -Ob -mv --ploidy-file /build/bcftools-1.16/test/mpileup.ploidy -S /build/bcftools-1.16/test/mpileup.2.samples /build/bcftools-1.16/test/mpileup.X.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.16/bcftools call --no-version -mv /build/bcftools-1.16/test/mpileup.NA19213.NA19129.vcf .. ok test_vcf_call: /build/bcftools-1.16/bcftools call -Ob -mv /build/bcftools-1.16/test/mpileup.NA19213.NA19129.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.16/bcftools call --no-version -mv -G - --group-samples-tag AD /build/bcftools-1.16/test/mpileup.NA19213.NA19129.vcf .. ok test_vcf_call: /build/bcftools-1.16/bcftools call -Ob -mv -G - --group-samples-tag AD /build/bcftools-1.16/test/mpileup.NA19213.NA19129.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.16/bcftools call --no-version -mv /build/bcftools-1.16/test/mpileup.hwe.vcf .. ok test_vcf_call: /build/bcftools-1.16/bcftools call -Ob -mv /build/bcftools-1.16/test/mpileup.hwe.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.16/bcftools call --no-version -mv -G - --group-samples-tag AD /build/bcftools-1.16/test/mpileup.hwe.vcf .. ok test_vcf_call: /build/bcftools-1.16/bcftools call -Ob -mv -G - --group-samples-tag AD /build/bcftools-1.16/test/mpileup.hwe.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.16/bcftools call --no-version -mv -G /build/bcftools-1.16/test/mpileup.hwe.samples --group-samples-tag AD /build/bcftools-1.16/test/mpileup.hwe.vcf .. ok test_vcf_call: /build/bcftools-1.16/bcftools call -Ob -mv -G /build/bcftools-1.16/test/mpileup.hwe.samples --group-samples-tag AD /build/bcftools-1.16/test/mpileup.hwe.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-1.16/bcftools call --no-version -mA -C alleles -T /tmp/NK5uwruTra/mpileup.tab.gz /build/bcftools-1.16/test/mpileup.vcf .. ok test_vcf_call_cAls: /build/bcftools-1.16/bcftools call -Ob -mA -C alleles -T /tmp/NK5uwruTra/mpileup.tab.gz /build/bcftools-1.16/test/mpileup.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-1.16/bcftools call --no-version -mA -C alleles -T /tmp/NK5uwruTra/mpileup.2.tab.gz /build/bcftools-1.16/test/mpileup.2.vcf .. ok test_vcf_call_cAls: /build/bcftools-1.16/bcftools call -Ob -mA -C alleles -T /tmp/NK5uwruTra/mpileup.2.tab.gz /build/bcftools-1.16/test/mpileup.2.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-1.16/bcftools call --no-version -mA -C alleles -T /tmp/NK5uwruTra/mpileup.3.tab.gz -i /build/bcftools-1.16/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /build/bcftools-1.16/bcftools call -Ob -mA -C alleles -T /tmp/NK5uwruTra/mpileup.3.tab.gz -i /build/bcftools-1.16/test/mpileup.3.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-1.16/bcftools call --no-version -mA -C alleles -T /tmp/NK5uwruTra/mpileup.4.tab.gz -i /build/bcftools-1.16/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /build/bcftools-1.16/bcftools call -Ob -mA -C alleles -T /tmp/NK5uwruTra/mpileup.4.tab.gz -i /build/bcftools-1.16/test/mpileup.3.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-1.16/bcftools call --no-version -mA -C alleles -T /tmp/NK5uwruTra/mpileup.5.tab.gz -i /build/bcftools-1.16/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /build/bcftools-1.16/bcftools call -Ob -mA -C alleles -T /tmp/NK5uwruTra/mpileup.5.tab.gz -i /build/bcftools-1.16/test/mpileup.3.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-1.16/bcftools call --no-version -mA -C alleles -T /tmp/NK5uwruTra/mpileup.6.tab.gz -i /build/bcftools-1.16/test/mpileup.4.vcf .. ok test_vcf_call_cAls: /build/bcftools-1.16/bcftools call -Ob -mA -C alleles -T /tmp/NK5uwruTra/mpileup.6.tab.gz -i /build/bcftools-1.16/test/mpileup.4.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-1.16/bcftools call --no-version -mA -C alleles -T /tmp/NK5uwruTra/mpileup.7.tab.gz -i /build/bcftools-1.16/test/mpileup.5.vcf .. ok test_vcf_call_cAls: /build/bcftools-1.16/bcftools call -Ob -mA -C alleles -T /tmp/NK5uwruTra/mpileup.7.tab.gz -i /build/bcftools-1.16/test/mpileup.5.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-1.16/bcftools call --no-version -mA -C alleles -T /tmp/NK5uwruTra/mpileup.cals.1.tab.gz /build/bcftools-1.16/test/mpileup.cals.1.vcf .. ok test_vcf_call_cAls: /build/bcftools-1.16/bcftools call -Ob -mA -C alleles -T /tmp/NK5uwruTra/mpileup.cals.1.tab.gz /build/bcftools-1.16/test/mpileup.cals.1.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-1.16/bcftools call --no-version -mA -C alleles -T /tmp/NK5uwruTra/mpileup.cals.2.tab.gz /build/bcftools-1.16/test/mpileup.cals.2.vcf .. ok test_vcf_call_cAls: /build/bcftools-1.16/bcftools call -Ob -mA -C alleles -T /tmp/NK5uwruTra/mpileup.cals.2.tab.gz /build/bcftools-1.16/test/mpileup.cals.2.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.16/bcftools call --no-version -cv /build/bcftools-1.16/test/mpileup.c.vcf .. ok test_vcf_call: /build/bcftools-1.16/bcftools call -Ob -cv /build/bcftools-1.16/test/mpileup.c.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.16/bcftools call --no-version -cv --ploidy-file /build/bcftools-1.16/test/mpileup.ploidy -S /build/bcftools-1.16/test/mpileup.samples /build/bcftools-1.16/test/mpileup.c.X.vcf .. ok test_vcf_call: /build/bcftools-1.16/bcftools call -Ob -cv --ploidy-file /build/bcftools-1.16/test/mpileup.ploidy -S /build/bcftools-1.16/test/mpileup.samples /build/bcftools-1.16/test/mpileup.c.X.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.16/bcftools call --no-version -cv --ploidy-file /build/bcftools-1.16/test/mpileup.ploidy -S /build/bcftools-1.16/test/mpileup.ped /build/bcftools-1.16/test/mpileup.c.X.vcf .. ok test_vcf_call: /build/bcftools-1.16/bcftools call -Ob -cv --ploidy-file /build/bcftools-1.16/test/mpileup.ploidy -S /build/bcftools-1.16/test/mpileup.ped /build/bcftools-1.16/test/mpileup.c.X.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.16/bcftools call --no-version -cv --ploidy-file /build/bcftools-1.16/test/mpileup.ploidy -S /build/bcftools-1.16/test/mpileup.2.samples /build/bcftools-1.16/test/mpileup.c.X.vcf .. ok test_vcf_call: /build/bcftools-1.16/bcftools call -Ob -cv --ploidy-file /build/bcftools-1.16/test/mpileup.ploidy -S /build/bcftools-1.16/test/mpileup.2.samples /build/bcftools-1.16/test/mpileup.c.X.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.16/bcftools call --no-version -mv /build/bcftools-1.16/test/call-G.vcf .. ok test_vcf_call: /build/bcftools-1.16/bcftools call -Ob -mv /build/bcftools-1.16/test/call-G.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.16/bcftools call --no-version -mv -G - --group-samples-tag AD /build/bcftools-1.16/test/call-G.vcf .. ok test_vcf_call: /build/bcftools-1.16/bcftools call -Ob -mv -G - --group-samples-tag AD /build/bcftools-1.16/test/call-G.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.16/bcftools call --no-version -mv -F AN_POP,AC_POP /build/bcftools-1.16/test/call-G.2.vcf .. ok test_vcf_call: /build/bcftools-1.16/bcftools call -Ob -mv -F AN_POP,AC_POP /build/bcftools-1.16/test/call-G.2.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.16/bcftools call --no-version -m /build/bcftools-1.16/test/call.af-fixation.vcf .. ok test_vcf_call: /build/bcftools-1.16/bcftools call -Ob -m /build/bcftools-1.16/test/call.af-fixation.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.16/bcftools call --no-version -m -G /build/bcftools-1.16/test/call.af-fixation.txt /build/bcftools-1.16/test/call.af-fixation.vcf .. ok test_vcf_call: /build/bcftools-1.16/bcftools call -Ob -m -G /build/bcftools-1.16/test/call.af-fixation.txt /build/bcftools-1.16/test/call.af-fixation.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.16/bcftools call --no-version -m -G /build/bcftools-1.16/test/call.af-fixation.txt -a GP,GQ /build/bcftools-1.16/test/call.af-fixation.vcf .. ok test_vcf_call: /build/bcftools-1.16/bcftools call -Ob -m -G /build/bcftools-1.16/test/call.af-fixation.txt -a GP,GQ /build/bcftools-1.16/test/call.af-fixation.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -S. -e'TXT0="text"' /build/bcftools-1.16/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -S. -e'TXT0="text"' /build/bcftools-1.16/test/view.filter.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -S. -e'FMT/FRS[*:1]="BB"' /build/bcftools-1.16/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -S. -e'FMT/FRS[*:1]="BB"' /build/bcftools-1.16/test/view.filter.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -S. -e'FMT/FGS[*:0]="AAAAAA"' /build/bcftools-1.16/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -S. -e'FMT/FGS[*:0]="AAAAAA"' /build/bcftools-1.16/test/view.filter.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -S. -e'FMT/FGS[*:1]="BBB"' /build/bcftools-1.16/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -S. -e'FMT/FGS[*:1]="BBB"' /build/bcftools-1.16/test/view.filter.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -S. -e'FMT/FGS[*:4]="EE"' /build/bcftools-1.16/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -S. -e'FMT/FGS[*:4]="EE"' /build/bcftools-1.16/test/view.filter.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -S. -e'FMT/STR="XX"' /build/bcftools-1.16/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -S. -e'FMT/STR="XX"' /build/bcftools-1.16/test/view.filter.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -S. -e'FMT/FILTER="aaa"' /build/bcftools-1.16/test/view.filter.2.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -S. -e'FMT/FILTER="aaa"' /build/bcftools-1.16/test/view.filter.2.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -mx -g2 -G2 /build/bcftools-1.16/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -mx -g2 -G2 /build/bcftools-1.16/test/filter.1.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /build/bcftools-1.16/test/filter.2.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /build/bcftools-1.16/test/filter.2.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -e'INFO/DP=19' /build/bcftools-1.16/test/filter.3.vcf | /build/bcftools-1.16/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -e'INFO/DP=19' /build/bcftools-1.16/test/filter.3.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -e'INFO/DP=19' -s XX /build/bcftools-1.16/test/filter.3.vcf | /build/bcftools-1.16/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -e'INFO/DP=19' -s XX /build/bcftools-1.16/test/filter.3.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -e'INFO/DP=19' -s XX -m+ /build/bcftools-1.16/test/filter.3.vcf | /build/bcftools-1.16/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+ /build/bcftools-1.16/test/filter.3.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -e'INFO/DP=19' -s XX -mx /build/bcftools-1.16/test/filter.3.vcf | /build/bcftools-1.16/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -e'INFO/DP=19' -s XX -mx /build/bcftools-1.16/test/filter.3.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -e'INFO/DP=19' -s XX -m+x /build/bcftools-1.16/test/filter.3.vcf | /build/bcftools-1.16/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+x /build/bcftools-1.16/test/filter.3.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -e'FMT/GT="0/2"' /build/bcftools-1.16/test/filter.3.vcf | /build/bcftools-1.16/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -e'FMT/GT="0/2"' /build/bcftools-1.16/test/filter.3.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -e'FMT/GT="0/2"' -s XX /build/bcftools-1.16/test/filter.3.vcf | /build/bcftools-1.16/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX /build/bcftools-1.16/test/filter.3.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -e'FMT/GT="0/2"' -s XX -m+ /build/bcftools-1.16/test/filter.3.vcf | /build/bcftools-1.16/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+ /build/bcftools-1.16/test/filter.3.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -e'FMT/GT="0/2"' -s XX -mx /build/bcftools-1.16/test/filter.3.vcf | /build/bcftools-1.16/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -mx /build/bcftools-1.16/test/filter.3.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -e'FMT/GT="0/2"' -s XX -m+x /build/bcftools-1.16/test/filter.3.vcf | /build/bcftools-1.16/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+x /build/bcftools-1.16/test/filter.3.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -i'FMT/GT="0/0" && AC[*]=2' /build/bcftools-1.16/test/filter.2.vcf | /build/bcftools-1.16/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -i'FMT/GT="0/0" && AC[*]=2' /build/bcftools-1.16/test/filter.2.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -i'AC[*]=2 && FMT/GT="0/0"' /build/bcftools-1.16/test/filter.2.vcf | /build/bcftools-1.16/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -i'AC[*]=2 && FMT/GT="0/0"' /build/bcftools-1.16/test/filter.2.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -i'ALT="."' /build/bcftools-1.16/test/filter.2.vcf | /build/bcftools-1.16/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -i'ALT="."' /build/bcftools-1.16/test/filter.2.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -S . -i 'FORMAT/TEST3<25' /build/bcftools-1.16/test/filter.4.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -S . -i 'FORMAT/TEST3<25' /build/bcftools-1.16/test/filter.4.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -S . -i 'FORMAT/TEST4<25' /build/bcftools-1.16/test/filter.4.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -S . -i 'FORMAT/TEST4<25' /build/bcftools-1.16/test/filter.4.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -i'GT="A"' /build/bcftools-1.16/test/filter.2.vcf | /build/bcftools-1.16/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -i'GT="A"' /build/bcftools-1.16/test/filter.2.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -i'GT="RR"' /build/bcftools-1.16/test/filter.2.vcf | /build/bcftools-1.16/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -i'GT="RR"' /build/bcftools-1.16/test/filter.2.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -i'GT="RA"' /build/bcftools-1.16/test/filter.2.vcf | /build/bcftools-1.16/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -i'GT="RA"' /build/bcftools-1.16/test/filter.2.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -i'GT="AR"' /build/bcftools-1.16/test/filter.2.vcf | /build/bcftools-1.16/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -i'GT="AR"' /build/bcftools-1.16/test/filter.2.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -i'GT="AA"' /build/bcftools-1.16/test/filter.2.vcf | /build/bcftools-1.16/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -i'GT="AA"' /build/bcftools-1.16/test/filter.2.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -i'GT="aA"' /build/bcftools-1.16/test/filter.2.vcf | /build/bcftools-1.16/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -i'GT="aA"' /build/bcftools-1.16/test/filter.2.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -i'GT="Aa"' /build/bcftools-1.16/test/filter.2.vcf | /build/bcftools-1.16/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -i'GT="Aa"' /build/bcftools-1.16/test/filter.2.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -i'GT="HOM"' /build/bcftools-1.16/test/filter.2.vcf | /build/bcftools-1.16/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -i'GT="HOM"' /build/bcftools-1.16/test/filter.2.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -i'GT="HET"' /build/bcftools-1.16/test/filter.2.vcf | /build/bcftools-1.16/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -i'GT="HET"' /build/bcftools-1.16/test/filter.2.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -i'GT="HAP"' /build/bcftools-1.16/test/filter.2.vcf | /build/bcftools-1.16/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -i'GT="HAP"' /build/bcftools-1.16/test/filter.2.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -i'AD[:1]=11' /build/bcftools-1.16/test/filter.5.vcf | /build/bcftools-1.16/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -i'AD[:1]=11' /build/bcftools-1.16/test/filter.5.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -i'AD[1:]=11' /build/bcftools-1.16/test/filter.5.vcf | /build/bcftools-1.16/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -i'AD[1:]=11' /build/bcftools-1.16/test/filter.5.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -i'FR[0:1]=11' /build/bcftools-1.16/test/filter.5.vcf | /build/bcftools-1.16/bcftools query -f '%POS[\t%FR]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -i'FR[0:1]=11' /build/bcftools-1.16/test/filter.5.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS[\t%FR]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -i'AD[*]="."' /build/bcftools-1.16/test/filter.5.vcf | /build/bcftools-1.16/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -i'AD[*]="."' /build/bcftools-1.16/test/filter.5.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -i'AD[0:0]=="."' /build/bcftools-1.16/test/filter.5.vcf | /build/bcftools-1.16/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -i'AD[0:0]=="."' /build/bcftools-1.16/test/filter.5.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -i'AD[0:0]!="."' /build/bcftools-1.16/test/filter.5.vcf | /build/bcftools-1.16/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -i'AD[0:0]!="."' /build/bcftools-1.16/test/filter.5.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -i'QUAL=="."' /build/bcftools-1.16/test/filter.5.vcf | /build/bcftools-1.16/bcftools query -f '%POS\t%QUAL\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -i'QUAL=="."' /build/bcftools-1.16/test/filter.5.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS\t%QUAL\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -i'N_PASS(DP>32)=1' /build/bcftools-1.16/test/filter.2.vcf | /build/bcftools-1.16/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -i'N_PASS(DP>32)=1' /build/bcftools-1.16/test/filter.2.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -i'F_PASS(DP>32)=0.5' /build/bcftools-1.16/test/filter.2.vcf | /build/bcftools-1.16/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -i'F_PASS(DP>32)=0.5' /build/bcftools-1.16/test/filter.2.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -i'F_MISSING>=1/5' /build/bcftools-1.16/test/filter.6.vcf | /build/bcftools-1.16/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -i'F_MISSING>=1/5' /build/bcftools-1.16/test/filter.6.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -i'F_MISSING>=0.2' /build/bcftools-1.16/test/filter.6.vcf | /build/bcftools-1.16/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -i'F_MISSING>=0.2' /build/bcftools-1.16/test/filter.6.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -i'F_PASS(GT=="mis")>=1/5' /build/bcftools-1.16/test/filter.6.vcf | /build/bcftools-1.16/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -i'F_PASS(GT=="mis")>=1/5' /build/bcftools-1.16/test/filter.6.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -i'F_PASS(GT=="mis")>=0.2' /build/bcftools-1.16/test/filter.6.vcf | /build/bcftools-1.16/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -i'F_PASS(GT=="mis")>=0.2' /build/bcftools-1.16/test/filter.6.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -mx -s + -g2:mnp,indel,other /build/bcftools-1.16/test/filter.7.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -mx -s + -g2:mnp,indel,other /build/bcftools-1.16/test/filter.7.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -S . -e 'FORMAT/AO==4' /build/bcftools-1.16/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -S . -e 'FORMAT/AO==4' /build/bcftools-1.16/test/filter.8.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -S . -e 'MAX(FORMAT/AO[0:])==4' /build/bcftools-1.16/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -S . -e 'MAX(FORMAT/AO[0:])==4' /build/bcftools-1.16/test/filter.8.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -S . -e 'MAX(FORMAT/AO)==4' /build/bcftools-1.16/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -S . -e 'MAX(FORMAT/AO)==4' /build/bcftools-1.16/test/filter.8.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -S . -e 'MIN(FORMAT/AO[0:])==3' /build/bcftools-1.16/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO[0:])==3' /build/bcftools-1.16/test/filter.8.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -S . -e 'MIN(FORMAT/AO)==2' /build/bcftools-1.16/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO)==2' /build/bcftools-1.16/test/filter.8.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -S . -e 'MIN(FORMAT/AO[0:])==3' /build/bcftools-1.16/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO[0:])==3' /build/bcftools-1.16/test/filter.8.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -S . -e 'AVG(FORMAT/AO[2:])==4' /build/bcftools-1.16/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -S . -e 'AVG(FORMAT/AO[2:])==4' /build/bcftools-1.16/test/filter.8.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -S . -e 'MEDIAN(FORMAT/AO[2:])==4' /build/bcftools-1.16/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -S . -e 'MEDIAN(FORMAT/AO[2:])==4' /build/bcftools-1.16/test/filter.8.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -S . -e 'STDEV(FORMAT/AO[0:])=0.5' /build/bcftools-1.16/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -S . -e 'STDEV(FORMAT/AO[0:])=0.5' /build/bcftools-1.16/test/filter.8.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -S . -e 'SUM(FORMAT/AO[0:])=7' /build/bcftools-1.16/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -S . -e 'SUM(FORMAT/AO[0:])=7' /build/bcftools-1.16/test/filter.8.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -S . -e 'SMPL_MAX(FORMAT/AO)==4' /build/bcftools-1.16/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -S . -e 'SMPL_MAX(FORMAT/AO)==4' /build/bcftools-1.16/test/filter.8.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -S . -e 'sMIN(FORMAT/AO)==2' /build/bcftools-1.16/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -S . -e 'sMIN(FORMAT/AO)==2' /build/bcftools-1.16/test/filter.8.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -S . -e 'ABS(sAVG(FORMAT/AO)-3.66666)<1e-5' /build/bcftools-1.16/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -S . -e 'ABS(sAVG(FORMAT/AO)-3.66666)<1e-5' /build/bcftools-1.16/test/filter.8.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -S . -e 'sMEDIAN(FORMAT/AO)==4' /build/bcftools-1.16/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -S . -e 'sMEDIAN(FORMAT/AO)==4' /build/bcftools-1.16/test/filter.8.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -S . -e 'ABS(sSTDEV(FORMAT/AO)-1.2472191)<1e-5' /build/bcftools-1.16/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -S . -e 'ABS(sSTDEV(FORMAT/AO)-1.2472191)<1e-5' /build/bcftools-1.16/test/filter.8.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -S . -e 'sSUM(FORMAT/AO)==11' /build/bcftools-1.16/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -S . -e 'sSUM(FORMAT/AO)==11' /build/bcftools-1.16/test/filter.8.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -i 'QUAL/FMT/AD==55' /build/bcftools-1.16/test/filter.9.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -i 'QUAL/FMT/AD==55' /build/bcftools-1.16/test/filter.9.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -i 'QUAL/INFO/AD==10' /build/bcftools-1.16/test/filter.9.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -i 'QUAL/INFO/AD==10' /build/bcftools-1.16/test/filter.9.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -S . -e 'ABS(SMPL_MAX(FORMAT/AO))=5' /build/bcftools-1.16/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -S . -e 'ABS(SMPL_MAX(FORMAT/AO))=5' /build/bcftools-1.16/test/filter.8.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -S . -e 'PHRED(AO[1:])>-4' /build/bcftools-1.16/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -S . -e 'PHRED(AO[1:])>-4' /build/bcftools-1.16/test/filter.8.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -S . -e 'ABS(AO[1:])==2' /build/bcftools-1.16/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -S . -e 'ABS(AO[1:])==2' /build/bcftools-1.16/test/filter.8.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -i 'sum(AD[*]) > FORMAT/DP' /build/bcftools-1.16/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -i 'sum(AD[*]) > FORMAT/DP' /build/bcftools-1.16/test/filter.10.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -i 'FORMAT/DP < sum(AD[*])' /build/bcftools-1.16/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -i 'FORMAT/DP < sum(AD[*])' /build/bcftools-1.16/test/filter.10.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -i 'sum(AD[*]) < FORMAT/DP' /build/bcftools-1.16/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -i 'sum(AD[*]) < FORMAT/DP' /build/bcftools-1.16/test/filter.10.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -i 'FORMAT/DP > sum(AD[*])' /build/bcftools-1.16/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob -i 'FORMAT/DP > sum(AD[*])' /build/bcftools-1.16/test/filter.10.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 0 /build/bcftools-1.16/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 0 /build/bcftools-1.16/test/filter.1.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 1 /build/bcftools-1.16/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 1 /build/bcftools-1.16/test/filter.1.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 2 /build/bcftools-1.16/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 2 /build/bcftools-1.16/test/filter.1.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter --soft-filter xxx --mask ^2:1005-1008 /build/bcftools-1.16/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.16/bcftools filter -Ob --soft-filter xxx --mask ^2:1005-1008 /build/bcftools-1.16/test/filter.1.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_sort: /build/bcftools-1.16/bcftools sort -m 0 /build/bcftools-1.16/test/sort.vcf | /build/bcftools-1.16/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /build/bcftools-1.16/bcftools sort -Ob -m 0 /build/bcftools-1.16/test/sort.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /build/bcftools-1.16/bcftools sort -m 1000 /build/bcftools-1.16/test/sort.vcf | /build/bcftools-1.16/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /build/bcftools-1.16/bcftools sort -Ob -m 1000 /build/bcftools-1.16/test/sort.vcf | /build/bcftools-1.16/bcftools view | /build/bcftools-1.16/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_regions: /build/bcftools-1.16/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /build/bcftools-1.16/test/regions.tab /tmp/NK5uwruTra/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/regions.vcf.gz | /build/bcftools-1.16/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /build/bcftools-1.16/test/regions.tab .. ok test_vcf_regions: /build/bcftools-1.16/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /build/bcftools-1.16/test/regions.tab /tmp/NK5uwruTra/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-1.16/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/NK5uwruTra/regions.tab.gz /tmp/NK5uwruTra/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/regions.vcf.gz | /build/bcftools-1.16/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/NK5uwruTra/regions.tab.gz .. ok test_vcf_regions: /build/bcftools-1.16/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/NK5uwruTra/regions.tab.gz /tmp/NK5uwruTra/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-1.16/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/NK5uwruTra/regions.bed /tmp/NK5uwruTra/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/regions.vcf.gz | /build/bcftools-1.16/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/NK5uwruTra/regions.bed .. ok test_vcf_regions: /build/bcftools-1.16/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/NK5uwruTra/regions.bed /tmp/NK5uwruTra/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-1.16/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/NK5uwruTra/regions.bed.gz /tmp/NK5uwruTra/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/regions.vcf.gz | /build/bcftools-1.16/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/NK5uwruTra/regions.bed.gz .. ok test_vcf_regions: /build/bcftools-1.16/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/NK5uwruTra/regions.bed.gz /tmp/NK5uwruTra/regions.vcf.gz .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/NK5uwruTra/annotate.tab.gz -h /build/bcftools-1.16/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /build/bcftools-1.16/test/annotate.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/NK5uwruTra/annotate.tab.gz -h /build/bcftools-1.16/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /build/bcftools-1.16/test/annotate.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/NK5uwruTra/annotate2.tab.gz -h /build/bcftools-1.16/test/annotate.hdr -c CHROM,POS,-,T_STR /build/bcftools-1.16/test/annotate.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/NK5uwruTra/annotate2.tab.gz -h /build/bcftools-1.16/test/annotate.hdr -c CHROM,POS,-,T_STR /build/bcftools-1.16/test/annotate.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/NK5uwruTra/annotate2.tab.gz -h /build/bcftools-1.16/test/annotate.hdr -c CHROM,FROM,TO,T_STR /build/bcftools-1.16/test/annotate.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/NK5uwruTra/annotate2.tab.gz -h /build/bcftools-1.16/test/annotate.hdr -c CHROM,FROM,TO,T_STR /build/bcftools-1.16/test/annotate.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/NK5uwruTra/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/NK5uwruTra/annotate.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/NK5uwruTra/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/NK5uwruTra/annotate.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/NK5uwruTra/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/NK5uwruTra/annotate2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/NK5uwruTra/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/NK5uwruTra/annotate2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/NK5uwruTra/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/NK5uwruTra/annotate2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/NK5uwruTra/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/NK5uwruTra/annotate2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/NK5uwruTra/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/NK5uwruTra/annotate2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/NK5uwruTra/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/NK5uwruTra/annotate2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/NK5uwruTra/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/NK5uwruTra/annotate2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/NK5uwruTra/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/NK5uwruTra/annotate2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/NK5uwruTra/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/NK5uwruTra/annotate2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/NK5uwruTra/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/NK5uwruTra/annotate2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /build/bcftools-1.16/test/annotate3.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /build/bcftools-1.16/test/annotate3.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -x FORMAT /build/bcftools-1.16/test/annotate3.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -x FORMAT /build/bcftools-1.16/test/annotate3.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/NK5uwruTra/annots4.vcf.gz -c +INFO /tmp/NK5uwruTra/annotate4.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/NK5uwruTra/annots4.vcf.gz -c +INFO /tmp/NK5uwruTra/annotate4.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/NK5uwruTra/annots4.tab.gz -h /build/bcftools-1.16/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /build/bcftools-1.16/test/annotate4.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/NK5uwruTra/annots4.tab.gz -h /build/bcftools-1.16/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /build/bcftools-1.16/test/annotate4.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/NK5uwruTra/annots10.tab.gz -h /build/bcftools-1.16/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /build/bcftools-1.16/test/annotate10.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/NK5uwruTra/annots10.tab.gz -h /build/bcftools-1.16/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /build/bcftools-1.16/test/annotate10.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/NK5uwruTra/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/NK5uwruTra/annotate2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/NK5uwruTra/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/NK5uwruTra/annotate2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/NK5uwruTra/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /build/bcftools-1.16/test/annotate2.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/NK5uwruTra/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /build/bcftools-1.16/test/annotate2.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/NK5uwruTra/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/NK5uwruTra/annotate2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/NK5uwruTra/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/NK5uwruTra/annotate2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/NK5uwruTra/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/NK5uwruTra/annotate2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/NK5uwruTra/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/NK5uwruTra/annotate2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/NK5uwruTra/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/NK5uwruTra/annotate2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/NK5uwruTra/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/NK5uwruTra/annotate2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/NK5uwruTra/annots11.vcf.gz -c FMT /tmp/NK5uwruTra/annotate11.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/NK5uwruTra/annots11.vcf.gz -c FMT /tmp/NK5uwruTra/annotate11.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/NK5uwruTra/annots2.vcf.gz -c FMT/newGT:=GT /tmp/NK5uwruTra/annotate2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/NK5uwruTra/annots2.vcf.gz -c FMT/newGT:=GT /tmp/NK5uwruTra/annotate2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/NK5uwruTra/annots12.vcf.gz -c FMT/GT:=newGT /tmp/NK5uwruTra/annotate2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/NK5uwruTra/annots12.vcf.gz -c FMT/GT:=newGT /tmp/NK5uwruTra/annotate2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/NK5uwruTra/annots13.tab.gz -h /build/bcftools-1.16/test/annotate13.hdr -c CHROM,BEG,END,ABC /build/bcftools-1.16/test/annotate13.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/NK5uwruTra/annots13.tab.gz -h /build/bcftools-1.16/test/annotate13.hdr -c CHROM,BEG,END,ABC /build/bcftools-1.16/test/annotate13.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/NK5uwruTra/annots13.tab.gz -h /build/bcftools-1.16/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:append /build/bcftools-1.16/test/annotate13.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/NK5uwruTra/annots13.tab.gz -h /build/bcftools-1.16/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:append /build/bcftools-1.16/test/annotate13.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/NK5uwruTra/annots13.tab.gz -h /build/bcftools-1.16/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:unique /build/bcftools-1.16/test/annotate13.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/NK5uwruTra/annots13.tab.gz -h /build/bcftools-1.16/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:unique /build/bcftools-1.16/test/annotate13.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -x FILTER/XX,INFO/XX --force /build/bcftools-1.16/test/annotate14.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -x FILTER/XX,INFO/XX --force /build/bcftools-1.16/test/annotate14.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/NK5uwruTra/annotate15.tab.gz -h /build/bcftools-1.16/test/annotate15.hdr -s SAMPLE1 -c CHROM,FROM,TO,FMT/FOO,BAR /build/bcftools-1.16/test/annotate15.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/NK5uwruTra/annotate15.tab.gz -h /build/bcftools-1.16/test/annotate15.hdr -s SAMPLE1 -c CHROM,FROM,TO,FMT/FOO,BAR /build/bcftools-1.16/test/annotate15.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/NK5uwruTra/annotate15.tab.gz -h /build/bcftools-1.16/test/annotate15.hdr -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR /build/bcftools-1.16/test/annotate15.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/NK5uwruTra/annotate15.tab.gz -h /build/bcftools-1.16/test/annotate15.hdr -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR /build/bcftools-1.16/test/annotate15.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/NK5uwruTra/annotate15.tab.gz -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR -H '##FORMAT=' -H '##INFO=' /build/bcftools-1.16/test/annotate15.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/NK5uwruTra/annotate15.tab.gz -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR -H '##FORMAT=' -H '##INFO=' /build/bcftools-1.16/test/annotate15.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -x FILTER /build/bcftools-1.16/test/annotate16.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -x FILTER /build/bcftools-1.16/test/annotate16.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/NK5uwruTra/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/bcftools-1.16/test/annotate17.1.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/NK5uwruTra/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/bcftools-1.16/test/annotate17.1.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/NK5uwruTra/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/bcftools-1.16/test/annotate17.2.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/NK5uwruTra/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/bcftools-1.16/test/annotate17.2.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/NK5uwruTra/annotate17.3.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/bcftools-1.16/test/annotate17.3.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/NK5uwruTra/annotate17.3.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/bcftools-1.16/test/annotate17.3.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/NK5uwruTra/annotate18.1.tab.gz -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /build/bcftools-1.16/test/annotate18.1.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/NK5uwruTra/annotate18.1.tab.gz -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /build/bcftools-1.16/test/annotate18.1.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/NK5uwruTra/annotate18.2.tab.gz -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /build/bcftools-1.16/test/annotate18.2.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/NK5uwruTra/annotate18.2.tab.gz -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /build/bcftools-1.16/test/annotate18.2.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/NK5uwruTra/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/NK5uwruTra/annotate19.dst.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/NK5uwruTra/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/NK5uwruTra/annotate19.dst.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/NK5uwruTra/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/NK5uwruTra/annotate19.dst.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/NK5uwruTra/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/NK5uwruTra/annotate19.dst.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/NK5uwruTra/annotate20.src.vcf.gz -c FMT/GT /tmp/NK5uwruTra/annotate20.dst.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/NK5uwruTra/annotate20.src.vcf.gz -c FMT/GT /tmp/NK5uwruTra/annotate20.dst.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/NK5uwruTra/annotate20.src.vcf.gz -c +FMT/GT /tmp/NK5uwruTra/annotate20.dst.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/NK5uwruTra/annotate20.src.vcf.gz -c +FMT/GT /tmp/NK5uwruTra/annotate20.dst.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/NK5uwruTra/annotate20.src.vcf.gz -c -FMT/GT /tmp/NK5uwruTra/annotate20.dst.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/NK5uwruTra/annotate20.src.vcf.gz -c -FMT/GT /tmp/NK5uwruTra/annotate20.dst.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/NK5uwruTra/annotate.multi.tab.gz -c CHROM,POS,REF,ALT,ANN -l ANN:append /build/bcftools-1.16/test/annotate.multi.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/NK5uwruTra/annotate.multi.tab.gz -c CHROM,POS,REF,ALT,ANN -l ANN:append /build/bcftools-1.16/test/annotate.multi.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/NK5uwruTra/annotate.missing-append.tab.gz -c CHROM,POS,REF,ALT,STR,INT,FLT -l STR:append-missing,INT:append-missing,FLT:append-missing /build/bcftools-1.16/test/annotate.missing-append.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/NK5uwruTra/annotate.missing-append.tab.gz -c CHROM,POS,REF,ALT,STR,INT,FLT -l STR:append-missing,INT:append-missing,FLT:append-missing /build/bcftools-1.16/test/annotate.missing-append.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/NK5uwruTra/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /build/bcftools-1.16/test/annotate9.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/NK5uwruTra/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /build/bcftools-1.16/test/annotate9.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate --rename-annots /build/bcftools-1.16/test/annotate21.txt /build/bcftools-1.16/test/annotate21.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob --rename-annots /build/bcftools-1.16/test/annotate21.txt /build/bcftools-1.16/test/annotate21.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -c XX:=FORMAT/X-X,YY:=FORMAT/Y-Y,AA:=FORMAT/A-A,AA:=INFO/A-A,BB:=INFO/B-B,XX:=INFO/X-X,YY:=INFO/Y-Y,fltA:=FILTER/flt-A,fltB:=FILTER/flt-B,fltX:=FILTER/flt-X,fltY:=FILTER/flt-Y /build/bcftools-1.16/test/annotate21.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -c XX:=FORMAT/X-X,YY:=FORMAT/Y-Y,AA:=FORMAT/A-A,AA:=INFO/A-A,BB:=INFO/B-B,XX:=INFO/X-X,YY:=INFO/Y-Y,fltA:=FILTER/flt-A,fltB:=FILTER/flt-B,fltX:=FILTER/flt-X,fltY:=FILTER/flt-Y /build/bcftools-1.16/test/annotate21.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/NK5uwruTra/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/NK5uwruTra/annotate22.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/NK5uwruTra/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/NK5uwruTra/annotate22.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/NK5uwruTra/annotate23.tab.gz -c CHROM,POS,~ID,REF,ALT,INFO/END /build/bcftools-1.16/test/annotate23.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/NK5uwruTra/annotate23.tab.gz -c CHROM,POS,~ID,REF,ALT,INFO/END /build/bcftools-1.16/test/annotate23.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/NK5uwruTra/annotate24.src.vcf.gz -c XX /tmp/NK5uwruTra/annotate24.dst.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/NK5uwruTra/annotate24.src.vcf.gz -c XX /tmp/NK5uwruTra/annotate24.dst.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/NK5uwruTra/annotate25.tab.gz -c CHROM,POS,ID,REF,ALT,~INFO/END /build/bcftools-1.16/test/annotate25.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/NK5uwruTra/annotate25.tab.gz -c CHROM,POS,ID,REF,ALT,~INFO/END /build/bcftools-1.16/test/annotate25.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/NK5uwruTra/annotate26.tab.gz -c CHROM,POS,~POS /build/bcftools-1.16/test/annotate26.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/NK5uwruTra/annotate26.tab.gz -c CHROM,POS,~POS /build/bcftools-1.16/test/annotate26.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/NK5uwruTra/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,TSTR,TFLT,TINT /build/bcftools-1.16/test/annotate.missing.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/NK5uwruTra/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,TSTR,TFLT,TINT /build/bcftools-1.16/test/annotate.missing.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/NK5uwruTra/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.TSTR,.TFLT,.TINT /build/bcftools-1.16/test/annotate.missing.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/NK5uwruTra/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.TSTR,.TFLT,.TINT /build/bcftools-1.16/test/annotate.missing.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/NK5uwruTra/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.+TSTR,.+TFLT,.+TINT /build/bcftools-1.16/test/annotate.missing.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/NK5uwruTra/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.+TSTR,.+TFLT,.+TINT /build/bcftools-1.16/test/annotate.missing.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/NK5uwruTra/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,+TSTR,+TFLT,+TINT /build/bcftools-1.16/test/annotate.missing.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/NK5uwruTra/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,+TSTR,+TFLT,+TINT /build/bcftools-1.16/test/annotate.missing.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/NK5uwruTra/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.=TSTR,.=TFLT,.=TINT /build/bcftools-1.16/test/annotate.missing.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/NK5uwruTra/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.=TSTR,.=TFLT,.=TINT /build/bcftools-1.16/test/annotate.missing.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/NK5uwruTra/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,=TSTR,=TFLT,=TINT /build/bcftools-1.16/test/annotate.missing.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/NK5uwruTra/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,=TSTR,=TFLT,=TINT /build/bcftools-1.16/test/annotate.missing.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/NK5uwruTra/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique /build/bcftools-1.16/test/annotate.olap.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/NK5uwruTra/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique /build/bcftools-1.16/test/annotate.olap.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/NK5uwruTra/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique --min-overlap 0.4:0.5 /build/bcftools-1.16/test/annotate.olap.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/NK5uwruTra/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique --min-overlap 0.4:0.5 /build/bcftools-1.16/test/annotate.olap.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/NK5uwruTra/annots.id.vcf.gz -c ALT /tmp/NK5uwruTra/annotate.id.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/NK5uwruTra/annots.id.vcf.gz -c ALT /tmp/NK5uwruTra/annotate.id.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/NK5uwruTra/annots.id.vcf.gz -c +ALT /tmp/NK5uwruTra/annotate.id.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/NK5uwruTra/annots.id.vcf.gz -c +ALT /tmp/NK5uwruTra/annotate.id.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/NK5uwruTra/annotate27.tab.gz -c CHROM,POS,REF,ALT,EVIDENCE /build/bcftools-1.16/test/annotate27.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -Ob -a /tmp/NK5uwruTra/annotate27.tab.gz -c CHROM,POS,REF,ALT,EVIDENCE /build/bcftools-1.16/test/annotate27.vcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-1.16/bcftools concat --no-version /tmp/NK5uwruTra/concat.1.a.vcf.gz /tmp/NK5uwruTra/concat.1.b.vcf.gz .. ok test_vcf_concat: /build/bcftools-1.16/bcftools concat -Ob /tmp/NK5uwruTra/concat.1.a.vcf.gz /tmp/NK5uwruTra/concat.1.b.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-1.16/bcftools concat --no-version /tmp/NK5uwruTra/concat.1.a.bcf /tmp/NK5uwruTra/concat.1.b.bcf .. ok test_vcf_concat: /build/bcftools-1.16/bcftools concat -Ob /tmp/NK5uwruTra/concat.1.a.bcf /tmp/NK5uwruTra/concat.1.b.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-1.16/bcftools concat --no-version -a /tmp/NK5uwruTra/concat.2.a.vcf.gz /tmp/NK5uwruTra/concat.2.b.vcf.gz .. ok test_vcf_concat: /build/bcftools-1.16/bcftools concat -Ob -a /tmp/NK5uwruTra/concat.2.a.vcf.gz /tmp/NK5uwruTra/concat.2.b.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-1.16/bcftools concat --no-version -a /tmp/NK5uwruTra/concat.2.a.bcf /tmp/NK5uwruTra/concat.2.b.bcf .. ok test_vcf_concat: /build/bcftools-1.16/bcftools concat -Ob -a /tmp/NK5uwruTra/concat.2.a.bcf /tmp/NK5uwruTra/concat.2.b.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-1.16/bcftools concat --no-version -aD /tmp/NK5uwruTra/concat.2.a.vcf.gz /tmp/NK5uwruTra/concat.2.b.vcf.gz .. ok test_vcf_concat: /build/bcftools-1.16/bcftools concat -Ob -aD /tmp/NK5uwruTra/concat.2.a.vcf.gz /tmp/NK5uwruTra/concat.2.b.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-1.16/bcftools concat --no-version -aD /tmp/NK5uwruTra/concat.2.a.bcf /tmp/NK5uwruTra/concat.2.b.bcf .. ok test_vcf_concat: /build/bcftools-1.16/bcftools concat -Ob -aD /tmp/NK5uwruTra/concat.2.a.bcf /tmp/NK5uwruTra/concat.2.b.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-1.16/bcftools concat --no-version -l --ligate-warn /tmp/NK5uwruTra/concat.3.a.vcf.gz /tmp/NK5uwruTra/concat.3.b.vcf.gz /tmp/NK5uwruTra/concat.3.0.vcf.gz /tmp/NK5uwruTra/concat.3.c.vcf.gz /tmp/NK5uwruTra/concat.3.d.vcf.gz /tmp/NK5uwruTra/concat.3.e.vcf.gz /tmp/NK5uwruTra/concat.3.f.vcf.gz .. ok test_vcf_concat: /build/bcftools-1.16/bcftools concat -Ob -l --ligate-warn /tmp/NK5uwruTra/concat.3.a.vcf.gz /tmp/NK5uwruTra/concat.3.b.vcf.gz /tmp/NK5uwruTra/concat.3.0.vcf.gz /tmp/NK5uwruTra/concat.3.c.vcf.gz /tmp/NK5uwruTra/concat.3.d.vcf.gz /tmp/NK5uwruTra/concat.3.e.vcf.gz /tmp/NK5uwruTra/concat.3.f.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-1.16/bcftools concat --no-version -l --ligate-warn /tmp/NK5uwruTra/concat.3.a.bcf /tmp/NK5uwruTra/concat.3.b.bcf /tmp/NK5uwruTra/concat.3.0.bcf /tmp/NK5uwruTra/concat.3.c.bcf /tmp/NK5uwruTra/concat.3.d.bcf /tmp/NK5uwruTra/concat.3.e.bcf /tmp/NK5uwruTra/concat.3.f.bcf .. ok test_vcf_concat: /build/bcftools-1.16/bcftools concat -Ob -l --ligate-warn /tmp/NK5uwruTra/concat.3.a.bcf /tmp/NK5uwruTra/concat.3.b.bcf /tmp/NK5uwruTra/concat.3.0.bcf /tmp/NK5uwruTra/concat.3.c.bcf /tmp/NK5uwruTra/concat.3.d.bcf /tmp/NK5uwruTra/concat.3.e.bcf /tmp/NK5uwruTra/concat.3.f.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ Random seed for test_naive_concat: 2601152263 .. ok test_naive_concat: /build/bcftools-1.16/bcftools concat --naive-force /tmp/NK5uwruTra/naive_concat.0.bcf /tmp/NK5uwruTra/naive_concat.1.bcf /tmp/NK5uwruTra/naive_concat.2.bcf /tmp/NK5uwruTra/naive_concat.3.bcf /tmp/NK5uwruTra/naive_concat.4.bcf /tmp/NK5uwruTra/naive_concat.5.bcf /tmp/NK5uwruTra/naive_concat.6.bcf /tmp/NK5uwruTra/naive_concat.7.bcf /tmp/NK5uwruTra/naive_concat.8.bcf /tmp/NK5uwruTra/naive_concat.9.bcf | /build/bcftools-1.16/bcftools view -H .. ok test_naive_concat: /build/bcftools-1.16/bcftools concat --naive /tmp/NK5uwruTra/naive_concat.0.vcf.gz /tmp/NK5uwruTra/naive_concat.1.vcf.gz /tmp/NK5uwruTra/naive_concat.2.vcf.gz /tmp/NK5uwruTra/naive_concat.3.vcf.gz /tmp/NK5uwruTra/naive_concat.4.vcf.gz /tmp/NK5uwruTra/naive_concat.5.vcf.gz /tmp/NK5uwruTra/naive_concat.6.vcf.gz /tmp/NK5uwruTra/naive_concat.7.vcf.gz /tmp/NK5uwruTra/naive_concat.8.vcf.gz /tmp/NK5uwruTra/naive_concat.9.vcf.gz | /build/bcftools-1.16/bcftools view -H .. ok test_vcf_concat: /build/bcftools-1.16/bcftools concat --no-version -l /tmp/NK5uwruTra/concat.4.a.vcf.gz /tmp/NK5uwruTra/concat.4.b.vcf.gz .. ok test_vcf_concat: /build/bcftools-1.16/bcftools concat -Ob -l /tmp/NK5uwruTra/concat.4.a.vcf.gz /tmp/NK5uwruTra/concat.4.b.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-1.16/bcftools concat --no-version -l /tmp/NK5uwruTra/concat.4.a.bcf /tmp/NK5uwruTra/concat.4.b.bcf .. ok test_vcf_concat: /build/bcftools-1.16/bcftools concat -Ob -l /tmp/NK5uwruTra/concat.4.a.bcf /tmp/NK5uwruTra/concat.4.b.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-1.16/bcftools concat --no-version -l --ligate-warn /tmp/NK5uwruTra/concat.5.a.vcf.gz /tmp/NK5uwruTra/concat.5.b.vcf.gz /tmp/NK5uwruTra/concat.5.c.vcf.gz .. ok test_vcf_concat: /build/bcftools-1.16/bcftools concat -Ob -l --ligate-warn /tmp/NK5uwruTra/concat.5.a.vcf.gz /tmp/NK5uwruTra/concat.5.b.vcf.gz /tmp/NK5uwruTra/concat.5.c.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-1.16/bcftools concat --no-version -l --ligate-warn /tmp/NK5uwruTra/concat.5.a.bcf /tmp/NK5uwruTra/concat.5.b.bcf /tmp/NK5uwruTra/concat.5.c.bcf .. ok test_vcf_concat: /build/bcftools-1.16/bcftools concat -Ob -l --ligate-warn /tmp/NK5uwruTra/concat.5.a.bcf /tmp/NK5uwruTra/concat.5.b.bcf /tmp/NK5uwruTra/concat.5.c.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-1.16/bcftools concat --no-version -l --ligate-force /tmp/NK5uwruTra/concat.5.a.bcf /tmp/NK5uwruTra/concat.5.b.bcf /tmp/NK5uwruTra/concat.5.c.bcf .. ok test_vcf_concat: /build/bcftools-1.16/bcftools concat -Ob -l --ligate-force /tmp/NK5uwruTra/concat.5.a.bcf /tmp/NK5uwruTra/concat.5.b.bcf /tmp/NK5uwruTra/concat.5.c.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_reheader: /build/bcftools-1.16/bcftools reheader -h /build/bcftools-1.16/test/reheader.hdr /build/bcftools-1.16/test/reheader.vcf | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-1.16/test/reheader.vcf | /build/bcftools-1.16/bcftools reheader -h /build/bcftools-1.16/test/reheader.hdr | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.16/bcftools reheader -h /build/bcftools-1.16/test/reheader.hdr /tmp/NK5uwruTra/reheader.bcf | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/NK5uwruTra/reheader.bcf | /build/bcftools-1.16/bcftools reheader -h /build/bcftools-1.16/test/reheader.hdr | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.16/bcftools reheader -h /build/bcftools-1.16/test/reheader.hdr /tmp/NK5uwruTra/reheader.vcf.gz | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/NK5uwruTra/reheader.vcf.gz | /build/bcftools-1.16/bcftools reheader -h /build/bcftools-1.16/test/reheader.hdr | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.16/bcftools reheader -s /build/bcftools-1.16/test/reheader.samples /build/bcftools-1.16/test/reheader.vcf | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-1.16/test/reheader.vcf | /build/bcftools-1.16/bcftools reheader -s /build/bcftools-1.16/test/reheader.samples | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.16/bcftools reheader -s /build/bcftools-1.16/test/reheader.samples /tmp/NK5uwruTra/reheader.bcf | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/NK5uwruTra/reheader.bcf | /build/bcftools-1.16/bcftools reheader -s /build/bcftools-1.16/test/reheader.samples | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.16/bcftools reheader -s /build/bcftools-1.16/test/reheader.samples /tmp/NK5uwruTra/reheader.vcf.gz | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/NK5uwruTra/reheader.vcf.gz | /build/bcftools-1.16/bcftools reheader -s /build/bcftools-1.16/test/reheader.samples | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.16/bcftools reheader -s /build/bcftools-1.16/test/reheader.samples2 /build/bcftools-1.16/test/reheader.vcf | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-1.16/test/reheader.vcf | /build/bcftools-1.16/bcftools reheader -s /build/bcftools-1.16/test/reheader.samples2 | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.16/bcftools reheader -s /build/bcftools-1.16/test/reheader.samples2 /tmp/NK5uwruTra/reheader.bcf | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/NK5uwruTra/reheader.bcf | /build/bcftools-1.16/bcftools reheader -s /build/bcftools-1.16/test/reheader.samples2 | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.16/bcftools reheader -s /build/bcftools-1.16/test/reheader.samples2 /tmp/NK5uwruTra/reheader.vcf.gz | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/NK5uwruTra/reheader.vcf.gz | /build/bcftools-1.16/bcftools reheader -s /build/bcftools-1.16/test/reheader.samples2 | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.16/bcftools reheader -s /build/bcftools-1.16/test/reheader.samples3 /build/bcftools-1.16/test/reheader.vcf | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-1.16/test/reheader.vcf | /build/bcftools-1.16/bcftools reheader -s /build/bcftools-1.16/test/reheader.samples3 | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.16/bcftools reheader -s /build/bcftools-1.16/test/reheader.samples3 /tmp/NK5uwruTra/reheader.bcf | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/NK5uwruTra/reheader.bcf | /build/bcftools-1.16/bcftools reheader -s /build/bcftools-1.16/test/reheader.samples3 | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.16/bcftools reheader -s /build/bcftools-1.16/test/reheader.samples3 /tmp/NK5uwruTra/reheader.vcf.gz | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/NK5uwruTra/reheader.vcf.gz | /build/bcftools-1.16/bcftools reheader -s /build/bcftools-1.16/test/reheader.samples3 | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.16/bcftools reheader -s /build/bcftools-1.16/test/reheader.samples4 /build/bcftools-1.16/test/reheader.vcf | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-1.16/test/reheader.vcf | /build/bcftools-1.16/bcftools reheader -s /build/bcftools-1.16/test/reheader.samples4 | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.16/bcftools reheader -s /build/bcftools-1.16/test/reheader.samples4 /tmp/NK5uwruTra/reheader.bcf | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/NK5uwruTra/reheader.bcf | /build/bcftools-1.16/bcftools reheader -s /build/bcftools-1.16/test/reheader.samples4 | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.16/bcftools reheader -s /build/bcftools-1.16/test/reheader.samples4 /tmp/NK5uwruTra/reheader.vcf.gz | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/NK5uwruTra/reheader.vcf.gz | /build/bcftools-1.16/bcftools reheader -s /build/bcftools-1.16/test/reheader.samples4 | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.16/bcftools reheader -h /build/bcftools-1.16/test/reheader.empty.hdr /build/bcftools-1.16/test/empty.vcf | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-1.16/test/empty.vcf | /build/bcftools-1.16/bcftools reheader -h /build/bcftools-1.16/test/reheader.empty.hdr | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.16/bcftools reheader -h /build/bcftools-1.16/test/reheader.empty.hdr /tmp/NK5uwruTra/empty.bcf | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/NK5uwruTra/empty.bcf | /build/bcftools-1.16/bcftools reheader -h /build/bcftools-1.16/test/reheader.empty.hdr | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.16/bcftools reheader -h /build/bcftools-1.16/test/reheader.empty.hdr /tmp/NK5uwruTra/empty.vcf.gz | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/NK5uwruTra/empty.vcf.gz | /build/bcftools-1.16/bcftools reheader -h /build/bcftools-1.16/test/reheader.empty.hdr | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.16/bcftools reheader -f /build/bcftools-1.16/test/reheader.fai /build/bcftools-1.16/test/reheader.2.vcf | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.16/bcftools reheader -f /build/bcftools-1.16/test/reheader.fai /tmp/NK5uwruTra/reheader.2.bcf | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.16/bcftools reheader -f /build/bcftools-1.16/test/reheader.fai /tmp/NK5uwruTra/reheader.2.vcf.gz | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.16/bcftools reheader -h /build/bcftools-1.16/test/reheader.2.hdr -f /build/bcftools-1.16/test/reheader.fai /build/bcftools-1.16/test/reheader.2.vcf | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.16/bcftools reheader -h /build/bcftools-1.16/test/reheader.2.hdr -f /build/bcftools-1.16/test/reheader.fai /tmp/NK5uwruTra/reheader.2.bcf | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.16/bcftools reheader -h /build/bcftools-1.16/test/reheader.2.hdr -f /build/bcftools-1.16/test/reheader.fai /tmp/NK5uwruTra/reheader.2.vcf.gz | /build/bcftools-1.16/bcftools view --no-version .. ok test_rename_chrs: /build/bcftools-1.16/bcftools annotate --rename-chrs /tmp/NK5uwruTra/rename.map -Ov /tmp/NK5uwruTra/annotate.bcf | /build/bcftools-1.16/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /build/bcftools-1.16/bcftools annotate --rename-chrs /tmp/NK5uwruTra/rename.map -Ob /tmp/NK5uwruTra/annotate.bcf | /build/bcftools-1.16/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /build/bcftools-1.16/bcftools annotate --rename-chrs /tmp/NK5uwruTra/rename.map -Ov /build/bcftools-1.16/test/annotate.vcf | /build/bcftools-1.16/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /build/bcftools-1.16/bcftools annotate --rename-chrs /tmp/NK5uwruTra/rename.map -Ob /build/bcftools-1.16/test/annotate.vcf | /build/bcftools-1.16/bcftools query -f'%CHROM\t%POS\n' .. ok test_vcf_convert: /build/bcftools-1.16/bcftools convert -g -,. /tmp/NK5uwruTra/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/convert.vcf.gz | /build/bcftools-1.16/bcftools convert -g -,. .. ok test_vcf_convert: /build/bcftools-1.16/bcftools convert -g -,. --vcf-ids /tmp/NK5uwruTra/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/convert.vcf.gz | /build/bcftools-1.16/bcftools convert -g -,. --vcf-ids .. ok test_vcf_convert: /build/bcftools-1.16/bcftools convert -g -,. --vcf-ids --3N6 /tmp/NK5uwruTra/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/convert.vcf.gz | /build/bcftools-1.16/bcftools convert -g -,. --vcf-ids --3N6 .. ok test_vcf_convert: /build/bcftools-1.16/bcftools convert -g .,- /tmp/NK5uwruTra/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/convert.vcf.gz | /build/bcftools-1.16/bcftools convert -g .,- .. ok test_vcf_convert_hs2vcf: /build/bcftools-1.16/bcftools convert --vcf-ids -G /build/bcftools-1.16/test/convert.gs.gt.ids.gen,/build/bcftools-1.16/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-1.16/bcftools convert --vcf-ids -G /build/bcftools-1.16/test/convert.gs.gt.ids.gen,/build/bcftools-1.16/test/convert.gs.gt.samples -Ou | /build/bcftools-1.16/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-1.16/bcftools convert -G /build/bcftools-1.16/test/convert.gs.gt.ids.gen,/build/bcftools-1.16/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-1.16/bcftools convert -G /build/bcftools-1.16/test/convert.gs.gt.ids.gen,/build/bcftools-1.16/test/convert.gs.gt.samples -Ou | /build/bcftools-1.16/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-1.16/bcftools convert --3N6 -G /build/bcftools-1.16/test/convert.gs.gt.ids.3N6.gen,/build/bcftools-1.16/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-1.16/bcftools convert --3N6 -G /build/bcftools-1.16/test/convert.gs.gt.ids.3N6.gen,/build/bcftools-1.16/test/convert.gs.gt.samples -Ou | /build/bcftools-1.16/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-1.16/bcftools convert --vcf-ids -G /build/bcftools-1.16/test/convert.gs.gt.ids.gen.rev,/build/bcftools-1.16/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-1.16/bcftools convert --vcf-ids -G /build/bcftools-1.16/test/convert.gs.gt.ids.gen.rev,/build/bcftools-1.16/test/convert.gs.gt.samples -Ou | /build/bcftools-1.16/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-1.16/bcftools convert -G /build/bcftools-1.16/test/convert.gs.gt.ids.gen.rev,/build/bcftools-1.16/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-1.16/bcftools convert -G /build/bcftools-1.16/test/convert.gs.gt.ids.gen.rev,/build/bcftools-1.16/test/convert.gs.gt.samples -Ou | /build/bcftools-1.16/bcftools view | grep -v ^## .. ok test_vcf_convert: /build/bcftools-1.16/bcftools convert -g -,. --tag PL /tmp/NK5uwruTra/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/convert.vcf.gz | /build/bcftools-1.16/bcftools convert -g -,. --tag PL .. ok test_vcf_convert: /build/bcftools-1.16/bcftools convert -g .,- --tag PL /tmp/NK5uwruTra/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/convert.vcf.gz | /build/bcftools-1.16/bcftools convert -g .,- --tag PL .. ok test_vcf_convert: /build/bcftools-1.16/bcftools convert -g -,. --vcf-ids /tmp/NK5uwruTra/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/check.vcf.gz | /build/bcftools-1.16/bcftools convert -g -,. --vcf-ids .. ok test_vcf_convert: /build/bcftools-1.16/bcftools convert -g .,- --vcf-ids /tmp/NK5uwruTra/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/check.vcf.gz | /build/bcftools-1.16/bcftools convert -g .,- --vcf-ids .. ok test_vcf_convert: /build/bcftools-1.16/bcftools convert -g -,. --3N6 /tmp/NK5uwruTra/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/check.vcf.gz | /build/bcftools-1.16/bcftools convert -g -,. --3N6 .. ok test_vcf_convert: /build/bcftools-1.16/bcftools convert -g .,- --3N6 /tmp/NK5uwruTra/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/check.vcf.gz | /build/bcftools-1.16/bcftools convert -g .,- --3N6 .. ok test_vcf_convert: /build/bcftools-1.16/bcftools convert -g -,. --3N6 --vcf-ids /tmp/NK5uwruTra/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/check.vcf.gz | /build/bcftools-1.16/bcftools convert -g -,. --3N6 --vcf-ids .. ok test_vcf_convert: /build/bcftools-1.16/bcftools convert -g .,- --3N6 --vcf-ids /tmp/NK5uwruTra/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/check.vcf.gz | /build/bcftools-1.16/bcftools convert -g .,- --3N6 --vcf-ids .. ok test_vcf_convert: /build/bcftools-1.16/bcftools convert -h -,.,. /tmp/NK5uwruTra/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/convert.vcf.gz | /build/bcftools-1.16/bcftools convert -h -,.,. .. ok test_vcf_convert: /build/bcftools-1.16/bcftools convert -h .,-,. /tmp/NK5uwruTra/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/convert.vcf.gz | /build/bcftools-1.16/bcftools convert -h .,-,. .. ok test_vcf_convert: /build/bcftools-1.16/bcftools convert -h .,-,. --vcf-ids /tmp/NK5uwruTra/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/convert.vcf.gz | /build/bcftools-1.16/bcftools convert -h .,-,. --vcf-ids .. ok test_vcf_convert: /build/bcftools-1.16/bcftools convert -h .,.,- /tmp/NK5uwruTra/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/convert.vcf.gz | /build/bcftools-1.16/bcftools convert -h .,.,- .. ok test_vcf_convert_hls2vcf: /build/bcftools-1.16/bcftools convert -H /build/bcftools-1.16/test/convert.hls.gt.hap,/build/bcftools-1.16/test/convert.hls.gt.legend,/build/bcftools-1.16/test/convert.hls.gt.samples | grep -v ^## .. ok test_vcf_convert_hls2vcf: /build/bcftools-1.16/bcftools convert -H /build/bcftools-1.16/test/convert.hls.gt.hap,/build/bcftools-1.16/test/convert.hls.gt.legend,/build/bcftools-1.16/test/convert.hls.gt.samples -Ou | /build/bcftools-1.16/bcftools view | grep -v ^## .. ok test_vcf_convert: /build/bcftools-1.16/bcftools convert --haplegendsample -,.,. /tmp/NK5uwruTra/convert.hap-missing.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/convert.hap-missing.vcf.gz | /build/bcftools-1.16/bcftools convert --haplegendsample -,.,. .. ok test_vcf_convert: /build/bcftools-1.16/bcftools convert --hapsample -,. /tmp/NK5uwruTra/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/convert.vcf.gz | /build/bcftools-1.16/bcftools convert --hapsample -,. .. ok test_vcf_convert: /build/bcftools-1.16/bcftools convert --hapsample -,. --vcf-ids /tmp/NK5uwruTra/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/convert.vcf.gz | /build/bcftools-1.16/bcftools convert --hapsample -,. --vcf-ids .. ok test_vcf_convert: /build/bcftools-1.16/bcftools convert --hapsample .,- /tmp/NK5uwruTra/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/convert.vcf.gz | /build/bcftools-1.16/bcftools convert --hapsample .,- .. ok test_vcf_convert_hs2vcf: /build/bcftools-1.16/bcftools convert --hapsample2vcf /build/bcftools-1.16/test/convert.hs.gt.hap,/build/bcftools-1.16/test/convert.hs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-1.16/bcftools convert --hapsample2vcf /build/bcftools-1.16/test/convert.hs.gt.hap,/build/bcftools-1.16/test/convert.hs.gt.samples -Ou | /build/bcftools-1.16/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-1.16/bcftools convert --vcf-ids --hapsample2vcf /build/bcftools-1.16/test/convert.hs.gt.ids.hap,/build/bcftools-1.16/test/convert.hs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-1.16/bcftools convert --vcf-ids --hapsample2vcf /build/bcftools-1.16/test/convert.hs.gt.ids.hap,/build/bcftools-1.16/test/convert.hs.gt.samples -Ou | /build/bcftools-1.16/bcftools view | grep -v ^## .. ok test_vcf_convert_gvcf: /build/bcftools-1.16/bcftools convert --no-version --gvcf2vcf -i'FILTER="PASS"' -f /build/bcftools-1.16/test/gvcf.fa /tmp/NK5uwruTra/convert.gvcf.vcf.gz .. ok test_vcf_convert_gvcf: /build/bcftools-1.16/bcftools view -Ob /tmp/NK5uwruTra/convert.gvcf.vcf.gz | /build/bcftools-1.16/bcftools convert --gvcf2vcf -i'FILTER="PASS"' -f /build/bcftools-1.16/test/gvcf.fa | grep -v ^##bcftools .. ok test_vcf_convert_tsv2vcf: /build/bcftools-1.16/bcftools convert --no-version -c ID,CHROM,POS,AA -s SAMPLE1 -f /build/bcftools-1.16/test/23andme.fa --tsv2vcf /build/bcftools-1.16/test/convert.23andme .. ok test_vcf_convert_tsv2vcf: /build/bcftools-1.16/bcftools convert -Ou -c ID,CHROM,POS,AA -s SAMPLE1 -f /build/bcftools-1.16/test/23andme.fa --tsv2vcf /build/bcftools-1.16/test/convert.23andme | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/NK5uwruTra/consensus.vcf.gz -f /build/bcftools-1.16/test/consensus.fa -m /build/bcftools-1.16/test/consensus.tab .. ok test_vcf_consensus_chain: /build/bcftools-1.16/bcftools consensus /tmp/NK5uwruTra/consensus.vcf.gz -f /build/bcftools-1.16/test/consensus.fa -m /build/bcftools-1.16/test/consensus.tab -c /tmp/NK5uwruTra/consensus.1.chain.new >/dev/null; cat /tmp/NK5uwruTra/consensus.1.chain.new .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/NK5uwruTra/consensus.vcf.gz -f /build/bcftools-1.16/test/consensus.fa -H 1 -m /build/bcftools-1.16/test/consensus.tab .. ok test_vcf_consensus_chain: /build/bcftools-1.16/bcftools consensus /tmp/NK5uwruTra/consensus.vcf.gz -f /build/bcftools-1.16/test/consensus.fa -H 1 -m /build/bcftools-1.16/test/consensus.tab -c /tmp/NK5uwruTra/consensus.2.chain.new >/dev/null; cat /tmp/NK5uwruTra/consensus.2.chain.new .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/NK5uwruTra/consensus.vcf.gz -f /build/bcftools-1.16/test/consensus.fa -I -m /build/bcftools-1.16/test/consensus.tab .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/NK5uwruTra/consensus.vcf.gz -f /build/bcftools-1.16/test/consensus.fa -I -m /build/bcftools-1.16/test/consensus.tab --mask-with X -m /build/bcftools-1.16/test/consensus.tab --mask-with lc .. ok test_vcf_consensus_chain: /build/bcftools-1.16/bcftools consensus /tmp/NK5uwruTra/consensus.vcf.gz -f /build/bcftools-1.16/test/consensus.fa -I -m /build/bcftools-1.16/test/consensus.tab -c /tmp/NK5uwruTra/consensus.3.chain.new >/dev/null; cat /tmp/NK5uwruTra/consensus.3.chain.new .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/NK5uwruTra/consensus.vcf.gz -f /build/bcftools-1.16/test/consensus.fa -H 1 .. ok test_vcf_consensus_chain: /build/bcftools-1.16/bcftools consensus /tmp/NK5uwruTra/consensus.vcf.gz -f /build/bcftools-1.16/test/consensus.fa -H 1 -c /tmp/NK5uwruTra/consensus.4.chain.new >/dev/null; cat /tmp/NK5uwruTra/consensus.4.chain.new .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/NK5uwruTra/consensus2.vcf.gz -f /build/bcftools-1.16/test/consensus2.fa -H 1 .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/NK5uwruTra/consensus2.vcf.gz -f /build/bcftools-1.16/test/consensus2.fa -H 2 .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/NK5uwruTra/empty.vcf.gz -f /build/bcftools-1.16/test/consensus.fa .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/NK5uwruTra/consensus3.vcf.gz -f /build/bcftools-1.16/test/consensus2.fa -H 2 -M "?" .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/NK5uwruTra/consensus3.vcf.gz -f /build/bcftools-1.16/test/consensus2.fa -H 2 -M "?" -p xx_ .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/NK5uwruTra/consensus4.vcf.gz -f /build/bcftools-1.16/test/consensus2.fa .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/NK5uwruTra/consensus5.vcf.gz -f /build/bcftools-1.16/test/consensus5.fa --haplotype LA .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/NK5uwruTra/consensus6.vcf.gz -f /build/bcftools-1.16/test/consensus6.fa .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/NK5uwruTra/consensus7.vcf.gz -f /build/bcftools-1.16/test/consensus7.fa -H 2 .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/NK5uwruTra/consensus7.vcf.gz -f /build/bcftools-1.16/test/consensus7.fa -H 2pIu .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/NK5uwruTra/consensus7.vcf.gz -f /build/bcftools-1.16/test/consensus7.fa -H 1 .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/NK5uwruTra/consensus7.vcf.gz -f /build/bcftools-1.16/test/consensus7.fa -H 1pIu .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/NK5uwruTra/consensus8.vcf.gz -f /build/bcftools-1.16/test/consensus.fa .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/NK5uwruTra/consensus8.vcf.gz -f /build/bcftools-1.16/test/consensus.fa -a . .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/NK5uwruTra/consensus8.vcf.gz -f /build/bcftools-1.16/test/consensus.fa -a . -i 'type="snp" || type="ref"' .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/NK5uwruTra/consensus8.vcf.gz -f /build/bcftools-1.16/test/consensus.fa -a . -i 'ALT!=""' .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/NK5uwruTra/consensus8.vcf.gz -f /build/bcftools-1.16/test/consensus.fa -a . -e 'MinDP>15' .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/NK5uwruTra/consensus8.vcf.gz -f /build/bcftools-1.16/test/consensus.fa -a . -e 'MinDP<15' .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/NK5uwruTra/consensus.9.vcf.gz -f /build/bcftools-1.16/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/NK5uwruTra/consensus.9.vcf.gz -f /build/bcftools-1.16/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/NK5uwruTra/consensus.10.vcf.gz -f /build/bcftools-1.16/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/NK5uwruTra/consensus.10.vcf.gz -f /build/bcftools-1.16/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/NK5uwruTra/consensus.11.vcf.gz -f /build/bcftools-1.16/test/consensus.11.fa -s smpl .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/NK5uwruTra/consensus.11.vcf.gz -f /build/bcftools-1.16/test/consensus.11.fa -s smpl -a N .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/NK5uwruTra/consensus.12.vcf.gz -f /build/bcftools-1.16/test/consensus.12.fa .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/NK5uwruTra/consensus.13.vcf.gz -f /build/bcftools-1.16/test/consensus.13.fa .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/NK5uwruTra/consensus.14.vcf.gz -f /build/bcftools-1.16/test/consensus.14.fa .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/NK5uwruTra/consensus.12.vcf.gz -f /build/bcftools-1.16/test/consensus.12.fa --mark-del - --mark-ins uc --mark-snv uc .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/NK5uwruTra/consensus.15.vcf.gz -f /build/bcftools-1.16/test/consensus.15.fa -H I --mark-ins lc --mark-snv lc .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/NK5uwruTra/consensus.16.vcf.gz -f /build/bcftools-1.16/test/consensus.fa -I .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/NK5uwruTra/consensus.16.vcf.gz -f /build/bcftools-1.16/test/consensus.fa -H I .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/NK5uwruTra/consensus.17.vcf.gz -f /build/bcftools-1.16/test/consensus2.fa -M N -m /build/bcftools-1.16/test/consensus.17.bed .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/NK5uwruTra/consensus.18.vcf.gz -f /build/bcftools-1.16/test/consensus.18.fa .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/NK5uwruTra/consensus.19.vcf.gz -f /build/bcftools-1.16/test/consensus.19.fa .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r17:100-150 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r17:100-150 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r17:100-150 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -b /tmp/NK5uwruTra/mpileup.bam.list --no-version | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r17:100-150 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob -b /tmp/NK5uwruTra/mpileup.bam.urllist | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r17:100-150 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r17:100-150 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r17:100-150 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -b /tmp/NK5uwruTra/mpileup.cram.list --no-version | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r17:100-150 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob -b /tmp/NK5uwruTra/mpileup.cram.urllist | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a DP,DV -r17:100-600 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a DP,DV -r17:100-600 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a DP,DV -r17:100-600 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a DP,DV -r17:100-600 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r17:100-150 -S /build/bcftools-1.16/test/mplp.samples -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r17:100-150 -S /build/bcftools-1.16/test/mplp.samples -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r17:100-150 -S /build/bcftools-1.16/test/mplp.samples -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r17:100-150 -S /build/bcftools-1.16/test/mplp.samples -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r17:100-150 -S ^/build/bcftools-1.16/test/mplp.samples -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r17:100-150 -S ^/build/bcftools-1.16/test/mplp.samples -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r17:100-150 -S ^/build/bcftools-1.16/test/mplp.samples -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r17:100-150 -S ^/build/bcftools-1.16/test/mplp.samples -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -t17:100-150 -S /build/bcftools-1.16/test/mplp.9.samples -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.sam /build/bcftools-1.16/test/mpileup/mpileup.2.sam /build/bcftools-1.16/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -t17:100-150 -S /build/bcftools-1.16/test/mplp.9.samples -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.sam /build/bcftools-1.16/test/mpileup/mpileup.2.sam /build/bcftools-1.16/test/mpileup/mpileup.3.sam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -t17:100-150 -S /build/bcftools-1.16/test/mplp.9.samples -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -t17:100-150 -S /build/bcftools-1.16/test/mplp.9.samples -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -t17:100-150 -S /build/bcftools-1.16/test/mplp.9.samples -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -t17:100-150 -S /build/bcftools-1.16/test/mplp.9.samples -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -t17:100-150 -G /build/bcftools-1.16/test/mplp.10.samples -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.sam /build/bcftools-1.16/test/mpileup/mpileup.2.sam /build/bcftools-1.16/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -t17:100-150 -G /build/bcftools-1.16/test/mplp.10.samples -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.sam /build/bcftools-1.16/test/mpileup/mpileup.2.sam /build/bcftools-1.16/test/mpileup/mpileup.3.sam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -t17:100-150 -G /build/bcftools-1.16/test/mplp.10.samples -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -t17:100-150 -G /build/bcftools-1.16/test/mplp.10.samples -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -t17:100-150 -G /build/bcftools-1.16/test/mplp.10.samples -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -t17:100-150 -G /build/bcftools-1.16/test/mplp.10.samples -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.3.sam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.3.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.3.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -s HG00102 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.3.sam /build/bcftools-1.16/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -s HG00102 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.3.sam /build/bcftools-1.16/test/mpileup/mpileup.4.sam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -s HG00102 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.3.bam /build/bcftools-1.16/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -s HG00102 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.3.bam /build/bcftools-1.16/test/mpileup/mpileup.4.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -s HG00102 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.3.cram /build/bcftools-1.16/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -s HG00102 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.3.cram /build/bcftools-1.16/test/mpileup/mpileup.4.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -s ^HG99999 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.3.sam /build/bcftools-1.16/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -s ^HG99999 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.3.sam /build/bcftools-1.16/test/mpileup/mpileup.4.sam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -s ^HG99999 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.3.bam /build/bcftools-1.16/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -s ^HG99999 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.3.bam /build/bcftools-1.16/test/mpileup/mpileup.4.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -s ^HG99999 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.3.cram /build/bcftools-1.16/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -s ^HG99999 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.3.cram /build/bcftools-1.16/test/mpileup/mpileup.4.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -G /build/bcftools-1.16/test/mplp.11.rgs -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.3.sam /build/bcftools-1.16/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -G /build/bcftools-1.16/test/mplp.11.rgs -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.3.sam /build/bcftools-1.16/test/mpileup/mpileup.4.sam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -G /build/bcftools-1.16/test/mplp.11.rgs -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.3.bam /build/bcftools-1.16/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -G /build/bcftools-1.16/test/mplp.11.rgs -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.3.bam /build/bcftools-1.16/test/mpileup/mpileup.4.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -G /build/bcftools-1.16/test/mplp.11.rgs -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.3.cram /build/bcftools-1.16/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -G /build/bcftools-1.16/test/mplp.11.rgs -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.3.cram /build/bcftools-1.16/test/mpileup/mpileup.4.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -G /build/bcftools-1.16/test/mplp.11.rgs -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.3.sam /build/bcftools-1.16/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -G /build/bcftools-1.16/test/mplp.11.rgs -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.3.sam /build/bcftools-1.16/test/mpileup/mpileup.4.sam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -G /build/bcftools-1.16/test/mplp.11.rgs -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.3.bam /build/bcftools-1.16/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -G /build/bcftools-1.16/test/mplp.11.rgs -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.3.bam /build/bcftools-1.16/test/mpileup/mpileup.4.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -G /build/bcftools-1.16/test/mplp.11.rgs -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.3.cram /build/bcftools-1.16/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -G /build/bcftools-1.16/test/mplp.11.rgs -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.3.cram /build/bcftools-1.16/test/mpileup/mpileup.4.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a AD -f /build/bcftools-1.16/test/mpileup/indel-AD.1.fa /build/bcftools-1.16/test/mpileup/indel-AD.1.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a AD -f /build/bcftools-1.16/test/mpileup/indel-AD.1.fa -Ob /build/bcftools-1.16/test/mpileup/indel-AD.1.sam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a AD -f /build/bcftools-1.16/test/mpileup/indel-AD.1.fa /build/bcftools-1.16/test/mpileup/indel-AD.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a AD -f /build/bcftools-1.16/test/mpileup/indel-AD.1.fa -Ob /build/bcftools-1.16/test/mpileup/indel-AD.1.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a AD -f /build/bcftools-1.16/test/mpileup/indel-AD.1.fa /build/bcftools-1.16/test/mpileup/indel-AD.1.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a AD -f /build/bcftools-1.16/test/mpileup/indel-AD.1.fa -Ob /build/bcftools-1.16/test/mpileup/indel-AD.1.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a AD -r 11:75 -f /build/bcftools-1.16/test/mpileup/indel-AD.2.fa /build/bcftools-1.16/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a AD -r 11:75 -f /build/bcftools-1.16/test/mpileup/indel-AD.2.fa -Ob /build/bcftools-1.16/test/mpileup/indel-AD.2.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a AD -r 11:75 -f /build/bcftools-1.16/test/mpileup/indel-AD.2.fa /build/bcftools-1.16/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a AD -r 11:75 -f /build/bcftools-1.16/test/mpileup/indel-AD.2.fa -Ob /build/bcftools-1.16/test/mpileup/indel-AD.2.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /build/bcftools-1.16/test/mpileup/indel-AD.2.fa /build/bcftools-1.16/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /build/bcftools-1.16/test/mpileup/indel-AD.2.fa -Ob /build/bcftools-1.16/test/mpileup/indel-AD.2.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /build/bcftools-1.16/test/mpileup/indel-AD.2.fa /build/bcftools-1.16/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /build/bcftools-1.16/test/mpileup/indel-AD.2.fa -Ob /build/bcftools-1.16/test/mpileup/indel-AD.2.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /build/bcftools-1.16/test/mpileup/indel-AD.2.fa /build/bcftools-1.16/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /build/bcftools-1.16/test/mpileup/indel-AD.2.fa -Ob /build/bcftools-1.16/test/mpileup/indel-AD.2.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /build/bcftools-1.16/test/mpileup/indel-AD.2.fa /build/bcftools-1.16/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /build/bcftools-1.16/test/mpileup/indel-AD.2.fa -Ob /build/bcftools-1.16/test/mpileup/indel-AD.2.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a INFO/SCR,FMT/SCR -f /build/bcftools-1.16/test/mpileup/mpileup-SCR.fa /build/bcftools-1.16/test/mpileup/mpileup-SCR.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a INFO/SCR,FMT/SCR -f /build/bcftools-1.16/test/mpileup/mpileup-SCR.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup-SCR.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a INFO/SCR,FMT/SCR -f /build/bcftools-1.16/test/mpileup/mpileup-SCR.fa /build/bcftools-1.16/test/mpileup/mpileup-SCR.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a INFO/SCR,FMT/SCR -f /build/bcftools-1.16/test/mpileup/mpileup-SCR.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup-SCR.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -t 1:100 --skip-all-set PAIRED,PROPER_PAIR,MREVERSE -f /build/bcftools-1.16/test/mpileup/mpileup-SCR.fa /build/bcftools-1.16/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -t 1:100 --skip-all-set PAIRED,PROPER_PAIR,MREVERSE -f /build/bcftools-1.16/test/mpileup/mpileup-SCR.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup-filter.sam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -t 1:100 --skip-any-set READ1 -f /build/bcftools-1.16/test/mpileup/mpileup-SCR.fa /build/bcftools-1.16/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -t 1:100 --skip-any-set READ1 -f /build/bcftools-1.16/test/mpileup/mpileup-SCR.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup-filter.sam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -t 1:100 --skip-all-unset READ1 -f /build/bcftools-1.16/test/mpileup/mpileup-SCR.fa /build/bcftools-1.16/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -t 1:100 --skip-all-unset READ1 -f /build/bcftools-1.16/test/mpileup/mpileup-SCR.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup-filter.sam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -t 1:100 --skip-any-unset READ1 -f /build/bcftools-1.16/test/mpileup/mpileup-SCR.fa /build/bcftools-1.16/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -t 1:100 --skip-any-unset READ1 -f /build/bcftools-1.16/test/mpileup/mpileup-SCR.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup-filter.sam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r chr19:69-99 -f /build/bcftools-1.16/test/mpileup/annot-NMBZ.1.fa /build/bcftools-1.16/test/mpileup/annot-NMBZ.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r chr19:69-99 -f /build/bcftools-1.16/test/mpileup/annot-NMBZ.1.fa -Ob /build/bcftools-1.16/test/mpileup/annot-NMBZ.1.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r chr6:75 -f /build/bcftools-1.16/test/mpileup/annot-NMBZ.2.fa /build/bcftools-1.16/test/mpileup/annot-NMBZ.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r chr6:75 -f /build/bcftools-1.16/test/mpileup/annot-NMBZ.2.fa -Ob /build/bcftools-1.16/test/mpileup/annot-NMBZ.2.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r chr16:75 -f /build/bcftools-1.16/test/mpileup/annot-NMBZ.3.fa /build/bcftools-1.16/test/mpileup/annot-NMBZ.3.1.bam /build/bcftools-1.16/test/mpileup/annot-NMBZ.3.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r chr16:75 -f /build/bcftools-1.16/test/mpileup/annot-NMBZ.3.fa -Ob /build/bcftools-1.16/test/mpileup/annot-NMBZ.3.1.bam /build/bcftools-1.16/test/mpileup/annot-NMBZ.3.2.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_csq: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq.fa -g /build/bcftools-1.16/test/csq.gff3 /build/bcftools-1.16/test/csq.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq.fa -g /build/bcftools-1.16/test/csq.chr.gff3 /build/bcftools-1.16/test/csq.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq.fa -g /build/bcftools-1.16/test/csq.2.gff /build/bcftools-1.16/test/csq.2.vcf | /build/bcftools-1.16/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq.fa -g /build/bcftools-1.16/test/csq.2.gff --ncsq 64 /build/bcftools-1.16/test/csq.2.vcf | /build/bcftools-1.16/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENSG00000173376/ENSG00000173376.fa -g /build/bcftools-1.16/test/csq/ENSG00000173376/ENSG00000173376.gff /build/bcftools-1.16/test/csq/ENSG00000173376/synon.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000573314/ENST00000573314.fa -g /build/bcftools-1.16/test/csq/ENST00000573314/ENST00000573314.gff /build/bcftools-1.16/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000573314/ENST00000573314.fa -g /build/bcftools-1.16/test/csq/ENST00000573314/ENST00000573314.gff /build/bcftools-1.16/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000285021/ENST00000285021.fa -g /build/bcftools-1.16/test/csq/ENST00000285021/ENST00000285021.gff /build/bcftools-1.16/test/csq/ENST00000285021/stop-gained-inframe-indel.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000410009/ENST00000410009.fa -g /build/bcftools-1.16/test/csq/ENST00000410009/ENST00000410009.gff /build/bcftools-1.16/test/csq/ENST00000410009/frameshift.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /build/bcftools-1.16/test/csq/ENST00000410009 && /build/bcftools-1.16/bcftools csq -B 5 -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/bcftools-1.16/test/csq/ENST00000410009 && /build/bcftools-1.16/bcftools csq -lb -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/bcftools-1.16/test/csq/ENST00000410009 && /build/bcftools-1.16/bcftools csq -b -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/bcftools-1.16/test/csq/ENST00000422159 && /build/bcftools-1.16/bcftools csq -f ENST00000422159.fa -g ENST00000422159.gff multiallelic.vcf | /build/bcftools-1.16/bcftools query -f'[%POS\t%REF\t%ALT\t%GT\t%TBCSQ\n]' | ../sort-csq -q ; echo ; /build/bcftools-1.16/bcftools csq -f ENST00000422159.fa -g short.gff multiallelic.vcf | /build/bcftools-1.16/bcftools query -f'[%POS\t%REF\t%ALT\t%GT\t%TBCSQ\n]' | ../sort-csq -q .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000303039/ENST00000303039.fa -g /build/bcftools-1.16/test/csq/ENST00000303039/ENST00000303039.gff /build/bcftools-1.16/test/csq/ENST00000303039/not-a-stop.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000303039/ENST00000303039.fa -g /build/bcftools-1.16/test/csq/ENST00000303039/ENST00000303039.gff /build/bcftools-1.16/test/csq/ENST00000303039/not-a-stop.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000543077/ENST00000543077.fa -g /build/bcftools-1.16/test/csq/ENST00000543077/ENST00000543077.gff /build/bcftools-1.16/test/csq/ENST00000543077/not-a-start-lost.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000543077/ENST00000543077.fa -g /build/bcftools-1.16/test/csq/ENST00000543077/ENST00000543077.gff /build/bcftools-1.16/test/csq/ENST00000543077/not-a-start-lost.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000423372/ENST00000423372.fa -g /build/bcftools-1.16/test/csq/ENST00000423372/ENST00000423372.gff /build/bcftools-1.16/test/csq/ENST00000423372/snps.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000423372/ENST00000423372.fa -g /build/bcftools-1.16/test/csq/ENST00000423372/ENST00000423372.gff /build/bcftools-1.16/test/csq/ENST00000423372/snps.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000423372/ENST00000423372.fa -g /build/bcftools-1.16/test/csq/ENST00000423372/ENST00000423372.gff /build/bcftools-1.16/test/csq/ENST00000423372/insert3.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000423372/ENST00000423372.fa -g /build/bcftools-1.16/test/csq/ENST00000423372/ENST00000423372.gff /build/bcftools-1.16/test/csq/ENST00000423372/insert3.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000420190/ENST00000420190.fa -g /build/bcftools-1.16/test/csq/ENST00000420190/ENST00000420190.gff /build/bcftools-1.16/test/csq/ENST00000420190/abort-in-csq-push.vcf | /build/bcftools-1.16/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000230048/ENST00000230048.fa -g /build/bcftools-1.16/test/csq/ENST00000230048/ENST00000230048.gff /build/bcftools-1.16/test/csq/ENST00000230048/start-del.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000227471/ENST00000227471.fa -g /build/bcftools-1.16/test/csq/ENST00000227471/ENST00000227471.gff /build/bcftools-1.16/test/csq/ENST00000227471/insert-splice-vs-frameshift.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000263103-INS/ENST00000263103-INS.fa -g /build/bcftools-1.16/test/csq/ENST00000263103-INS/ENST00000263103-INS.gff /build/bcftools-1.16/test/csq/ENST00000263103-INS/insertions.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000295641/ENST00000295641.fa -g /build/bcftools-1.16/test/csq/ENST00000295641/ENST00000295641.gff /build/bcftools-1.16/test/csq/ENST00000295641/not-a-start-lost.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000295641/ENST00000295641.fa -g /build/bcftools-1.16/test/csq/ENST00000295641/ENST00000295641.gff /build/bcftools-1.16/test/csq/ENST00000295641/not-a-start-lost.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000373833/ENST00000373833.fa -g /build/bcftools-1.16/test/csq/ENST00000373833/ENST00000373833.gff /build/bcftools-1.16/test/csq/ENST00000373833/boundary-insertion.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000373833/ENST00000373833.fa -g /build/bcftools-1.16/test/csq/ENST00000373833/ENST00000373833.gff /build/bcftools-1.16/test/csq/ENST00000373833/boundary-insertion.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000375992/ENST00000375992.fa -g /build/bcftools-1.16/test/csq/ENST00000375992/ENST00000375992.gff /build/bcftools-1.16/test/csq/ENST00000375992/incorrect-synon-del-not-start-lost.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000409523/ENST00000409523.fa -g /build/bcftools-1.16/test/csq/ENST00000409523/ENST00000409523.gff /build/bcftools-1.16/test/csq/ENST00000409523/long-overlapping-del.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000536784/ENST00000536784.fa -g /build/bcftools-1.16/test/csq/ENST00000536784/ENST00000536784.gff /build/bcftools-1.16/test/csq/ENST00000536784/not-a-start-lost.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000536784/ENST00000536784.fa -g /build/bcftools-1.16/test/csq/ENST00000536784/ENST00000536784.gff /build/bcftools-1.16/test/csq/ENST00000536784/not-a-start-lost.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000557788/ENST00000557788.fa -g /build/bcftools-1.16/test/csq/ENST00000557788/ENST00000557788.gff /build/bcftools-1.16/test/csq/ENST00000557788/long-overlap-del.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000381157/ENST00000381157.fa -g /build/bcftools-1.16/test/csq/ENST00000381157/ENST00000381157.gff /build/bcftools-1.16/test/csq/ENST00000381157/haploid-diploid.vcf | /build/bcftools-1.16/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n' .. ok test_csq_real: cd /build/bcftools-1.16/test/csq/ENST00000379416 && /build/bcftools-1.16/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.del-snp.vcf | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-1.16/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-del.vcf | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-1.16/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-ins.vcf | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-1.16/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-snp.vcf | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-1.16/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff single.vcf | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000545279/ENST00000545279.fa -g /build/bcftools-1.16/test/csq/ENST00000545279/ENST00000545279.gff /build/bcftools-1.16/test/csq/ENST00000545279/splice-region-insert.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000542803/ENST00000542803.fa -g /build/bcftools-1.16/test/csq/ENST00000542803/ENST00000542803.gff /build/bcftools-1.16/test/csq/ENST00000542803/splice-region.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000542803/ENST00000542803.fa -g /build/bcftools-1.16/test/csq/ENST00000542803/ENST00000542803.gff /build/bcftools-1.16/test/csq/ENST00000542803/splice-region.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000382647/ENST00000382647.fa -g /build/bcftools-1.16/test/csq/ENST00000382647/ENST00000382647.gff /build/bcftools-1.16/test/csq/ENST00000382647/synon-splice-region-insert.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000294661/ENST00000294661.fa -g /build/bcftools-1.16/test/csq/ENST00000294661/ENST00000294661.gff /build/bcftools-1.16/test/csq/ENST00000294661/non-coding-boundary.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000294661/ENST00000294661.fa -g /build/bcftools-1.16/test/csq/ENST00000294661/ENST00000294661.gff /build/bcftools-1.16/test/csq/ENST00000294661/non-coding-boundary.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000318249/ENST00000318249.fa -g /build/bcftools-1.16/test/csq/ENST00000318249/ENST00000318249.gff /build/bcftools-1.16/test/csq/ENST00000318249/start-lost.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000318249/ENST00000318249.fa -g /build/bcftools-1.16/test/csq/ENST00000318249/ENST00000318249.gff /build/bcftools-1.16/test/csq/ENST00000318249/start-lost.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000390520/ENST00000390520.fa -g /build/bcftools-1.16/test/csq/ENST00000390520/ENST00000390520.gff /build/bcftools-1.16/test/csq/ENST00000390520/deletion-overlap.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/EDUMMY0003/EDUMMY0003.fa -g /build/bcftools-1.16/test/csq/EDUMMY0003/EDUMMY0003.gff /build/bcftools-1.16/test/csq/EDUMMY0003/long-del.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000479739/ENST00000479739.fa -g /build/bcftools-1.16/test/csq/ENST00000479739/ENST00000479739.gff /build/bcftools-1.16/test/csq/ENST00000479739/short-cds-start-lost.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000479739/ENST00000479739.fa -g /build/bcftools-1.16/test/csq/ENST00000479739/ENST00000479739.gff /build/bcftools-1.16/test/csq/ENST00000479739/short-cds-start-lost.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000269081/ENST00000269081.fa -g /build/bcftools-1.16/test/csq/ENST00000269081/ENST00000269081.gff /build/bcftools-1.16/test/csq/ENST00000269081/stop-gained-not-inframe-insertion.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000218032/ENST00000218032.fa -g /build/bcftools-1.16/test/csq/ENST00000218032/ENST00000218032.gff /build/bcftools-1.16/test/csq/ENST00000218032/start-lost-del.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000218032/ENST00000218032.fa -g /build/bcftools-1.16/test/csq/ENST00000218032/ENST00000218032.gff /build/bcftools-1.16/test/csq/ENST00000218032/start-lost.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000218032/ENST00000218032.fa -g /build/bcftools-1.16/test/csq/ENST00000218032/ENST00000218032.gff /build/bcftools-1.16/test/csq/ENST00000218032/start-lost.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000256452/ENST00000256452.fa -g /build/bcftools-1.16/test/csq/ENST00000256452/ENST00000256452.gff /build/bcftools-1.16/test/csq/ENST00000256452/intron.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000624631/ENST00000624631.fa -g /build/bcftools-1.16/test/csq/ENST00000624631/ENST00000624631.gff /build/bcftools-1.16/test/csq/ENST00000624631/ambiguous.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000368801.2/ENST00000368801.2.fa -g /build/bcftools-1.16/test/csq/ENST00000368801.2/ENST00000368801.2.gff /build/bcftools-1.16/test/csq/ENST00000368801.2/start-lost.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /build/bcftools-1.16/test/csq/ENST00000000000 && /build/bcftools-1.16/bcftools csq -p a -f ENST00000000000.fa -g ENST00000000000.gff upstream-stop.vcf | /build/bcftools-1.16/bcftools query -f'[%POS\t%REF\t%ALT\t%SAMPLE\t%GT\t%TBCSQ\n]' | ../sort-csq -q .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/EDUMMY0002/EDUMMY0002.fa -g /build/bcftools-1.16/test/csq/EDUMMY0002/EDUMMY0002.gff /build/bcftools-1.16/test/csq/EDUMMY0002/boundaries.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000520795/ENST00000520795.fa -g /build/bcftools-1.16/test/csq/ENST00000520795/ENST00000520795.gff /build/bcftools-1.16/test/csq/ENST00000520795/long-inside-del.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000520795/ENST00000520795.fa -g /build/bcftools-1.16/test/csq/ENST00000520795/ENST00000520795.gff /build/bcftools-1.16/test/csq/ENST00000520795/long-inside-del.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000518414/ENST00000518414.fa -g /build/bcftools-1.16/test/csq/ENST00000518414/ENST00000518414.gff /build/bcftools-1.16/test/csq/ENST00000518414/incorrect-inframe-del.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /build/bcftools-1.16/test/csq/ENSMUST00000121418 && /build/bcftools-1.16/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25500' --phase m | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/bcftools-1.16/test/csq/ENSMUST00000121418 && /build/bcftools-1.16/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25105' --phase m | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/bcftools-1.16/test/csq/ENSMUST00000121418 && /build/bcftools-1.16/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25496' --phase m | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.fa -g /build/bcftools-1.16/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.gff /build/bcftools-1.16/test/csq/ENST00000518414-ENST00000521270/valgrind.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000400151/ENST00000400151.fa -g /build/bcftools-1.16/test/csq/ENST00000400151/ENST00000400151.gff /build/bcftools-1.16/test/csq/ENST00000400151/long-del.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000301246/ENST00000301246.fa -g /build/bcftools-1.16/test/csq/ENST00000301246/ENST00000301246.gff /build/bcftools-1.16/test/csq/ENST00000301246/15bp-insert.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /build/bcftools-1.16/test/csq/ENST00000580206 && /build/bcftools-1.16/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.ins-snv.vcf | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-1.16/bcftools csq -f ENST00000580206.fa -g short.gff compound.ins-snv.vcf | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-1.16/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff single.ins-snv.vcf | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-1.16/bcftools csq -f ENST00000580206.fa -g short.gff single.ins-snv.vcf | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-1.16/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.del-snv.vcf | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-1.16/bcftools csq -f ENST00000580206.fa -g short.gff compound.del-snv.vcf | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-1.16/bcftools csq -f ENST00000580206.fa -g short.gff single.del-snv.vcf | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-1.16/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.del-ins.vcf | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-1.16/bcftools csq -f ENST00000580206.fa -g short.gff compound.del-ins.vcf | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-1.16/bcftools csq -f ENST00000580206.fa -g short.gff single.del-ins.vcf | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000357367/ENST00000357367.fa -g /build/bcftools-1.16/test/csq/ENST00000357367/ENST00000357367.gff /build/bcftools-1.16/test/csq/ENST00000357367/stop-retained.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000378322/ENST00000378322.fa -g /build/bcftools-1.16/test/csq/ENST00000378322/ENST00000378322.gff /build/bcftools-1.16/test/csq/ENST00000378322/end-overlap-tscript.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000378322/ENST00000378322.fa -g /build/bcftools-1.16/test/csq/ENST00000378322/ENST00000378322.gff /build/bcftools-1.16/test/csq/ENST00000378322/end-overlap-tscript.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000420670/ENST00000420670.fa -g /build/bcftools-1.16/test/csq/ENST00000420670/ENST00000420670.gff /build/bcftools-1.16/test/csq/ENST00000420670/start-stop-lost.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000420670/ENST00000420670.fa -g /build/bcftools-1.16/test/csq/ENST00000420670/ENST00000420670.gff /build/bcftools-1.16/test/csq/ENST00000420670/segfault.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/frame1.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/frame1.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/frame2.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/frame2.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/not-a-start-lost.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/not-a-start-lost.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/frame3.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/frame3.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000413103/ENST00000413103.fa -g /build/bcftools-1.16/test/csq/ENST00000413103/ENST00000413103.gff /build/bcftools-1.16/test/csq/ENST00000413103/long-deletion.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000520868/ENST00000520868.fa -g /build/bcftools-1.16/test/csq/ENST00000520868/ENST00000520868.gff /build/bcftools-1.16/test/csq/ENST00000520868/long-deletion.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000318249.2/ENST00000318249.2.fa -g /build/bcftools-1.16/test/csq/ENST00000318249.2/ENST00000318249.2.gff /build/bcftools-1.16/test/csq/ENST00000318249.2/synonymous-start-lost.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000593942/ENST00000593942.fa -g /build/bcftools-1.16/test/csq/ENST00000593942/ENST00000593942.gff /build/bcftools-1.16/test/csq/ENST00000593942/last-codon-deletion.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000448695/ENST00000448695.fa -g /build/bcftools-1.16/test/csq/ENST00000448695/ENST00000448695.gff /build/bcftools-1.16/test/csq/ENST00000448695/syn-and-splice-reg.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000368801/ENST00000368801.fa -g /build/bcftools-1.16/test/csq/ENST00000368801/ENST00000368801.gff /build/bcftools-1.16/test/csq/ENST00000368801/compound-lost.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /build/bcftools-1.16/test/csq/EMN908947 && /build/bcftools-1.16/bcftools csq -f EMN908947.fa -g ribosomal-slippage.gff ribosomal-slippage.vcf --force | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /build/bcftools-1.16/test/csq/EMN908947 && /build/bcftools-1.16/bcftools csq -f EMN908947.fa -g simple.gff simple.vcf | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000436063/ENST00000436063.fa -g /build/bcftools-1.16/test/csq/ENST00000436063/ENST00000436063.gff /build/bcftools-1.16/test/csq/ENST00000436063/insert-before-utr.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000528237/ENST00000528237.fa -g /build/bcftools-1.16/test/csq/ENST00000528237/ENST00000528237.gff /build/bcftools-1.16/test/csq/ENST00000528237/retained-stop-incomplete-cds.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000519442/ENST00000519442.fa -g /build/bcftools-1.16/test/csq/ENST00000519442/ENST00000519442.gff /build/bcftools-1.16/test/csq/ENST00000519442/synon-splice-region-del.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000271583/ENST00000271583.fa -g /build/bcftools-1.16/test/csq/ENST00000271583/ENST00000271583.gff /build/bcftools-1.16/test/csq/ENST00000271583/splice-acceptor.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000329454/ENST00000329454.fa -g /build/bcftools-1.16/test/csq/ENST00000329454/ENST00000329454.gff /build/bcftools-1.16/test/csq/ENST00000329454/boundary-deletion.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000329454/ENST00000329454.fa -g /build/bcftools-1.16/test/csq/ENST00000329454/ENST00000329454.gff /build/bcftools-1.16/test/csq/ENST00000329454/boundary-deletion.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /build/bcftools-1.16/test/csq/ENSMUST00000133836 && /build/bcftools-1.16/bcftools csq -f ENSMUST00000133836.fa -g ENSMUST00000133836.gff filter-problem.vcf -i 'FILTER="PASS"' --phase m | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/EDUMMY0001/EDUMMY0001.fa -g /build/bcftools-1.16/test/csq/EDUMMY0001/EDUMMY0001.gff /build/bcftools-1.16/test/csq/EDUMMY0001/starts-with-1.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/EDUMMY0001/EDUMMY0001.fa -g /build/bcftools-1.16/test/csq/EDUMMY0001/EDUMMY0001.gff /build/bcftools-1.16/test/csq/EDUMMY0001/starts-with-1.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_roh: /build/bcftools-1.16/bcftools roh /build/bcftools-1.16/test/roh.1.vcf.gz -Or -G30 --AF-dflt 0.4| grep -v ^# .. ok test_roh: /build/bcftools-1.16/bcftools roh /build/bcftools-1.16/test/roh.1.vcf.gz -Or -G30 --AF-file /build/bcftools-1.16/test/roh.1.tab.gz| grep -v ^# .. ok test_roh: /build/bcftools-1.16/bcftools roh /build/bcftools-1.16/test/roh.1.vcf.gz -Or -G30 --AF-file /build/bcftools-1.16/test/roh.1.tab.gz --ignore-homref| grep -v ^# .. ok test_roh: /build/bcftools-1.16/bcftools roh /build/bcftools-1.16/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245| grep -v ^# .. ok test_roh: /build/bcftools-1.16/bcftools roh /build/bcftools-1.16/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --ignore-homref| grep -v ^# .. ok test_roh: /build/bcftools-1.16/bcftools roh /build/bcftools-1.16/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --ignore-homref --include-noalt| grep -v ^# .. ok test_roh: /build/bcftools-1.16/bcftools roh /build/bcftools-1.16/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --include-noalt| grep -v ^# .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck -e 0 /tmp/NK5uwruTra/gtcheck.1.vcf.gz -g /tmp/NK5uwruTra/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck -e 0 -u GT,GT /tmp/NK5uwruTra/gtcheck.1.vcf.gz -g /tmp/NK5uwruTra/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck -e 0 -u GT,PL /tmp/NK5uwruTra/gtcheck.1.vcf.gz -g /tmp/NK5uwruTra/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck -e 0 -u PL,GT /tmp/NK5uwruTra/gtcheck.1.vcf.gz -g /tmp/NK5uwruTra/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck -e 0 -u PL,PL /tmp/NK5uwruTra/gtcheck.1.vcf.gz -g /tmp/NK5uwruTra/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck -e 0 -p s1,s1 /tmp/NK5uwruTra/gtcheck.1.vcf.gz -g /tmp/NK5uwruTra/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck -e 0 /tmp/NK5uwruTra/gtcheck.2.vcf.gz -g /tmp/NK5uwruTra/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck -e 0 /tmp/NK5uwruTra/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck -e 0 -p B,A,C,A,C,B,D,A,D,B,D,C,E,A,E,B,E,C,E,D /tmp/NK5uwruTra/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck -e 0 -P /build/bcftools-1.16/test/gtcheck.3.pairs /tmp/NK5uwruTra/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck -e 0 -u PL /tmp/NK5uwruTra/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck -e 0 --n-matches 4 /tmp/NK5uwruTra/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO | sort .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck -e 0 -s qry:E,D,C /tmp/NK5uwruTra/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck -e 0 -s qry:E,D,C -u PL /tmp/NK5uwruTra/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck -e 0 -s qry:B -s gt:D /tmp/NK5uwruTra/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck -e 0 -s qry:B -s gt:D -u PL /tmp/NK5uwruTra/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck -e 0 -s qry:B -s gt:D,C /tmp/NK5uwruTra/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck -e 0 -p B,C,B,D /tmp/NK5uwruTra/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck -e 0 -u GT,GT -H /tmp/NK5uwruTra/gtcheck.1.vcf.gz -g /tmp/NK5uwruTra/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck -e 0 -u GT,PL -H /tmp/NK5uwruTra/gtcheck.1.vcf.gz -g /tmp/NK5uwruTra/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck -e 0 -u PL,GT -H /tmp/NK5uwruTra/gtcheck.1.vcf.gz -g /tmp/NK5uwruTra/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck -e 0 -u PL,PL -H /tmp/NK5uwruTra/gtcheck.1.vcf.gz -g /tmp/NK5uwruTra/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck -e 0 -P /build/bcftools-1.16/test/gtcheck.4.pairs --distinctive-sites 3 /tmp/NK5uwruTra/gtcheck.4.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck -e 0 -P /build/bcftools-1.16/test/gtcheck.4.pairs --distinctive-sites 3,1 /tmp/NK5uwruTra/gtcheck.4.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck -u GT -e 30 /tmp/NK5uwruTra/gtcheck.1.vcf.gz -g /tmp/NK5uwruTra/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck -u GT -e 30 -p s1,s1 /tmp/NK5uwruTra/gtcheck.1.vcf.gz -g /tmp/NK5uwruTra/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck -u GT -e 300 /tmp/NK5uwruTra/gtcheck.1.vcf.gz -g /tmp/NK5uwruTra/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck -u PL -e 30 /tmp/NK5uwruTra/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck /tmp/NK5uwruTra/gtcheck.ntop.vcf.gz -g /tmp/NK5uwruTra/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck --n-matches 2 /tmp/NK5uwruTra/gtcheck.ntop.vcf.gz -g /tmp/NK5uwruTra/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck /tmp/NK5uwruTra/gtcheck.5.vcf.gz -g /tmp/NK5uwruTra/gtcheck.5.gts.vcf.gz | grep -v ^# | grep -v Time .. ok Number of tests: total .. 1477 passed .. 1477 failed .. 0 make[2]: Leaving directory '/build/bcftools-1.16' make[1]: Leaving directory '/build/bcftools-1.16' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/bcftools/ make -j3 install DESTDIR=/build/bcftools-1.16/debian/bcftools AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/bcftools-1.16' mkdir -p -m 755 /build/bcftools-1.16/debian/bcftools/usr/bin /build/bcftools-1.16/debian/bcftools/usr/share/man/man1 /build/bcftools-1.16/debian/bcftools/usr/lib/arm-linux-gnueabihf/bcftools install -p bcftools /build/bcftools-1.16/debian/bcftools/usr/bin install -p misc/color-chrs.pl misc/gff2gff.py misc/guess-ploidy.py misc/plot-vcfstats misc/plot-roh.py misc/run-roh.pl misc/vcfutils.pl /build/bcftools-1.16/debian/bcftools/usr/bin install -p -m 644 doc/bcftools.1 /build/bcftools-1.16/debian/bcftools/usr/share/man/man1 install -p plugins/*.so /build/bcftools-1.16/debian/bcftools/usr/lib/arm-linux-gnueabihf/bcftools make[1]: Leaving directory '/build/bcftools-1.16' debian/rules override_dh_install make[1]: Entering directory '/build/bcftools-1.16' dh_install # Fix Perl interpreter PATH for pscript in `grep -Rl '#!/usr/bin/env \+perl' debian/*` ; do \ sed -i '1s?#!/usr/bin/env \+perl?#!/usr/bin/perl?' ${pscript} ; \ done make[1]: Leaving directory '/build/bcftools-1.16' dh_installdocs dh_installchangelogs debian/rules override_dh_installman make[1]: Entering directory '/build/bcftools-1.16' dh_installman --language=C make[1]: Leaving directory '/build/bcftools-1.16' dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dpkg-gencontrol: warning: package bcftools: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package bcftools: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'bcftools-dbgsym' in '../bcftools-dbgsym_1.16-1_armhf.deb'. dpkg-deb: building package 'bcftools' in '../bcftools_1.16-1_armhf.deb'. dpkg-genbuildinfo --build=binary -O../bcftools_1.16-1_armhf.buildinfo dpkg-genchanges --build=binary -O../bcftools_1.16-1_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/7757 and its subdirectories I: Current time: Mon May 22 22:46:09 -12 2023 I: pbuilder-time-stamp: 1684838769 Tue May 23 10:46:35 UTC 2023 I: 1st build successful. Starting 2nd build on remote node virt64b-armhf-rb.debian.net. Tue May 23 10:46:35 UTC 2023 I: Preparing to do remote build '2' on virt64b-armhf-rb.debian.net. Tue May 23 10:54:25 UTC 2023 I: Deleting $TMPDIR on virt64b-armhf-rb.debian.net. Tue May 23 10:54:28 UTC 2023 I: bcftools_1.16-1_armhf.changes: Format: 1.8 Date: Fri, 30 Sep 2022 11:48:40 +0200 Source: bcftools Binary: bcftools bcftools-dbgsym Architecture: armhf Version: 1.16-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: bcftools - genomic variant calling and manipulation of VCF/BCF files Changes: bcftools (1.16-1) unstable; urgency=medium . * Team upload. * Fix watch file * Standards-Version: 4.6.1 (routine-update) Checksums-Sha1: 4ff5b09a7586e0df299ff06105de92c2613b43f0 1816240 bcftools-dbgsym_1.16-1_armhf.deb bbac79928cc83ca5c5bd45c0ef18828deaf2607b 5849 bcftools_1.16-1_armhf.buildinfo 3b49d5ae7cda82a073517920565eb81b2c5fe39e 609120 bcftools_1.16-1_armhf.deb Checksums-Sha256: 38ac155aea9823d332f904fab7e72a3c46ec701bfd5446c8224ab3a7873a8911 1816240 bcftools-dbgsym_1.16-1_armhf.deb 787d7018196b4126d4989f31f6fa9de81ddb961f2eb94214f687900f8f8d635e 5849 bcftools_1.16-1_armhf.buildinfo 1b02b8bd49233910c73dada00edc0a030cf514f26a7820815c25212ac04cedbc 609120 bcftools_1.16-1_armhf.deb Files: 4a3aa5a8b455a3c323f82afd02aaf14d 1816240 debug optional bcftools-dbgsym_1.16-1_armhf.deb e084b6ae6290023fe1d83ab044a66079 5849 science optional bcftools_1.16-1_armhf.buildinfo 4279c9e06822dfc223bd010ec8db5186 609120 science optional bcftools_1.16-1_armhf.deb Tue May 23 10:54:29 UTC 2023 I: diffoscope 242 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.p7KDElAa/bcftools_1.16-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.p7KDElAa/bcftools_1.16-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.p7KDElAa/bcftools_1.16-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.p7KDElAa/b1/bcftools_1.16-1_armhf.changes /srv/reproducible-results/rbuild-debian/r-b-build.p7KDElAa/b2/bcftools_1.16-1_armhf.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.319s) 0.319s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.039s) 0.038s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Tue May 23 10:54:30 UTC 2023 I: diffoscope 242 found no differences in the changes files, and a .buildinfo file also exists. Tue May 23 10:54:30 UTC 2023 I: bcftools from bookworm built successfully and reproducibly on armhf. Tue May 23 10:54:31 UTC 2023 I: Submitting .buildinfo files to external archives: Tue May 23 10:54:31 UTC 2023 I: Submitting 8.0K b1/bcftools_1.16-1_armhf.buildinfo.asc Tue May 23 10:54:33 UTC 2023 I: Submitting 8.0K b2/bcftools_1.16-1_armhf.buildinfo.asc Tue May 23 10:54:34 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue May 23 10:54:34 UTC 2023 I: Done submitting .buildinfo files. Tue May 23 10:54:34 UTC 2023 I: Removing signed bcftools_1.16-1_armhf.buildinfo.asc files: removed './b1/bcftools_1.16-1_armhf.buildinfo.asc' removed './b2/bcftools_1.16-1_armhf.buildinfo.asc'