Tue Apr 25 01:58:19 UTC 2023 I: starting to build bcftools/bookworm/arm64 on jenkins on '2023-04-25 01:58' Tue Apr 25 01:58:19 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_1/76/console.log Tue Apr 25 01:58:19 UTC 2023 I: Downloading source for bookworm/bcftools=1.16-1 --2023-04-25 01:58:19-- 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% 180M=0s 2023-04-25 01:58:19 (180 MB/s) - ‘bcftools_1.16-1.dsc’ saved [2150/2150] Tue Apr 25 01:58:20 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 Apr 25 01:58:20 UTC 2023 I: Checking whether the package is not for us Tue Apr 25 01:58:20 UTC 2023 I: Starting 1st build on remote node codethink9-arm64.debian.net. Tue Apr 25 01:58:20 UTC 2023 I: Preparing to do remote build '1' on codethink9-arm64.debian.net. Tue Apr 25 02:05:46 UTC 2023 I: Deleting $TMPDIR on codethink9-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun May 26 20:21:24 -12 2024 I: pbuilder-time-stamp: 1716798084 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/15637/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='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' DISTRIBUTION='bookworm' HOME='/var/lib/jenkins' HOST_ARCH='arm64' IFS=' ' 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='15637' 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.TKD4aCl8/pbuilderrc_TniV --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.TKD4aCl8/b1 --logfile b1/build.log bcftools_1.16-1.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a Linux codethink9-arm64 4.15.0-209-generic #220-Ubuntu SMP Tue Mar 21 19:52:44 UTC 2023 aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 26 08:41 /bin -> usr/bin I: user script /srv/workspace/pbuilder/15637/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), zlib1g-dev, libbz2-dev, liblzma-dev, libhts-dev (>= 1.14), 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 ... 19616 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 25.7 MB of archives. After unpacking 103 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main arm64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 2 http://deb.debian.org/debian bookworm/main arm64 libmagic-mgc arm64 1:5.44-3 [305 kB] Get: 3 http://deb.debian.org/debian bookworm/main arm64 libmagic1 arm64 1:5.44-3 [98.5 kB] Get: 4 http://deb.debian.org/debian bookworm/main arm64 file arm64 1:5.44-3 [42.5 kB] Get: 5 http://deb.debian.org/debian bookworm/main arm64 gettext-base arm64 0.21-12 [159 kB] Get: 6 http://deb.debian.org/debian bookworm/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 7 http://deb.debian.org/debian bookworm/main arm64 groff-base arm64 1.22.4-10 [861 kB] Get: 8 http://deb.debian.org/debian bookworm/main arm64 bsdextrautils arm64 2.38.1-5+b1 [86.9 kB] Get: 9 http://deb.debian.org/debian bookworm/main arm64 libpipeline1 arm64 1.5.7-1 [36.4 kB] Get: 10 http://deb.debian.org/debian bookworm/main arm64 man-db arm64 2.11.2-2 [1369 kB] Get: 11 http://deb.debian.org/debian bookworm/main arm64 m4 arm64 1.4.19-3 [276 kB] Get: 12 http://deb.debian.org/debian bookworm/main arm64 autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian bookworm/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian bookworm/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian bookworm/main arm64 autopoint all 0.21-12 [495 kB] Get: 16 http://deb.debian.org/debian bookworm/main arm64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 17 http://deb.debian.org/debian bookworm/main arm64 libtool all 2.4.7-5 [517 kB] Get: 18 http://deb.debian.org/debian bookworm/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian bookworm/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian bookworm/main arm64 libsub-override-perl all 0.09-4 [9304 B] Get: 21 http://deb.debian.org/debian bookworm/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 22 http://deb.debian.org/debian bookworm/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 23 http://deb.debian.org/debian bookworm/main arm64 libelf1 arm64 0.188-2.1 [173 kB] Get: 24 http://deb.debian.org/debian bookworm/main arm64 dwz arm64 0.15-1 [101 kB] Get: 25 http://deb.debian.org/debian bookworm/main arm64 libicu72 arm64 72.1-3 [9204 kB] Get: 26 http://deb.debian.org/debian bookworm/main arm64 libxml2 arm64 2.9.14+dfsg-1.2 [620 kB] Get: 27 http://deb.debian.org/debian bookworm/main arm64 gettext arm64 0.21-12 [1248 kB] Get: 28 http://deb.debian.org/debian bookworm/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian bookworm/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian bookworm/main arm64 debhelper all 13.11.4 [942 kB] Get: 31 http://deb.debian.org/debian bookworm/main arm64 libbrotli1 arm64 1.0.9-2+b6 [269 kB] Get: 32 http://deb.debian.org/debian bookworm/main arm64 libbz2-dev arm64 1.0.8-5+b1 [31.5 kB] Get: 33 http://deb.debian.org/debian bookworm/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg-10 [20.8 kB] Get: 34 http://deb.debian.org/debian bookworm/main arm64 libsasl2-2 arm64 2.1.28+dfsg-10 [58.0 kB] Get: 35 http://deb.debian.org/debian bookworm/main arm64 libldap-2.5-0 arm64 2.5.13+dfsg-5 [171 kB] Get: 36 http://deb.debian.org/debian bookworm/main arm64 libnghttp2-14 arm64 1.52.0-1 [67.9 kB] Get: 37 http://deb.debian.org/debian bookworm/main arm64 libpsl5 arm64 0.21.2-1 [58.6 kB] Get: 38 http://deb.debian.org/debian bookworm/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b2 [59.4 kB] Get: 39 http://deb.debian.org/debian bookworm/main arm64 libssh2-1 arm64 1.10.0-3+b1 [172 kB] Get: 40 http://deb.debian.org/debian bookworm/main arm64 libcurl3-gnutls arm64 7.88.1-8 [357 kB] Get: 41 http://deb.debian.org/debian bookworm/main arm64 libcurl4-gnutls-dev arm64 7.88.1-8 [466 kB] Get: 42 http://deb.debian.org/debian bookworm/main arm64 libdeflate0 arm64 1.14-1 [54.3 kB] Get: 43 http://deb.debian.org/debian bookworm/main arm64 libdeflate-dev arm64 1.14-1 [50.0 kB] Get: 44 http://deb.debian.org/debian bookworm/main arm64 libgslcblas0 arm64 2.7.1+dfsg-3+b1 [82.3 kB] Get: 45 http://deb.debian.org/debian bookworm/main arm64 libgsl27 arm64 2.7.1+dfsg-3+b1 [824 kB] Get: 46 http://deb.debian.org/debian bookworm/main arm64 libgsl-dev arm64 2.7.1+dfsg-3+b1 [1035 kB] Get: 47 http://deb.debian.org/debian bookworm/main arm64 libhtscodecs2 arm64 1.3.0-4 [70.5 kB] Get: 48 http://deb.debian.org/debian bookworm/main arm64 libhts3 arm64 1.16+ds-3 [392 kB] Get: 49 http://deb.debian.org/debian bookworm/main arm64 liblzma-dev arm64 5.4.1-0.2 [255 kB] Get: 50 http://deb.debian.org/debian bookworm/main arm64 zlib1g-dev arm64 1:1.2.13.dfsg-1 [913 kB] Get: 51 http://deb.debian.org/debian bookworm/main arm64 libhts-dev arm64 1.16+ds-3 [1525 kB] Get: 52 http://deb.debian.org/debian bookworm/main arm64 libio-pty-perl arm64 1:1.17-1 [34.5 kB] Get: 53 http://deb.debian.org/debian bookworm/main arm64 tabix arm64 1.16+ds-3 [427 kB] Fetched 25.7 MB in 3s (7755 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 ... 19616 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_arm64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../02-libmagic1_1%3a5.44-3_arm64.deb ... Unpacking libmagic1:arm64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.44-3_arm64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-12_arm64.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../05-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.22.4-10_arm64.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.38.1-5+b1_arm64.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../08-libpipeline1_1.5.7-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.11.2-2_arm64.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-3_arm64.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.11.4_all.deb ... Unpacking libdebhelper-perl (13.11.4) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-5_all.deb ... Unpacking libtool (2.4.7-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../19-libsub-override-perl_0.09-4_all.deb ... Unpacking libsub-override-perl (0.09-4) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:arm64. Preparing to unpack .../22-libelf1_0.188-2.1_arm64.deb ... Unpacking libelf1:arm64 (0.188-2.1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1_arm64.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../24-libicu72_72.1-3_arm64.deb ... Unpacking libicu72:arm64 (72.1-3) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../25-libxml2_2.9.14+dfsg-1.2_arm64.deb ... Unpacking libxml2:arm64 (2.9.14+dfsg-1.2) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.21-12_arm64.deb ... Unpacking gettext (0.21-12) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../28-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../29-debhelper_13.11.4_all.deb ... Unpacking debhelper (13.11.4) ... Selecting previously unselected package libbrotli1:arm64. Preparing to unpack .../30-libbrotli1_1.0.9-2+b6_arm64.deb ... Unpacking libbrotli1:arm64 (1.0.9-2+b6) ... Selecting previously unselected package libbz2-dev:arm64. Preparing to unpack .../31-libbz2-dev_1.0.8-5+b1_arm64.deb ... Unpacking libbz2-dev:arm64 (1.0.8-5+b1) ... Selecting previously unselected package libsasl2-modules-db:arm64. Preparing to unpack .../32-libsasl2-modules-db_2.1.28+dfsg-10_arm64.deb ... Unpacking libsasl2-modules-db:arm64 (2.1.28+dfsg-10) ... Selecting previously unselected package libsasl2-2:arm64. Preparing to unpack .../33-libsasl2-2_2.1.28+dfsg-10_arm64.deb ... 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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:arm64 (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:arm64 (7.88.1-8) ... Setting up libcurl4-gnutls-dev:arm64 (7.88.1-8) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libhts3:arm64 (1.16+ds-3) ... Setting up libhts-dev:arm64 (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 arm64 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 -j8 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/aarch64-linux-gnu/bcftools ./configure --build=aarch64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/aarch64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system --enable-gsl --with-cblas=gslcblas --with-bcf-plugin-dir=/usr/lib/aarch64-linux-gnu/bcftools checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for htslib/sam.h... yes checking for hts_version in -lhts... yes checking shared library type... plain .so checking for library containing dlopen... none required checking if the compiler accepts -rdynamic... yes checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing regcomp... none required configure: creating ./config.status config.status: creating config.mk config.status: creating config.h make[1]: Leaving directory '/build/bcftools-1.16' dh_auto_build make -j8 make[1]: Entering directory '/build/bcftools-1.16' echo '#define BCFTOOLS_VERSION "1.16"' > version.h gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfindex.o vcfindex.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tabix.o tabix.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfstats.o vcfstats.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfisec.o vcfisec.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfmerge.o vcfmerge.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfquery.o vcfquery.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcffilter.o vcffilter.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o filter.o filter.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfsom.o vcfsom.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfnorm.o vcfnorm.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfgtcheck.o vcfgtcheck.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfview.o vcfview.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfannotate.o vcfannotate.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfroh.o vcfroh.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfconcat.o vcfconcat.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcall.o vcfcall.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mcall.o mcall.c gcc -Wall -g -O2 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-D_FORTIFY_SOURCE=2 -c -o tsv2vcf.o tsv2vcf.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcnv.o vcfcnv.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfhead.o vcfhead.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o HMM.o HMM.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o consensus.o consensus.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ploidy.o ploidy.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bin.o bin.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hclust.o hclust.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o version.o version.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o regidx.o regidx.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o smpl_ilist.o smpl_ilist.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o csq.o csq.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfbuf.o vcfbuf.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mpileup.o mpileup.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sample.o bam_sample.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfsort.o vcfsort.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cols.o cols.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o extsort.o extsort.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dist.o dist.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o abuf.o abuf.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ccall.o ccall.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o em.o em.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o prob1.o prob1.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kmin.o kmin.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o str_finder.o str_finder.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DPLUGINPATH='"/usr/lib/aarch64-linux-gnu/bcftools"' -c -o vcfplugin.o vcfplugin.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-rbuf.o test/test-rbuf.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-regidx.o test/test-regidx.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/GTisec.so version.c plugins/GTisec.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/GTsubset.so version.c plugins/GTsubset.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/ad-bias.so convert.c version.c plugins/ad-bias.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/add-variantkey.so version.c plugins/add-variantkey.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/af-dist.so bin.c version.c plugins/af-dist.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/allele-length.so version.c plugins/allele-length.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/check-ploidy.so version.c plugins/check-ploidy.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/check-sparsity.so version.c plugins/check-sparsity.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/color-chrs.so HMM.c version.c plugins/color-chrs.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/contrast.so version.c plugins/contrast.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/counts.so version.c plugins/counts.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/dosage.so version.c plugins/dosage.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fill-AN-AC.so version.c plugins/fill-AN-AC.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fill-from-fasta.so filter.c version.c plugins/fill-from-fasta.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fill-tags.so version.c plugins/fill-tags.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fixploidy.so ploidy.c regidx.c version.c plugins/fixploidy.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fixref.so version.c plugins/fixref.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/frameshifts.so version.c plugins/frameshifts.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/guess-ploidy.so version.c plugins/guess-ploidy.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/gvcfz.so version.c plugins/gvcfz.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/impute-info.so version.c plugins/impute-info.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/indel-stats.so version.c plugins/indel-stats.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/isecGT.so smpl_ilist.c version.c plugins/isecGT.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/mendelian.so version.c plugins/mendelian.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/missing2ref.so version.c plugins/missing2ref.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/parental-origin.so version.c plugins/parental-origin.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/prune.so version.c plugins/prune.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/remove-overlaps.so version.c plugins/remove-overlaps.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/scatter.so version.c plugins/scatter.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/setGT.so version.c plugins/setGT.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/smpl-stats.so version.c plugins/smpl-stats.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/split-vep.so version.c plugins/split-vep.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/split.so version.c plugins/split.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/tag2tag.so version.c plugins/tag2tag.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/trio-dnm2.so version.c plugins/trio-dnm2.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/trio-stats.so version.c plugins/trio-stats.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/trio-switch-rate.so version.c plugins/trio-switch-rate.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/variant-distance.so version.c plugins/variant-distance.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/variantkey-hex.so version.c plugins/variantkey-hex.c gcc -Wall -g -O2 -ffile-prefix-map=/build/bcftools-1.16=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o main.o main.c gcc -Wl,-z,relro -o test/test-rbuf test/test-rbuf.o -lz gcc -Wl,-z,relro -o test/test-regidx test/test-regidx.o regidx.o -lhts -lpthread -lz gcc -rdynamic -Wl,-z,relro -o bcftools main.o vcfindex.o tabix.o vcfstats.o vcfisec.o vcfmerge.o vcfquery.o vcffilter.o filter.o vcfsom.o vcfnorm.o vcfgtcheck.o vcfview.o vcfannotate.o vcfroh.o vcfconcat.o vcfcall.o mcall.o vcmp.o gvcf.o reheader.o convert.o vcfconvert.o tsv2vcf.o vcfcnv.o vcfhead.o HMM.o consensus.o ploidy.o bin.o hclust.o version.o regidx.o smpl_ilist.o csq.o vcfbuf.o mpileup.o bam2bcf.o bam2bcf_indel.o bam_sample.o vcfsort.o cols.o extsort.o dist.o abuf.o ccall.o em.o prob1.o kmin.o str_finder.o vcfplugin.o -lhts -lm -lz -lpthread make[1]: Leaving directory '/build/bcftools-1.16' debian/rules override_dh_auto_test make[1]: Entering directory '/build/bcftools-1.16' make test-no-plugins VERBOSE=1 make[2]: Entering directory '/build/bcftools-1.16' ./test/test-rbuf Inserted 1-9 starting at offset 5: 5 6 7 8 9 0 1 2 3 1 2 3 4 5 6 7 8 9 4th is 4 Deleting 1-2: 7 8 9 0 1 2 3 3 4 5 6 7 8 9 Prepending 0-8: 8 9 0 1 2 3 4 5 6 7 8 7 6 5 4 3 2 1 0 3 Expanding: 8 9 10 11 12 13 14 15 16 17 8 7 6 5 4 3 2 1 0 3 ./test/test-regidx REF_PATH=: ./test/test.pl --exec bgzip= --exec tabix= --htsdir= ${TEST_OPTS:-} test_usage: bcftools .. ok test_usage_subcommand: bcftools index .. ok test_usage_subcommand: bcftools annotate .. ok test_usage_subcommand: bcftools concat .. ok test_usage_subcommand: bcftools convert .. ok test_usage_subcommand: bcftools head .. ok test_usage_subcommand: bcftools isec .. ok test_usage_subcommand: bcftools merge .. ok test_usage_subcommand: bcftools norm .. ok test_usage_subcommand: bcftools plugin .. ok test_usage_subcommand: bcftools query .. ok test_usage_subcommand: bcftools reheader .. ok test_usage_subcommand: bcftools sort .. ok test_usage_subcommand: bcftools view .. ok test_usage_subcommand: bcftools call .. ok test_usage_subcommand: bcftools consensus .. ok test_usage_subcommand: bcftools cnv .. ok test_usage_subcommand: bcftools csq .. ok test_usage_subcommand: bcftools filter .. ok test_usage_subcommand: bcftools gtcheck .. ok test_usage_subcommand: bcftools mpileup .. ok test_usage_subcommand: bcftools roh .. ok test_usage_subcommand: bcftools stats .. ok test_tabix: tabix /tmp/lFdI2HY7eC/merge.a.vcf.gz 2:3199812-3199812 .. ok test_tabix: /build/bcftools-1.16/bcftools view -H /tmp/lFdI2HY7eC/merge.a.bcf 2:3199812-3199812 .. ok test_tabix: tabix /tmp/lFdI2HY7eC/merge.a.vcf.gz 1:3000151-3000151 .. ok test_tabix: /build/bcftools-1.16/bcftools view -H /tmp/lFdI2HY7eC/merge.a.bcf 1:3000151-3000151 .. ok test_index: /build/bcftools-1.16/bcftools view -H /tmp/lFdI2HY7eC/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /build/bcftools-1.16/bcftools view -H /tmp/lFdI2HY7eC/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/bcftools-1.16/bcftools view -H /tmp/lFdI2HY7eC/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/bcftools-1.16/bcftools view -H /tmp/lFdI2HY7eC/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /build/bcftools-1.16/bcftools view -H /tmp/lFdI2HY7eC/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/bcftools-1.16/bcftools view -H /tmp/lFdI2HY7eC/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /build/bcftools-1.16/bcftools view -H /tmp/lFdI2HY7eC/large_chrom_csi_limit.bcf chr20 .. ok test_index: /build/bcftools-1.16/bcftools view -H /tmp/lFdI2HY7eC/large_chrom_csi_limit.bcf chr20 .. ok test_index: /build/bcftools-1.16/bcftools view -H /tmp/lFdI2HY7eC/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /build/bcftools-1.16/bcftools view -H /tmp/lFdI2HY7eC/large_chrom_csi_limit.bcf chr20 .. ok test_vcf_idxstats: /build/bcftools-1.16/bcftools index -s /tmp/lFdI2HY7eC/idx.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.16/bcftools index -s /tmp/lFdI2HY7eC/idx.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.16/bcftools index -s /tmp/lFdI2HY7eC/idx.bcf .. ok test_vcf_idxstats: /build/bcftools-1.16/bcftools index -n /tmp/lFdI2HY7eC/idx.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.16/bcftools index -n /tmp/lFdI2HY7eC/idx.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.16/bcftools index -n /tmp/lFdI2HY7eC/idx.vcf.gz.csi .. ok test_vcf_idxstats: /build/bcftools-1.16/bcftools index -n /tmp/lFdI2HY7eC/idx.bcf .. ok test_vcf_idxstats: /build/bcftools-1.16/bcftools index -n /tmp/lFdI2HY7eC/idx.bcf.csi .. ok test_vcf_idxstats: /build/bcftools-1.16/bcftools index -s /tmp/lFdI2HY7eC/empty.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.16/bcftools index -s /tmp/lFdI2HY7eC/empty.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.16/bcftools index -s /tmp/lFdI2HY7eC/empty.bcf .. ok test_vcf_idxstats: /build/bcftools-1.16/bcftools index -n /tmp/lFdI2HY7eC/empty.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.16/bcftools index -n /tmp/lFdI2HY7eC/empty.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.16/bcftools index -n /tmp/lFdI2HY7eC/empty.vcf.gz.csi .. ok test_vcf_idxstats: /build/bcftools-1.16/bcftools index -n /tmp/lFdI2HY7eC/empty.bcf .. ok test_vcf_idxstats: /build/bcftools-1.16/bcftools index -n /tmp/lFdI2HY7eC/empty.bcf.csi .. ok test_vcf_check: /build/bcftools-1.16/bcftools stats -s - /tmp/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/check.1.chk /tmp/lFdI2HY7eC/check.2.chk /tmp/lFdI2HY7eC/check.3.chk /tmp/lFdI2HY7eC/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/lFdI2HY7eC/stats.a.vcf.gz /tmp/lFdI2HY7eC/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/bcftools-1.16/bcftools stats -s B /tmp/lFdI2HY7eC/stats.a.vcf.gz /tmp/lFdI2HY7eC/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/bcftools-1.16/bcftools stats -s - /tmp/lFdI2HY7eC/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_isec: /build/bcftools-1.16/bcftools isec -n =2 /tmp/lFdI2HY7eC/isec.a.vcf.gz /tmp/lFdI2HY7eC/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.16/bcftools isec -Ob -n =2 /tmp/lFdI2HY7eC/isec.a.vcf.gz /tmp/lFdI2HY7eC/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.16/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/lFdI2HY7eC/isec.a.vcf.gz /tmp/lFdI2HY7eC/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.16/bcftools isec -Ob -n =2 -i"STRLEN(REF)==2" /tmp/lFdI2HY7eC/isec.a.vcf.gz /tmp/lFdI2HY7eC/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.16/bcftools isec -n =2 -c both /tmp/lFdI2HY7eC/isec.a.vcf.gz /tmp/lFdI2HY7eC/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.16/bcftools isec -Ob -n =2 -c both /tmp/lFdI2HY7eC/isec.a.vcf.gz /tmp/lFdI2HY7eC/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.16/bcftools isec -n =2 -c any /tmp/lFdI2HY7eC/isec.a.vcf.gz /tmp/lFdI2HY7eC/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.16/bcftools isec -Ob -n =2 -c any /tmp/lFdI2HY7eC/isec.a.vcf.gz /tmp/lFdI2HY7eC/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.16/bcftools isec -C -c any /tmp/lFdI2HY7eC/isec.a.vcf.gz /tmp/lFdI2HY7eC/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.16/bcftools isec -Ob -C -c any /tmp/lFdI2HY7eC/isec.a.vcf.gz /tmp/lFdI2HY7eC/isec.b.vcf.gz .. ok test_vcf_isec2: /build/bcftools-1.16/bcftools isec --no-version -T /tmp/lFdI2HY7eC/isec.tab.gz /tmp/lFdI2HY7eC/isec.a.vcf.gz .. ok test_vcf_isec2: /build/bcftools-1.16/bcftools isec -Ob -T /tmp/lFdI2HY7eC/isec.tab.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/isec-miss.1.1.vcf.gz /tmp/lFdI2HY7eC/isec-miss.1.2.vcf.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/isec-miss.1.1.vcf.gz /tmp/lFdI2HY7eC/isec-miss.1.2.vcf.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/isec-miss.1.1.vcf.gz /tmp/lFdI2HY7eC/isec-miss.1.2.vcf.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/isec-miss.1.1.vcf.gz /tmp/lFdI2HY7eC/isec-miss.1.2.vcf.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/isec-miss.2.1.vcf.gz /tmp/lFdI2HY7eC/isec-miss.2.2.vcf.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/isec-miss.2.1.vcf.gz /tmp/lFdI2HY7eC/isec-miss.2.2.vcf.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/isec-miss.2.1.vcf.gz /tmp/lFdI2HY7eC/isec-miss.2.2.vcf.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/isec-miss.2.1.vcf.gz /tmp/lFdI2HY7eC/isec-miss.2.2.vcf.gz /tmp/lFdI2HY7eC/isec-miss.2.3.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge --no-version -i AF:join /tmp/lFdI2HY7eC/merge.join.a.vcf.gz /tmp/lFdI2HY7eC/merge.join.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob -i AF:join /tmp/lFdI2HY7eC/merge.join.a.vcf.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.join.a.bcf /tmp/lFdI2HY7eC/merge.join.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob -i AF:join /tmp/lFdI2HY7eC/merge.join.a.bcf /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.LPL.a.vcf.gz /tmp/lFdI2HY7eC/merge.LPL.b.vcf.gz /tmp/lFdI2HY7eC/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples /tmp/lFdI2HY7eC/merge.LPL.a.vcf.gz /tmp/lFdI2HY7eC/merge.LPL.b.vcf.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.LPL.a.bcf /tmp/lFdI2HY7eC/merge.LPL.b.bcf /tmp/lFdI2HY7eC/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples /tmp/lFdI2HY7eC/merge.LPL.a.bcf /tmp/lFdI2HY7eC/merge.LPL.b.bcf /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.LPL.a.vcf.gz /tmp/lFdI2HY7eC/merge.LPL.b.vcf.gz /tmp/lFdI2HY7eC/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -L 1 /tmp/lFdI2HY7eC/merge.LPL.a.vcf.gz /tmp/lFdI2HY7eC/merge.LPL.b.vcf.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.LPL.a.bcf /tmp/lFdI2HY7eC/merge.LPL.b.bcf /tmp/lFdI2HY7eC/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -L 1 /tmp/lFdI2HY7eC/merge.LPL.a.bcf /tmp/lFdI2HY7eC/merge.LPL.b.bcf /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.LPL.a.vcf.gz /tmp/lFdI2HY7eC/merge.LPL.b.vcf.gz /tmp/lFdI2HY7eC/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -L 2 /tmp/lFdI2HY7eC/merge.LPL.a.vcf.gz /tmp/lFdI2HY7eC/merge.LPL.b.vcf.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.LPL.a.bcf /tmp/lFdI2HY7eC/merge.LPL.b.bcf /tmp/lFdI2HY7eC/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -L 2 /tmp/lFdI2HY7eC/merge.LPL.a.bcf /tmp/lFdI2HY7eC/merge.LPL.b.bcf /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.LPL.a.vcf.gz /tmp/lFdI2HY7eC/merge.LPL.b.vcf.gz /tmp/lFdI2HY7eC/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -L 3 /tmp/lFdI2HY7eC/merge.LPL.a.vcf.gz /tmp/lFdI2HY7eC/merge.LPL.b.vcf.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.LPL.a.bcf /tmp/lFdI2HY7eC/merge.LPL.b.bcf /tmp/lFdI2HY7eC/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -L 3 /tmp/lFdI2HY7eC/merge.LPL.a.bcf /tmp/lFdI2HY7eC/merge.LPL.b.bcf /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.LPL.a.vcf.gz /tmp/lFdI2HY7eC/merge.LPL.b.vcf.gz /tmp/lFdI2HY7eC/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -L 4 /tmp/lFdI2HY7eC/merge.LPL.a.vcf.gz /tmp/lFdI2HY7eC/merge.LPL.b.vcf.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.LPL.a.bcf /tmp/lFdI2HY7eC/merge.LPL.b.bcf /tmp/lFdI2HY7eC/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -L 4 /tmp/lFdI2HY7eC/merge.LPL.a.bcf /tmp/lFdI2HY7eC/merge.LPL.b.bcf /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.LPL.a.vcf.gz /tmp/lFdI2HY7eC/merge.LPL.b.vcf.gz /tmp/lFdI2HY7eC/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -L 5 /tmp/lFdI2HY7eC/merge.LPL.a.vcf.gz /tmp/lFdI2HY7eC/merge.LPL.b.vcf.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.LPL.a.bcf /tmp/lFdI2HY7eC/merge.LPL.b.bcf /tmp/lFdI2HY7eC/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -L 5 /tmp/lFdI2HY7eC/merge.LPL.a.bcf /tmp/lFdI2HY7eC/merge.LPL.b.bcf /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.a.vcf.gz /tmp/lFdI2HY7eC/merge.b.vcf.gz /tmp/lFdI2HY7eC/merge.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples /tmp/lFdI2HY7eC/merge.a.vcf.gz /tmp/lFdI2HY7eC/merge.b.vcf.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.a.bcf /tmp/lFdI2HY7eC/merge.b.bcf /tmp/lFdI2HY7eC/merge.c.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples /tmp/lFdI2HY7eC/merge.a.bcf /tmp/lFdI2HY7eC/merge.b.bcf /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.a.vcf.gz /tmp/lFdI2HY7eC/merge.b.vcf.gz /tmp/lFdI2HY7eC/merge.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -Fx /tmp/lFdI2HY7eC/merge.a.vcf.gz /tmp/lFdI2HY7eC/merge.b.vcf.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.a.bcf /tmp/lFdI2HY7eC/merge.b.bcf /tmp/lFdI2HY7eC/merge.c.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -Fx /tmp/lFdI2HY7eC/merge.a.bcf /tmp/lFdI2HY7eC/merge.b.bcf /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.a.vcf.gz /tmp/lFdI2HY7eC/merge.b.vcf.gz /tmp/lFdI2HY7eC/merge.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -0 /tmp/lFdI2HY7eC/merge.a.vcf.gz /tmp/lFdI2HY7eC/merge.b.vcf.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.a.bcf /tmp/lFdI2HY7eC/merge.b.bcf /tmp/lFdI2HY7eC/merge.c.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -0 /tmp/lFdI2HY7eC/merge.a.bcf /tmp/lFdI2HY7eC/merge.b.bcf /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.2.a.vcf.gz /tmp/lFdI2HY7eC/merge.2.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -m none /tmp/lFdI2HY7eC/merge.2.a.vcf.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.2.a.bcf /tmp/lFdI2HY7eC/merge.2.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -m none /tmp/lFdI2HY7eC/merge.2.a.bcf /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.2.a.vcf.gz /tmp/lFdI2HY7eC/merge.2.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -m both /tmp/lFdI2HY7eC/merge.2.a.vcf.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.2.a.bcf /tmp/lFdI2HY7eC/merge.2.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -m both /tmp/lFdI2HY7eC/merge.2.a.bcf /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.2.a.vcf.gz /tmp/lFdI2HY7eC/merge.2.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -m all /tmp/lFdI2HY7eC/merge.2.a.vcf.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.2.a.bcf /tmp/lFdI2HY7eC/merge.2.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -m all /tmp/lFdI2HY7eC/merge.2.a.bcf /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.3.a.vcf.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.3.a.vcf.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.3.a.bcf /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.3.a.bcf /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.4.a.vcf.gz /tmp/lFdI2HY7eC/merge.4.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -m id /tmp/lFdI2HY7eC/merge.4.a.vcf.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.4.a.bcf /tmp/lFdI2HY7eC/merge.4.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples -m id /tmp/lFdI2HY7eC/merge.4.a.bcf /tmp/lFdI2HY7eC/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/lFdI2HY7eC/gvcf.merge.1.vcf.gz /tmp/lFdI2HY7eC/gvcf.merge.2.vcf.gz /tmp/lFdI2HY7eC/gvcf.merge.3.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --gvcf - /tmp/lFdI2HY7eC/gvcf.merge.1.vcf.gz /tmp/lFdI2HY7eC/gvcf.merge.2.vcf.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/gvcf.merge.1.bcf /tmp/lFdI2HY7eC/gvcf.merge.2.bcf /tmp/lFdI2HY7eC/gvcf.merge.3.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --gvcf - /tmp/lFdI2HY7eC/gvcf.merge.1.bcf /tmp/lFdI2HY7eC/gvcf.merge.2.bcf /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.gvcf.2.a.vcf.gz /tmp/lFdI2HY7eC/merge.gvcf.2.b.vcf.gz /tmp/lFdI2HY7eC/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --gvcf - /tmp/lFdI2HY7eC/merge.gvcf.2.a.vcf.gz /tmp/lFdI2HY7eC/merge.gvcf.2.b.vcf.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.gvcf.3.a.vcf.gz /tmp/lFdI2HY7eC/merge.gvcf.3.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --gvcf - -i SRC:join /tmp/lFdI2HY7eC/merge.gvcf.3.a.vcf.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.gvcf.4.a.vcf.gz /tmp/lFdI2HY7eC/merge.gvcf.4.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --gvcf - /tmp/lFdI2HY7eC/merge.gvcf.4.a.vcf.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.gvcf.4.a.bcf /tmp/lFdI2HY7eC/merge.gvcf.4.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --gvcf - /tmp/lFdI2HY7eC/merge.gvcf.4.a.bcf /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.5.a.vcf.gz /tmp/lFdI2HY7eC/merge.5.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob /tmp/lFdI2HY7eC/merge.5.a.vcf.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.5.a.bcf /tmp/lFdI2HY7eC/merge.5.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob /tmp/lFdI2HY7eC/merge.5.a.bcf /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.6.a.vcf.gz /tmp/lFdI2HY7eC/merge.6.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob /tmp/lFdI2HY7eC/merge.6.a.vcf.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.6.a.bcf /tmp/lFdI2HY7eC/merge.6.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob /tmp/lFdI2HY7eC/merge.6.a.bcf /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.gvcf.7.a.vcf.gz /tmp/lFdI2HY7eC/merge.gvcf.7.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --gvcf - /tmp/lFdI2HY7eC/merge.gvcf.7.a.vcf.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.gvcf.7.a.bcf /tmp/lFdI2HY7eC/merge.gvcf.7.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --gvcf - /tmp/lFdI2HY7eC/merge.gvcf.7.a.bcf /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.gvcf.8.a.vcf.gz /tmp/lFdI2HY7eC/merge.gvcf.8.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --gvcf - /tmp/lFdI2HY7eC/merge.gvcf.8.a.vcf.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.gvcf.8.a.bcf /tmp/lFdI2HY7eC/merge.gvcf.8.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --gvcf - /tmp/lFdI2HY7eC/merge.gvcf.8.a.bcf /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.7.a.vcf.gz /tmp/lFdI2HY7eC/merge.7.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples /tmp/lFdI2HY7eC/merge.7.a.vcf.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.7.a.bcf /tmp/lFdI2HY7eC/merge.7.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --force-samples /tmp/lFdI2HY7eC/merge.7.a.bcf /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.gvcf.9a.vcf.gz /tmp/lFdI2HY7eC/merge.gvcf.9b.vcf.gz /tmp/lFdI2HY7eC/merge.gvcf.9c.vcf.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.gvcf.9a.vcf.gz /tmp/lFdI2HY7eC/merge.gvcf.9b.vcf.gz /tmp/lFdI2HY7eC/merge.gvcf.9c.vcf.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.gvcf.9a.bcf /tmp/lFdI2HY7eC/merge.gvcf.9b.bcf /tmp/lFdI2HY7eC/merge.gvcf.9c.bcf /tmp/lFdI2HY7eC/merge.gvcf.9d.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --gvcf /build/bcftools-1.16/test/gvcf.fa /tmp/lFdI2HY7eC/merge.gvcf.9a.bcf /tmp/lFdI2HY7eC/merge.gvcf.9b.bcf /tmp/lFdI2HY7eC/merge.gvcf.9c.bcf /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.gvcf.9a.vcf.gz /tmp/lFdI2HY7eC/merge.gvcf.9b.vcf.gz /tmp/lFdI2HY7eC/merge.gvcf.9c.vcf.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.gvcf.9a.vcf.gz /tmp/lFdI2HY7eC/merge.gvcf.9b.vcf.gz /tmp/lFdI2HY7eC/merge.gvcf.9c.vcf.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.gvcf.9a.bcf /tmp/lFdI2HY7eC/merge.gvcf.9b.bcf /tmp/lFdI2HY7eC/merge.gvcf.9c.bcf /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.gvcf.9a.bcf /tmp/lFdI2HY7eC/merge.gvcf.9b.bcf /tmp/lFdI2HY7eC/merge.gvcf.9c.bcf /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.gvcf.9a.vcf.gz /tmp/lFdI2HY7eC/merge.gvcf.9b.vcf.gz /tmp/lFdI2HY7eC/merge.gvcf.9c.vcf.gz /tmp/lFdI2HY7eC/merge.gvcf.9d.vcf.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.gvcf.9a.vcf.gz /tmp/lFdI2HY7eC/merge.gvcf.9b.vcf.gz /tmp/lFdI2HY7eC/merge.gvcf.9c.vcf.gz /tmp/lFdI2HY7eC/merge.gvcf.9d.vcf.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.gvcf.9a.bcf /tmp/lFdI2HY7eC/merge.gvcf.9b.bcf /tmp/lFdI2HY7eC/merge.gvcf.9c.bcf /tmp/lFdI2HY7eC/merge.gvcf.9d.bcf /tmp/lFdI2HY7eC/merge.gvcf.9e.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --gvcf /build/bcftools-1.16/test/gvcf.fa /tmp/lFdI2HY7eC/merge.gvcf.9a.bcf /tmp/lFdI2HY7eC/merge.gvcf.9b.bcf /tmp/lFdI2HY7eC/merge.gvcf.9c.bcf /tmp/lFdI2HY7eC/merge.gvcf.9d.bcf /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.gvcf.9a.vcf.gz /tmp/lFdI2HY7eC/merge.gvcf.9b.vcf.gz /tmp/lFdI2HY7eC/merge.gvcf.9c.vcf.gz /tmp/lFdI2HY7eC/merge.gvcf.9d.vcf.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.gvcf.9a.vcf.gz /tmp/lFdI2HY7eC/merge.gvcf.9b.vcf.gz /tmp/lFdI2HY7eC/merge.gvcf.9c.vcf.gz /tmp/lFdI2HY7eC/merge.gvcf.9d.vcf.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.gvcf.9a.bcf /tmp/lFdI2HY7eC/merge.gvcf.9b.bcf /tmp/lFdI2HY7eC/merge.gvcf.9c.bcf /tmp/lFdI2HY7eC/merge.gvcf.9d.bcf /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.gvcf.9a.bcf /tmp/lFdI2HY7eC/merge.gvcf.9b.bcf /tmp/lFdI2HY7eC/merge.gvcf.9c.bcf /tmp/lFdI2HY7eC/merge.gvcf.9d.bcf /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.gvcf.10.a.vcf.gz /tmp/lFdI2HY7eC/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob /tmp/lFdI2HY7eC/merge.gvcf.10.a.vcf.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.gvcf.10.a.bcf /tmp/lFdI2HY7eC/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob /tmp/lFdI2HY7eC/merge.gvcf.10.a.bcf /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.gvcf.10.a.vcf.gz /tmp/lFdI2HY7eC/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob -m none /tmp/lFdI2HY7eC/merge.gvcf.10.a.vcf.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.gvcf.10.a.bcf /tmp/lFdI2HY7eC/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob -m none /tmp/lFdI2HY7eC/merge.gvcf.10.a.bcf /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.gvcf.10.a.vcf.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.gvcf.10.a.vcf.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.gvcf.10.a.bcf /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.gvcf.10.a.bcf /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.gvcf.10.a.vcf.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.gvcf.10.a.vcf.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.gvcf.10.a.bcf /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.gvcf.10.a.bcf /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.gvcf.10.b.vcf.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.gvcf.10.b.vcf.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.gvcf.10.b.bcf /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.gvcf.10.b.bcf /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.gvcf.10.b.vcf.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.gvcf.10.b.vcf.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.gvcf.10.b.bcf /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.gvcf.10.b.bcf /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.noidx.a.vcf.gz /tmp/lFdI2HY7eC/merge.noidx.b.vcf.gz /tmp/lFdI2HY7eC/merge.noidx.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob /tmp/lFdI2HY7eC/merge.noidx.a.vcf.gz /tmp/lFdI2HY7eC/merge.noidx.b.vcf.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.noidx.a.bcf /tmp/lFdI2HY7eC/merge.noidx.b.bcf /tmp/lFdI2HY7eC/merge.noidx.c.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob /tmp/lFdI2HY7eC/merge.noidx.a.bcf /tmp/lFdI2HY7eC/merge.noidx.b.bcf /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.noidx.a.bcf /tmp/lFdI2HY7eC/merge.noidx.b.bcf /tmp/lFdI2HY7eC/merge.noidx.c.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob --no-index /tmp/lFdI2HY7eC/merge.noidx.a.bcf /tmp/lFdI2HY7eC/merge.noidx.b.bcf /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.8.a.vcf.gz /tmp/lFdI2HY7eC/merge.8.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob /tmp/lFdI2HY7eC/merge.8.a.vcf.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.8.a.bcf /tmp/lFdI2HY7eC/merge.8.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob /tmp/lFdI2HY7eC/merge.8.a.bcf /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.8.a.vcf.gz /tmp/lFdI2HY7eC/merge.8.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob -i AN:sum,AC:sum /tmp/lFdI2HY7eC/merge.8.a.vcf.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.8.a.bcf /tmp/lFdI2HY7eC/merge.8.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob -i AN:sum,AC:sum /tmp/lFdI2HY7eC/merge.8.a.bcf /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.9.a.vcf.gz /tmp/lFdI2HY7eC/merge.9.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob /tmp/lFdI2HY7eC/merge.9.a.vcf.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.9.a.bcf /tmp/lFdI2HY7eC/merge.9.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob /tmp/lFdI2HY7eC/merge.9.a.bcf /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.9.a.vcf.gz /tmp/lFdI2HY7eC/merge.9.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob -i AN:sum,AC:sum /tmp/lFdI2HY7eC/merge.9.a.vcf.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.9.a.bcf /tmp/lFdI2HY7eC/merge.9.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob -i AN:sum,AC:sum /tmp/lFdI2HY7eC/merge.9.a.bcf /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.10.a.vcf.gz /tmp/lFdI2HY7eC/merge.10.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob -m none /tmp/lFdI2HY7eC/merge.10.a.vcf.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.10.a.bcf /tmp/lFdI2HY7eC/merge.10.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob -m none /tmp/lFdI2HY7eC/merge.10.a.bcf /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.10.a.vcf.gz /tmp/lFdI2HY7eC/merge.10.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob -m both /tmp/lFdI2HY7eC/merge.10.a.vcf.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.10.a.bcf /tmp/lFdI2HY7eC/merge.10.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob -m both /tmp/lFdI2HY7eC/merge.10.a.bcf /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.10.a.vcf.gz /tmp/lFdI2HY7eC/merge.10.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob -m snp-ins-del /tmp/lFdI2HY7eC/merge.10.a.vcf.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/merge.10.a.bcf /tmp/lFdI2HY7eC/merge.10.b.bcf .. ok test_vcf_merge: /build/bcftools-1.16/bcftools merge -Ob -m snp-ins-del /tmp/lFdI2HY7eC/merge.10.a.bcf /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.string.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.string.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.string.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.variantkey.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/view.vectors.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.2.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/filter-missing-floats.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/filter-missing-floats.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.filter.2.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.filter.3.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.filter.3.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.filter.3.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.filter.4.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/view.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.negative.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.negative.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.negative.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.negative.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.filter.6.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.filter.8.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.filter.8.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.filter.9.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.filter.9.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.filter.13.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.filter.10.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.filter.10.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.filter.12.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.filter.12.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.smpl.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.smpl.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.smpl.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.smpl.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.smpl.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.smpl.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.filter.id.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/query.filter.id.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/filter.12.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/filter.12.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/filter.12.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/filter.12.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/filter.12.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/filter.12.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/filter.10.vcf.gz .. ok test_vcf_query: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/norm.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -cx -f /build/bcftools-1.16/test/norm.fa /tmp/lFdI2HY7eC/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/lFdI2HY7eC/norm.split.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -m- /tmp/lFdI2HY7eC/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/lFdI2HY7eC/norm.split.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -m- /tmp/lFdI2HY7eC/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/lFdI2HY7eC/norm.split.3.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -m- --force /tmp/lFdI2HY7eC/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/lFdI2HY7eC/norm.split.4.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -m- /tmp/lFdI2HY7eC/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/lFdI2HY7eC/norm.split.4.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -m- --keep-sum AD /tmp/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/norm.merge.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -m+ /tmp/lFdI2HY7eC/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/lFdI2HY7eC/norm.merge.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -m+ /tmp/lFdI2HY7eC/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/lFdI2HY7eC/norm.merge.3.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -m+ /tmp/lFdI2HY7eC/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/lFdI2HY7eC/norm.merge.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -m+ -s /tmp/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/norm.telomere.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -f /build/bcftools-1.16/test/norm.fa /tmp/lFdI2HY7eC/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/lFdI2HY7eC/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -d snps /tmp/lFdI2HY7eC/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/lFdI2HY7eC/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -d indels /tmp/lFdI2HY7eC/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/lFdI2HY7eC/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -d both /tmp/lFdI2HY7eC/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/lFdI2HY7eC/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -d all /tmp/lFdI2HY7eC/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/lFdI2HY7eC/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -d none /tmp/lFdI2HY7eC/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/lFdI2HY7eC/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -d exact /tmp/lFdI2HY7eC/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/lFdI2HY7eC/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -d none /tmp/lFdI2HY7eC/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/lFdI2HY7eC/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -d exact /tmp/lFdI2HY7eC/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/lFdI2HY7eC/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -d indels /tmp/lFdI2HY7eC/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/lFdI2HY7eC/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -d any /tmp/lFdI2HY7eC/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/lFdI2HY7eC/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -d both /tmp/lFdI2HY7eC/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/lFdI2HY7eC/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -d snps /tmp/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/atomize.split.1.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob --atomize --old-rec-tag OLD_REC /tmp/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/atomize.split.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob --atomize --old-rec-tag OLD_REC /tmp/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/atomize.split.3.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob --atomize --atom-overlaps . /tmp/lFdI2HY7eC/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/lFdI2HY7eC/norm.4.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -m +both /tmp/lFdI2HY7eC/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/lFdI2HY7eC/norm.4.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.16/bcftools norm -Ob -m +any /tmp/lFdI2HY7eC/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/lFdI2HY7eC/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/lFdI2HY7eC/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/lFdI2HY7eC/view.vcf.gz -r20,Y .. ok test_vcf_view: /build/bcftools-1.16/bcftools view -Ob -f PASS -Xks NA00003 /tmp/lFdI2HY7eC/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/lFdI2HY7eC/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view -Ob -xs NA00003 /tmp/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view -Ob -p /tmp/lFdI2HY7eC/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/lFdI2HY7eC/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view -Ob -P /tmp/lFdI2HY7eC/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/lFdI2HY7eC/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/lFdI2HY7eC/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/lFdI2HY7eC/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -GVsnps /tmp/lFdI2HY7eC/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view -Ob -GVsnps /tmp/lFdI2HY7eC/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/lFdI2HY7eC/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/lFdI2HY7eC/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/lFdI2HY7eC/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view -Ob -s ^NA00003 /tmp/lFdI2HY7eC/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/lFdI2HY7eC/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view -Ob -G /tmp/lFdI2HY7eC/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/lFdI2HY7eC/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -a /tmp/lFdI2HY7eC/many.alleles.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view -Ob -a /tmp/lFdI2HY7eC/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/lFdI2HY7eC/view.vectors.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view -Ob -asA /tmp/lFdI2HY7eC/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/lFdI2HY7eC/view.vectors.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view -Ob -asB /tmp/lFdI2HY7eC/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/lFdI2HY7eC/view.vectors.2.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view -Ob -asA /tmp/lFdI2HY7eC/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/lFdI2HY7eC/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -i'FMT/FGS[*:2]="C"' /tmp/lFdI2HY7eC/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -i'FMT/FGS[*:4]="EE"' /tmp/lFdI2HY7eC/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -i'FMT/FRS[*:1]="BB"' /tmp/lFdI2HY7eC/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -i'TXT0="text"' /tmp/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/filter.2.vcf.gz 1:3062917-3157410 .. ok test_vcf_view: /build/bcftools-1.16/bcftools view -Ob -i 'POS>=3062917' /tmp/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/idx.4.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -Ht 2 /tmp/lFdI2HY7eC/view-t.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -Ht 3 /tmp/lFdI2HY7eC/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/lFdI2HY7eC/overlap.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 1 /tmp/lFdI2HY7eC/overlap.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 2 /tmp/lFdI2HY7eC/overlap.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 0 /tmp/lFdI2HY7eC/overlap.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 1 /tmp/lFdI2HY7eC/overlap.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 2 /tmp/lFdI2HY7eC/overlap.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 0 /tmp/lFdI2HY7eC/overlap.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 1 /tmp/lFdI2HY7eC/overlap.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 2 /tmp/lFdI2HY7eC/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/lFdI2HY7eC/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -c6:nonmajor /tmp/lFdI2HY7eC/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -q0.3:major /tmp/lFdI2HY7eC/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/lFdI2HY7eC/view.filter.annovar.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -i 'Gene.refGene~"NOD"' /tmp/lFdI2HY7eC/view.filter.annovar.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -i 'LJB2_MutationTaster=="0.291000"' /tmp/lFdI2HY7eC/view.filter.annovar.vcf.gz .. ok test_vcf_view: /build/bcftools-1.16/bcftools view --no-version -H -a /tmp/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-1.16/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/lFdI2HY7eC/regions.tab.gz /tmp/lFdI2HY7eC/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/regions.vcf.gz | /build/bcftools-1.16/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/lFdI2HY7eC/regions.tab.gz .. ok test_vcf_regions: /build/bcftools-1.16/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/lFdI2HY7eC/regions.tab.gz /tmp/lFdI2HY7eC/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-1.16/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/lFdI2HY7eC/regions.bed /tmp/lFdI2HY7eC/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/regions.vcf.gz | /build/bcftools-1.16/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/lFdI2HY7eC/regions.bed .. ok test_vcf_regions: /build/bcftools-1.16/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/lFdI2HY7eC/regions.bed /tmp/lFdI2HY7eC/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-1.16/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/lFdI2HY7eC/regions.bed.gz /tmp/lFdI2HY7eC/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/regions.vcf.gz | /build/bcftools-1.16/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/lFdI2HY7eC/regions.bed.gz .. ok test_vcf_regions: /build/bcftools-1.16/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/lFdI2HY7eC/regions.bed.gz /tmp/lFdI2HY7eC/regions.vcf.gz .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/lFdI2HY7eC/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/lFdI2HY7eC/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/lFdI2HY7eC/annotate.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/lFdI2HY7eC/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/lFdI2HY7eC/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/lFdI2HY7eC/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/lFdI2HY7eC/annotate2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/lFdI2HY7eC/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/lFdI2HY7eC/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/lFdI2HY7eC/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/lFdI2HY7eC/annotate2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/lFdI2HY7eC/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/lFdI2HY7eC/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/lFdI2HY7eC/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/lFdI2HY7eC/annotate2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/lFdI2HY7eC/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/lFdI2HY7eC/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/lFdI2HY7eC/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/lFdI2HY7eC/annotate2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/lFdI2HY7eC/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/lFdI2HY7eC/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/lFdI2HY7eC/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/lFdI2HY7eC/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/lFdI2HY7eC/annots4.vcf.gz -c +INFO /tmp/lFdI2HY7eC/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/lFdI2HY7eC/annots4.vcf.gz -c +INFO /tmp/lFdI2HY7eC/annotate4.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/lFdI2HY7eC/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/lFdI2HY7eC/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/lFdI2HY7eC/annotate2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/lFdI2HY7eC/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/lFdI2HY7eC/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/lFdI2HY7eC/annotate2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/lFdI2HY7eC/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/lFdI2HY7eC/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/lFdI2HY7eC/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/lFdI2HY7eC/annotate2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/lFdI2HY7eC/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/lFdI2HY7eC/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/lFdI2HY7eC/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/lFdI2HY7eC/annotate2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/lFdI2HY7eC/annots11.vcf.gz -c FMT /tmp/lFdI2HY7eC/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/lFdI2HY7eC/annots11.vcf.gz -c FMT /tmp/lFdI2HY7eC/annotate11.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/lFdI2HY7eC/annots2.vcf.gz -c FMT/newGT:=GT /tmp/lFdI2HY7eC/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/lFdI2HY7eC/annots2.vcf.gz -c FMT/newGT:=GT /tmp/lFdI2HY7eC/annotate2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/lFdI2HY7eC/annots12.vcf.gz -c FMT/GT:=newGT /tmp/lFdI2HY7eC/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/lFdI2HY7eC/annots12.vcf.gz -c FMT/GT:=newGT /tmp/lFdI2HY7eC/annotate2.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/lFdI2HY7eC/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/lFdI2HY7eC/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/lFdI2HY7eC/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/lFdI2HY7eC/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/lFdI2HY7eC/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/lFdI2HY7eC/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/lFdI2HY7eC/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/lFdI2HY7eC/annotate20.src.vcf.gz -c FMT/GT /tmp/lFdI2HY7eC/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/lFdI2HY7eC/annotate20.src.vcf.gz -c FMT/GT /tmp/lFdI2HY7eC/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/lFdI2HY7eC/annotate20.src.vcf.gz -c +FMT/GT /tmp/lFdI2HY7eC/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/lFdI2HY7eC/annotate20.src.vcf.gz -c +FMT/GT /tmp/lFdI2HY7eC/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/lFdI2HY7eC/annotate20.src.vcf.gz -c -FMT/GT /tmp/lFdI2HY7eC/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/lFdI2HY7eC/annotate20.src.vcf.gz -c -FMT/GT /tmp/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/lFdI2HY7eC/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/lFdI2HY7eC/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/lFdI2HY7eC/annotate22.vcf.gz | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.16/bcftools annotate -a /tmp/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/annotate24.src.vcf.gz -c XX /tmp/lFdI2HY7eC/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/lFdI2HY7eC/annotate24.src.vcf.gz -c XX /tmp/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/annots.id.vcf.gz -c ALT /tmp/lFdI2HY7eC/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/lFdI2HY7eC/annots.id.vcf.gz -c ALT /tmp/lFdI2HY7eC/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/lFdI2HY7eC/annots.id.vcf.gz -c +ALT /tmp/lFdI2HY7eC/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/lFdI2HY7eC/annots.id.vcf.gz -c +ALT /tmp/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/concat.1.a.vcf.gz /tmp/lFdI2HY7eC/concat.1.b.vcf.gz .. ok test_vcf_concat: /build/bcftools-1.16/bcftools concat -Ob /tmp/lFdI2HY7eC/concat.1.a.vcf.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/concat.1.a.bcf /tmp/lFdI2HY7eC/concat.1.b.bcf .. ok test_vcf_concat: /build/bcftools-1.16/bcftools concat -Ob /tmp/lFdI2HY7eC/concat.1.a.bcf /tmp/lFdI2HY7eC/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/lFdI2HY7eC/concat.2.a.vcf.gz /tmp/lFdI2HY7eC/concat.2.b.vcf.gz .. ok test_vcf_concat: /build/bcftools-1.16/bcftools concat -Ob -a /tmp/lFdI2HY7eC/concat.2.a.vcf.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/concat.2.a.bcf /tmp/lFdI2HY7eC/concat.2.b.bcf .. ok test_vcf_concat: /build/bcftools-1.16/bcftools concat -Ob -a /tmp/lFdI2HY7eC/concat.2.a.bcf /tmp/lFdI2HY7eC/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/lFdI2HY7eC/concat.2.a.vcf.gz /tmp/lFdI2HY7eC/concat.2.b.vcf.gz .. ok test_vcf_concat: /build/bcftools-1.16/bcftools concat -Ob -aD /tmp/lFdI2HY7eC/concat.2.a.vcf.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/concat.2.a.bcf /tmp/lFdI2HY7eC/concat.2.b.bcf .. ok test_vcf_concat: /build/bcftools-1.16/bcftools concat -Ob -aD /tmp/lFdI2HY7eC/concat.2.a.bcf /tmp/lFdI2HY7eC/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/lFdI2HY7eC/concat.3.a.vcf.gz /tmp/lFdI2HY7eC/concat.3.b.vcf.gz /tmp/lFdI2HY7eC/concat.3.0.vcf.gz /tmp/lFdI2HY7eC/concat.3.c.vcf.gz /tmp/lFdI2HY7eC/concat.3.d.vcf.gz /tmp/lFdI2HY7eC/concat.3.e.vcf.gz /tmp/lFdI2HY7eC/concat.3.f.vcf.gz .. ok test_vcf_concat: /build/bcftools-1.16/bcftools concat -Ob -l --ligate-warn /tmp/lFdI2HY7eC/concat.3.a.vcf.gz /tmp/lFdI2HY7eC/concat.3.b.vcf.gz /tmp/lFdI2HY7eC/concat.3.0.vcf.gz /tmp/lFdI2HY7eC/concat.3.c.vcf.gz /tmp/lFdI2HY7eC/concat.3.d.vcf.gz /tmp/lFdI2HY7eC/concat.3.e.vcf.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/concat.3.a.bcf /tmp/lFdI2HY7eC/concat.3.b.bcf /tmp/lFdI2HY7eC/concat.3.0.bcf /tmp/lFdI2HY7eC/concat.3.c.bcf /tmp/lFdI2HY7eC/concat.3.d.bcf /tmp/lFdI2HY7eC/concat.3.e.bcf /tmp/lFdI2HY7eC/concat.3.f.bcf .. ok test_vcf_concat: /build/bcftools-1.16/bcftools concat -Ob -l --ligate-warn /tmp/lFdI2HY7eC/concat.3.a.bcf /tmp/lFdI2HY7eC/concat.3.b.bcf /tmp/lFdI2HY7eC/concat.3.0.bcf /tmp/lFdI2HY7eC/concat.3.c.bcf /tmp/lFdI2HY7eC/concat.3.d.bcf /tmp/lFdI2HY7eC/concat.3.e.bcf /tmp/lFdI2HY7eC/concat.3.f.bcf | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools_ Random seed for test_naive_concat: 2013862142 .. ok test_naive_concat: /build/bcftools-1.16/bcftools concat --naive-force /tmp/lFdI2HY7eC/naive_concat.0.bcf /tmp/lFdI2HY7eC/naive_concat.1.bcf /tmp/lFdI2HY7eC/naive_concat.2.bcf /tmp/lFdI2HY7eC/naive_concat.3.bcf /tmp/lFdI2HY7eC/naive_concat.4.bcf /tmp/lFdI2HY7eC/naive_concat.5.bcf /tmp/lFdI2HY7eC/naive_concat.6.bcf /tmp/lFdI2HY7eC/naive_concat.7.bcf /tmp/lFdI2HY7eC/naive_concat.8.bcf /tmp/lFdI2HY7eC/naive_concat.9.bcf | /build/bcftools-1.16/bcftools view -H .. ok test_naive_concat: /build/bcftools-1.16/bcftools concat --naive /tmp/lFdI2HY7eC/naive_concat.0.vcf.gz /tmp/lFdI2HY7eC/naive_concat.1.vcf.gz /tmp/lFdI2HY7eC/naive_concat.2.vcf.gz /tmp/lFdI2HY7eC/naive_concat.3.vcf.gz /tmp/lFdI2HY7eC/naive_concat.4.vcf.gz /tmp/lFdI2HY7eC/naive_concat.5.vcf.gz /tmp/lFdI2HY7eC/naive_concat.6.vcf.gz /tmp/lFdI2HY7eC/naive_concat.7.vcf.gz /tmp/lFdI2HY7eC/naive_concat.8.vcf.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/concat.4.a.vcf.gz /tmp/lFdI2HY7eC/concat.4.b.vcf.gz .. ok test_vcf_concat: /build/bcftools-1.16/bcftools concat -Ob -l /tmp/lFdI2HY7eC/concat.4.a.vcf.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/concat.4.a.bcf /tmp/lFdI2HY7eC/concat.4.b.bcf .. ok test_vcf_concat: /build/bcftools-1.16/bcftools concat -Ob -l /tmp/lFdI2HY7eC/concat.4.a.bcf /tmp/lFdI2HY7eC/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/lFdI2HY7eC/concat.5.a.vcf.gz /tmp/lFdI2HY7eC/concat.5.b.vcf.gz /tmp/lFdI2HY7eC/concat.5.c.vcf.gz .. ok test_vcf_concat: /build/bcftools-1.16/bcftools concat -Ob -l --ligate-warn /tmp/lFdI2HY7eC/concat.5.a.vcf.gz /tmp/lFdI2HY7eC/concat.5.b.vcf.gz /tmp/lFdI2HY7eC/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/lFdI2HY7eC/concat.5.a.bcf /tmp/lFdI2HY7eC/concat.5.b.bcf /tmp/lFdI2HY7eC/concat.5.c.bcf .. ok test_vcf_concat: /build/bcftools-1.16/bcftools concat -Ob -l --ligate-warn /tmp/lFdI2HY7eC/concat.5.a.bcf /tmp/lFdI2HY7eC/concat.5.b.bcf /tmp/lFdI2HY7eC/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/lFdI2HY7eC/concat.5.a.bcf /tmp/lFdI2HY7eC/concat.5.b.bcf /tmp/lFdI2HY7eC/concat.5.c.bcf .. ok test_vcf_concat: /build/bcftools-1.16/bcftools concat -Ob -l --ligate-force /tmp/lFdI2HY7eC/concat.5.a.bcf /tmp/lFdI2HY7eC/concat.5.b.bcf /tmp/lFdI2HY7eC/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/lFdI2HY7eC/reheader.bcf | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/lFdI2HY7eC/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/lFdI2HY7eC/reheader.vcf.gz | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/lFdI2HY7eC/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/lFdI2HY7eC/reheader.bcf | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/lFdI2HY7eC/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/lFdI2HY7eC/reheader.vcf.gz | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/lFdI2HY7eC/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/lFdI2HY7eC/reheader.bcf | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/lFdI2HY7eC/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/lFdI2HY7eC/reheader.vcf.gz | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/lFdI2HY7eC/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/lFdI2HY7eC/reheader.bcf | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/lFdI2HY7eC/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/lFdI2HY7eC/reheader.vcf.gz | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/lFdI2HY7eC/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/lFdI2HY7eC/reheader.bcf | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/lFdI2HY7eC/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/lFdI2HY7eC/reheader.vcf.gz | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/lFdI2HY7eC/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/lFdI2HY7eC/empty.bcf | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/lFdI2HY7eC/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/lFdI2HY7eC/empty.vcf.gz | /build/bcftools-1.16/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/rename.map -Ov /tmp/lFdI2HY7eC/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/lFdI2HY7eC/rename.map -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/convert.vcf.gz | /build/bcftools-1.16/bcftools convert -g -,. .. ok test_vcf_convert: /build/bcftools-1.16/bcftools convert -g -,. --vcf-ids /tmp/lFdI2HY7eC/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/check.vcf.gz | /build/bcftools-1.16/bcftools convert -g -,. --3N6 .. ok test_vcf_convert: /build/bcftools-1.16/bcftools convert -g .,- --3N6 /tmp/lFdI2HY7eC/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/convert.vcf.gz | /build/bcftools-1.16/bcftools convert -h -,.,. .. ok test_vcf_convert: /build/bcftools-1.16/bcftools convert -h .,-,. /tmp/lFdI2HY7eC/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/convert.vcf.gz | /build/bcftools-1.16/bcftools convert -h .,-,. .. ok test_vcf_convert: /build/bcftools-1.16/bcftools convert -h .,-,. --vcf-ids /tmp/lFdI2HY7eC/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/convert.vcf.gz | /build/bcftools-1.16/bcftools convert -h .,-,. --vcf-ids .. ok test_vcf_convert: /build/bcftools-1.16/bcftools convert -h .,.,- /tmp/lFdI2HY7eC/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/convert.hap-missing.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/convert.hap-missing.vcf.gz | /build/bcftools-1.16/bcftools convert --haplegendsample -,.,. .. ok test_vcf_convert: /build/bcftools-1.16/bcftools convert --hapsample -,. /tmp/lFdI2HY7eC/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/convert.vcf.gz | /build/bcftools-1.16/bcftools convert --hapsample -,. .. ok test_vcf_convert: /build/bcftools-1.16/bcftools convert --hapsample -,. --vcf-ids /tmp/lFdI2HY7eC/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/convert.vcf.gz | /build/bcftools-1.16/bcftools convert --hapsample -,. --vcf-ids .. ok test_vcf_convert: /build/bcftools-1.16/bcftools convert --hapsample .,- /tmp/lFdI2HY7eC/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/convert.gvcf.vcf.gz .. ok test_vcf_convert_gvcf: /build/bcftools-1.16/bcftools view -Ob /tmp/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/consensus.vcf.gz -f /build/bcftools-1.16/test/consensus.fa -m /build/bcftools-1.16/test/consensus.tab -c /tmp/lFdI2HY7eC/consensus.1.chain.new >/dev/null; cat /tmp/lFdI2HY7eC/consensus.1.chain.new .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/lFdI2HY7eC/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/lFdI2HY7eC/consensus.vcf.gz -f /build/bcftools-1.16/test/consensus.fa -H 1 -m /build/bcftools-1.16/test/consensus.tab -c /tmp/lFdI2HY7eC/consensus.2.chain.new >/dev/null; cat /tmp/lFdI2HY7eC/consensus.2.chain.new .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/consensus.vcf.gz -f /build/bcftools-1.16/test/consensus.fa -I -m /build/bcftools-1.16/test/consensus.tab -c /tmp/lFdI2HY7eC/consensus.3.chain.new >/dev/null; cat /tmp/lFdI2HY7eC/consensus.3.chain.new .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/lFdI2HY7eC/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/lFdI2HY7eC/consensus.vcf.gz -f /build/bcftools-1.16/test/consensus.fa -H 1 -c /tmp/lFdI2HY7eC/consensus.4.chain.new >/dev/null; cat /tmp/lFdI2HY7eC/consensus.4.chain.new .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/lFdI2HY7eC/consensus2.vcf.gz -f /build/bcftools-1.16/test/consensus2.fa -H 1 .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/lFdI2HY7eC/consensus2.vcf.gz -f /build/bcftools-1.16/test/consensus2.fa -H 2 .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/lFdI2HY7eC/empty.vcf.gz -f /build/bcftools-1.16/test/consensus.fa .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/consensus4.vcf.gz -f /build/bcftools-1.16/test/consensus2.fa .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/lFdI2HY7eC/consensus5.vcf.gz -f /build/bcftools-1.16/test/consensus5.fa --haplotype LA .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/lFdI2HY7eC/consensus6.vcf.gz -f /build/bcftools-1.16/test/consensus6.fa .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/lFdI2HY7eC/consensus7.vcf.gz -f /build/bcftools-1.16/test/consensus7.fa -H 2 .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/lFdI2HY7eC/consensus7.vcf.gz -f /build/bcftools-1.16/test/consensus7.fa -H 2pIu .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/lFdI2HY7eC/consensus7.vcf.gz -f /build/bcftools-1.16/test/consensus7.fa -H 1 .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/lFdI2HY7eC/consensus7.vcf.gz -f /build/bcftools-1.16/test/consensus7.fa -H 1pIu .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/lFdI2HY7eC/consensus8.vcf.gz -f /build/bcftools-1.16/test/consensus.fa .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/lFdI2HY7eC/consensus8.vcf.gz -f /build/bcftools-1.16/test/consensus.fa -a . .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/consensus.12.vcf.gz -f /build/bcftools-1.16/test/consensus.12.fa .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/lFdI2HY7eC/consensus.13.vcf.gz -f /build/bcftools-1.16/test/consensus.13.fa .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/lFdI2HY7eC/consensus.14.vcf.gz -f /build/bcftools-1.16/test/consensus.14.fa .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/consensus.16.vcf.gz -f /build/bcftools-1.16/test/consensus.fa -I .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/consensus.18.vcf.gz -f /build/bcftools-1.16/test/consensus.18.fa .. ok test_vcf_consensus: /build/bcftools-1.16/bcftools consensus /tmp/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/mpileup.cram.urllist | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a DP,DV -r17:100-600 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a DP,DV -r17:100-600 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a DP,DV -r17:100-600 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a DP,DV -r17:100-600 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r17:100-150 -S /build/bcftools-1.16/test/mplp.samples -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r17:100-150 -S /build/bcftools-1.16/test/mplp.samples -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r17:100-150 -S /build/bcftools-1.16/test/mplp.samples -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r17:100-150 -S /build/bcftools-1.16/test/mplp.samples -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r17:100-150 -S ^/build/bcftools-1.16/test/mplp.samples -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r17:100-150 -S ^/build/bcftools-1.16/test/mplp.samples -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r17:100-150 -S ^/build/bcftools-1.16/test/mplp.samples -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r17:100-150 -S ^/build/bcftools-1.16/test/mplp.samples -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -t17:100-150 -S /build/bcftools-1.16/test/mplp.9.samples -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.sam /build/bcftools-1.16/test/mpileup/mpileup.2.sam /build/bcftools-1.16/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -t17:100-150 -S /build/bcftools-1.16/test/mplp.9.samples -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.sam /build/bcftools-1.16/test/mpileup/mpileup.2.sam /build/bcftools-1.16/test/mpileup/mpileup.3.sam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -t17:100-150 -S /build/bcftools-1.16/test/mplp.9.samples -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -t17:100-150 -S /build/bcftools-1.16/test/mplp.9.samples -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -t17:100-150 -S /build/bcftools-1.16/test/mplp.9.samples -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -t17:100-150 -S /build/bcftools-1.16/test/mplp.9.samples -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -t17:100-150 -G /build/bcftools-1.16/test/mplp.10.samples -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.sam /build/bcftools-1.16/test/mpileup/mpileup.2.sam /build/bcftools-1.16/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -t17:100-150 -G /build/bcftools-1.16/test/mplp.10.samples -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.sam /build/bcftools-1.16/test/mpileup/mpileup.2.sam /build/bcftools-1.16/test/mpileup/mpileup.3.sam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -t17:100-150 -G /build/bcftools-1.16/test/mplp.10.samples -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -t17:100-150 -G /build/bcftools-1.16/test/mplp.10.samples -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.bam /build/bcftools-1.16/test/mpileup/mpileup.2.bam /build/bcftools-1.16/test/mpileup/mpileup.3.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -t17:100-150 -G /build/bcftools-1.16/test/mplp.10.samples -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -t17:100-150 -G /build/bcftools-1.16/test/mplp.10.samples -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.1.cram /build/bcftools-1.16/test/mpileup/mpileup.2.cram /build/bcftools-1.16/test/mpileup/mpileup.3.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.3.sam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.3.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.3.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -s HG00102 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.3.sam /build/bcftools-1.16/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -s HG00102 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.3.sam /build/bcftools-1.16/test/mpileup/mpileup.4.sam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -s HG00102 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.3.bam /build/bcftools-1.16/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -s HG00102 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.3.bam /build/bcftools-1.16/test/mpileup/mpileup.4.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -s HG00102 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.3.cram /build/bcftools-1.16/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -s HG00102 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.3.cram /build/bcftools-1.16/test/mpileup/mpileup.4.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -s ^HG99999 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.3.sam /build/bcftools-1.16/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -s ^HG99999 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.3.sam /build/bcftools-1.16/test/mpileup/mpileup.4.sam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -s ^HG99999 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.3.bam /build/bcftools-1.16/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -s ^HG99999 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.3.bam /build/bcftools-1.16/test/mpileup/mpileup.4.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -s ^HG99999 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.3.cram /build/bcftools-1.16/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -s ^HG99999 -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.3.cram /build/bcftools-1.16/test/mpileup/mpileup.4.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -G /build/bcftools-1.16/test/mplp.11.rgs -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.3.sam /build/bcftools-1.16/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -G /build/bcftools-1.16/test/mplp.11.rgs -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.3.sam /build/bcftools-1.16/test/mpileup/mpileup.4.sam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -G /build/bcftools-1.16/test/mplp.11.rgs -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.3.bam /build/bcftools-1.16/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -G /build/bcftools-1.16/test/mplp.11.rgs -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.3.bam /build/bcftools-1.16/test/mpileup/mpileup.4.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -G /build/bcftools-1.16/test/mplp.11.rgs -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.3.cram /build/bcftools-1.16/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -G /build/bcftools-1.16/test/mplp.11.rgs -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.3.cram /build/bcftools-1.16/test/mpileup/mpileup.4.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -G /build/bcftools-1.16/test/mplp.11.rgs -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.3.sam /build/bcftools-1.16/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -G /build/bcftools-1.16/test/mplp.11.rgs -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.3.sam /build/bcftools-1.16/test/mpileup/mpileup.4.sam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -G /build/bcftools-1.16/test/mplp.11.rgs -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.3.bam /build/bcftools-1.16/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -G /build/bcftools-1.16/test/mplp.11.rgs -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.3.bam /build/bcftools-1.16/test/mpileup/mpileup.4.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -G /build/bcftools-1.16/test/mplp.11.rgs -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa /build/bcftools-1.16/test/mpileup/mpileup.3.cram /build/bcftools-1.16/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -G /build/bcftools-1.16/test/mplp.11.rgs -f /build/bcftools-1.16/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup.3.cram /build/bcftools-1.16/test/mpileup/mpileup.4.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a AD -f /build/bcftools-1.16/test/mpileup/indel-AD.1.fa /build/bcftools-1.16/test/mpileup/indel-AD.1.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a AD -f /build/bcftools-1.16/test/mpileup/indel-AD.1.fa -Ob /build/bcftools-1.16/test/mpileup/indel-AD.1.sam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a AD -f /build/bcftools-1.16/test/mpileup/indel-AD.1.fa /build/bcftools-1.16/test/mpileup/indel-AD.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a AD -f /build/bcftools-1.16/test/mpileup/indel-AD.1.fa -Ob /build/bcftools-1.16/test/mpileup/indel-AD.1.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a AD -f /build/bcftools-1.16/test/mpileup/indel-AD.1.fa /build/bcftools-1.16/test/mpileup/indel-AD.1.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a AD -f /build/bcftools-1.16/test/mpileup/indel-AD.1.fa -Ob /build/bcftools-1.16/test/mpileup/indel-AD.1.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a AD -r 11:75 -f /build/bcftools-1.16/test/mpileup/indel-AD.2.fa /build/bcftools-1.16/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a AD -r 11:75 -f /build/bcftools-1.16/test/mpileup/indel-AD.2.fa -Ob /build/bcftools-1.16/test/mpileup/indel-AD.2.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a AD -r 11:75 -f /build/bcftools-1.16/test/mpileup/indel-AD.2.fa /build/bcftools-1.16/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a AD -r 11:75 -f /build/bcftools-1.16/test/mpileup/indel-AD.2.fa -Ob /build/bcftools-1.16/test/mpileup/indel-AD.2.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /build/bcftools-1.16/test/mpileup/indel-AD.2.fa /build/bcftools-1.16/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /build/bcftools-1.16/test/mpileup/indel-AD.2.fa -Ob /build/bcftools-1.16/test/mpileup/indel-AD.2.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /build/bcftools-1.16/test/mpileup/indel-AD.2.fa /build/bcftools-1.16/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /build/bcftools-1.16/test/mpileup/indel-AD.2.fa -Ob /build/bcftools-1.16/test/mpileup/indel-AD.2.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /build/bcftools-1.16/test/mpileup/indel-AD.2.fa /build/bcftools-1.16/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /build/bcftools-1.16/test/mpileup/indel-AD.2.fa -Ob /build/bcftools-1.16/test/mpileup/indel-AD.2.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /build/bcftools-1.16/test/mpileup/indel-AD.2.fa /build/bcftools-1.16/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /build/bcftools-1.16/test/mpileup/indel-AD.2.fa -Ob /build/bcftools-1.16/test/mpileup/indel-AD.2.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a INFO/SCR,FMT/SCR -f /build/bcftools-1.16/test/mpileup/mpileup-SCR.fa /build/bcftools-1.16/test/mpileup/mpileup-SCR.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a INFO/SCR,FMT/SCR -f /build/bcftools-1.16/test/mpileup/mpileup-SCR.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup-SCR.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a INFO/SCR,FMT/SCR -f /build/bcftools-1.16/test/mpileup/mpileup-SCR.fa /build/bcftools-1.16/test/mpileup/mpileup-SCR.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -a INFO/SCR,FMT/SCR -f /build/bcftools-1.16/test/mpileup/mpileup-SCR.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup-SCR.cram | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -t 1:100 --skip-all-set PAIRED,PROPER_PAIR,MREVERSE -f /build/bcftools-1.16/test/mpileup/mpileup-SCR.fa /build/bcftools-1.16/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -t 1:100 --skip-all-set PAIRED,PROPER_PAIR,MREVERSE -f /build/bcftools-1.16/test/mpileup/mpileup-SCR.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup-filter.sam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -t 1:100 --skip-any-set READ1 -f /build/bcftools-1.16/test/mpileup/mpileup-SCR.fa /build/bcftools-1.16/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -t 1:100 --skip-any-set READ1 -f /build/bcftools-1.16/test/mpileup/mpileup-SCR.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup-filter.sam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -t 1:100 --skip-all-unset READ1 -f /build/bcftools-1.16/test/mpileup/mpileup-SCR.fa /build/bcftools-1.16/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -t 1:100 --skip-all-unset READ1 -f /build/bcftools-1.16/test/mpileup/mpileup-SCR.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup-filter.sam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -t 1:100 --skip-any-unset READ1 -f /build/bcftools-1.16/test/mpileup/mpileup-SCR.fa /build/bcftools-1.16/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -t 1:100 --skip-any-unset READ1 -f /build/bcftools-1.16/test/mpileup/mpileup-SCR.fa -Ob /build/bcftools-1.16/test/mpileup/mpileup-filter.sam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r chr19:69-99 -f /build/bcftools-1.16/test/mpileup/annot-NMBZ.1.fa /build/bcftools-1.16/test/mpileup/annot-NMBZ.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r chr19:69-99 -f /build/bcftools-1.16/test/mpileup/annot-NMBZ.1.fa -Ob /build/bcftools-1.16/test/mpileup/annot-NMBZ.1.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r chr6:75 -f /build/bcftools-1.16/test/mpileup/annot-NMBZ.2.fa /build/bcftools-1.16/test/mpileup/annot-NMBZ.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r chr6:75 -f /build/bcftools-1.16/test/mpileup/annot-NMBZ.2.fa -Ob /build/bcftools-1.16/test/mpileup/annot-NMBZ.2.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r chr16:75 -f /build/bcftools-1.16/test/mpileup/annot-NMBZ.3.fa /build/bcftools-1.16/test/mpileup/annot-NMBZ.3.1.bam /build/bcftools-1.16/test/mpileup/annot-NMBZ.3.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.16/bcftools mpileup -r chr16:75 -f /build/bcftools-1.16/test/mpileup/annot-NMBZ.3.fa -Ob /build/bcftools-1.16/test/mpileup/annot-NMBZ.3.1.bam /build/bcftools-1.16/test/mpileup/annot-NMBZ.3.2.bam | /build/bcftools-1.16/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_csq: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq.fa -g /build/bcftools-1.16/test/csq.gff3 /build/bcftools-1.16/test/csq.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq.fa -g /build/bcftools-1.16/test/csq.chr.gff3 /build/bcftools-1.16/test/csq.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq.fa -g /build/bcftools-1.16/test/csq.2.gff /build/bcftools-1.16/test/csq.2.vcf | /build/bcftools-1.16/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq.fa -g /build/bcftools-1.16/test/csq.2.gff --ncsq 64 /build/bcftools-1.16/test/csq.2.vcf | /build/bcftools-1.16/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000624631/ENST00000624631.fa -g /build/bcftools-1.16/test/csq/ENST00000624631/ENST00000624631.gff /build/bcftools-1.16/test/csq/ENST00000624631/ambiguous.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000593942/ENST00000593942.fa -g /build/bcftools-1.16/test/csq/ENST00000593942/ENST00000593942.gff /build/bcftools-1.16/test/csq/ENST00000593942/last-codon-deletion.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /build/bcftools-1.16/test/csq/ENST00000580206 && /build/bcftools-1.16/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.ins-snv.vcf | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-1.16/bcftools csq -f ENST00000580206.fa -g short.gff compound.ins-snv.vcf | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-1.16/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff single.ins-snv.vcf | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-1.16/bcftools csq -f ENST00000580206.fa -g short.gff single.ins-snv.vcf | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-1.16/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.del-snv.vcf | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-1.16/bcftools csq -f ENST00000580206.fa -g short.gff compound.del-snv.vcf | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-1.16/bcftools csq -f ENST00000580206.fa -g short.gff single.del-snv.vcf | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-1.16/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.del-ins.vcf | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-1.16/bcftools csq -f ENST00000580206.fa -g short.gff compound.del-ins.vcf | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-1.16/bcftools csq -f ENST00000580206.fa -g short.gff single.del-ins.vcf | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000573314/ENST00000573314.fa -g /build/bcftools-1.16/test/csq/ENST00000573314/ENST00000573314.gff /build/bcftools-1.16/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000573314/ENST00000573314.fa -g /build/bcftools-1.16/test/csq/ENST00000573314/ENST00000573314.gff /build/bcftools-1.16/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000557788/ENST00000557788.fa -g /build/bcftools-1.16/test/csq/ENST00000557788/ENST00000557788.gff /build/bcftools-1.16/test/csq/ENST00000557788/long-overlap-del.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000545279/ENST00000545279.fa -g /build/bcftools-1.16/test/csq/ENST00000545279/ENST00000545279.gff /build/bcftools-1.16/test/csq/ENST00000545279/splice-region-insert.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000543077/ENST00000543077.fa -g /build/bcftools-1.16/test/csq/ENST00000543077/ENST00000543077.gff /build/bcftools-1.16/test/csq/ENST00000543077/not-a-start-lost.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000543077/ENST00000543077.fa -g /build/bcftools-1.16/test/csq/ENST00000543077/ENST00000543077.gff /build/bcftools-1.16/test/csq/ENST00000543077/not-a-start-lost.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000542803/ENST00000542803.fa -g /build/bcftools-1.16/test/csq/ENST00000542803/ENST00000542803.gff /build/bcftools-1.16/test/csq/ENST00000542803/splice-region.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000542803/ENST00000542803.fa -g /build/bcftools-1.16/test/csq/ENST00000542803/ENST00000542803.gff /build/bcftools-1.16/test/csq/ENST00000542803/splice-region.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000536784/ENST00000536784.fa -g /build/bcftools-1.16/test/csq/ENST00000536784/ENST00000536784.gff /build/bcftools-1.16/test/csq/ENST00000536784/not-a-start-lost.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000536784/ENST00000536784.fa -g /build/bcftools-1.16/test/csq/ENST00000536784/ENST00000536784.gff /build/bcftools-1.16/test/csq/ENST00000536784/not-a-start-lost.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000528237/ENST00000528237.fa -g /build/bcftools-1.16/test/csq/ENST00000528237/ENST00000528237.gff /build/bcftools-1.16/test/csq/ENST00000528237/retained-stop-incomplete-cds.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000520868/ENST00000520868.fa -g /build/bcftools-1.16/test/csq/ENST00000520868/ENST00000520868.gff /build/bcftools-1.16/test/csq/ENST00000520868/long-deletion.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000520795/ENST00000520795.fa -g /build/bcftools-1.16/test/csq/ENST00000520795/ENST00000520795.gff /build/bcftools-1.16/test/csq/ENST00000520795/long-inside-del.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000520795/ENST00000520795.fa -g /build/bcftools-1.16/test/csq/ENST00000520795/ENST00000520795.gff /build/bcftools-1.16/test/csq/ENST00000520795/long-inside-del.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000519442/ENST00000519442.fa -g /build/bcftools-1.16/test/csq/ENST00000519442/ENST00000519442.gff /build/bcftools-1.16/test/csq/ENST00000519442/synon-splice-region-del.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000518414/ENST00000518414.fa -g /build/bcftools-1.16/test/csq/ENST00000518414/ENST00000518414.gff /build/bcftools-1.16/test/csq/ENST00000518414/incorrect-inframe-del.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.fa -g /build/bcftools-1.16/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.gff /build/bcftools-1.16/test/csq/ENST00000518414-ENST00000521270/valgrind.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000479739/ENST00000479739.fa -g /build/bcftools-1.16/test/csq/ENST00000479739/ENST00000479739.gff /build/bcftools-1.16/test/csq/ENST00000479739/short-cds-start-lost.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000479739/ENST00000479739.fa -g /build/bcftools-1.16/test/csq/ENST00000479739/ENST00000479739.gff /build/bcftools-1.16/test/csq/ENST00000479739/short-cds-start-lost.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000448695/ENST00000448695.fa -g /build/bcftools-1.16/test/csq/ENST00000448695/ENST00000448695.gff /build/bcftools-1.16/test/csq/ENST00000448695/syn-and-splice-reg.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000436063/ENST00000436063.fa -g /build/bcftools-1.16/test/csq/ENST00000436063/ENST00000436063.gff /build/bcftools-1.16/test/csq/ENST00000436063/insert-before-utr.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000423372/ENST00000423372.fa -g /build/bcftools-1.16/test/csq/ENST00000423372/ENST00000423372.gff /build/bcftools-1.16/test/csq/ENST00000423372/snps.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000423372/ENST00000423372.fa -g /build/bcftools-1.16/test/csq/ENST00000423372/ENST00000423372.gff /build/bcftools-1.16/test/csq/ENST00000423372/snps.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000423372/ENST00000423372.fa -g /build/bcftools-1.16/test/csq/ENST00000423372/ENST00000423372.gff /build/bcftools-1.16/test/csq/ENST00000423372/insert3.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000423372/ENST00000423372.fa -g /build/bcftools-1.16/test/csq/ENST00000423372/ENST00000423372.gff /build/bcftools-1.16/test/csq/ENST00000423372/insert3.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /build/bcftools-1.16/test/csq/ENST00000422159 && /build/bcftools-1.16/bcftools csq -f ENST00000422159.fa -g ENST00000422159.gff multiallelic.vcf | /build/bcftools-1.16/bcftools query -f'[%POS\t%REF\t%ALT\t%GT\t%TBCSQ\n]' | ../sort-csq -q ; echo ; /build/bcftools-1.16/bcftools csq -f ENST00000422159.fa -g short.gff multiallelic.vcf | /build/bcftools-1.16/bcftools query -f'[%POS\t%REF\t%ALT\t%GT\t%TBCSQ\n]' | ../sort-csq -q .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000420670/ENST00000420670.fa -g /build/bcftools-1.16/test/csq/ENST00000420670/ENST00000420670.gff /build/bcftools-1.16/test/csq/ENST00000420670/start-stop-lost.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000420670/ENST00000420670.fa -g /build/bcftools-1.16/test/csq/ENST00000420670/ENST00000420670.gff /build/bcftools-1.16/test/csq/ENST00000420670/segfault.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000420190/ENST00000420190.fa -g /build/bcftools-1.16/test/csq/ENST00000420190/ENST00000420190.gff /build/bcftools-1.16/test/csq/ENST00000420190/abort-in-csq-push.vcf | /build/bcftools-1.16/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000413103/ENST00000413103.fa -g /build/bcftools-1.16/test/csq/ENST00000413103/ENST00000413103.gff /build/bcftools-1.16/test/csq/ENST00000413103/long-deletion.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000410009/ENST00000410009.fa -g /build/bcftools-1.16/test/csq/ENST00000410009/ENST00000410009.gff /build/bcftools-1.16/test/csq/ENST00000410009/frameshift.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /build/bcftools-1.16/test/csq/ENST00000410009 && /build/bcftools-1.16/bcftools csq -B 5 -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/bcftools-1.16/test/csq/ENST00000410009 && /build/bcftools-1.16/bcftools csq -lb -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/bcftools-1.16/test/csq/ENST00000410009 && /build/bcftools-1.16/bcftools csq -b -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000409523/ENST00000409523.fa -g /build/bcftools-1.16/test/csq/ENST00000409523/ENST00000409523.gff /build/bcftools-1.16/test/csq/ENST00000409523/long-overlapping-del.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000400151/ENST00000400151.fa -g /build/bcftools-1.16/test/csq/ENST00000400151/ENST00000400151.gff /build/bcftools-1.16/test/csq/ENST00000400151/long-del.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000390520/ENST00000390520.fa -g /build/bcftools-1.16/test/csq/ENST00000390520/ENST00000390520.gff /build/bcftools-1.16/test/csq/ENST00000390520/deletion-overlap.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000382647/ENST00000382647.fa -g /build/bcftools-1.16/test/csq/ENST00000382647/ENST00000382647.gff /build/bcftools-1.16/test/csq/ENST00000382647/synon-splice-region-insert.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000381157/ENST00000381157.fa -g /build/bcftools-1.16/test/csq/ENST00000381157/ENST00000381157.gff /build/bcftools-1.16/test/csq/ENST00000381157/haploid-diploid.vcf | /build/bcftools-1.16/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n' .. ok test_csq_real: cd /build/bcftools-1.16/test/csq/ENST00000379416 && /build/bcftools-1.16/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.del-snp.vcf | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-1.16/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-del.vcf | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-1.16/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-ins.vcf | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-1.16/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-snp.vcf | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-1.16/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff single.vcf | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000378322/ENST00000378322.fa -g /build/bcftools-1.16/test/csq/ENST00000378322/ENST00000378322.gff /build/bcftools-1.16/test/csq/ENST00000378322/end-overlap-tscript.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000378322/ENST00000378322.fa -g /build/bcftools-1.16/test/csq/ENST00000378322/ENST00000378322.gff /build/bcftools-1.16/test/csq/ENST00000378322/end-overlap-tscript.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000375992/ENST00000375992.fa -g /build/bcftools-1.16/test/csq/ENST00000375992/ENST00000375992.gff /build/bcftools-1.16/test/csq/ENST00000375992/incorrect-synon-del-not-start-lost.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000373833/ENST00000373833.fa -g /build/bcftools-1.16/test/csq/ENST00000373833/ENST00000373833.gff /build/bcftools-1.16/test/csq/ENST00000373833/boundary-insertion.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000373833/ENST00000373833.fa -g /build/bcftools-1.16/test/csq/ENST00000373833/ENST00000373833.gff /build/bcftools-1.16/test/csq/ENST00000373833/boundary-insertion.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000368801/ENST00000368801.fa -g /build/bcftools-1.16/test/csq/ENST00000368801/ENST00000368801.gff /build/bcftools-1.16/test/csq/ENST00000368801/compound-lost.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000368801.2/ENST00000368801.2.fa -g /build/bcftools-1.16/test/csq/ENST00000368801.2/ENST00000368801.2.gff /build/bcftools-1.16/test/csq/ENST00000368801.2/start-lost.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000357367/ENST00000357367.fa -g /build/bcftools-1.16/test/csq/ENST00000357367/ENST00000357367.gff /build/bcftools-1.16/test/csq/ENST00000357367/stop-retained.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/not-a-start-lost.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/not-a-start-lost.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/frame3.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/frame3.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/frame2.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/frame2.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/frame1.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.16/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.16/test/csq/ENST00000341065/frame1.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000329454/ENST00000329454.fa -g /build/bcftools-1.16/test/csq/ENST00000329454/ENST00000329454.gff /build/bcftools-1.16/test/csq/ENST00000329454/boundary-deletion.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000329454/ENST00000329454.fa -g /build/bcftools-1.16/test/csq/ENST00000329454/ENST00000329454.gff /build/bcftools-1.16/test/csq/ENST00000329454/boundary-deletion.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000318249/ENST00000318249.fa -g /build/bcftools-1.16/test/csq/ENST00000318249/ENST00000318249.gff /build/bcftools-1.16/test/csq/ENST00000318249/start-lost.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000318249/ENST00000318249.fa -g /build/bcftools-1.16/test/csq/ENST00000318249/ENST00000318249.gff /build/bcftools-1.16/test/csq/ENST00000318249/start-lost.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000318249.2/ENST00000318249.2.fa -g /build/bcftools-1.16/test/csq/ENST00000318249.2/ENST00000318249.2.gff /build/bcftools-1.16/test/csq/ENST00000318249.2/synonymous-start-lost.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000303039/ENST00000303039.fa -g /build/bcftools-1.16/test/csq/ENST00000303039/ENST00000303039.gff /build/bcftools-1.16/test/csq/ENST00000303039/not-a-stop.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000303039/ENST00000303039.fa -g /build/bcftools-1.16/test/csq/ENST00000303039/ENST00000303039.gff /build/bcftools-1.16/test/csq/ENST00000303039/not-a-stop.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000301246/ENST00000301246.fa -g /build/bcftools-1.16/test/csq/ENST00000301246/ENST00000301246.gff /build/bcftools-1.16/test/csq/ENST00000301246/15bp-insert.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000295641/ENST00000295641.fa -g /build/bcftools-1.16/test/csq/ENST00000295641/ENST00000295641.gff /build/bcftools-1.16/test/csq/ENST00000295641/not-a-start-lost.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000295641/ENST00000295641.fa -g /build/bcftools-1.16/test/csq/ENST00000295641/ENST00000295641.gff /build/bcftools-1.16/test/csq/ENST00000295641/not-a-start-lost.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000294661/ENST00000294661.fa -g /build/bcftools-1.16/test/csq/ENST00000294661/ENST00000294661.gff /build/bcftools-1.16/test/csq/ENST00000294661/non-coding-boundary.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000294661/ENST00000294661.fa -g /build/bcftools-1.16/test/csq/ENST00000294661/ENST00000294661.gff /build/bcftools-1.16/test/csq/ENST00000294661/non-coding-boundary.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000285021/ENST00000285021.fa -g /build/bcftools-1.16/test/csq/ENST00000285021/ENST00000285021.gff /build/bcftools-1.16/test/csq/ENST00000285021/stop-gained-inframe-indel.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000271583/ENST00000271583.fa -g /build/bcftools-1.16/test/csq/ENST00000271583/ENST00000271583.gff /build/bcftools-1.16/test/csq/ENST00000271583/splice-acceptor.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000269081/ENST00000269081.fa -g /build/bcftools-1.16/test/csq/ENST00000269081/ENST00000269081.gff /build/bcftools-1.16/test/csq/ENST00000269081/stop-gained-not-inframe-insertion.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000263103-INS/ENST00000263103-INS.fa -g /build/bcftools-1.16/test/csq/ENST00000263103-INS/ENST00000263103-INS.gff /build/bcftools-1.16/test/csq/ENST00000263103-INS/insertions.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000256452/ENST00000256452.fa -g /build/bcftools-1.16/test/csq/ENST00000256452/ENST00000256452.gff /build/bcftools-1.16/test/csq/ENST00000256452/intron.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000230048/ENST00000230048.fa -g /build/bcftools-1.16/test/csq/ENST00000230048/ENST00000230048.gff /build/bcftools-1.16/test/csq/ENST00000230048/start-del.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000227471/ENST00000227471.fa -g /build/bcftools-1.16/test/csq/ENST00000227471/ENST00000227471.gff /build/bcftools-1.16/test/csq/ENST00000227471/insert-splice-vs-frameshift.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000218032/ENST00000218032.fa -g /build/bcftools-1.16/test/csq/ENST00000218032/ENST00000218032.gff /build/bcftools-1.16/test/csq/ENST00000218032/start-lost.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/ENST00000218032/ENST00000218032.fa -g /build/bcftools-1.16/test/csq/ENST00000218032/ENST00000218032.gff /build/bcftools-1.16/test/csq/ENST00000218032/start-lost.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENST00000218032/ENST00000218032.fa -g /build/bcftools-1.16/test/csq/ENST00000218032/ENST00000218032.gff /build/bcftools-1.16/test/csq/ENST00000218032/start-lost-del.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /build/bcftools-1.16/test/csq/ENST00000000000 && /build/bcftools-1.16/bcftools csq -p a -f ENST00000000000.fa -g ENST00000000000.gff upstream-stop.vcf | /build/bcftools-1.16/bcftools query -f'[%POS\t%REF\t%ALT\t%SAMPLE\t%GT\t%TBCSQ\n]' | ../sort-csq -q .. ok test_csq_real: cd /build/bcftools-1.16/test/csq/ENSMUST00000133836 && /build/bcftools-1.16/bcftools csq -f ENSMUST00000133836.fa -g ENSMUST00000133836.gff filter-problem.vcf -i 'FILTER="PASS"' --phase m | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/bcftools-1.16/test/csq/ENSMUST00000121418 && /build/bcftools-1.16/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25500' --phase m | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/bcftools-1.16/test/csq/ENSMUST00000121418 && /build/bcftools-1.16/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25496' --phase m | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/bcftools-1.16/test/csq/ENSMUST00000121418 && /build/bcftools-1.16/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25105' --phase m | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/ENSG00000173376/ENSG00000173376.fa -g /build/bcftools-1.16/test/csq/ENSG00000173376/ENSG00000173376.gff /build/bcftools-1.16/test/csq/ENSG00000173376/synon.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /build/bcftools-1.16/test/csq/EMN908947 && /build/bcftools-1.16/bcftools csq -f EMN908947.fa -g simple.gff simple.vcf | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /build/bcftools-1.16/test/csq/EMN908947 && /build/bcftools-1.16/bcftools csq -f EMN908947.fa -g ribosomal-slippage.gff ribosomal-slippage.vcf --force | ../sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/EDUMMY0003/EDUMMY0003.fa -g /build/bcftools-1.16/test/csq/EDUMMY0003/EDUMMY0003.gff /build/bcftools-1.16/test/csq/EDUMMY0003/long-del.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/EDUMMY0002/EDUMMY0002.fa -g /build/bcftools-1.16/test/csq/EDUMMY0002/EDUMMY0002.gff /build/bcftools-1.16/test/csq/EDUMMY0002/boundaries.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -f /build/bcftools-1.16/test/csq/EDUMMY0001/EDUMMY0001.fa -g /build/bcftools-1.16/test/csq/EDUMMY0001/EDUMMY0001.gff /build/bcftools-1.16/test/csq/EDUMMY0001/starts-with-1.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.16/bcftools csq -l -f /build/bcftools-1.16/test/csq/EDUMMY0001/EDUMMY0001.fa -g /build/bcftools-1.16/test/csq/EDUMMY0001/EDUMMY0001.gff /build/bcftools-1.16/test/csq/EDUMMY0001/starts-with-1.vcf | /build/bcftools-1.16/test/csq/sort-csq | /build/bcftools-1.16/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_roh: /build/bcftools-1.16/bcftools roh /build/bcftools-1.16/test/roh.1.vcf.gz -Or -G30 --AF-dflt 0.4| grep -v ^# .. ok test_roh: /build/bcftools-1.16/bcftools roh /build/bcftools-1.16/test/roh.1.vcf.gz -Or -G30 --AF-file /build/bcftools-1.16/test/roh.1.tab.gz| grep -v ^# .. ok test_roh: /build/bcftools-1.16/bcftools roh /build/bcftools-1.16/test/roh.1.vcf.gz -Or -G30 --AF-file /build/bcftools-1.16/test/roh.1.tab.gz --ignore-homref| grep -v ^# .. ok test_roh: /build/bcftools-1.16/bcftools roh /build/bcftools-1.16/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245| grep -v ^# .. ok test_roh: /build/bcftools-1.16/bcftools roh /build/bcftools-1.16/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --ignore-homref| grep -v ^# .. ok test_roh: /build/bcftools-1.16/bcftools roh /build/bcftools-1.16/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --ignore-homref --include-noalt| grep -v ^# .. ok test_roh: /build/bcftools-1.16/bcftools roh /build/bcftools-1.16/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --include-noalt| grep -v ^# .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck -e 0 /tmp/lFdI2HY7eC/gtcheck.1.vcf.gz -g /tmp/lFdI2HY7eC/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/lFdI2HY7eC/gtcheck.1.vcf.gz -g /tmp/lFdI2HY7eC/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/lFdI2HY7eC/gtcheck.1.vcf.gz -g /tmp/lFdI2HY7eC/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/lFdI2HY7eC/gtcheck.1.vcf.gz -g /tmp/lFdI2HY7eC/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/lFdI2HY7eC/gtcheck.1.vcf.gz -g /tmp/lFdI2HY7eC/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/lFdI2HY7eC/gtcheck.1.vcf.gz -g /tmp/lFdI2HY7eC/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck -e 0 /tmp/lFdI2HY7eC/gtcheck.2.vcf.gz -g /tmp/lFdI2HY7eC/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck -e 0 /tmp/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck -e 0 -u PL /tmp/lFdI2HY7eC/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck -e 0 --n-matches 4 /tmp/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/gtcheck.1.vcf.gz -g /tmp/lFdI2HY7eC/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/lFdI2HY7eC/gtcheck.1.vcf.gz -g /tmp/lFdI2HY7eC/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/lFdI2HY7eC/gtcheck.1.vcf.gz -g /tmp/lFdI2HY7eC/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/lFdI2HY7eC/gtcheck.1.vcf.gz -g /tmp/lFdI2HY7eC/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/lFdI2HY7eC/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/lFdI2HY7eC/gtcheck.4.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck -u GT -e 30 /tmp/lFdI2HY7eC/gtcheck.1.vcf.gz -g /tmp/lFdI2HY7eC/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/lFdI2HY7eC/gtcheck.1.vcf.gz -g /tmp/lFdI2HY7eC/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck -u GT -e 300 /tmp/lFdI2HY7eC/gtcheck.1.vcf.gz -g /tmp/lFdI2HY7eC/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck -u PL -e 30 /tmp/lFdI2HY7eC/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck /tmp/lFdI2HY7eC/gtcheck.ntop.vcf.gz -g /tmp/lFdI2HY7eC/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck --n-matches 2 /tmp/lFdI2HY7eC/gtcheck.ntop.vcf.gz -g /tmp/lFdI2HY7eC/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.16/bcftools gtcheck /tmp/lFdI2HY7eC/gtcheck.5.vcf.gz -g /tmp/lFdI2HY7eC/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 -j8 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/aarch64-linux-gnu/bcftools install -p bcftools /build/bcftools-1.16/debian/bcftools/usr/bin install -p misc/color-chrs.pl misc/gff2gff.py misc/guess-ploidy.py misc/plot-vcfstats misc/plot-roh.py misc/run-roh.pl misc/vcfutils.pl /build/bcftools-1.16/debian/bcftools/usr/bin install -p -m 644 doc/bcftools.1 /build/bcftools-1.16/debian/bcftools/usr/share/man/man1 install -p plugins/*.so /build/bcftools-1.16/debian/bcftools/usr/lib/aarch64-linux-gnu/bcftools make[1]: Leaving directory '/build/bcftools-1.16' debian/rules override_dh_install make[1]: Entering directory '/build/bcftools-1.16' dh_install # Fix Perl interpreter PATH for pscript in `grep -Rl '#!/usr/bin/env \+perl' debian/*` ; do \ sed -i '1s?#!/usr/bin/env \+perl?#!/usr/bin/perl?' ${pscript} ; \ done make[1]: Leaving directory '/build/bcftools-1.16' dh_installdocs dh_installchangelogs debian/rules override_dh_installman make[1]: Entering directory '/build/bcftools-1.16' dh_installman --language=C make[1]: Leaving directory '/build/bcftools-1.16' dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dpkg-gencontrol: warning: package bcftools: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package bcftools: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'bcftools' in '../bcftools_1.16-1_arm64.deb'. dpkg-deb: building package 'bcftools-dbgsym' in '../bcftools-dbgsym_1.16-1_arm64.deb'. dpkg-genbuildinfo --build=binary -O../bcftools_1.16-1_arm64.buildinfo dpkg-genchanges --build=binary -O../bcftools_1.16-1_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: 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/15637 and its subdirectories I: Current time: Sun May 26 20:28:44 -12 2024 I: pbuilder-time-stamp: 1716798524 Tue Apr 25 02:05:47 UTC 2023 I: 1st build successful. Starting 2nd build on remote node codethink10-arm64.debian.net. Tue Apr 25 02:05:47 UTC 2023 I: Preparing to do remote build '2' on codethink10-arm64.debian.net. Tue Apr 25 02:10:30 UTC 2023 I: Deleting $TMPDIR on codethink10-arm64.debian.net. Tue Apr 25 02:10:31 UTC 2023 I: bcftools_1.16-1_arm64.changes: Format: 1.8 Date: Fri, 30 Sep 2022 11:48:40 +0200 Source: bcftools Binary: bcftools bcftools-dbgsym Architecture: arm64 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: 4a7c31d87680c5500d6190ebdda11f7d58cd2e5f 1866416 bcftools-dbgsym_1.16-1_arm64.deb a689479fe22e434c4d0e49ffdf7999c7758086b8 6001 bcftools_1.16-1_arm64.buildinfo 4f4a1b93d845f92e3664010cf69b4204d13629eb 623304 bcftools_1.16-1_arm64.deb Checksums-Sha256: c8e6151910f465c566ead75d8956b141796522dfa99b5a0232168af1e138bfa5 1866416 bcftools-dbgsym_1.16-1_arm64.deb e5c7583da87f08508ce58ee9b82a09d9276e0f4f57293b7c374b7dd345052f13 6001 bcftools_1.16-1_arm64.buildinfo 279656ace2b15d6343864e731ab9daab52c35b5dfdacaaeaee45247830066055 623304 bcftools_1.16-1_arm64.deb Files: 2f18e8ad16ddd90e588ee7aae9c8e27a 1866416 debug optional bcftools-dbgsym_1.16-1_arm64.deb a41b9d019aa8c994627de836e5586fb8 6001 science optional bcftools_1.16-1_arm64.buildinfo 19b31a2f802d8b7d8338f886260baa7b 623304 science optional bcftools_1.16-1_arm64.deb Tue Apr 25 02:10:32 UTC 2023 I: diffoscope 241 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.TKD4aCl8/bcftools_1.16-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.TKD4aCl8/bcftools_1.16-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.TKD4aCl8/bcftools_1.16-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.TKD4aCl8/b1/bcftools_1.16-1_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.TKD4aCl8/b2/bcftools_1.16-1_arm64.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: 0.392s) 0.392s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.052s) 0.052s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.001s) 0.001s 1 call specialize Tue Apr 25 02:10:34 UTC 2023 I: diffoscope 241 found no differences in the changes files, and a .buildinfo file also exists. Tue Apr 25 02:10:34 UTC 2023 I: bcftools from bookworm built successfully and reproducibly on arm64. Tue Apr 25 02:10:36 UTC 2023 I: Submitting .buildinfo files to external archives: Tue Apr 25 02:10:36 UTC 2023 I: Submitting 8.0K b1/bcftools_1.16-1_arm64.buildinfo.asc Tue Apr 25 02:10:36 UTC 2023 I: Submitting 8.0K b2/bcftools_1.16-1_arm64.buildinfo.asc Tue Apr 25 02:10:37 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Apr 25 02:10:37 UTC 2023 I: Done submitting .buildinfo files. Tue Apr 25 02:10:37 UTC 2023 I: Removing signed bcftools_1.16-1_arm64.buildinfo.asc files: removed './b1/bcftools_1.16-1_arm64.buildinfo.asc' removed './b2/bcftools_1.16-1_arm64.buildinfo.asc'