Tue Jul 27 23:49:14 UTC 2021 I: starting to build bcftools/bullseye/arm64 on jenkins on '2021-07-27 23:48' Tue Jul 27 23:49:14 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_10/682/console.log Tue Jul 27 23:49:14 UTC 2021 I: Downloading source for bullseye/bcftools=1.11-1 --2021-07-27 23:49:14-- http://cdn-fastly.deb.debian.org/debian/pool/main/b/bcftools/bcftools_1.11-1.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2109 (2.1K) Saving to: ‘bcftools_1.11-1.dsc’ 0K .. 100% 154M=0s 2021-07-27 23:49:14 (154 MB/s) - ‘bcftools_1.11-1.dsc’ saved [2109/2109] Tue Jul 27 23:49:14 UTC 2021 I: bcftools_1.11-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: bcftools Binary: bcftools Architecture: any Version: 1.11-1 Maintainer: Debian Med Packaging Team Uploaders: Michael R. Crusoe Homepage: http://samtools.github.io/bcftools/ Standards-Version: 4.5.0 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 (>= 1.11), libgsl-dev, tabix , libio-pty-perl Package-List: bcftools deb science optional arch=any Checksums-Sha1: 116d9652f6798d475613b8fd5c09af2c72417035 3004923 bcftools_1.11.orig.tar.gz abef7ee506d622313b83c0065b6c17ec533e2513 7044 bcftools_1.11-1.debian.tar.xz Checksums-Sha256: f2d9a09fd7920754b60948b81ec047882864213b93a0cd1ef0372b0e025cba3f 3004923 bcftools_1.11.orig.tar.gz 293866fddd4ef0d2cf411c7a92518e55e8fa6287081dd44ada42b437c7557ef3 7044 bcftools_1.11-1.debian.tar.xz Files: 96802da049663f4a07e36cfb5cb247f7 3004923 bcftools_1.11.orig.tar.gz aa79fb712862cc335b9beb15688f1d9f 7044 bcftools_1.11-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl913hsRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtHoMw//bcAx94RKC8bnxoB4fuozEivgoxnpCuao 7n4NccC9U+K81PLb9eylOytk2dYxnZV5PPKh2smTh524rMZU6zbN3g5+e58fgNK8 DOkkLbLbrMSJLRq/9m/UnyAG8DmVJONH+hXY9wevPaqYLGuJug1emRdEzom4mbhf Ws/DhF763qOMDpRYV9mfeSHLGR6UM/thNxwnfRPCr07JZj6WEGOoLdvvJP7chRot sm9uT8xCXoghmRgBNlC6WwwgkfLyALLB2yKPuTXhjV6yIMPeigCNlWX0mwiZjAKu dbEGuX3bdBxF0rLEvkPTZUBBw2EBDb6zk1SAgjcm8SDeNH5hp2BzImnMB5uW46KV r1H+73feVCde4GxXmBRRSmfJdZ/cCp94uLNLhX4edngGdSct6IY3yWmSK+TvIyZ6 5JLzf4pL+w/stlQvX82PM0/OIb+m6B7cqbn1/LSvz0hROK0d8TCf/s/QbS6S/sAe hkWIVfYtliu+BdyCDDk5m7w2r05a0kOXSH7fWd7bl1yJ68dYrjk89XqB/2Uvl/XP N5J+7GAYvvcv68U+kMNXqGRq3jUw9zDxUz2eKgA0Qclpba1L8D5TwHgrHqhPvmnr 70PfejKii0XzzVRYG4FuVXuTr0yqObGBw6TReAYnecRAf/GbbqJlWqM6TzP/7XWX UfZ3kJ8I/cY= =Tpca -----END PGP SIGNATURE----- Tue Jul 27 23:49:14 UTC 2021 I: Checking whether the package is not for us Tue Jul 27 23:49:14 UTC 2021 I: Starting 1st build on remote node codethink11-arm64.debian.net. Tue Jul 27 23:49:14 UTC 2021 I: Preparing to do remote build '1' on codethink11-arm64.debian.net. Tue Jul 27 23:54:05 UTC 2021 I: Deleting $TMPDIR on codethink11-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Aug 29 18:12:17 -12 2022 I: pbuilder-time-stamp: 1661839937 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [bcftools_1.11-1.dsc] I: copying [./bcftools_1.11.orig.tar.gz] I: copying [./bcftools_1.11-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.otiJPQ51/trustedkeys.kbx': General error gpgv: Signature made Thu Oct 1 01:48:11 2020 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./bcftools_1.11-1.dsc dpkg-source: info: extracting bcftools in bcftools-1.11 dpkg-source: info: unpacking bcftools_1.11.orig.tar.gz dpkg-source: info: unpacking bcftools_1.11-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying tests-pluginpath.patch dpkg-source: info: applying skip_new_test_failing_on_32bit.patch dpkg-source: info: applying 2to3.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/28602/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,-fixfilepath parallel=8' DISTRIBUTION='' 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='28602' 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/tmp.wrmUl1lcEW/pbuilderrc_RlgD --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.wrmUl1lcEW/b1 --logfile b1/build.log bcftools_1.11-1.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 codethink11-arm64 4.15.0-151-generic #157-Ubuntu SMP Fri Jul 9 21:03:48 UTC 2021 aarch64 GNU/Linux I: ls -l /bin total 5252 -rwxr-xr-x 1 root root 1282512 Jun 21 2021 bash -rwxr-xr-x 3 root root 34808 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 34808 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 34808 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 14264 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 39832 Sep 22 2020 cat -rwxr-xr-x 1 root root 64512 Sep 22 2020 chgrp -rwxr-xr-x 1 root root 60368 Sep 22 2020 chmod -rwxr-xr-x 1 root root 64528 Sep 22 2020 chown -rwxr-xr-x 1 root root 138896 Sep 22 2020 cp -rwxr-xr-x 1 root root 129544 Dec 10 2020 dash -rwxr-xr-x 1 root root 101384 Sep 22 2020 date -rwxr-xr-x 1 root root 80984 Sep 22 2020 dd -rwxr-xr-x 1 root root 89824 Sep 22 2020 df -rwxr-xr-x 1 root root 143088 Sep 22 2020 dir -rwxr-xr-x 1 root root 76152 Feb 7 2021 dmesg lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname -rwxr-xr-x 1 root root 35632 Sep 22 2020 echo -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep -rwxr-xr-x 1 root root 31512 Sep 22 2020 false -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep -rwxr-xr-x 1 root root 64856 Feb 7 2021 findmnt -rwsr-xr-x 1 root root 34824 Feb 26 2021 fusermount -rwxr-xr-x 1 root root 178400 Nov 9 2020 grep -rwxr-xr-x 2 root root 2346 Mar 2 2021 gunzip -rwxr-xr-x 1 root root 6376 Mar 2 2021 gzexe -rwxr-xr-x 1 root root 93744 Mar 2 2021 gzip -rwxr-xr-x 1 root root 18440 Nov 6 2019 hostname -rwxr-xr-x 1 root root 68720 Sep 22 2020 ln -rwxr-xr-x 1 root root 52720 Feb 7 2020 login -rwxr-xr-x 1 root root 143088 Sep 22 2020 ls -rwxr-xr-x 1 root root 161960 Feb 7 2021 lsblk -rwxr-xr-x 1 root root 85200 Sep 22 2020 mkdir -rwxr-xr-x 1 root root 68744 Sep 22 2020 mknod -rwxr-xr-x 1 root root 43976 Sep 22 2020 mktemp -rwxr-xr-x 1 root root 51368 Feb 7 2021 more -rwsr-xr-x 1 root root 51360 Feb 7 2021 mount -rwxr-xr-x 1 root root 14496 Feb 7 2021 mountpoint -rwxr-xr-x 1 root root 134808 Sep 22 2020 mv lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 18 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 35720 Sep 22 2020 pwd lrwxrwxrwx 1 root root 4 Jun 21 2021 rbash -> bash -rwxr-xr-x 1 root root 43872 Sep 22 2020 readlink -rwxr-xr-x 1 root root 68592 Sep 22 2020 rm -rwxr-xr-x 1 root root 43880 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 19208 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Aug 28 03:47 sh -> dash -rwxr-xr-x 1 root root 35656 Sep 22 2020 sleep -rwxr-xr-x 1 root root 72640 Sep 22 2020 stty -rwsr-xr-x 1 root root 67776 Feb 7 2021 su -rwxr-xr-x 1 root root 35672 Sep 22 2020 sync -rwxr-xr-x 1 root root 535768 Feb 16 2021 tar -rwxr-xr-x 1 root root 10568 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 89120 Sep 22 2020 touch -rwxr-xr-x 1 root root 31512 Sep 22 2020 true -rwxr-xr-x 1 root root 14264 Feb 26 2021 ulockmgr_server -rwsr-xr-x 1 root root 30880 Feb 7 2021 umount -rwxr-xr-x 1 root root 35640 Sep 22 2020 uname -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress -rwxr-xr-x 1 root root 143088 Sep 22 2020 vdir -rwxr-xr-x 1 root root 59584 Feb 7 2021 wdctl lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 2 2021 zcat -rwxr-xr-x 1 root root 1678 Mar 2 2021 zcmp -rwxr-xr-x 1 root root 5880 Mar 2 2021 zdiff -rwxr-xr-x 1 root root 29 Mar 2 2021 zegrep -rwxr-xr-x 1 root root 29 Mar 2 2021 zfgrep -rwxr-xr-x 1 root root 2081 Mar 2 2021 zforce -rwxr-xr-x 1 root root 7585 Mar 2 2021 zgrep -rwxr-xr-x 1 root root 2206 Mar 2 2021 zless -rwxr-xr-x 1 root root 1842 Mar 2 2021 zmore -rwxr-xr-x 1 root root 4553 Mar 2 2021 znew I: user script /srv/workspace/pbuilder/28602/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), zlib1g-dev, libbz2-dev, liblzma-dev, libhts-dev (>= 1.11), libgsl-dev, tabix, libio-pty-perl dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19646 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. pbuilder-satisfydepends-dummy depends on liblzma-dev; however: Package liblzma-dev is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev (>= 1.11); however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on libgsl-dev; however: Package libgsl-dev is not installed. pbuilder-satisfydepends-dummy depends on tabix; however: Package tabix is not installed. pbuilder-satisfydepends-dummy depends on libio-pty-perl; however: Package libio-pty-perl is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbrotli1{a} libbz2-dev{a} libcurl3-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1{a} libfile-stripnondeterminism-perl{a} libgsl-dev{a} libgsl25{a} libgslcblas0{a} libhts-dev{a} libhts3{a} libicu67{a} libio-pty-perl{a} libldap-2.4-2{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libnghttp2-14{a} libpipeline1{a} libpsl5{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libssh2-1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} tabix{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc ca-certificates curl libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix wget 0 packages upgraded, 53 newly installed, 0 to remove and 0 not upgraded. Need to get 26.7 MB of archives. After unpacking 91.0 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main arm64 bsdextrautils arm64 2.36.1-7 [141 kB] Get: 2 http://deb.debian.org/debian bullseye/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 3 http://deb.debian.org/debian bullseye/main arm64 groff-base arm64 1.22.4-6 [883 kB] Get: 4 http://deb.debian.org/debian bullseye/main arm64 libpipeline1 arm64 1.5.3-1 [33.0 kB] Get: 5 http://deb.debian.org/debian bullseye/main arm64 man-db arm64 2.9.4-2 [1336 kB] Get: 6 http://deb.debian.org/debian bullseye/main arm64 sensible-utils all 0.0.14 [14.8 kB] Get: 7 http://deb.debian.org/debian bullseye/main arm64 libmagic-mgc arm64 1:5.39-3 [273 kB] Get: 8 http://deb.debian.org/debian bullseye/main arm64 libmagic1 arm64 1:5.39-3 [121 kB] Get: 9 http://deb.debian.org/debian bullseye/main arm64 file arm64 1:5.39-3 [69.1 kB] Get: 10 http://deb.debian.org/debian bullseye/main arm64 gettext-base arm64 0.21-4 [173 kB] Get: 11 http://deb.debian.org/debian bullseye/main arm64 libsigsegv2 arm64 2.13-1 [34.7 kB] Get: 12 http://deb.debian.org/debian bullseye/main arm64 m4 arm64 1.4.18-5 [199 kB] Get: 13 http://deb.debian.org/debian bullseye/main arm64 autoconf all 2.69-14 [313 kB] Get: 14 http://deb.debian.org/debian bullseye/main arm64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 15 http://deb.debian.org/debian bullseye/main arm64 automake all 1:1.16.3-2 [814 kB] Get: 16 http://deb.debian.org/debian bullseye/main arm64 autopoint all 0.21-4 [510 kB] Get: 17 http://deb.debian.org/debian bullseye/main arm64 libdebhelper-perl all 13.3.4 [189 kB] Get: 18 http://deb.debian.org/debian bullseye/main arm64 libtool all 2.4.6-15 [513 kB] Get: 19 http://deb.debian.org/debian bullseye/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian bullseye/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian bullseye/main arm64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 22 http://deb.debian.org/debian bullseye/main arm64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 23 http://deb.debian.org/debian bullseye/main arm64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 24 http://deb.debian.org/debian bullseye/main arm64 libelf1 arm64 0.183-1 [164 kB] Get: 25 http://deb.debian.org/debian bullseye/main arm64 dwz arm64 0.13+20210201-1 [155 kB] Get: 26 http://deb.debian.org/debian bullseye/main arm64 libicu67 arm64 67.1-7 [8467 kB] Get: 27 http://deb.debian.org/debian bullseye/main arm64 libxml2 arm64 2.9.10+dfsg-6.7 [629 kB] Get: 28 http://deb.debian.org/debian bullseye/main arm64 gettext arm64 0.21-4 [1261 kB] Get: 29 http://deb.debian.org/debian bullseye/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 30 http://deb.debian.org/debian bullseye/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian bullseye/main arm64 debhelper all 13.3.4 [1049 kB] Get: 32 http://deb.debian.org/debian bullseye/main arm64 libbrotli1 arm64 1.0.9-2+b2 [267 kB] Get: 33 http://deb.debian.org/debian bullseye/main arm64 libbz2-dev arm64 1.0.8-4 [31.5 kB] Get: 34 http://deb.debian.org/debian bullseye/main arm64 libsasl2-modules-db arm64 2.1.27+dfsg-2.1 [69.3 kB] Get: 35 http://deb.debian.org/debian bullseye/main arm64 libsasl2-2 arm64 2.1.27+dfsg-2.1 [105 kB] Get: 36 http://deb.debian.org/debian bullseye/main arm64 libldap-2.4-2 arm64 2.4.57+dfsg-3 [222 kB] Get: 37 http://deb.debian.org/debian bullseye/main arm64 libnghttp2-14 arm64 1.43.0-1 [73.8 kB] Get: 38 http://deb.debian.org/debian bullseye/main arm64 libpsl5 arm64 0.21.0-1.2 [57.1 kB] Get: 39 http://deb.debian.org/debian bullseye/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b2 [59.4 kB] Get: 40 http://deb.debian.org/debian bullseye/main arm64 libssh2-1 arm64 1.9.0-2 [150 kB] Get: 41 http://deb.debian.org/debian bullseye/main arm64 libcurl3-gnutls arm64 7.74.0-1.3+b1 [318 kB] Get: 42 http://deb.debian.org/debian bullseye/main arm64 libcurl4-gnutls-dev arm64 7.74.0-1.3+b1 [419 kB] Get: 43 http://deb.debian.org/debian bullseye/main arm64 libdeflate0 arm64 1.7-1 [47.7 kB] Get: 44 http://deb.debian.org/debian bullseye/main arm64 libdeflate-dev arm64 1.7-1 [44.5 kB] Get: 45 http://deb.debian.org/debian bullseye/main arm64 libgslcblas0 arm64 2.6+dfsg-2 [73.4 kB] Get: 46 http://deb.debian.org/debian bullseye/main arm64 libgsl25 arm64 2.6+dfsg-2 [812 kB] Get: 47 http://deb.debian.org/debian bullseye/main arm64 libgsl-dev arm64 2.6+dfsg-2 [1006 kB] Get: 48 http://deb.debian.org/debian bullseye/main arm64 libhts3 arm64 1.11-4 [346 kB] Get: 49 http://deb.debian.org/debian bullseye/main arm64 liblzma-dev arm64 5.2.5-2 [227 kB] Get: 50 http://deb.debian.org/debian bullseye/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-2 [189 kB] Get: 51 http://deb.debian.org/debian bullseye/main arm64 libhts-dev arm64 1.11-4 [3856 kB] Get: 52 http://deb.debian.org/debian bullseye/main arm64 libio-pty-perl arm64 1:1.15-2 [36.0 kB] Get: 53 http://deb.debian.org/debian bullseye/main arm64 tabix arm64 1.11-4 [316 kB] Fetched 26.7 MB in 1s (26.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19646 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-7_arm64.deb ... Unpacking bsdextrautils (2.36.1-7) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../01-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-6_arm64.deb ... 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Setting up libsasl2-modules-db:arm64 (2.1.27+dfsg-2.1) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libsigsegv2:arm64 (2.13-1) ... Setting up autopoint (0.21-4) ... Setting up libsasl2-2:arm64 (2.1.27+dfsg-2.1) ... Setting up liblzma-dev:arm64 (5.2.5-2) ... Setting up zlib1g-dev:arm64 (1:1.2.11.dfsg-2) ... Setting up sensible-utils (0.0.14) ... Setting up libuchardet0:arm64 (0.0.7-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libssh2-1:arm64 (1.9.0-2) ... Setting up libdeflate-dev:arm64 (1.7-1) ... Setting up tabix (1.11-4) ... Setting up libelf1:arm64 (0.183-1) ... Setting up libxml2:arm64 (2.9.10+dfsg-6.7) ... Setting up libbz2-dev:arm64 (1.0.8-4) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up gettext (0.21-4) ... Setting up libgsl-dev (2.6+dfsg-2) ... Setting up libtool (2.4.6-15) ... Setting up libldap-2.4-2:arm64 (2.4.57+dfsg-3) ... Setting up m4 (1.4.18-5) ... Setting up libcurl3-gnutls:arm64 (7.74.0-1.3+b1) ... Setting up libcurl4-gnutls-dev:arm64 (7.74.0-1.3+b1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.12.0-1) ... Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libhts3:arm64 (1.11-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhts-dev:arm64 (1.11-4) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up dh-autoreconf (20) ... Setting up debhelper (13.3.4) ... Processing triggers for libc-bin (2.31-13) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/bcftools-1.11/ && 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_1.11-1_source.changes dpkg-buildpackage: info: source package bcftools dpkg-buildpackage: info: source version 1.11-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean rm -f config.mk && touch config.mk dh clean dh_auto_clean make -j8 distclean make[1]: Entering directory '/build/bcftools-1.11' rm -f test/*.o test/*~ test/test-rbuf test/test-regidx rm -f plugins/*.so plugins/*.P rm -rf plugins/*.dSYM rm -f test/*.hex rm -f gmon.out *.o *.a *~ bcftools version.h rm -rf *.dSYM test/*.dSYM rm -f config.cache config.h config.log config.mk config.status rm -rf autom4te.cache rm -f TAGS make[1]: Leaving directory '/build/bcftools-1.11' dh_clean debian/rules binary dh binary dh_update_autotools_config debian/rules override_dh_autoreconf make[1]: Entering directory '/build/bcftools-1.11' rm -f config.mk && touch config.mk export MAKEFLAGS="-s"; dh_autoreconf configure.ac:94: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:94: the top level configure.ac:94: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:94: the top level configure.ac:94: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:94: the top level configure.ac:94: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:94: the top level make[1]: Leaving directory '/build/bcftools-1.11' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/bcftools-1.11' dh_auto_configure -- \ --with-htslib=system \ --enable-gsl \ --with-cblas=gslcblas \ --with-bcf-plugin-dir=/usr/lib/aarch64-linux-gnu/bcftools ./configure --build=aarch64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/aarch64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system --enable-gsl --with-cblas=gslcblas --with-bcf-plugin-dir=/usr/lib/aarch64-linux-gnu/bcftools checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for grep that handles long lines and -e... /bin/grep checking for C compiler warning flags... -Wall checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for htslib/sam.h... yes checking for hts_version in -lhts... yes checking shared library type... plain .so checking for library containing dlopen... -ldl checking if the compiler accepts -rdynamic... yes checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing regcomp... none required configure: creating ./config.status config.status: creating config.mk config.status: creating config.h make[1]: Leaving directory '/build/bcftools-1.11' dh_auto_build make -j8 make[1]: Entering directory '/build/bcftools-1.11' echo '#define BCFTOOLS_VERSION "1.11"' > version.h gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfindex.o vcfindex.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tabix.o tabix.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfstats.o vcfstats.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfisec.o vcfisec.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfmerge.o vcfmerge.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfquery.o vcfquery.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcffilter.o vcffilter.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o filter.o filter.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfsom.o vcfsom.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfnorm.o vcfnorm.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfgtcheck.o vcfgtcheck.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfview.o vcfview.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfannotate.o vcfannotate.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfroh.o vcfroh.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfconcat.o vcfconcat.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcall.o vcfcall.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mcall.o mcall.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcmp.o vcmp.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gvcf.o gvcf.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o reheader.o reheader.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o convert.o convert.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfconvert.o vcfconvert.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tsv2vcf.o tsv2vcf.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcnv.o vcfcnv.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o HMM.o HMM.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o consensus.o consensus.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ploidy.o ploidy.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bin.o bin.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hclust.o hclust.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o version.o version.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o regidx.o regidx.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o smpl_ilist.o smpl_ilist.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o csq.o csq.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfbuf.o vcfbuf.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mpileup.o mpileup.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sample.o bam_sample.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfsort.o vcfsort.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cols.o cols.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o extsort.o extsort.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ccall.o ccall.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o em.o em.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o prob1.o prob1.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kmin.o kmin.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DPLUGINPATH='"/usr/lib/aarch64-linux-gnu/bcftools"' -c -o vcfplugin.o vcfplugin.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-rbuf.o test/test-rbuf.c gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-regidx.o test/test-regidx.c gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/GTisec.so version.c plugins/GTisec.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/GTsubset.so version.c plugins/GTsubset.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/ad-bias.so convert.c version.c plugins/ad-bias.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/add-variantkey.so version.c plugins/add-variantkey.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/af-dist.so bin.c version.c plugins/af-dist.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/allele-length.so version.c plugins/allele-length.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/check-ploidy.so version.c plugins/check-ploidy.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/check-sparsity.so version.c plugins/check-sparsity.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/color-chrs.so HMM.c version.c plugins/color-chrs.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/contrast.so version.c plugins/contrast.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/counts.so version.c plugins/counts.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/dosage.so version.c plugins/dosage.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fill-AN-AC.so version.c plugins/fill-AN-AC.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fill-from-fasta.so filter.c version.c plugins/fill-from-fasta.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fill-tags.so version.c plugins/fill-tags.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fixploidy.so ploidy.c regidx.c version.c plugins/fixploidy.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fixref.so version.c plugins/fixref.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/frameshifts.so version.c plugins/frameshifts.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/guess-ploidy.so version.c plugins/guess-ploidy.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/gvcfz.so version.c plugins/gvcfz.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/impute-info.so version.c plugins/impute-info.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/indel-stats.so version.c plugins/indel-stats.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/isecGT.so smpl_ilist.c version.c plugins/isecGT.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/mendelian.so version.c plugins/mendelian.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/missing2ref.so version.c plugins/missing2ref.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/parental-origin.so version.c plugins/parental-origin.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/prune.so version.c plugins/prune.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/remove-overlaps.so version.c plugins/remove-overlaps.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/scatter.so version.c plugins/scatter.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/setGT.so version.c plugins/setGT.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/smpl-stats.so version.c plugins/smpl-stats.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/split-vep.so version.c plugins/split-vep.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/split.so version.c plugins/split.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/tag2tag.so version.c plugins/tag2tag.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/trio-dnm.so version.c plugins/trio-dnm.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/trio-stats.so version.c plugins/trio-stats.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/trio-switch-rate.so version.c plugins/trio-switch-rate.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/variantkey-hex.so version.c plugins/variantkey-hex.c -ldl gcc -Wall -g -O2 -fdebug-prefix-map=/build/bcftools-1.11=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o main.o main.c gcc -Wl,-z,relro -o test/test-rbuf test/test-rbuf.o -lz -ldl gcc -Wl,-z,relro -o test/test-regidx test/test-regidx.o regidx.o -lhts -lpthread -lz -ldl gcc -rdynamic -Wl,-z,relro -o bcftools main.o vcfindex.o tabix.o vcfstats.o vcfisec.o vcfmerge.o vcfquery.o vcffilter.o filter.o vcfsom.o vcfnorm.o vcfgtcheck.o vcfview.o vcfannotate.o vcfroh.o vcfconcat.o vcfcall.o mcall.o vcmp.o gvcf.o reheader.o convert.o vcfconvert.o tsv2vcf.o vcfcnv.o HMM.o consensus.o ploidy.o bin.o hclust.o version.o regidx.o smpl_ilist.o csq.o vcfbuf.o mpileup.o bam2bcf.o bam2bcf_indel.o bam_sample.o vcfsort.o cols.o extsort.o ccall.o em.o prob1.o kmin.o vcfplugin.o -lhts -lm -lz -ldl -lpthread make[1]: Leaving directory '/build/bcftools-1.11' debian/rules override_dh_auto_test make[1]: Entering directory '/build/bcftools-1.11' make test-no-plugins VERBOSE=1 make[2]: Entering directory '/build/bcftools-1.11' ./test/test-rbuf Inserted 1-9 starting at offset 5: 5 6 7 8 9 0 1 2 3 1 2 3 4 5 6 7 8 9 4th is 4 Deleting 1-2: 7 8 9 0 1 2 3 3 4 5 6 7 8 9 Prepending 0-8: 8 9 0 1 2 3 4 5 6 7 8 7 6 5 4 3 2 1 0 3 Expanding: 8 9 10 11 12 13 14 15 16 17 8 7 6 5 4 3 2 1 0 3 ./test/test-regidx REF_PATH=: ./test/test.pl --exec bgzip= --exec tabix= --htsdir= ${TEST_OPTS:-} test_usage: bcftools .. ok test_usage_subcommand: bcftools index .. ok test_usage_subcommand: bcftools annotate .. ok test_usage_subcommand: bcftools concat .. ok test_usage_subcommand: bcftools convert .. ok test_usage_subcommand: bcftools isec .. ok test_usage_subcommand: bcftools merge .. ok test_usage_subcommand: bcftools norm .. ok test_usage_subcommand: bcftools plugin .. ok test_usage_subcommand: bcftools query .. ok test_usage_subcommand: bcftools reheader .. ok test_usage_subcommand: bcftools sort .. ok test_usage_subcommand: bcftools view .. ok test_usage_subcommand: bcftools call .. ok test_usage_subcommand: bcftools consensus .. ok test_usage_subcommand: bcftools cnv .. ok test_usage_subcommand: bcftools csq .. ok test_usage_subcommand: bcftools filter .. ok test_usage_subcommand: bcftools gtcheck .. ok test_usage_subcommand: bcftools mpileup .. ok test_usage_subcommand: bcftools roh .. ok test_usage_subcommand: bcftools stats .. ok test_tabix: tabix /tmp/urvXTTg_IK/merge.a.vcf.gz 2:3199812-3199812 .. ok test_tabix: /build/bcftools-1.11/bcftools view -H /tmp/urvXTTg_IK/merge.a.bcf 2:3199812-3199812 .. ok test_tabix: tabix /tmp/urvXTTg_IK/merge.a.vcf.gz 1:3000151-3000151 .. ok test_tabix: /build/bcftools-1.11/bcftools view -H /tmp/urvXTTg_IK/merge.a.bcf 1:3000151-3000151 .. ok test_index: /build/bcftools-1.11/bcftools view -H /tmp/urvXTTg_IK/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /build/bcftools-1.11/bcftools view -H /tmp/urvXTTg_IK/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/bcftools-1.11/bcftools view -H /tmp/urvXTTg_IK/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/bcftools-1.11/bcftools view -H /tmp/urvXTTg_IK/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /build/bcftools-1.11/bcftools view -H /tmp/urvXTTg_IK/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/bcftools-1.11/bcftools view -H /tmp/urvXTTg_IK/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /build/bcftools-1.11/bcftools view -H /tmp/urvXTTg_IK/large_chrom_csi_limit.bcf chr20 .. ok test_index: /build/bcftools-1.11/bcftools view -H /tmp/urvXTTg_IK/large_chrom_csi_limit.bcf chr20 .. ok test_index: /build/bcftools-1.11/bcftools view -H /tmp/urvXTTg_IK/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /build/bcftools-1.11/bcftools view -H /tmp/urvXTTg_IK/large_chrom_csi_limit.bcf chr20 .. ok test_vcf_idxstats: /build/bcftools-1.11/bcftools index -s /tmp/urvXTTg_IK/idx.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.11/bcftools index -s /tmp/urvXTTg_IK/idx.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.11/bcftools index -s /tmp/urvXTTg_IK/idx.bcf .. ok test_vcf_idxstats: /build/bcftools-1.11/bcftools index -n /tmp/urvXTTg_IK/idx.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.11/bcftools index -n /tmp/urvXTTg_IK/idx.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.11/bcftools index -n /tmp/urvXTTg_IK/idx.bcf .. ok test_vcf_idxstats: /build/bcftools-1.11/bcftools index -s /tmp/urvXTTg_IK/empty.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.11/bcftools index -s /tmp/urvXTTg_IK/empty.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.11/bcftools index -s /tmp/urvXTTg_IK/empty.bcf .. ok test_vcf_idxstats: /build/bcftools-1.11/bcftools index -n /tmp/urvXTTg_IK/empty.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.11/bcftools index -n /tmp/urvXTTg_IK/empty.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.11/bcftools index -n /tmp/urvXTTg_IK/empty.bcf .. ok test_vcf_check: /build/bcftools-1.11/bcftools stats -s - /tmp/urvXTTg_IK/check.vcf.gz | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/check.vcf.gz | /build/bcftools-1.11/bcftools stats -s - | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check_merge: /build/bcftools-1.11/misc/plot-vcfstats -m /tmp/urvXTTg_IK/check.1.chk /tmp/urvXTTg_IK/check.2.chk /tmp/urvXTTg_IK/check.3.chk /tmp/urvXTTg_IK/check.4.chk | grep -v 'plot-vcfstats' | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_stats: /build/bcftools-1.11/bcftools stats -s - /tmp/urvXTTg_IK/stats.a.vcf.gz /tmp/urvXTTg_IK/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/bcftools-1.11/bcftools stats -s B /tmp/urvXTTg_IK/stats.a.vcf.gz /tmp/urvXTTg_IK/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/bcftools-1.11/bcftools stats -s - /tmp/urvXTTg_IK/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_isec: /build/bcftools-1.11/bcftools isec -n =2 /tmp/urvXTTg_IK/isec.a.vcf.gz /tmp/urvXTTg_IK/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.11/bcftools isec -Ob -n =2 /tmp/urvXTTg_IK/isec.a.vcf.gz /tmp/urvXTTg_IK/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.11/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/urvXTTg_IK/isec.a.vcf.gz /tmp/urvXTTg_IK/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.11/bcftools isec -Ob -n =2 -i"STRLEN(REF)==2" /tmp/urvXTTg_IK/isec.a.vcf.gz /tmp/urvXTTg_IK/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.11/bcftools isec -n =2 -c both /tmp/urvXTTg_IK/isec.a.vcf.gz /tmp/urvXTTg_IK/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.11/bcftools isec -Ob -n =2 -c both /tmp/urvXTTg_IK/isec.a.vcf.gz /tmp/urvXTTg_IK/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.11/bcftools isec -n =2 -c any /tmp/urvXTTg_IK/isec.a.vcf.gz /tmp/urvXTTg_IK/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.11/bcftools isec -Ob -n =2 -c any /tmp/urvXTTg_IK/isec.a.vcf.gz /tmp/urvXTTg_IK/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.11/bcftools isec -C -c any /tmp/urvXTTg_IK/isec.a.vcf.gz /tmp/urvXTTg_IK/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.11/bcftools isec -Ob -C -c any /tmp/urvXTTg_IK/isec.a.vcf.gz /tmp/urvXTTg_IK/isec.b.vcf.gz .. ok test_vcf_isec2: /build/bcftools-1.11/bcftools isec --no-version -T /tmp/urvXTTg_IK/isec.tab.gz /tmp/urvXTTg_IK/isec.a.vcf.gz .. ok test_vcf_isec2: /build/bcftools-1.11/bcftools isec -Ob -T /tmp/urvXTTg_IK/isec.tab.gz /tmp/urvXTTg_IK/isec.a.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_isec: /build/bcftools-1.11/bcftools isec -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/urvXTTg_IK/isec-miss.1.1.vcf.gz /tmp/urvXTTg_IK/isec-miss.1.2.vcf.gz /tmp/urvXTTg_IK/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.11/bcftools isec -Ob -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/urvXTTg_IK/isec-miss.1.1.vcf.gz /tmp/urvXTTg_IK/isec-miss.1.2.vcf.gz /tmp/urvXTTg_IK/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.11/bcftools isec -R /build/bcftools-1.11/test/isec-miss.1.regs.txt -n +1 /tmp/urvXTTg_IK/isec-miss.1.1.vcf.gz /tmp/urvXTTg_IK/isec-miss.1.2.vcf.gz /tmp/urvXTTg_IK/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.11/bcftools isec -Ob -R /build/bcftools-1.11/test/isec-miss.1.regs.txt -n +1 /tmp/urvXTTg_IK/isec-miss.1.1.vcf.gz /tmp/urvXTTg_IK/isec-miss.1.2.vcf.gz /tmp/urvXTTg_IK/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.11/bcftools isec -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/urvXTTg_IK/isec-miss.2.1.vcf.gz /tmp/urvXTTg_IK/isec-miss.2.2.vcf.gz /tmp/urvXTTg_IK/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.11/bcftools isec -Ob -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/urvXTTg_IK/isec-miss.2.1.vcf.gz /tmp/urvXTTg_IK/isec-miss.2.2.vcf.gz /tmp/urvXTTg_IK/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.11/bcftools isec -R /build/bcftools-1.11/test/isec-miss.1.regs.txt -n +1 /tmp/urvXTTg_IK/isec-miss.2.1.vcf.gz /tmp/urvXTTg_IK/isec-miss.2.2.vcf.gz /tmp/urvXTTg_IK/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.11/bcftools isec -Ob -R /build/bcftools-1.11/test/isec-miss.1.regs.txt -n +1 /tmp/urvXTTg_IK/isec-miss.2.1.vcf.gz /tmp/urvXTTg_IK/isec-miss.2.2.vcf.gz /tmp/urvXTTg_IK/isec-miss.2.3.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version -i AF:join /tmp/urvXTTg_IK/merge.join.a.vcf.gz /tmp/urvXTTg_IK/merge.join.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob -i AF:join /tmp/urvXTTg_IK/merge.join.a.vcf.gz /tmp/urvXTTg_IK/merge.join.b.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version -i AF:join /tmp/urvXTTg_IK/merge.join.a.bcf /tmp/urvXTTg_IK/merge.join.b.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob -i AF:join /tmp/urvXTTg_IK/merge.join.a.bcf /tmp/urvXTTg_IK/merge.join.b.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --force-samples /tmp/urvXTTg_IK/merge.LPL.a.vcf.gz /tmp/urvXTTg_IK/merge.LPL.b.vcf.gz /tmp/urvXTTg_IK/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples /tmp/urvXTTg_IK/merge.LPL.a.vcf.gz /tmp/urvXTTg_IK/merge.LPL.b.vcf.gz /tmp/urvXTTg_IK/merge.LPL.c.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --force-samples /tmp/urvXTTg_IK/merge.LPL.a.bcf /tmp/urvXTTg_IK/merge.LPL.b.bcf /tmp/urvXTTg_IK/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples /tmp/urvXTTg_IK/merge.LPL.a.bcf /tmp/urvXTTg_IK/merge.LPL.b.bcf /tmp/urvXTTg_IK/merge.LPL.c.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --force-samples -L 1 /tmp/urvXTTg_IK/merge.LPL.a.vcf.gz /tmp/urvXTTg_IK/merge.LPL.b.vcf.gz /tmp/urvXTTg_IK/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -L 1 /tmp/urvXTTg_IK/merge.LPL.a.vcf.gz /tmp/urvXTTg_IK/merge.LPL.b.vcf.gz /tmp/urvXTTg_IK/merge.LPL.c.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --force-samples -L 1 /tmp/urvXTTg_IK/merge.LPL.a.bcf /tmp/urvXTTg_IK/merge.LPL.b.bcf /tmp/urvXTTg_IK/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -L 1 /tmp/urvXTTg_IK/merge.LPL.a.bcf /tmp/urvXTTg_IK/merge.LPL.b.bcf /tmp/urvXTTg_IK/merge.LPL.c.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --force-samples -L 2 /tmp/urvXTTg_IK/merge.LPL.a.vcf.gz /tmp/urvXTTg_IK/merge.LPL.b.vcf.gz /tmp/urvXTTg_IK/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -L 2 /tmp/urvXTTg_IK/merge.LPL.a.vcf.gz /tmp/urvXTTg_IK/merge.LPL.b.vcf.gz /tmp/urvXTTg_IK/merge.LPL.c.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --force-samples -L 2 /tmp/urvXTTg_IK/merge.LPL.a.bcf /tmp/urvXTTg_IK/merge.LPL.b.bcf /tmp/urvXTTg_IK/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -L 2 /tmp/urvXTTg_IK/merge.LPL.a.bcf /tmp/urvXTTg_IK/merge.LPL.b.bcf /tmp/urvXTTg_IK/merge.LPL.c.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --force-samples -L 3 /tmp/urvXTTg_IK/merge.LPL.a.vcf.gz /tmp/urvXTTg_IK/merge.LPL.b.vcf.gz /tmp/urvXTTg_IK/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -L 3 /tmp/urvXTTg_IK/merge.LPL.a.vcf.gz /tmp/urvXTTg_IK/merge.LPL.b.vcf.gz /tmp/urvXTTg_IK/merge.LPL.c.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --force-samples -L 3 /tmp/urvXTTg_IK/merge.LPL.a.bcf /tmp/urvXTTg_IK/merge.LPL.b.bcf /tmp/urvXTTg_IK/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -L 3 /tmp/urvXTTg_IK/merge.LPL.a.bcf /tmp/urvXTTg_IK/merge.LPL.b.bcf /tmp/urvXTTg_IK/merge.LPL.c.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --force-samples -L 4 /tmp/urvXTTg_IK/merge.LPL.a.vcf.gz /tmp/urvXTTg_IK/merge.LPL.b.vcf.gz /tmp/urvXTTg_IK/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -L 4 /tmp/urvXTTg_IK/merge.LPL.a.vcf.gz /tmp/urvXTTg_IK/merge.LPL.b.vcf.gz /tmp/urvXTTg_IK/merge.LPL.c.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --force-samples -L 4 /tmp/urvXTTg_IK/merge.LPL.a.bcf /tmp/urvXTTg_IK/merge.LPL.b.bcf /tmp/urvXTTg_IK/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -L 4 /tmp/urvXTTg_IK/merge.LPL.a.bcf /tmp/urvXTTg_IK/merge.LPL.b.bcf /tmp/urvXTTg_IK/merge.LPL.c.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --force-samples -L 5 /tmp/urvXTTg_IK/merge.LPL.a.vcf.gz /tmp/urvXTTg_IK/merge.LPL.b.vcf.gz /tmp/urvXTTg_IK/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -L 5 /tmp/urvXTTg_IK/merge.LPL.a.vcf.gz /tmp/urvXTTg_IK/merge.LPL.b.vcf.gz /tmp/urvXTTg_IK/merge.LPL.c.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --force-samples -L 5 /tmp/urvXTTg_IK/merge.LPL.a.bcf /tmp/urvXTTg_IK/merge.LPL.b.bcf /tmp/urvXTTg_IK/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -L 5 /tmp/urvXTTg_IK/merge.LPL.a.bcf /tmp/urvXTTg_IK/merge.LPL.b.bcf /tmp/urvXTTg_IK/merge.LPL.c.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --force-samples /tmp/urvXTTg_IK/merge.a.vcf.gz /tmp/urvXTTg_IK/merge.b.vcf.gz /tmp/urvXTTg_IK/merge.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples /tmp/urvXTTg_IK/merge.a.vcf.gz /tmp/urvXTTg_IK/merge.b.vcf.gz /tmp/urvXTTg_IK/merge.c.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --force-samples /tmp/urvXTTg_IK/merge.a.bcf /tmp/urvXTTg_IK/merge.b.bcf /tmp/urvXTTg_IK/merge.c.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples /tmp/urvXTTg_IK/merge.a.bcf /tmp/urvXTTg_IK/merge.b.bcf /tmp/urvXTTg_IK/merge.c.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --force-samples -Fx /tmp/urvXTTg_IK/merge.a.vcf.gz /tmp/urvXTTg_IK/merge.b.vcf.gz /tmp/urvXTTg_IK/merge.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -Fx /tmp/urvXTTg_IK/merge.a.vcf.gz /tmp/urvXTTg_IK/merge.b.vcf.gz /tmp/urvXTTg_IK/merge.c.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --force-samples -Fx /tmp/urvXTTg_IK/merge.a.bcf /tmp/urvXTTg_IK/merge.b.bcf /tmp/urvXTTg_IK/merge.c.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -Fx /tmp/urvXTTg_IK/merge.a.bcf /tmp/urvXTTg_IK/merge.b.bcf /tmp/urvXTTg_IK/merge.c.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --force-samples -0 /tmp/urvXTTg_IK/merge.a.vcf.gz /tmp/urvXTTg_IK/merge.b.vcf.gz /tmp/urvXTTg_IK/merge.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -0 /tmp/urvXTTg_IK/merge.a.vcf.gz /tmp/urvXTTg_IK/merge.b.vcf.gz /tmp/urvXTTg_IK/merge.c.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --force-samples -0 /tmp/urvXTTg_IK/merge.a.bcf /tmp/urvXTTg_IK/merge.b.bcf /tmp/urvXTTg_IK/merge.c.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -0 /tmp/urvXTTg_IK/merge.a.bcf /tmp/urvXTTg_IK/merge.b.bcf /tmp/urvXTTg_IK/merge.c.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --force-samples -m none /tmp/urvXTTg_IK/merge.2.a.vcf.gz /tmp/urvXTTg_IK/merge.2.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -m none /tmp/urvXTTg_IK/merge.2.a.vcf.gz /tmp/urvXTTg_IK/merge.2.b.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --force-samples -m none /tmp/urvXTTg_IK/merge.2.a.bcf /tmp/urvXTTg_IK/merge.2.b.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -m none /tmp/urvXTTg_IK/merge.2.a.bcf /tmp/urvXTTg_IK/merge.2.b.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --force-samples -m both /tmp/urvXTTg_IK/merge.2.a.vcf.gz /tmp/urvXTTg_IK/merge.2.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -m both /tmp/urvXTTg_IK/merge.2.a.vcf.gz /tmp/urvXTTg_IK/merge.2.b.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --force-samples -m both /tmp/urvXTTg_IK/merge.2.a.bcf /tmp/urvXTTg_IK/merge.2.b.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -m both /tmp/urvXTTg_IK/merge.2.a.bcf /tmp/urvXTTg_IK/merge.2.b.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --force-samples -m all /tmp/urvXTTg_IK/merge.2.a.vcf.gz /tmp/urvXTTg_IK/merge.2.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -m all /tmp/urvXTTg_IK/merge.2.a.vcf.gz /tmp/urvXTTg_IK/merge.2.b.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --force-samples -m all /tmp/urvXTTg_IK/merge.2.a.bcf /tmp/urvXTTg_IK/merge.2.b.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -m all /tmp/urvXTTg_IK/merge.2.a.bcf /tmp/urvXTTg_IK/merge.2.b.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/urvXTTg_IK/merge.3.a.vcf.gz /tmp/urvXTTg_IK/merge.3.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/urvXTTg_IK/merge.3.a.vcf.gz /tmp/urvXTTg_IK/merge.3.b.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/urvXTTg_IK/merge.3.a.bcf /tmp/urvXTTg_IK/merge.3.b.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/urvXTTg_IK/merge.3.a.bcf /tmp/urvXTTg_IK/merge.3.b.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --force-samples -m id /tmp/urvXTTg_IK/merge.4.a.vcf.gz /tmp/urvXTTg_IK/merge.4.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -m id /tmp/urvXTTg_IK/merge.4.a.vcf.gz /tmp/urvXTTg_IK/merge.4.b.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --force-samples -m id /tmp/urvXTTg_IK/merge.4.a.bcf /tmp/urvXTTg_IK/merge.4.b.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -m id /tmp/urvXTTg_IK/merge.4.a.bcf /tmp/urvXTTg_IK/merge.4.b.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --gvcf - /tmp/urvXTTg_IK/gvcf.merge.1.vcf.gz /tmp/urvXTTg_IK/gvcf.merge.2.vcf.gz /tmp/urvXTTg_IK/gvcf.merge.3.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --gvcf - /tmp/urvXTTg_IK/gvcf.merge.1.vcf.gz /tmp/urvXTTg_IK/gvcf.merge.2.vcf.gz /tmp/urvXTTg_IK/gvcf.merge.3.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --gvcf - /tmp/urvXTTg_IK/gvcf.merge.1.bcf /tmp/urvXTTg_IK/gvcf.merge.2.bcf /tmp/urvXTTg_IK/gvcf.merge.3.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --gvcf - /tmp/urvXTTg_IK/gvcf.merge.1.bcf /tmp/urvXTTg_IK/gvcf.merge.2.bcf /tmp/urvXTTg_IK/gvcf.merge.3.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --gvcf - /tmp/urvXTTg_IK/merge.gvcf.2.a.vcf.gz /tmp/urvXTTg_IK/merge.gvcf.2.b.vcf.gz /tmp/urvXTTg_IK/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --gvcf - /tmp/urvXTTg_IK/merge.gvcf.2.a.vcf.gz /tmp/urvXTTg_IK/merge.gvcf.2.b.vcf.gz /tmp/urvXTTg_IK/merge.gvcf.2.c.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --gvcf - -i SRC:join /tmp/urvXTTg_IK/merge.gvcf.3.a.vcf.gz /tmp/urvXTTg_IK/merge.gvcf.3.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --gvcf - -i SRC:join /tmp/urvXTTg_IK/merge.gvcf.3.a.vcf.gz /tmp/urvXTTg_IK/merge.gvcf.3.b.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --gvcf - /tmp/urvXTTg_IK/merge.gvcf.4.a.vcf.gz /tmp/urvXTTg_IK/merge.gvcf.4.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --gvcf - /tmp/urvXTTg_IK/merge.gvcf.4.a.vcf.gz /tmp/urvXTTg_IK/merge.gvcf.4.b.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --gvcf - /tmp/urvXTTg_IK/merge.gvcf.4.a.bcf /tmp/urvXTTg_IK/merge.gvcf.4.b.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --gvcf - /tmp/urvXTTg_IK/merge.gvcf.4.a.bcf /tmp/urvXTTg_IK/merge.gvcf.4.b.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version /tmp/urvXTTg_IK/merge.5.a.vcf.gz /tmp/urvXTTg_IK/merge.5.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob /tmp/urvXTTg_IK/merge.5.a.vcf.gz /tmp/urvXTTg_IK/merge.5.b.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version /tmp/urvXTTg_IK/merge.5.a.bcf /tmp/urvXTTg_IK/merge.5.b.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob /tmp/urvXTTg_IK/merge.5.a.bcf /tmp/urvXTTg_IK/merge.5.b.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version /tmp/urvXTTg_IK/merge.6.a.vcf.gz /tmp/urvXTTg_IK/merge.6.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob /tmp/urvXTTg_IK/merge.6.a.vcf.gz /tmp/urvXTTg_IK/merge.6.b.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version /tmp/urvXTTg_IK/merge.6.a.bcf /tmp/urvXTTg_IK/merge.6.b.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob /tmp/urvXTTg_IK/merge.6.a.bcf /tmp/urvXTTg_IK/merge.6.b.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --gvcf - /tmp/urvXTTg_IK/merge.gvcf.7.a.vcf.gz /tmp/urvXTTg_IK/merge.gvcf.7.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --gvcf - /tmp/urvXTTg_IK/merge.gvcf.7.a.vcf.gz /tmp/urvXTTg_IK/merge.gvcf.7.b.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --gvcf - /tmp/urvXTTg_IK/merge.gvcf.7.a.bcf /tmp/urvXTTg_IK/merge.gvcf.7.b.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --gvcf - /tmp/urvXTTg_IK/merge.gvcf.7.a.bcf /tmp/urvXTTg_IK/merge.gvcf.7.b.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --gvcf - /tmp/urvXTTg_IK/merge.gvcf.8.a.vcf.gz /tmp/urvXTTg_IK/merge.gvcf.8.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --gvcf - /tmp/urvXTTg_IK/merge.gvcf.8.a.vcf.gz /tmp/urvXTTg_IK/merge.gvcf.8.b.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --gvcf - /tmp/urvXTTg_IK/merge.gvcf.8.a.bcf /tmp/urvXTTg_IK/merge.gvcf.8.b.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --gvcf - /tmp/urvXTTg_IK/merge.gvcf.8.a.bcf /tmp/urvXTTg_IK/merge.gvcf.8.b.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --force-samples /tmp/urvXTTg_IK/merge.7.a.vcf.gz /tmp/urvXTTg_IK/merge.7.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples /tmp/urvXTTg_IK/merge.7.a.vcf.gz /tmp/urvXTTg_IK/merge.7.b.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --force-samples /tmp/urvXTTg_IK/merge.7.a.bcf /tmp/urvXTTg_IK/merge.7.b.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples /tmp/urvXTTg_IK/merge.7.a.bcf /tmp/urvXTTg_IK/merge.7.b.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --gvcf /build/bcftools-1.11/test/gvcf.fa /tmp/urvXTTg_IK/merge.gvcf.9a.vcf.gz /tmp/urvXTTg_IK/merge.gvcf.9b.vcf.gz /tmp/urvXTTg_IK/merge.gvcf.9c.vcf.gz /tmp/urvXTTg_IK/merge.gvcf.9d.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --gvcf /build/bcftools-1.11/test/gvcf.fa /tmp/urvXTTg_IK/merge.gvcf.9a.vcf.gz /tmp/urvXTTg_IK/merge.gvcf.9b.vcf.gz /tmp/urvXTTg_IK/merge.gvcf.9c.vcf.gz /tmp/urvXTTg_IK/merge.gvcf.9d.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --gvcf /build/bcftools-1.11/test/gvcf.fa /tmp/urvXTTg_IK/merge.gvcf.9a.bcf /tmp/urvXTTg_IK/merge.gvcf.9b.bcf /tmp/urvXTTg_IK/merge.gvcf.9c.bcf /tmp/urvXTTg_IK/merge.gvcf.9d.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --gvcf /build/bcftools-1.11/test/gvcf.fa /tmp/urvXTTg_IK/merge.gvcf.9a.bcf /tmp/urvXTTg_IK/merge.gvcf.9b.bcf /tmp/urvXTTg_IK/merge.gvcf.9c.bcf /tmp/urvXTTg_IK/merge.gvcf.9d.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --gvcf /build/bcftools-1.11/test/gvcf.fa -r 22:21-23 /tmp/urvXTTg_IK/merge.gvcf.9a.vcf.gz /tmp/urvXTTg_IK/merge.gvcf.9b.vcf.gz /tmp/urvXTTg_IK/merge.gvcf.9c.vcf.gz /tmp/urvXTTg_IK/merge.gvcf.9d.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --gvcf /build/bcftools-1.11/test/gvcf.fa -r 22:21-23 /tmp/urvXTTg_IK/merge.gvcf.9a.vcf.gz /tmp/urvXTTg_IK/merge.gvcf.9b.vcf.gz /tmp/urvXTTg_IK/merge.gvcf.9c.vcf.gz /tmp/urvXTTg_IK/merge.gvcf.9d.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --gvcf /build/bcftools-1.11/test/gvcf.fa -r 22:21-23 /tmp/urvXTTg_IK/merge.gvcf.9a.bcf /tmp/urvXTTg_IK/merge.gvcf.9b.bcf /tmp/urvXTTg_IK/merge.gvcf.9c.bcf /tmp/urvXTTg_IK/merge.gvcf.9d.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --gvcf /build/bcftools-1.11/test/gvcf.fa -r 22:21-23 /tmp/urvXTTg_IK/merge.gvcf.9a.bcf /tmp/urvXTTg_IK/merge.gvcf.9b.bcf /tmp/urvXTTg_IK/merge.gvcf.9c.bcf /tmp/urvXTTg_IK/merge.gvcf.9d.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --gvcf /build/bcftools-1.11/test/gvcf.fa /tmp/urvXTTg_IK/merge.gvcf.9a.vcf.gz /tmp/urvXTTg_IK/merge.gvcf.9b.vcf.gz /tmp/urvXTTg_IK/merge.gvcf.9c.vcf.gz /tmp/urvXTTg_IK/merge.gvcf.9d.vcf.gz /tmp/urvXTTg_IK/merge.gvcf.9e.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --gvcf /build/bcftools-1.11/test/gvcf.fa /tmp/urvXTTg_IK/merge.gvcf.9a.vcf.gz /tmp/urvXTTg_IK/merge.gvcf.9b.vcf.gz /tmp/urvXTTg_IK/merge.gvcf.9c.vcf.gz /tmp/urvXTTg_IK/merge.gvcf.9d.vcf.gz /tmp/urvXTTg_IK/merge.gvcf.9e.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --gvcf /build/bcftools-1.11/test/gvcf.fa /tmp/urvXTTg_IK/merge.gvcf.9a.bcf /tmp/urvXTTg_IK/merge.gvcf.9b.bcf /tmp/urvXTTg_IK/merge.gvcf.9c.bcf /tmp/urvXTTg_IK/merge.gvcf.9d.bcf /tmp/urvXTTg_IK/merge.gvcf.9e.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --gvcf /build/bcftools-1.11/test/gvcf.fa /tmp/urvXTTg_IK/merge.gvcf.9a.bcf /tmp/urvXTTg_IK/merge.gvcf.9b.bcf /tmp/urvXTTg_IK/merge.gvcf.9c.bcf /tmp/urvXTTg_IK/merge.gvcf.9d.bcf /tmp/urvXTTg_IK/merge.gvcf.9e.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --gvcf /build/bcftools-1.11/test/gvcf.fa -r 22:21-23 /tmp/urvXTTg_IK/merge.gvcf.9a.vcf.gz /tmp/urvXTTg_IK/merge.gvcf.9b.vcf.gz /tmp/urvXTTg_IK/merge.gvcf.9c.vcf.gz /tmp/urvXTTg_IK/merge.gvcf.9d.vcf.gz /tmp/urvXTTg_IK/merge.gvcf.9e.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --gvcf /build/bcftools-1.11/test/gvcf.fa -r 22:21-23 /tmp/urvXTTg_IK/merge.gvcf.9a.vcf.gz /tmp/urvXTTg_IK/merge.gvcf.9b.vcf.gz /tmp/urvXTTg_IK/merge.gvcf.9c.vcf.gz /tmp/urvXTTg_IK/merge.gvcf.9d.vcf.gz /tmp/urvXTTg_IK/merge.gvcf.9e.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --gvcf /build/bcftools-1.11/test/gvcf.fa -r 22:21-23 /tmp/urvXTTg_IK/merge.gvcf.9a.bcf /tmp/urvXTTg_IK/merge.gvcf.9b.bcf /tmp/urvXTTg_IK/merge.gvcf.9c.bcf /tmp/urvXTTg_IK/merge.gvcf.9d.bcf /tmp/urvXTTg_IK/merge.gvcf.9e.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --gvcf /build/bcftools-1.11/test/gvcf.fa -r 22:21-23 /tmp/urvXTTg_IK/merge.gvcf.9a.bcf /tmp/urvXTTg_IK/merge.gvcf.9b.bcf /tmp/urvXTTg_IK/merge.gvcf.9c.bcf /tmp/urvXTTg_IK/merge.gvcf.9d.bcf /tmp/urvXTTg_IK/merge.gvcf.9e.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version /tmp/urvXTTg_IK/merge.gvcf.10.a.vcf.gz /tmp/urvXTTg_IK/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob /tmp/urvXTTg_IK/merge.gvcf.10.a.vcf.gz /tmp/urvXTTg_IK/merge.gvcf.10.b.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version /tmp/urvXTTg_IK/merge.gvcf.10.a.bcf /tmp/urvXTTg_IK/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob /tmp/urvXTTg_IK/merge.gvcf.10.a.bcf /tmp/urvXTTg_IK/merge.gvcf.10.b.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version -m none /tmp/urvXTTg_IK/merge.gvcf.10.a.vcf.gz /tmp/urvXTTg_IK/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob -m none /tmp/urvXTTg_IK/merge.gvcf.10.a.vcf.gz /tmp/urvXTTg_IK/merge.gvcf.10.b.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version -m none /tmp/urvXTTg_IK/merge.gvcf.10.a.bcf /tmp/urvXTTg_IK/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob -m none /tmp/urvXTTg_IK/merge.gvcf.10.a.bcf /tmp/urvXTTg_IK/merge.gvcf.10.b.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version -g /build/bcftools-1.11/test/merge.gvcf.10.fa /tmp/urvXTTg_IK/merge.gvcf.10.a.vcf.gz /tmp/urvXTTg_IK/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob -g /build/bcftools-1.11/test/merge.gvcf.10.fa /tmp/urvXTTg_IK/merge.gvcf.10.a.vcf.gz /tmp/urvXTTg_IK/merge.gvcf.10.b.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version -g /build/bcftools-1.11/test/merge.gvcf.10.fa /tmp/urvXTTg_IK/merge.gvcf.10.a.bcf /tmp/urvXTTg_IK/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob -g /build/bcftools-1.11/test/merge.gvcf.10.fa /tmp/urvXTTg_IK/merge.gvcf.10.a.bcf /tmp/urvXTTg_IK/merge.gvcf.10.b.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version -g /build/bcftools-1.11/test/merge.gvcf.10.fa -m none /tmp/urvXTTg_IK/merge.gvcf.10.a.vcf.gz /tmp/urvXTTg_IK/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob -g /build/bcftools-1.11/test/merge.gvcf.10.fa -m none /tmp/urvXTTg_IK/merge.gvcf.10.a.vcf.gz /tmp/urvXTTg_IK/merge.gvcf.10.b.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version -g /build/bcftools-1.11/test/merge.gvcf.10.fa -m none /tmp/urvXTTg_IK/merge.gvcf.10.a.bcf /tmp/urvXTTg_IK/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob -g /build/bcftools-1.11/test/merge.gvcf.10.fa -m none /tmp/urvXTTg_IK/merge.gvcf.10.a.bcf /tmp/urvXTTg_IK/merge.gvcf.10.b.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version -g /build/bcftools-1.11/test/merge.gvcf.10.fa /tmp/urvXTTg_IK/merge.gvcf.10.b.vcf.gz /tmp/urvXTTg_IK/merge.gvcf.10.a.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob -g /build/bcftools-1.11/test/merge.gvcf.10.fa /tmp/urvXTTg_IK/merge.gvcf.10.b.vcf.gz /tmp/urvXTTg_IK/merge.gvcf.10.a.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version -g /build/bcftools-1.11/test/merge.gvcf.10.fa /tmp/urvXTTg_IK/merge.gvcf.10.b.bcf /tmp/urvXTTg_IK/merge.gvcf.10.a.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob -g /build/bcftools-1.11/test/merge.gvcf.10.fa /tmp/urvXTTg_IK/merge.gvcf.10.b.bcf /tmp/urvXTTg_IK/merge.gvcf.10.a.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version -g /build/bcftools-1.11/test/merge.gvcf.10.fa -m none /tmp/urvXTTg_IK/merge.gvcf.10.b.vcf.gz /tmp/urvXTTg_IK/merge.gvcf.10.a.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob -g /build/bcftools-1.11/test/merge.gvcf.10.fa -m none /tmp/urvXTTg_IK/merge.gvcf.10.b.vcf.gz /tmp/urvXTTg_IK/merge.gvcf.10.a.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version -g /build/bcftools-1.11/test/merge.gvcf.10.fa -m none /tmp/urvXTTg_IK/merge.gvcf.10.b.bcf /tmp/urvXTTg_IK/merge.gvcf.10.a.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob -g /build/bcftools-1.11/test/merge.gvcf.10.fa -m none /tmp/urvXTTg_IK/merge.gvcf.10.b.bcf /tmp/urvXTTg_IK/merge.gvcf.10.a.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version /tmp/urvXTTg_IK/merge.noidx.a.vcf.gz /tmp/urvXTTg_IK/merge.noidx.b.vcf.gz /tmp/urvXTTg_IK/merge.noidx.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob /tmp/urvXTTg_IK/merge.noidx.a.vcf.gz /tmp/urvXTTg_IK/merge.noidx.b.vcf.gz /tmp/urvXTTg_IK/merge.noidx.c.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version /tmp/urvXTTg_IK/merge.noidx.a.bcf /tmp/urvXTTg_IK/merge.noidx.b.bcf /tmp/urvXTTg_IK/merge.noidx.c.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob /tmp/urvXTTg_IK/merge.noidx.a.bcf /tmp/urvXTTg_IK/merge.noidx.b.bcf /tmp/urvXTTg_IK/merge.noidx.c.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --no-index /build/bcftools-1.11/test/merge.noidx.a.vcf /build/bcftools-1.11/test/merge.noidx.b.vcf /build/bcftools-1.11/test/merge.noidx.c.vcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --no-index /build/bcftools-1.11/test/merge.noidx.a.vcf /build/bcftools-1.11/test/merge.noidx.b.vcf /build/bcftools-1.11/test/merge.noidx.c.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version --no-index /tmp/urvXTTg_IK/merge.noidx.a.bcf /tmp/urvXTTg_IK/merge.noidx.b.bcf /tmp/urvXTTg_IK/merge.noidx.c.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --no-index /tmp/urvXTTg_IK/merge.noidx.a.bcf /tmp/urvXTTg_IK/merge.noidx.b.bcf /tmp/urvXTTg_IK/merge.noidx.c.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided,_conflicting_interpretations"' /tmp/urvXTTg_IK/query.string.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/query.string.vcf.gz | /build/bcftools-1.11/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided,_conflicting_interpretations"' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" || CLNREVSTAT="_conflicting_interpretations"' /tmp/urvXTTg_IK/query.string.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/query.string.vcf.gz | /build/bcftools-1.11/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" || CLNREVSTAT="_conflicting_interpretations"' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" && CLNREVSTAT="_conflicting_interpretations"' /tmp/urvXTTg_IK/query.string.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/query.string.vcf.gz | /build/bcftools-1.11/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" && CLNREVSTAT="_conflicting_interpretations"' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' /tmp/urvXTTg_IK/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/query.vcf.gz | /build/bcftools-1.11/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f '%RSX\t%VKX\n' /tmp/urvXTTg_IK/query.variantkey.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/query.variantkey.vcf.gz | /build/bcftools-1.11/bcftools query -f '%RSX\t%VKX\n' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%XRI\n' -i'XRI[*]>1111' /tmp/urvXTTg_IK/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/view.filter.vcf.gz | /build/bcftools-1.11/bcftools query -f'%XRI\n' -i'XRI[*]>1111' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' /tmp/urvXTTg_IK/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/view.filter.vcf.gz | /build/bcftools-1.11/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' /tmp/urvXTTg_IK/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/view.filter.vcf.gz | /build/bcftools-1.11/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' /tmp/urvXTTg_IK/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/view.filter.vcf.gz | /build/bcftools-1.11/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' /tmp/urvXTTg_IK/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/view.filter.vcf.gz | /build/bcftools-1.11/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' /tmp/urvXTTg_IK/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/view.filter.vcf.gz | /build/bcftools-1.11/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' /tmp/urvXTTg_IK/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/view.filter.vcf.gz | /build/bcftools-1.11/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' /tmp/urvXTTg_IK/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/query.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' /tmp/urvXTTg_IK/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/query.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' /tmp/urvXTTg_IK/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/query.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' /tmp/urvXTTg_IK/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/query.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' /tmp/urvXTTg_IK/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/view.filter.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' /tmp/urvXTTg_IK/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/query.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' /tmp/urvXTTg_IK/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/query.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' /tmp/urvXTTg_IK/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/query.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' /tmp/urvXTTg_IK/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/query.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'I8=%I8 I16=%I16 I32=%I32 IF=%IF IA8=%IA8 IA16=%IA16 IA32=%IA32 IAF=%IAF IA8=%IA8{1} IA16=%IA16{1} IA32=%IA32{1} IAF=%IAF{1} [ %F8:%F16:%F32:%FF]\n' /tmp/urvXTTg_IK/view.vectors.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/view.vectors.vcf.gz | /build/bcftools-1.11/bcftools query -f'I8=%I8 I16=%I16 I32=%I32 IF=%IF IA8=%IA8 IA16=%IA16 IA32=%IA32 IAF=%IAF IA8=%IA8{1} IA16=%IA16{1} IA32=%IA32{1} IAF=%IAF{1} [ %F8:%F16:%F32:%FF]\n' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' /tmp/urvXTTg_IK/query.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/query.filter.vcf.gz | /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' /tmp/urvXTTg_IK/query.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/query.filter.vcf.gz | /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' /tmp/urvXTTg_IK/query.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/query.filter.vcf.gz | /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' /tmp/urvXTTg_IK/query.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/query.filter.vcf.gz | /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' /tmp/urvXTTg_IK/query.2.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/query.2.vcf.gz | /build/bcftools-1.11/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -i'IINT="."' -f'%POS %IINT\n' /tmp/urvXTTg_IK/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/missing.vcf.gz | /build/bcftools-1.11/bcftools query -i'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -i'IINT!="."' -f'%POS %IINT\n' /tmp/urvXTTg_IK/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/missing.vcf.gz | /build/bcftools-1.11/bcftools query -i'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -e'IINT!="."' -f'%POS %IINT\n' /tmp/urvXTTg_IK/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/missing.vcf.gz | /build/bcftools-1.11/bcftools query -e'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -e'IINT="."' -f'%POS %IINT\n' /tmp/urvXTTg_IK/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/missing.vcf.gz | /build/bcftools-1.11/bcftools query -e'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' /tmp/urvXTTg_IK/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/missing.vcf.gz | /build/bcftools-1.11/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' /tmp/urvXTTg_IK/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/missing.vcf.gz | /build/bcftools-1.11/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' /tmp/urvXTTg_IK/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/missing.vcf.gz | /build/bcftools-1.11/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' /tmp/urvXTTg_IK/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/missing.vcf.gz | /build/bcftools-1.11/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' /tmp/urvXTTg_IK/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/missing.vcf.gz | /build/bcftools-1.11/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' /tmp/urvXTTg_IK/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/missing.vcf.gz | /build/bcftools-1.11/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' /tmp/urvXTTg_IK/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/missing.vcf.gz | /build/bcftools-1.11/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' /tmp/urvXTTg_IK/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/missing.vcf.gz | /build/bcftools-1.11/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' /tmp/urvXTTg_IK/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/missing.vcf.gz | /build/bcftools-1.11/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -i'FILTER="A"' -f'%POS %FILTER\n' /tmp/urvXTTg_IK/filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/filter.11.vcf.gz | /build/bcftools-1.11/bcftools query -i'FILTER="A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -i'FILTER!="A"' -f'%POS %FILTER\n' /tmp/urvXTTg_IK/filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/filter.11.vcf.gz | /build/bcftools-1.11/bcftools query -i'FILTER!="A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -i'FILTER~"A"' -f'%POS %FILTER\n' /tmp/urvXTTg_IK/filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/filter.11.vcf.gz | /build/bcftools-1.11/bcftools query -i'FILTER~"A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n' /tmp/urvXTTg_IK/filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/filter.11.vcf.gz | /build/bcftools-1.11/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%LINE' /tmp/urvXTTg_IK/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/query.vcf.gz | /build/bcftools-1.11/bcftools query -f'%LINE' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' /tmp/urvXTTg_IK/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/query.filter-type.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' /tmp/urvXTTg_IK/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/query.filter-type.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' /tmp/urvXTTg_IK/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/query.filter-type.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' /tmp/urvXTTg_IK/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/query.filter-type.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\n' -i'INFO/TYPE="xxx"' /tmp/urvXTTg_IK/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/query.filter-type.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\n' -i'INFO/TYPE="xxx"' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -i'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001' /tmp/urvXTTg_IK/filter-missing-floats.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/filter-missing-floats.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -i'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -e'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001' /tmp/urvXTTg_IK/filter-missing-floats.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/filter-missing-floats.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -e'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' /tmp/urvXTTg_IK/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/missing.vcf.gz | /build/bcftools-1.11/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' /tmp/urvXTTg_IK/query.filter.2.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/query.filter.2.vcf.gz | /build/bcftools-1.11/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' /tmp/urvXTTg_IK/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/view.filter.vcf.gz | /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' /tmp/urvXTTg_IK/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/view.filter.vcf.gz | /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' /tmp/urvXTTg_IK/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/view.filter.vcf.gz | /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' /tmp/urvXTTg_IK/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/view.filter.vcf.gz | /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' /tmp/urvXTTg_IK/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/view.filter.vcf.gz | /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' /tmp/urvXTTg_IK/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/view.filter.vcf.gz | /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' /tmp/urvXTTg_IK/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/view.filter.vcf.gz | /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' /tmp/urvXTTg_IK/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/view.filter.vcf.gz | /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' /tmp/urvXTTg_IK/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/view.filter.vcf.gz | /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' /tmp/urvXTTg_IK/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/view.filter.vcf.gz | /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' /tmp/urvXTTg_IK/filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/filter.5.vcf.gz | /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' /tmp/urvXTTg_IK/filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/filter.5.vcf.gz | /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' /tmp/urvXTTg_IK/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/view.filter.vcf.gz | /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' /tmp/urvXTTg_IK/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/view.filter.vcf.gz | /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' /tmp/urvXTTg_IK/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/view.filter.vcf.gz | /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' /tmp/urvXTTg_IK/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/view.filter.vcf.gz | /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' /tmp/urvXTTg_IK/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/view.filter.vcf.gz | /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 & FMT/GQ=589' /tmp/urvXTTg_IK/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/view.filter.vcf.gz | /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 & FMT/GQ=589' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' /tmp/urvXTTg_IK/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/view.filter.vcf.gz | /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' /tmp/urvXTTg_IK/query.filter.3.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/query.filter.3.vcf.gz | /build/bcftools-1.11/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"' /tmp/urvXTTg_IK/query.filter.3.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/query.filter.3.vcf.gz | /build/bcftools-1.11/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' /tmp/urvXTTg_IK/query.filter.3.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/query.filter.3.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %AD\n]\n' -i'AD[:0]+AD[:1] > 12' /tmp/urvXTTg_IK/filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/filter.5.vcf.gz | /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %AD\n]\n' -i'AD[:0]+AD[:1] > 12' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' /tmp/urvXTTg_IK/query.filter.4.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/query.filter.4.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%ID\n' -i 'ID=@/build/bcftools-1.11/test/query.56.out' /tmp/urvXTTg_IK/view.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/view.vcf.gz | /build/bcftools-1.11/bcftools query -f'%ID\n' -i 'ID=@/build/bcftools-1.11/test/query.56.out' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD)>0.01' /tmp/urvXTTg_IK/query.filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/query.filter.5.vcf.gz | /build/bcftools-1.11/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD)>0.01' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD[:0],FMT/AD[:1])>0.01' /tmp/urvXTTg_IK/query.filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/query.filter.5.vcf.gz | /build/bcftools-1.11/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD[:0],FMT/AD[:1])>0.01' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS\t%AD\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01' /tmp/urvXTTg_IK/query.filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/query.filter.5.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS\t%AD\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%CHROM %POS\n' -i'CHROM="4"' /tmp/urvXTTg_IK/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/query.vcf.gz | /build/bcftools-1.11/bcftools query -f'%CHROM %POS\n' -i'CHROM="4"' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS\t%TAG1\n' -i'(TAG1>=-129 && TAG1<=-120) || (TAG1>=-32769 && TAG1<=-32760)' /tmp/urvXTTg_IK/query.negative.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/query.negative.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS\t%TAG1\n' -i'(TAG1>=-129 && TAG1<=-120) || (TAG1>=-32769 && TAG1<=-32760)' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS\t%TAGV1\n' -i'(TAGV1>=-129 && TAGV1<=-120) || (TAGV1>=-32769 && TAGV1<=-32760)' /tmp/urvXTTg_IK/query.negative.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/query.negative.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS\t%TAGV1\n' -i'(TAGV1>=-129 && TAGV1<=-120) || (TAGV1>=-32769 && TAGV1<=-32760)' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS\t%TAG2\n' -i'(TAG2>=-129 && TAG2<=-120) || (TAG2>=-32769 && TAG2<=-32760)' /tmp/urvXTTg_IK/query.negative.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/query.negative.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS\t%TAG2\n' -i'(TAG2>=-129 && TAG2<=-120) || (TAG2>=-32769 && TAG2<=-32760)' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS\t%TAGV2\n' -i'(TAGV2>=-129 && TAGV2<=-120) || (TAGV2>=-32769 && TAGV2<=-32760)' /tmp/urvXTTg_IK/query.negative.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/query.negative.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS\t%TAGV2\n' -i'(TAGV2>=-129 && TAGV2<=-120) || (TAGV2>=-32769 && TAGV2<=-32760)' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'[%POS\t%SAMPLE\t%GQ\n]' -i'N_PASS(GQ<20)==1' /tmp/urvXTTg_IK/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/query.vcf.gz | /build/bcftools-1.11/bcftools query -f'[%POS\t%SAMPLE\t%GQ\n]' -i'N_PASS(GQ<20)==1' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%CHROM\t%POS\t%INFO\t%FORMAT\n' -s D,C /tmp/urvXTTg_IK/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/query.vcf.gz | /build/bcftools-1.11/bcftools query -f'%CHROM\t%POS\t%INFO\t%FORMAT\n' -s D,C .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS\n' -i'POS==16777217 || POS==33554432 || POS=118673904' /tmp/urvXTTg_IK/query.filter.6.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/query.filter.6.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS\n' -i'POS==16777217 || POS==33554432 || POS=118673904' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(II)==6' /tmp/urvXTTg_IK/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/query.filter.7.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(II)==6' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(FORMAT/FI)==7' /tmp/urvXTTg_IK/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/query.filter.7.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(FORMAT/FI)==7' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(II)==2' /tmp/urvXTTg_IK/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/query.filter.7.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(II)==2' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(FORMAT/FI)==1.75' /tmp/urvXTTg_IK/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/query.filter.7.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(FORMAT/FI)==1.75' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(II)==2' /tmp/urvXTTg_IK/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/query.filter.7.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(II)==2' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(FORMAT/FI)==1.75' /tmp/urvXTTg_IK/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/query.filter.7.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(FORMAT/FI)==1.75' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(II)==2' /tmp/urvXTTg_IK/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/query.filter.7.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(II)==2' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(FORMAT/FI)==1.5' /tmp/urvXTTg_IK/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/query.filter.7.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(FORMAT/FI)==1.5' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'%ILEN==1' /tmp/urvXTTg_IK/query.filter.8.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/query.filter.8.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'%ILEN==1' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'ILEN==1' /tmp/urvXTTg_IK/query.filter.8.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/query.filter.8.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'ILEN==1' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] < FMT/AD[:1]' /tmp/urvXTTg_IK/query.filter.9.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/query.filter.9.vcf.gz | /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] < FMT/AD[:1]' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] > FMT/AD[:1]' /tmp/urvXTTg_IK/query.filter.9.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/query.filter.9.vcf.gz | /build/bcftools-1.11/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] > FMT/AD[:1]' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS %NUM_TAG\n' -i'COUNT(INFO/NUM_TAG)=2' /tmp/urvXTTg_IK/query.filter.10.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/query.filter.10.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS %NUM_TAG\n' -i'COUNT(INFO/NUM_TAG)=2' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f'%POS %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2' /tmp/urvXTTg_IK/query.filter.10.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/query.filter.10.vcf.gz | /build/bcftools-1.11/bcftools query -f'%POS %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2' .. ok test_vcf_query: /build/bcftools-1.11/bcftools query -f '%CHROM:%POS\t%N_PASS(GT="alt" & GQ>110)\t[\t%GT]\t[\t%GQ]\n' /tmp/urvXTTg_IK/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/query.vcf.gz | /build/bcftools-1.11/bcftools query -f '%CHROM:%POS\t%N_PASS(GT="alt" & GQ>110)\t[\t%GT]\t[\t%GQ]\n' .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm --no-version -cx -f /build/bcftools-1.11/test/norm.fa /tmp/urvXTTg_IK/norm.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -cx -f /build/bcftools-1.11/test/norm.fa /tmp/urvXTTg_IK/norm.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm --no-version -m- /tmp/urvXTTg_IK/norm.split.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -m- /tmp/urvXTTg_IK/norm.split.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm --no-version -m- /tmp/urvXTTg_IK/norm.split.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -m- /tmp/urvXTTg_IK/norm.split.2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm --no-version -m- --force /tmp/urvXTTg_IK/norm.split.3.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -m- --force /tmp/urvXTTg_IK/norm.split.3.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm --no-version -m- /tmp/urvXTTg_IK/norm.split.4.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -m- /tmp/urvXTTg_IK/norm.split.4.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm --no-version -m- --keep-sum AD /tmp/urvXTTg_IK/norm.split.4.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -m- --keep-sum AD /tmp/urvXTTg_IK/norm.split.4.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm --no-version -m- -f /build/bcftools-1.11/test/norm.fa /tmp/urvXTTg_IK/norm.split.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -m- -f /build/bcftools-1.11/test/norm.fa /tmp/urvXTTg_IK/norm.split.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm --no-version -m+ /tmp/urvXTTg_IK/norm.merge.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -m+ /tmp/urvXTTg_IK/norm.merge.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm --no-version -m+ /tmp/urvXTTg_IK/norm.merge.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -m+ /tmp/urvXTTg_IK/norm.merge.2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm --no-version -m+ /tmp/urvXTTg_IK/norm.merge.3.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -m+ /tmp/urvXTTg_IK/norm.merge.3.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm --no-version -m+ -s /tmp/urvXTTg_IK/norm.merge.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -m+ -s /tmp/urvXTTg_IK/norm.merge.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm --no-version -Nc s -f /build/bcftools-1.11/test/norm.fa /tmp/urvXTTg_IK/norm.setref.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -Nc s -f /build/bcftools-1.11/test/norm.fa /tmp/urvXTTg_IK/norm.setref.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm --no-version -f /build/bcftools-1.11/test/norm.fa /tmp/urvXTTg_IK/norm.telomere.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -f /build/bcftools-1.11/test/norm.fa /tmp/urvXTTg_IK/norm.telomere.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm --no-version -d snps /tmp/urvXTTg_IK/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -d snps /tmp/urvXTTg_IK/norm.rmdup.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm --no-version -d indels /tmp/urvXTTg_IK/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -d indels /tmp/urvXTTg_IK/norm.rmdup.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm --no-version -d both /tmp/urvXTTg_IK/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -d both /tmp/urvXTTg_IK/norm.rmdup.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm --no-version -d all /tmp/urvXTTg_IK/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -d all /tmp/urvXTTg_IK/norm.rmdup.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm --no-version -d none /tmp/urvXTTg_IK/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -d none /tmp/urvXTTg_IK/norm.rmdup.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm --no-version -d exact /tmp/urvXTTg_IK/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -d exact /tmp/urvXTTg_IK/norm.rmdup.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm --no-version -d none /tmp/urvXTTg_IK/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -d none /tmp/urvXTTg_IK/norm.rmdup.2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm --no-version -d exact /tmp/urvXTTg_IK/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -d exact /tmp/urvXTTg_IK/norm.rmdup.2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm --no-version -d indels /tmp/urvXTTg_IK/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -d indels /tmp/urvXTTg_IK/norm.rmdup.2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm --no-version -d any /tmp/urvXTTg_IK/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -d any /tmp/urvXTTg_IK/norm.rmdup.2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm --no-version -d both /tmp/urvXTTg_IK/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -d both /tmp/urvXTTg_IK/norm.rmdup.2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm --no-version -d snps /tmp/urvXTTg_IK/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -d snps /tmp/urvXTTg_IK/norm.rmdup.2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm --no-version -f /build/bcftools-1.11/test/norm.2.fa /tmp/urvXTTg_IK/norm.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -f /build/bcftools-1.11/test/norm.2.fa /tmp/urvXTTg_IK/norm.2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm --no-version -c s -f /build/bcftools-1.11/test/norm.iupac.fa /tmp/urvXTTg_IK/norm.iupac.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -c s -f /build/bcftools-1.11/test/norm.iupac.fa /tmp/urvXTTg_IK/norm.iupac.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm --no-version -c s -f /build/bcftools-1.11/test/norm.3.fa /tmp/urvXTTg_IK/norm.3.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -c s -f /build/bcftools-1.11/test/norm.3.fa /tmp/urvXTTg_IK/norm.3.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -aUc1 -C1 -s NA00002 -v snps /tmp/urvXTTg_IK/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/urvXTTg_IK/view.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -f PASS -Xks NA00003 /tmp/urvXTTg_IK/view.vcf.gz -r20,Y .. ok test_vcf_view: /build/bcftools-1.11/bcftools view -Ob -f PASS -Xks NA00003 /tmp/urvXTTg_IK/view.vcf.gz -r20,Y | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -xs NA00003 /tmp/urvXTTg_IK/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view -Ob -xs NA00003 /tmp/urvXTTg_IK/view.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/urvXTTg_IK/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view -Ob -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/urvXTTg_IK/view.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -p /tmp/urvXTTg_IK/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view -Ob -p /tmp/urvXTTg_IK/view.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -P /tmp/urvXTTg_IK/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view -Ob -P /tmp/urvXTTg_IK/view.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -hm2 -M2 -q0.3 -Q0.7 /tmp/urvXTTg_IK/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/urvXTTg_IK/view.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -Hu /tmp/urvXTTg_IK/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -GVsnps /tmp/urvXTTg_IK/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view -Ob -GVsnps /tmp/urvXTTg_IK/view.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -ne 'INDEL=1 || PV4[0]<0.006' /tmp/urvXTTg_IK/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/urvXTTg_IK/view.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -s ^NA00003 /tmp/urvXTTg_IK/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view -Ob -s ^NA00003 /tmp/urvXTTg_IK/view.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version /tmp/urvXTTg_IK/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/view.omitgenotypes.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -G /tmp/urvXTTg_IK/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view -Ob -G /tmp/urvXTTg_IK/view.omitgenotypes.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -HG /tmp/urvXTTg_IK/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -a /tmp/urvXTTg_IK/many.alleles.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view -Ob -a /tmp/urvXTTg_IK/many.alleles.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -asA /tmp/urvXTTg_IK/view.vectors.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view -Ob -asA /tmp/urvXTTg_IK/view.vectors.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -asB /tmp/urvXTTg_IK/view.vectors.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view -Ob -asB /tmp/urvXTTg_IK/view.vectors.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -asA /tmp/urvXTTg_IK/view.vectors.2.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view -Ob -asA /tmp/urvXTTg_IK/view.vectors.2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -H -i'FMT/FGS[*:0]="AAAAAA"' /tmp/urvXTTg_IK/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -H -i'FMT/FGS[*:2]="C"' /tmp/urvXTTg_IK/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -H -i'FMT/FGS[*:4]="EE"' /tmp/urvXTTg_IK/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -H -i'FMT/FRS[*:1]="BB"' /tmp/urvXTTg_IK/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -H -i'TXT0="text"' /tmp/urvXTTg_IK/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -T /build/bcftools-1.11/test/view.chrs.tab /tmp/urvXTTg_IK/view.chrs.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view -Ob -T /build/bcftools-1.11/test/view.chrs.tab /tmp/urvXTTg_IK/view.chrs.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -i 'POS>=3062917' /tmp/urvXTTg_IK/filter.2.vcf.gz 1:3062917-3157410 .. ok test_vcf_view: /build/bcftools-1.11/bcftools view -Ob -i 'POS>=3062917' /tmp/urvXTTg_IK/filter.2.vcf.gz 1:3062917-3157410 | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -H -r 1:10,1:12,1:10 /tmp/urvXTTg_IK/idx.1.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -H -r 1:1172777-1172804,1:1172806-1172808 /tmp/urvXTTg_IK/idx.2.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -H -R /build/bcftools-1.11/test/idx.2.bed /tmp/urvXTTg_IK/idx.2.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -H -R /build/bcftools-1.11/test/idx.3.bed /tmp/urvXTTg_IK/idx.3.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -H -R /build/bcftools-1.11/test/idx.4.bed /tmp/urvXTTg_IK/idx.4.vcf.gz .. ok test_vcf_64bit: /build/bcftools-1.11/bcftools view /build/bcftools-1.11/test/view64bit.1.vcf -H .. ok test_vcf_64bit: /build/bcftools-1.11/bcftools view /build/bcftools-1.11/test/view64bit.1.vcf | /build/bcftools-1.11/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-1.11/bcftools view /build/bcftools-1.11/test/view64bit.1.vcf -Ou | /build/bcftools-1.11/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-1.11/bcftools view /build/bcftools-1.11/test/view64bit.2.vcf -H .. ok test_vcf_64bit: /build/bcftools-1.11/bcftools view /build/bcftools-1.11/test/view64bit.2.vcf | /build/bcftools-1.11/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-1.11/bcftools view /build/bcftools-1.11/test/view64bit.2.vcf -Ou | /build/bcftools-1.11/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-1.11/bcftools view /build/bcftools-1.11/test/view64bit.3.vcf -H .. ok test_vcf_64bit: /build/bcftools-1.11/bcftools view /build/bcftools-1.11/test/view64bit.3.vcf | /build/bcftools-1.11/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-1.11/bcftools view /build/bcftools-1.11/test/view64bit.4.vcf -H .. ok test_vcf_64bit: /build/bcftools-1.11/bcftools view /build/bcftools-1.11/test/view64bit.4.vcf | /build/bcftools-1.11/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-1.11/bcftools view /build/bcftools-1.11/test/view64bit.4.vcf -Ou | /build/bcftools-1.11/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-1.11/bcftools view /build/bcftools-1.11/test/view64bit.5.vcf -H .. ok test_vcf_64bit: /build/bcftools-1.11/bcftools view /build/bcftools-1.11/test/view64bit.5.vcf | /build/bcftools-1.11/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-1.11/bcftools view /build/bcftools-1.11/test/view64bit.5.vcf -Ou | /build/bcftools-1.11/bcftools view -H .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -H -C5:nonmajor /tmp/urvXTTg_IK/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -H -c6:nonmajor /tmp/urvXTTg_IK/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -H -q0.3:major /tmp/urvXTTg_IK/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/urvXTTg_IK/view.filter.annovar.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -H -i 'Gene.refGene~"NOD"' /tmp/urvXTTg_IK/view.filter.annovar.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -H -i 'LJB2_MutationTaster=="0.291000"' /tmp/urvXTTg_IK/view.filter.annovar.vcf.gz .. ok test_vcf_call: /build/bcftools-1.11/bcftools call --no-version -mv /build/bcftools-1.11/test/mpileup.vcf .. ok test_vcf_call: /build/bcftools-1.11/bcftools call -Ob -mv /build/bcftools-1.11/test/mpileup.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.11/bcftools call --no-version -mg0 /build/bcftools-1.11/test/mpileup.vcf .. ok test_vcf_call: /build/bcftools-1.11/bcftools call -Ob -mg0 /build/bcftools-1.11/test/mpileup.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.11/bcftools call --no-version -mv -S /build/bcftools-1.11/test/mpileup.3.samples /build/bcftools-1.11/test/mpileup.vcf .. ok test_vcf_call: /build/bcftools-1.11/bcftools call -Ob -mv -S /build/bcftools-1.11/test/mpileup.3.samples /build/bcftools-1.11/test/mpileup.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.11/bcftools call --no-version -mv -S /build/bcftools-1.11/test/mpileup.4.samples /build/bcftools-1.11/test/mpileup.vcf .. ok test_vcf_call: /build/bcftools-1.11/bcftools call -Ob -mv -S /build/bcftools-1.11/test/mpileup.4.samples /build/bcftools-1.11/test/mpileup.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.11/bcftools call --no-version -mv -S /build/bcftools-1.11/test/mpileup.5.samples /build/bcftools-1.11/test/mpileup.vcf .. ok test_vcf_call: /build/bcftools-1.11/bcftools call -Ob -mv -S /build/bcftools-1.11/test/mpileup.5.samples /build/bcftools-1.11/test/mpileup.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.11/bcftools call --no-version -mv --ploidy-file /build/bcftools-1.11/test/mpileup.ploidy -S /build/bcftools-1.11/test/mpileup.samples /build/bcftools-1.11/test/mpileup.X.vcf .. ok test_vcf_call: /build/bcftools-1.11/bcftools call -Ob -mv --ploidy-file /build/bcftools-1.11/test/mpileup.ploidy -S /build/bcftools-1.11/test/mpileup.samples /build/bcftools-1.11/test/mpileup.X.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.11/bcftools call --no-version -mv --ploidy-file /build/bcftools-1.11/test/mpileup.ploidy -S /build/bcftools-1.11/test/mpileup.ped /build/bcftools-1.11/test/mpileup.X.vcf .. ok test_vcf_call: /build/bcftools-1.11/bcftools call -Ob -mv --ploidy-file /build/bcftools-1.11/test/mpileup.ploidy -S /build/bcftools-1.11/test/mpileup.ped /build/bcftools-1.11/test/mpileup.X.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.11/bcftools call --no-version -mv --ploidy-file /build/bcftools-1.11/test/mpileup.ploidy -S /build/bcftools-1.11/test/mpileup.2.samples /build/bcftools-1.11/test/mpileup.X.vcf .. ok test_vcf_call: /build/bcftools-1.11/bcftools call -Ob -mv --ploidy-file /build/bcftools-1.11/test/mpileup.ploidy -S /build/bcftools-1.11/test/mpileup.2.samples /build/bcftools-1.11/test/mpileup.X.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.11/bcftools call --no-version -mv /build/bcftools-1.11/test/mpileup.NA19213.NA19129.vcf .. ok test_vcf_call: /build/bcftools-1.11/bcftools call -Ob -mv /build/bcftools-1.11/test/mpileup.NA19213.NA19129.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.11/bcftools call --no-version -mv -G - /build/bcftools-1.11/test/mpileup.NA19213.NA19129.vcf .. ok test_vcf_call: /build/bcftools-1.11/bcftools call -Ob -mv -G - /build/bcftools-1.11/test/mpileup.NA19213.NA19129.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.11/bcftools call --no-version -mv /build/bcftools-1.11/test/mpileup.hwe.vcf .. ok test_vcf_call: /build/bcftools-1.11/bcftools call -Ob -mv /build/bcftools-1.11/test/mpileup.hwe.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.11/bcftools call --no-version -mv -G - /build/bcftools-1.11/test/mpileup.hwe.vcf .. ok test_vcf_call: /build/bcftools-1.11/bcftools call -Ob -mv -G - /build/bcftools-1.11/test/mpileup.hwe.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.11/bcftools call --no-version -mv -G /build/bcftools-1.11/test/mpileup.hwe.samples /build/bcftools-1.11/test/mpileup.hwe.vcf .. ok test_vcf_call: /build/bcftools-1.11/bcftools call -Ob -mv -G /build/bcftools-1.11/test/mpileup.hwe.samples /build/bcftools-1.11/test/mpileup.hwe.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-1.11/bcftools call --no-version -mA -C alleles -T /tmp/urvXTTg_IK/mpileup.tab.gz /build/bcftools-1.11/test/mpileup.vcf .. ok test_vcf_call_cAls: /build/bcftools-1.11/bcftools call -Ob -mA -C alleles -T /tmp/urvXTTg_IK/mpileup.tab.gz /build/bcftools-1.11/test/mpileup.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-1.11/bcftools call --no-version -mA -C alleles -T /tmp/urvXTTg_IK/mpileup.2.tab.gz /build/bcftools-1.11/test/mpileup.2.vcf .. ok test_vcf_call_cAls: /build/bcftools-1.11/bcftools call -Ob -mA -C alleles -T /tmp/urvXTTg_IK/mpileup.2.tab.gz /build/bcftools-1.11/test/mpileup.2.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-1.11/bcftools call --no-version -mA -C alleles -T /tmp/urvXTTg_IK/mpileup.3.tab.gz -i /build/bcftools-1.11/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /build/bcftools-1.11/bcftools call -Ob -mA -C alleles -T /tmp/urvXTTg_IK/mpileup.3.tab.gz -i /build/bcftools-1.11/test/mpileup.3.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-1.11/bcftools call --no-version -mA -C alleles -T /tmp/urvXTTg_IK/mpileup.4.tab.gz -i /build/bcftools-1.11/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /build/bcftools-1.11/bcftools call -Ob -mA -C alleles -T /tmp/urvXTTg_IK/mpileup.4.tab.gz -i /build/bcftools-1.11/test/mpileup.3.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-1.11/bcftools call --no-version -mA -C alleles -T /tmp/urvXTTg_IK/mpileup.5.tab.gz -i /build/bcftools-1.11/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /build/bcftools-1.11/bcftools call -Ob -mA -C alleles -T /tmp/urvXTTg_IK/mpileup.5.tab.gz -i /build/bcftools-1.11/test/mpileup.3.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-1.11/bcftools call --no-version -mA -C alleles -T /tmp/urvXTTg_IK/mpileup.6.tab.gz -i /build/bcftools-1.11/test/mpileup.4.vcf .. ok test_vcf_call_cAls: /build/bcftools-1.11/bcftools call -Ob -mA -C alleles -T /tmp/urvXTTg_IK/mpileup.6.tab.gz -i /build/bcftools-1.11/test/mpileup.4.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-1.11/bcftools call --no-version -mA -C alleles -T /tmp/urvXTTg_IK/mpileup.7.tab.gz -i /build/bcftools-1.11/test/mpileup.5.vcf .. ok test_vcf_call_cAls: /build/bcftools-1.11/bcftools call -Ob -mA -C alleles -T /tmp/urvXTTg_IK/mpileup.7.tab.gz -i /build/bcftools-1.11/test/mpileup.5.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-1.11/bcftools call --no-version -mA -C alleles -T /tmp/urvXTTg_IK/mpileup.cals.1.tab.gz /build/bcftools-1.11/test/mpileup.cals.1.vcf .. ok test_vcf_call_cAls: /build/bcftools-1.11/bcftools call -Ob -mA -C alleles -T /tmp/urvXTTg_IK/mpileup.cals.1.tab.gz /build/bcftools-1.11/test/mpileup.cals.1.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-1.11/bcftools call --no-version -mA -C alleles -T /tmp/urvXTTg_IK/mpileup.cals.2.tab.gz /build/bcftools-1.11/test/mpileup.cals.2.vcf .. ok test_vcf_call_cAls: /build/bcftools-1.11/bcftools call -Ob -mA -C alleles -T /tmp/urvXTTg_IK/mpileup.cals.2.tab.gz /build/bcftools-1.11/test/mpileup.cals.2.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.11/bcftools call --no-version -cv /build/bcftools-1.11/test/mpileup.c.vcf .. ok test_vcf_call: /build/bcftools-1.11/bcftools call -Ob -cv /build/bcftools-1.11/test/mpileup.c.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.11/bcftools call --no-version -cv --ploidy-file /build/bcftools-1.11/test/mpileup.ploidy -S /build/bcftools-1.11/test/mpileup.samples /build/bcftools-1.11/test/mpileup.c.X.vcf .. ok test_vcf_call: /build/bcftools-1.11/bcftools call -Ob -cv --ploidy-file /build/bcftools-1.11/test/mpileup.ploidy -S /build/bcftools-1.11/test/mpileup.samples /build/bcftools-1.11/test/mpileup.c.X.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.11/bcftools call --no-version -cv --ploidy-file /build/bcftools-1.11/test/mpileup.ploidy -S /build/bcftools-1.11/test/mpileup.ped /build/bcftools-1.11/test/mpileup.c.X.vcf .. ok test_vcf_call: /build/bcftools-1.11/bcftools call -Ob -cv --ploidy-file /build/bcftools-1.11/test/mpileup.ploidy -S /build/bcftools-1.11/test/mpileup.ped /build/bcftools-1.11/test/mpileup.c.X.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-1.11/bcftools call --no-version -cv --ploidy-file /build/bcftools-1.11/test/mpileup.ploidy -S /build/bcftools-1.11/test/mpileup.2.samples /build/bcftools-1.11/test/mpileup.c.X.vcf .. ok test_vcf_call: /build/bcftools-1.11/bcftools call -Ob -cv --ploidy-file /build/bcftools-1.11/test/mpileup.ploidy -S /build/bcftools-1.11/test/mpileup.2.samples /build/bcftools-1.11/test/mpileup.c.X.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -S. -e'TXT0="text"' /build/bcftools-1.11/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -S. -e'TXT0="text"' /build/bcftools-1.11/test/view.filter.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -S. -e'FMT/FRS[*:1]="BB"' /build/bcftools-1.11/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -S. -e'FMT/FRS[*:1]="BB"' /build/bcftools-1.11/test/view.filter.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -S. -e'FMT/FGS[*:0]="AAAAAA"' /build/bcftools-1.11/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -S. -e'FMT/FGS[*:0]="AAAAAA"' /build/bcftools-1.11/test/view.filter.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -S. -e'FMT/FGS[*:1]="BBB"' /build/bcftools-1.11/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -S. -e'FMT/FGS[*:1]="BBB"' /build/bcftools-1.11/test/view.filter.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -S. -e'FMT/FGS[*:4]="EE"' /build/bcftools-1.11/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -S. -e'FMT/FGS[*:4]="EE"' /build/bcftools-1.11/test/view.filter.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -S. -e'FMT/STR="XX"' /build/bcftools-1.11/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -S. -e'FMT/STR="XX"' /build/bcftools-1.11/test/view.filter.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -S. -e'FMT/FILTER="aaa"' /build/bcftools-1.11/test/view.filter.2.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -S. -e'FMT/FILTER="aaa"' /build/bcftools-1.11/test/view.filter.2.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -mx -g2 -G2 /build/bcftools-1.11/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -mx -g2 -G2 /build/bcftools-1.11/test/filter.1.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /build/bcftools-1.11/test/filter.2.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /build/bcftools-1.11/test/filter.2.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -e'INFO/DP=19' /build/bcftools-1.11/test/filter.3.vcf | /build/bcftools-1.11/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -e'INFO/DP=19' /build/bcftools-1.11/test/filter.3.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -e'INFO/DP=19' -s XX /build/bcftools-1.11/test/filter.3.vcf | /build/bcftools-1.11/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -e'INFO/DP=19' -s XX /build/bcftools-1.11/test/filter.3.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -e'INFO/DP=19' -s XX -m+ /build/bcftools-1.11/test/filter.3.vcf | /build/bcftools-1.11/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+ /build/bcftools-1.11/test/filter.3.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -e'INFO/DP=19' -s XX -mx /build/bcftools-1.11/test/filter.3.vcf | /build/bcftools-1.11/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -e'INFO/DP=19' -s XX -mx /build/bcftools-1.11/test/filter.3.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -e'INFO/DP=19' -s XX -m+x /build/bcftools-1.11/test/filter.3.vcf | /build/bcftools-1.11/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+x /build/bcftools-1.11/test/filter.3.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -e'FMT/GT="0/2"' /build/bcftools-1.11/test/filter.3.vcf | /build/bcftools-1.11/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -e'FMT/GT="0/2"' /build/bcftools-1.11/test/filter.3.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -e'FMT/GT="0/2"' -s XX /build/bcftools-1.11/test/filter.3.vcf | /build/bcftools-1.11/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX /build/bcftools-1.11/test/filter.3.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -e'FMT/GT="0/2"' -s XX -m+ /build/bcftools-1.11/test/filter.3.vcf | /build/bcftools-1.11/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+ /build/bcftools-1.11/test/filter.3.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -e'FMT/GT="0/2"' -s XX -mx /build/bcftools-1.11/test/filter.3.vcf | /build/bcftools-1.11/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -mx /build/bcftools-1.11/test/filter.3.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -e'FMT/GT="0/2"' -s XX -m+x /build/bcftools-1.11/test/filter.3.vcf | /build/bcftools-1.11/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+x /build/bcftools-1.11/test/filter.3.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -i'FMT/GT="0/0" && AC[*]=2' /build/bcftools-1.11/test/filter.2.vcf | /build/bcftools-1.11/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -i'FMT/GT="0/0" && AC[*]=2' /build/bcftools-1.11/test/filter.2.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -i'AC[*]=2 && FMT/GT="0/0"' /build/bcftools-1.11/test/filter.2.vcf | /build/bcftools-1.11/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -i'AC[*]=2 && FMT/GT="0/0"' /build/bcftools-1.11/test/filter.2.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -i'ALT="."' /build/bcftools-1.11/test/filter.2.vcf | /build/bcftools-1.11/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -i'ALT="."' /build/bcftools-1.11/test/filter.2.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -S . -i 'FORMAT/TEST3<25' /build/bcftools-1.11/test/filter.4.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -S . -i 'FORMAT/TEST3<25' /build/bcftools-1.11/test/filter.4.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -S . -i 'FORMAT/TEST4<25' /build/bcftools-1.11/test/filter.4.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -S . -i 'FORMAT/TEST4<25' /build/bcftools-1.11/test/filter.4.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -i'GT="A"' /build/bcftools-1.11/test/filter.2.vcf | /build/bcftools-1.11/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -i'GT="A"' /build/bcftools-1.11/test/filter.2.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -i'GT="RR"' /build/bcftools-1.11/test/filter.2.vcf | /build/bcftools-1.11/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -i'GT="RR"' /build/bcftools-1.11/test/filter.2.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -i'GT="RA"' /build/bcftools-1.11/test/filter.2.vcf | /build/bcftools-1.11/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -i'GT="RA"' /build/bcftools-1.11/test/filter.2.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -i'GT="AR"' /build/bcftools-1.11/test/filter.2.vcf | /build/bcftools-1.11/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -i'GT="AR"' /build/bcftools-1.11/test/filter.2.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -i'GT="AA"' /build/bcftools-1.11/test/filter.2.vcf | /build/bcftools-1.11/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -i'GT="AA"' /build/bcftools-1.11/test/filter.2.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -i'GT="aA"' /build/bcftools-1.11/test/filter.2.vcf | /build/bcftools-1.11/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -i'GT="aA"' /build/bcftools-1.11/test/filter.2.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -i'GT="Aa"' /build/bcftools-1.11/test/filter.2.vcf | /build/bcftools-1.11/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -i'GT="Aa"' /build/bcftools-1.11/test/filter.2.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -i'GT="HOM"' /build/bcftools-1.11/test/filter.2.vcf | /build/bcftools-1.11/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -i'GT="HOM"' /build/bcftools-1.11/test/filter.2.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -i'GT="HET"' /build/bcftools-1.11/test/filter.2.vcf | /build/bcftools-1.11/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -i'GT="HET"' /build/bcftools-1.11/test/filter.2.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -i'GT="HAP"' /build/bcftools-1.11/test/filter.2.vcf | /build/bcftools-1.11/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -i'GT="HAP"' /build/bcftools-1.11/test/filter.2.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -i'AD[:1]=11' /build/bcftools-1.11/test/filter.5.vcf | /build/bcftools-1.11/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -i'AD[:1]=11' /build/bcftools-1.11/test/filter.5.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -i'AD[1:]=11' /build/bcftools-1.11/test/filter.5.vcf | /build/bcftools-1.11/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -i'AD[1:]=11' /build/bcftools-1.11/test/filter.5.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -i'FR[0:1]=11' /build/bcftools-1.11/test/filter.5.vcf | /build/bcftools-1.11/bcftools query -f '%POS[\t%FR]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -i'FR[0:1]=11' /build/bcftools-1.11/test/filter.5.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS[\t%FR]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -i'AD[*]="."' /build/bcftools-1.11/test/filter.5.vcf | /build/bcftools-1.11/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -i'AD[*]="."' /build/bcftools-1.11/test/filter.5.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -i'AD[0:0]=="."' /build/bcftools-1.11/test/filter.5.vcf | /build/bcftools-1.11/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -i'AD[0:0]=="."' /build/bcftools-1.11/test/filter.5.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -i'AD[0:0]!="."' /build/bcftools-1.11/test/filter.5.vcf | /build/bcftools-1.11/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -i'AD[0:0]!="."' /build/bcftools-1.11/test/filter.5.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -i'QUAL=="."' /build/bcftools-1.11/test/filter.5.vcf | /build/bcftools-1.11/bcftools query -f '%POS\t%QUAL\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -i'QUAL=="."' /build/bcftools-1.11/test/filter.5.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS\t%QUAL\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -i'N_PASS(DP>32)=1' /build/bcftools-1.11/test/filter.2.vcf | /build/bcftools-1.11/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -i'N_PASS(DP>32)=1' /build/bcftools-1.11/test/filter.2.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -i'F_PASS(DP>32)=0.5' /build/bcftools-1.11/test/filter.2.vcf | /build/bcftools-1.11/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -i'F_PASS(DP>32)=0.5' /build/bcftools-1.11/test/filter.2.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -i'F_MISSING>=1/5' /build/bcftools-1.11/test/filter.6.vcf | /build/bcftools-1.11/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -i'F_MISSING>=1/5' /build/bcftools-1.11/test/filter.6.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -i'F_MISSING>=0.2' /build/bcftools-1.11/test/filter.6.vcf | /build/bcftools-1.11/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -i'F_MISSING>=0.2' /build/bcftools-1.11/test/filter.6.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -i'F_PASS(GT=="mis")>=1/5' /build/bcftools-1.11/test/filter.6.vcf | /build/bcftools-1.11/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -i'F_PASS(GT=="mis")>=1/5' /build/bcftools-1.11/test/filter.6.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -i'F_PASS(GT=="mis")>=0.2' /build/bcftools-1.11/test/filter.6.vcf | /build/bcftools-1.11/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -i'F_PASS(GT=="mis")>=0.2' /build/bcftools-1.11/test/filter.6.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -mx -s + -g2:mnp,indel,other /build/bcftools-1.11/test/filter.7.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -mx -s + -g2:mnp,indel,other /build/bcftools-1.11/test/filter.7.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -S . -e 'FORMAT/AO==4' /build/bcftools-1.11/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -S . -e 'FORMAT/AO==4' /build/bcftools-1.11/test/filter.8.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -S . -e 'MAX(FORMAT/AO[0:])==4' /build/bcftools-1.11/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -S . -e 'MAX(FORMAT/AO[0:])==4' /build/bcftools-1.11/test/filter.8.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -S . -e 'MAX(FORMAT/AO)==4' /build/bcftools-1.11/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -S . -e 'MAX(FORMAT/AO)==4' /build/bcftools-1.11/test/filter.8.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -S . -e 'MIN(FORMAT/AO[0:])==3' /build/bcftools-1.11/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO[0:])==3' /build/bcftools-1.11/test/filter.8.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -S . -e 'MIN(FORMAT/AO)==2' /build/bcftools-1.11/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO)==2' /build/bcftools-1.11/test/filter.8.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -S . -e 'MIN(FORMAT/AO[0:])==3' /build/bcftools-1.11/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO[0:])==3' /build/bcftools-1.11/test/filter.8.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -S . -e 'AVG(FORMAT/AO[2:])==4' /build/bcftools-1.11/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -S . -e 'AVG(FORMAT/AO[2:])==4' /build/bcftools-1.11/test/filter.8.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -S . -e 'MEDIAN(FORMAT/AO[2:])==4' /build/bcftools-1.11/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -S . -e 'MEDIAN(FORMAT/AO[2:])==4' /build/bcftools-1.11/test/filter.8.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -S . -e 'STDEV(FORMAT/AO[0:])=0.5' /build/bcftools-1.11/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -S . -e 'STDEV(FORMAT/AO[0:])=0.5' /build/bcftools-1.11/test/filter.8.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -S . -e 'SUM(FORMAT/AO[0:])=7' /build/bcftools-1.11/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -S . -e 'SUM(FORMAT/AO[0:])=7' /build/bcftools-1.11/test/filter.8.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -S . -e 'SMPL_MAX(FORMAT/AO)==4' /build/bcftools-1.11/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -S . -e 'SMPL_MAX(FORMAT/AO)==4' /build/bcftools-1.11/test/filter.8.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -S . -e 'sMIN(FORMAT/AO)==2' /build/bcftools-1.11/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -S . -e 'sMIN(FORMAT/AO)==2' /build/bcftools-1.11/test/filter.8.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -S . -e 'ABS(sAVG(FORMAT/AO)-3.66666)<1e-5' /build/bcftools-1.11/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -S . -e 'ABS(sAVG(FORMAT/AO)-3.66666)<1e-5' /build/bcftools-1.11/test/filter.8.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -S . -e 'sMEDIAN(FORMAT/AO)==4' /build/bcftools-1.11/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -S . -e 'sMEDIAN(FORMAT/AO)==4' /build/bcftools-1.11/test/filter.8.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -S . -e 'ABS(sSTDEV(FORMAT/AO)-1.2472191)<1e-5' /build/bcftools-1.11/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -S . -e 'ABS(sSTDEV(FORMAT/AO)-1.2472191)<1e-5' /build/bcftools-1.11/test/filter.8.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -S . -e 'sSUM(FORMAT/AO)==11' /build/bcftools-1.11/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -S . -e 'sSUM(FORMAT/AO)==11' /build/bcftools-1.11/test/filter.8.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -i 'QUAL/FMT/AD==55' /build/bcftools-1.11/test/filter.9.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -i 'QUAL/FMT/AD==55' /build/bcftools-1.11/test/filter.9.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -i 'QUAL/INFO/AD==10' /build/bcftools-1.11/test/filter.9.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -i 'QUAL/INFO/AD==10' /build/bcftools-1.11/test/filter.9.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -S . -e 'ABS(SMPL_MAX(FORMAT/AO))=5' /build/bcftools-1.11/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -S . -e 'ABS(SMPL_MAX(FORMAT/AO))=5' /build/bcftools-1.11/test/filter.8.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -S . -e 'PHRED(AO[1:])>-4' /build/bcftools-1.11/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -S . -e 'PHRED(AO[1:])>-4' /build/bcftools-1.11/test/filter.8.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -S . -e 'ABS(AO[1:])==2' /build/bcftools-1.11/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -S . -e 'ABS(AO[1:])==2' /build/bcftools-1.11/test/filter.8.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -i 'sum(AD[*]) > FORMAT/DP' /build/bcftools-1.11/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -i 'sum(AD[*]) > FORMAT/DP' /build/bcftools-1.11/test/filter.10.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -i 'FORMAT/DP < sum(AD[*])' /build/bcftools-1.11/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -i 'FORMAT/DP < sum(AD[*])' /build/bcftools-1.11/test/filter.10.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -i 'sum(AD[*]) < FORMAT/DP' /build/bcftools-1.11/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -i 'sum(AD[*]) < FORMAT/DP' /build/bcftools-1.11/test/filter.10.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -i 'FORMAT/DP > sum(AD[*])' /build/bcftools-1.11/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-1.11/bcftools filter -Ob -i 'FORMAT/DP > sum(AD[*])' /build/bcftools-1.11/test/filter.10.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_sort: /build/bcftools-1.11/bcftools sort -m 0 /build/bcftools-1.11/test/sort.vcf | /build/bcftools-1.11/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /build/bcftools-1.11/bcftools sort -Ob -m 0 /build/bcftools-1.11/test/sort.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /build/bcftools-1.11/bcftools sort -m 1000 /build/bcftools-1.11/test/sort.vcf | /build/bcftools-1.11/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /build/bcftools-1.11/bcftools sort -Ob -m 1000 /build/bcftools-1.11/test/sort.vcf | /build/bcftools-1.11/bcftools view | /build/bcftools-1.11/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_regions: /build/bcftools-1.11/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /build/bcftools-1.11/test/regions.tab /tmp/urvXTTg_IK/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/regions.vcf.gz | /build/bcftools-1.11/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /build/bcftools-1.11/test/regions.tab .. ok test_vcf_regions: /build/bcftools-1.11/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /build/bcftools-1.11/test/regions.tab /tmp/urvXTTg_IK/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-1.11/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/urvXTTg_IK/regions.tab.gz /tmp/urvXTTg_IK/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/regions.vcf.gz | /build/bcftools-1.11/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/urvXTTg_IK/regions.tab.gz .. ok test_vcf_regions: /build/bcftools-1.11/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/urvXTTg_IK/regions.tab.gz /tmp/urvXTTg_IK/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-1.11/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/urvXTTg_IK/regions.bed /tmp/urvXTTg_IK/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/regions.vcf.gz | /build/bcftools-1.11/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/urvXTTg_IK/regions.bed .. ok test_vcf_regions: /build/bcftools-1.11/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/urvXTTg_IK/regions.bed /tmp/urvXTTg_IK/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-1.11/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/urvXTTg_IK/regions.bed.gz /tmp/urvXTTg_IK/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/regions.vcf.gz | /build/bcftools-1.11/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/urvXTTg_IK/regions.bed.gz .. ok test_vcf_regions: /build/bcftools-1.11/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/urvXTTg_IK/regions.bed.gz /tmp/urvXTTg_IK/regions.vcf.gz .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/urvXTTg_IK/annotate.tab.gz -h /build/bcftools-1.11/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /build/bcftools-1.11/test/annotate.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/urvXTTg_IK/annotate.tab.gz -h /build/bcftools-1.11/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /build/bcftools-1.11/test/annotate.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/urvXTTg_IK/annotate2.tab.gz -h /build/bcftools-1.11/test/annotate.hdr -c CHROM,POS,-,T_STR /build/bcftools-1.11/test/annotate.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/urvXTTg_IK/annotate2.tab.gz -h /build/bcftools-1.11/test/annotate.hdr -c CHROM,POS,-,T_STR /build/bcftools-1.11/test/annotate.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/urvXTTg_IK/annotate2.tab.gz -h /build/bcftools-1.11/test/annotate.hdr -c CHROM,FROM,TO,T_STR /build/bcftools-1.11/test/annotate.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/urvXTTg_IK/annotate2.tab.gz -h /build/bcftools-1.11/test/annotate.hdr -c CHROM,FROM,TO,T_STR /build/bcftools-1.11/test/annotate.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/urvXTTg_IK/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/urvXTTg_IK/annotate.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/urvXTTg_IK/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/urvXTTg_IK/annotate.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/urvXTTg_IK/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/urvXTTg_IK/annotate2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/urvXTTg_IK/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/urvXTTg_IK/annotate2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/urvXTTg_IK/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/urvXTTg_IK/annotate2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/urvXTTg_IK/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/urvXTTg_IK/annotate2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/urvXTTg_IK/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/urvXTTg_IK/annotate2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/urvXTTg_IK/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/urvXTTg_IK/annotate2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/urvXTTg_IK/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/urvXTTg_IK/annotate2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/urvXTTg_IK/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/urvXTTg_IK/annotate2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/urvXTTg_IK/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/urvXTTg_IK/annotate2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/urvXTTg_IK/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/urvXTTg_IK/annotate2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /build/bcftools-1.11/test/annotate3.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /build/bcftools-1.11/test/annotate3.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -x FORMAT /build/bcftools-1.11/test/annotate3.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -x FORMAT /build/bcftools-1.11/test/annotate3.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/urvXTTg_IK/annots4.vcf.gz -c +INFO /tmp/urvXTTg_IK/annotate4.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/urvXTTg_IK/annots4.vcf.gz -c +INFO /tmp/urvXTTg_IK/annotate4.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/urvXTTg_IK/annots4.tab.gz -h /build/bcftools-1.11/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /build/bcftools-1.11/test/annotate4.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/urvXTTg_IK/annots4.tab.gz -h /build/bcftools-1.11/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /build/bcftools-1.11/test/annotate4.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/urvXTTg_IK/annots10.tab.gz -h /build/bcftools-1.11/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /build/bcftools-1.11/test/annotate10.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/urvXTTg_IK/annots10.tab.gz -h /build/bcftools-1.11/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /build/bcftools-1.11/test/annotate10.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/urvXTTg_IK/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/urvXTTg_IK/annotate2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/urvXTTg_IK/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/urvXTTg_IK/annotate2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/urvXTTg_IK/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /build/bcftools-1.11/test/annotate2.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/urvXTTg_IK/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /build/bcftools-1.11/test/annotate2.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/urvXTTg_IK/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/urvXTTg_IK/annotate2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/urvXTTg_IK/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/urvXTTg_IK/annotate2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/urvXTTg_IK/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/urvXTTg_IK/annotate2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/urvXTTg_IK/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/urvXTTg_IK/annotate2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/urvXTTg_IK/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/urvXTTg_IK/annotate2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/urvXTTg_IK/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/urvXTTg_IK/annotate2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/urvXTTg_IK/annots11.vcf.gz -c FMT /tmp/urvXTTg_IK/annotate11.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/urvXTTg_IK/annots11.vcf.gz -c FMT /tmp/urvXTTg_IK/annotate11.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/urvXTTg_IK/annots2.vcf.gz -c FMT/newGT:=GT /tmp/urvXTTg_IK/annotate2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/urvXTTg_IK/annots2.vcf.gz -c FMT/newGT:=GT /tmp/urvXTTg_IK/annotate2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/urvXTTg_IK/annots12.vcf.gz -c FMT/GT:=newGT /tmp/urvXTTg_IK/annotate2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/urvXTTg_IK/annots12.vcf.gz -c FMT/GT:=newGT /tmp/urvXTTg_IK/annotate2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/urvXTTg_IK/annots13.tab.gz -h /build/bcftools-1.11/test/annotate13.hdr -c CHROM,BEG,END,ABC /build/bcftools-1.11/test/annotate13.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/urvXTTg_IK/annots13.tab.gz -h /build/bcftools-1.11/test/annotate13.hdr -c CHROM,BEG,END,ABC /build/bcftools-1.11/test/annotate13.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/urvXTTg_IK/annots13.tab.gz -h /build/bcftools-1.11/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:append /build/bcftools-1.11/test/annotate13.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/urvXTTg_IK/annots13.tab.gz -h /build/bcftools-1.11/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:append /build/bcftools-1.11/test/annotate13.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/urvXTTg_IK/annots13.tab.gz -h /build/bcftools-1.11/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:unique /build/bcftools-1.11/test/annotate13.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/urvXTTg_IK/annots13.tab.gz -h /build/bcftools-1.11/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:unique /build/bcftools-1.11/test/annotate13.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -x FILTER/XX,INFO/XX --force /build/bcftools-1.11/test/annotate14.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -x FILTER/XX,INFO/XX --force /build/bcftools-1.11/test/annotate14.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/urvXTTg_IK/annotate15.tab.gz -h /build/bcftools-1.11/test/annotate15.hdr -s SAMPLE1 -c CHROM,FROM,TO,FMT/FOO,BAR /build/bcftools-1.11/test/annotate15.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/urvXTTg_IK/annotate15.tab.gz -h /build/bcftools-1.11/test/annotate15.hdr -s SAMPLE1 -c CHROM,FROM,TO,FMT/FOO,BAR /build/bcftools-1.11/test/annotate15.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/urvXTTg_IK/annotate15.tab.gz -h /build/bcftools-1.11/test/annotate15.hdr -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR /build/bcftools-1.11/test/annotate15.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/urvXTTg_IK/annotate15.tab.gz -h /build/bcftools-1.11/test/annotate15.hdr -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR /build/bcftools-1.11/test/annotate15.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -x FILTER /build/bcftools-1.11/test/annotate16.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -x FILTER /build/bcftools-1.11/test/annotate16.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/urvXTTg_IK/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/bcftools-1.11/test/annotate17.1.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/urvXTTg_IK/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/bcftools-1.11/test/annotate17.1.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/urvXTTg_IK/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/bcftools-1.11/test/annotate17.2.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/urvXTTg_IK/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/bcftools-1.11/test/annotate17.2.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/urvXTTg_IK/annotate17.3.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/bcftools-1.11/test/annotate17.3.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/urvXTTg_IK/annotate17.3.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/bcftools-1.11/test/annotate17.3.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/urvXTTg_IK/annotate18.1.tab.gz -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /build/bcftools-1.11/test/annotate18.1.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/urvXTTg_IK/annotate18.1.tab.gz -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /build/bcftools-1.11/test/annotate18.1.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/urvXTTg_IK/annotate18.2.tab.gz -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /build/bcftools-1.11/test/annotate18.2.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/urvXTTg_IK/annotate18.2.tab.gz -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /build/bcftools-1.11/test/annotate18.2.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/urvXTTg_IK/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/urvXTTg_IK/annotate19.dst.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/urvXTTg_IK/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/urvXTTg_IK/annotate19.dst.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/urvXTTg_IK/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/urvXTTg_IK/annotate19.dst.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/urvXTTg_IK/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/urvXTTg_IK/annotate19.dst.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/urvXTTg_IK/annotate20.src.vcf.gz -c FMT/GT /tmp/urvXTTg_IK/annotate20.dst.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/urvXTTg_IK/annotate20.src.vcf.gz -c FMT/GT /tmp/urvXTTg_IK/annotate20.dst.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/urvXTTg_IK/annotate20.src.vcf.gz -c +FMT/GT /tmp/urvXTTg_IK/annotate20.dst.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/urvXTTg_IK/annotate20.src.vcf.gz -c +FMT/GT /tmp/urvXTTg_IK/annotate20.dst.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/urvXTTg_IK/annotate20.src.vcf.gz -c -FMT/GT /tmp/urvXTTg_IK/annotate20.dst.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/urvXTTg_IK/annotate20.src.vcf.gz -c -FMT/GT /tmp/urvXTTg_IK/annotate20.dst.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/urvXTTg_IK/annotate.multi.tab.gz -c CHROM,POS,REF,ALT,ANN -l ANN:append /build/bcftools-1.11/test/annotate.multi.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/urvXTTg_IK/annotate.multi.tab.gz -c CHROM,POS,REF,ALT,ANN -l ANN:append /build/bcftools-1.11/test/annotate.multi.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/urvXTTg_IK/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /build/bcftools-1.11/test/annotate9.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -Ob -a /tmp/urvXTTg_IK/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /build/bcftools-1.11/test/annotate9.vcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-1.11/bcftools concat --no-version /tmp/urvXTTg_IK/concat.1.a.vcf.gz /tmp/urvXTTg_IK/concat.1.b.vcf.gz .. ok test_vcf_concat: /build/bcftools-1.11/bcftools concat -Ob /tmp/urvXTTg_IK/concat.1.a.vcf.gz /tmp/urvXTTg_IK/concat.1.b.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-1.11/bcftools concat --no-version /tmp/urvXTTg_IK/concat.1.a.bcf /tmp/urvXTTg_IK/concat.1.b.bcf .. ok test_vcf_concat: /build/bcftools-1.11/bcftools concat -Ob /tmp/urvXTTg_IK/concat.1.a.bcf /tmp/urvXTTg_IK/concat.1.b.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-1.11/bcftools concat --no-version -a /tmp/urvXTTg_IK/concat.2.a.vcf.gz /tmp/urvXTTg_IK/concat.2.b.vcf.gz .. ok test_vcf_concat: /build/bcftools-1.11/bcftools concat -Ob -a /tmp/urvXTTg_IK/concat.2.a.vcf.gz /tmp/urvXTTg_IK/concat.2.b.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-1.11/bcftools concat --no-version -a /tmp/urvXTTg_IK/concat.2.a.bcf /tmp/urvXTTg_IK/concat.2.b.bcf .. ok test_vcf_concat: /build/bcftools-1.11/bcftools concat -Ob -a /tmp/urvXTTg_IK/concat.2.a.bcf /tmp/urvXTTg_IK/concat.2.b.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-1.11/bcftools concat --no-version -aD /tmp/urvXTTg_IK/concat.2.a.vcf.gz /tmp/urvXTTg_IK/concat.2.b.vcf.gz .. ok test_vcf_concat: /build/bcftools-1.11/bcftools concat -Ob -aD /tmp/urvXTTg_IK/concat.2.a.vcf.gz /tmp/urvXTTg_IK/concat.2.b.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-1.11/bcftools concat --no-version -aD /tmp/urvXTTg_IK/concat.2.a.bcf /tmp/urvXTTg_IK/concat.2.b.bcf .. ok test_vcf_concat: /build/bcftools-1.11/bcftools concat -Ob -aD /tmp/urvXTTg_IK/concat.2.a.bcf /tmp/urvXTTg_IK/concat.2.b.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-1.11/bcftools concat --no-version -l /tmp/urvXTTg_IK/concat.3.a.vcf.gz /tmp/urvXTTg_IK/concat.3.b.vcf.gz /tmp/urvXTTg_IK/concat.3.0.vcf.gz /tmp/urvXTTg_IK/concat.3.c.vcf.gz /tmp/urvXTTg_IK/concat.3.d.vcf.gz /tmp/urvXTTg_IK/concat.3.e.vcf.gz /tmp/urvXTTg_IK/concat.3.f.vcf.gz .. ok test_vcf_concat: /build/bcftools-1.11/bcftools concat -Ob -l /tmp/urvXTTg_IK/concat.3.a.vcf.gz /tmp/urvXTTg_IK/concat.3.b.vcf.gz /tmp/urvXTTg_IK/concat.3.0.vcf.gz /tmp/urvXTTg_IK/concat.3.c.vcf.gz /tmp/urvXTTg_IK/concat.3.d.vcf.gz /tmp/urvXTTg_IK/concat.3.e.vcf.gz /tmp/urvXTTg_IK/concat.3.f.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-1.11/bcftools concat --no-version -l /tmp/urvXTTg_IK/concat.3.a.bcf /tmp/urvXTTg_IK/concat.3.b.bcf /tmp/urvXTTg_IK/concat.3.0.bcf /tmp/urvXTTg_IK/concat.3.c.bcf /tmp/urvXTTg_IK/concat.3.d.bcf /tmp/urvXTTg_IK/concat.3.e.bcf /tmp/urvXTTg_IK/concat.3.f.bcf .. ok test_vcf_concat: /build/bcftools-1.11/bcftools concat -Ob -l /tmp/urvXTTg_IK/concat.3.a.bcf /tmp/urvXTTg_IK/concat.3.b.bcf /tmp/urvXTTg_IK/concat.3.0.bcf /tmp/urvXTTg_IK/concat.3.c.bcf /tmp/urvXTTg_IK/concat.3.d.bcf /tmp/urvXTTg_IK/concat.3.e.bcf /tmp/urvXTTg_IK/concat.3.f.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ Random seed for test_naive_concat: 77680373 .. ok test_naive_concat: /build/bcftools-1.11/bcftools concat --naive-force /tmp/urvXTTg_IK/naive_concat.0.bcf /tmp/urvXTTg_IK/naive_concat.1.bcf /tmp/urvXTTg_IK/naive_concat.2.bcf /tmp/urvXTTg_IK/naive_concat.3.bcf /tmp/urvXTTg_IK/naive_concat.4.bcf /tmp/urvXTTg_IK/naive_concat.5.bcf /tmp/urvXTTg_IK/naive_concat.6.bcf /tmp/urvXTTg_IK/naive_concat.7.bcf /tmp/urvXTTg_IK/naive_concat.8.bcf /tmp/urvXTTg_IK/naive_concat.9.bcf | /build/bcftools-1.11/bcftools view -H .. ok test_naive_concat: /build/bcftools-1.11/bcftools concat --naive /tmp/urvXTTg_IK/naive_concat.0.vcf.gz /tmp/urvXTTg_IK/naive_concat.1.vcf.gz /tmp/urvXTTg_IK/naive_concat.2.vcf.gz /tmp/urvXTTg_IK/naive_concat.3.vcf.gz /tmp/urvXTTg_IK/naive_concat.4.vcf.gz /tmp/urvXTTg_IK/naive_concat.5.vcf.gz /tmp/urvXTTg_IK/naive_concat.6.vcf.gz /tmp/urvXTTg_IK/naive_concat.7.vcf.gz /tmp/urvXTTg_IK/naive_concat.8.vcf.gz /tmp/urvXTTg_IK/naive_concat.9.vcf.gz | /build/bcftools-1.11/bcftools view -H .. ok test_vcf_reheader: /build/bcftools-1.11/bcftools reheader -h /build/bcftools-1.11/test/reheader.hdr /build/bcftools-1.11/test/reheader.vcf | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-1.11/test/reheader.vcf | /build/bcftools-1.11/bcftools reheader -h /build/bcftools-1.11/test/reheader.hdr | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.11/bcftools reheader -h /build/bcftools-1.11/test/reheader.hdr /tmp/urvXTTg_IK/reheader.bcf | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/urvXTTg_IK/reheader.bcf | /build/bcftools-1.11/bcftools reheader -h /build/bcftools-1.11/test/reheader.hdr | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.11/bcftools reheader -h /build/bcftools-1.11/test/reheader.hdr /tmp/urvXTTg_IK/reheader.vcf.gz | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/urvXTTg_IK/reheader.vcf.gz | /build/bcftools-1.11/bcftools reheader -h /build/bcftools-1.11/test/reheader.hdr | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.11/bcftools reheader -s /build/bcftools-1.11/test/reheader.samples /build/bcftools-1.11/test/reheader.vcf | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-1.11/test/reheader.vcf | /build/bcftools-1.11/bcftools reheader -s /build/bcftools-1.11/test/reheader.samples | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.11/bcftools reheader -s /build/bcftools-1.11/test/reheader.samples /tmp/urvXTTg_IK/reheader.bcf | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/urvXTTg_IK/reheader.bcf | /build/bcftools-1.11/bcftools reheader -s /build/bcftools-1.11/test/reheader.samples | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.11/bcftools reheader -s /build/bcftools-1.11/test/reheader.samples /tmp/urvXTTg_IK/reheader.vcf.gz | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/urvXTTg_IK/reheader.vcf.gz | /build/bcftools-1.11/bcftools reheader -s /build/bcftools-1.11/test/reheader.samples | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.11/bcftools reheader -s /build/bcftools-1.11/test/reheader.samples2 /build/bcftools-1.11/test/reheader.vcf | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-1.11/test/reheader.vcf | /build/bcftools-1.11/bcftools reheader -s /build/bcftools-1.11/test/reheader.samples2 | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.11/bcftools reheader -s /build/bcftools-1.11/test/reheader.samples2 /tmp/urvXTTg_IK/reheader.bcf | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/urvXTTg_IK/reheader.bcf | /build/bcftools-1.11/bcftools reheader -s /build/bcftools-1.11/test/reheader.samples2 | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.11/bcftools reheader -s /build/bcftools-1.11/test/reheader.samples2 /tmp/urvXTTg_IK/reheader.vcf.gz | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/urvXTTg_IK/reheader.vcf.gz | /build/bcftools-1.11/bcftools reheader -s /build/bcftools-1.11/test/reheader.samples2 | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.11/bcftools reheader -s /build/bcftools-1.11/test/reheader.samples3 /build/bcftools-1.11/test/reheader.vcf | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-1.11/test/reheader.vcf | /build/bcftools-1.11/bcftools reheader -s /build/bcftools-1.11/test/reheader.samples3 | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.11/bcftools reheader -s /build/bcftools-1.11/test/reheader.samples3 /tmp/urvXTTg_IK/reheader.bcf | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/urvXTTg_IK/reheader.bcf | /build/bcftools-1.11/bcftools reheader -s /build/bcftools-1.11/test/reheader.samples3 | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.11/bcftools reheader -s /build/bcftools-1.11/test/reheader.samples3 /tmp/urvXTTg_IK/reheader.vcf.gz | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/urvXTTg_IK/reheader.vcf.gz | /build/bcftools-1.11/bcftools reheader -s /build/bcftools-1.11/test/reheader.samples3 | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.11/bcftools reheader -s /build/bcftools-1.11/test/reheader.samples4 /build/bcftools-1.11/test/reheader.vcf | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-1.11/test/reheader.vcf | /build/bcftools-1.11/bcftools reheader -s /build/bcftools-1.11/test/reheader.samples4 | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.11/bcftools reheader -s /build/bcftools-1.11/test/reheader.samples4 /tmp/urvXTTg_IK/reheader.bcf | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/urvXTTg_IK/reheader.bcf | /build/bcftools-1.11/bcftools reheader -s /build/bcftools-1.11/test/reheader.samples4 | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.11/bcftools reheader -s /build/bcftools-1.11/test/reheader.samples4 /tmp/urvXTTg_IK/reheader.vcf.gz | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/urvXTTg_IK/reheader.vcf.gz | /build/bcftools-1.11/bcftools reheader -s /build/bcftools-1.11/test/reheader.samples4 | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.11/bcftools reheader -h /build/bcftools-1.11/test/reheader.empty.hdr /build/bcftools-1.11/test/empty.vcf | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-1.11/test/empty.vcf | /build/bcftools-1.11/bcftools reheader -h /build/bcftools-1.11/test/reheader.empty.hdr | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.11/bcftools reheader -h /build/bcftools-1.11/test/reheader.empty.hdr /tmp/urvXTTg_IK/empty.bcf | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/urvXTTg_IK/empty.bcf | /build/bcftools-1.11/bcftools reheader -h /build/bcftools-1.11/test/reheader.empty.hdr | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.11/bcftools reheader -h /build/bcftools-1.11/test/reheader.empty.hdr /tmp/urvXTTg_IK/empty.vcf.gz | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/urvXTTg_IK/empty.vcf.gz | /build/bcftools-1.11/bcftools reheader -h /build/bcftools-1.11/test/reheader.empty.hdr | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.11/bcftools reheader -f /build/bcftools-1.11/test/reheader.fai /build/bcftools-1.11/test/reheader.2.vcf | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.11/bcftools reheader -f /build/bcftools-1.11/test/reheader.fai /tmp/urvXTTg_IK/reheader.2.bcf | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.11/bcftools reheader -f /build/bcftools-1.11/test/reheader.fai /tmp/urvXTTg_IK/reheader.2.vcf.gz | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.11/bcftools reheader -h /build/bcftools-1.11/test/reheader.2.hdr -f /build/bcftools-1.11/test/reheader.fai /build/bcftools-1.11/test/reheader.2.vcf | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.11/bcftools reheader -h /build/bcftools-1.11/test/reheader.2.hdr -f /build/bcftools-1.11/test/reheader.fai /tmp/urvXTTg_IK/reheader.2.bcf | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-1.11/bcftools reheader -h /build/bcftools-1.11/test/reheader.2.hdr -f /build/bcftools-1.11/test/reheader.fai /tmp/urvXTTg_IK/reheader.2.vcf.gz | /build/bcftools-1.11/bcftools view --no-version .. ok test_rename_chrs: /build/bcftools-1.11/bcftools annotate --rename-chrs /tmp/urvXTTg_IK/rename.map -Ov /tmp/urvXTTg_IK/annotate.bcf | /build/bcftools-1.11/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /build/bcftools-1.11/bcftools annotate --rename-chrs /tmp/urvXTTg_IK/rename.map -Ob /tmp/urvXTTg_IK/annotate.bcf | /build/bcftools-1.11/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /build/bcftools-1.11/bcftools annotate --rename-chrs /tmp/urvXTTg_IK/rename.map -Ov /build/bcftools-1.11/test/annotate.vcf | /build/bcftools-1.11/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /build/bcftools-1.11/bcftools annotate --rename-chrs /tmp/urvXTTg_IK/rename.map -Ob /build/bcftools-1.11/test/annotate.vcf | /build/bcftools-1.11/bcftools query -f'%CHROM\t%POS\n' .. ok test_vcf_convert: /build/bcftools-1.11/bcftools convert -g -,. /tmp/urvXTTg_IK/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/convert.vcf.gz | /build/bcftools-1.11/bcftools convert -g -,. .. ok test_vcf_convert: /build/bcftools-1.11/bcftools convert -g .,- /tmp/urvXTTg_IK/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/convert.vcf.gz | /build/bcftools-1.11/bcftools convert -g .,- .. ok test_vcf_convert: /build/bcftools-1.11/bcftools convert -g -,. --tag PL /tmp/urvXTTg_IK/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/convert.vcf.gz | /build/bcftools-1.11/bcftools convert -g -,. --tag PL .. ok test_vcf_convert: /build/bcftools-1.11/bcftools convert -g .,- --tag PL /tmp/urvXTTg_IK/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/convert.vcf.gz | /build/bcftools-1.11/bcftools convert -g .,- --tag PL .. ok test_vcf_convert: /build/bcftools-1.11/bcftools convert -g -,. --vcf-ids /tmp/urvXTTg_IK/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/check.vcf.gz | /build/bcftools-1.11/bcftools convert -g -,. --vcf-ids .. ok test_vcf_convert: /build/bcftools-1.11/bcftools convert -g .,- --vcf-ids /tmp/urvXTTg_IK/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/check.vcf.gz | /build/bcftools-1.11/bcftools convert -g .,- --vcf-ids .. ok test_vcf_convert: /build/bcftools-1.11/bcftools convert -g -,. --chrom /tmp/urvXTTg_IK/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/check.vcf.gz | /build/bcftools-1.11/bcftools convert -g -,. --chrom .. ok test_vcf_convert: /build/bcftools-1.11/bcftools convert -g .,- --chrom /tmp/urvXTTg_IK/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/check.vcf.gz | /build/bcftools-1.11/bcftools convert -g .,- --chrom .. ok test_vcf_convert: /build/bcftools-1.11/bcftools convert -g -,. --chrom --vcf-ids /tmp/urvXTTg_IK/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/check.vcf.gz | /build/bcftools-1.11/bcftools convert -g -,. --chrom --vcf-ids .. ok test_vcf_convert: /build/bcftools-1.11/bcftools convert -g .,- --chrom --vcf-ids /tmp/urvXTTg_IK/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/check.vcf.gz | /build/bcftools-1.11/bcftools convert -g .,- --chrom --vcf-ids .. ok test_vcf_convert: /build/bcftools-1.11/bcftools convert -h -,.,. /tmp/urvXTTg_IK/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/convert.vcf.gz | /build/bcftools-1.11/bcftools convert -h -,.,. .. ok test_vcf_convert: /build/bcftools-1.11/bcftools convert -h .,-,. /tmp/urvXTTg_IK/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/convert.vcf.gz | /build/bcftools-1.11/bcftools convert -h .,-,. .. ok test_vcf_convert: /build/bcftools-1.11/bcftools convert -h .,.,- /tmp/urvXTTg_IK/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/convert.vcf.gz | /build/bcftools-1.11/bcftools convert -h .,.,- .. ok test_vcf_convert_hls2vcf: /build/bcftools-1.11/bcftools convert -H /build/bcftools-1.11/test/convert.hls.gt.hap,/build/bcftools-1.11/test/convert.hls.gt.legend,/build/bcftools-1.11/test/convert.hls.gt.samples | grep -v ^## .. ok test_vcf_convert_hls2vcf: /build/bcftools-1.11/bcftools convert -H /build/bcftools-1.11/test/convert.hls.gt.hap,/build/bcftools-1.11/test/convert.hls.gt.legend,/build/bcftools-1.11/test/convert.hls.gt.samples -Ou | /build/bcftools-1.11/bcftools view | grep -v ^## .. ok test_vcf_convert_hls2vcf: /build/bcftools-1.11/bcftools convert --vcf-ids -H /build/bcftools-1.11/test/convert.hls.gt.hap,/build/bcftools-1.11/test/convert.hls.gt.legend,/build/bcftools-1.11/test/convert.hls.gt.samples | grep -v ^## .. ok test_vcf_convert_hls2vcf: /build/bcftools-1.11/bcftools convert --vcf-ids -H /build/bcftools-1.11/test/convert.hls.gt.hap,/build/bcftools-1.11/test/convert.hls.gt.legend,/build/bcftools-1.11/test/convert.hls.gt.samples -Ou | /build/bcftools-1.11/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-1.11/bcftools convert --hapsample2vcf /build/bcftools-1.11/test/convert.hs.gt.hap,/build/bcftools-1.11/test/convert.hs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-1.11/bcftools convert --hapsample2vcf /build/bcftools-1.11/test/convert.hs.gt.hap,/build/bcftools-1.11/test/convert.hs.gt.samples -Ou | /build/bcftools-1.11/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-1.11/bcftools convert --vcf-ids --hapsample2vcf /build/bcftools-1.11/test/convert.hs.gt.hap,/build/bcftools-1.11/test/convert.hs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-1.11/bcftools convert --vcf-ids --hapsample2vcf /build/bcftools-1.11/test/convert.hs.gt.hap,/build/bcftools-1.11/test/convert.hs.gt.samples -Ou | /build/bcftools-1.11/bcftools view | grep -v ^## .. ok test_vcf_convert: /build/bcftools-1.11/bcftools convert --hapsample -,. /tmp/urvXTTg_IK/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/convert.vcf.gz | /build/bcftools-1.11/bcftools convert --hapsample -,. .. ok test_vcf_convert: /build/bcftools-1.11/bcftools convert --hapsample .,- /tmp/urvXTTg_IK/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/convert.vcf.gz | /build/bcftools-1.11/bcftools convert --hapsample .,- .. ok test_vcf_convert: /build/bcftools-1.11/bcftools convert --haplegendsample -,.,. /tmp/urvXTTg_IK/convert.hap-missing.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/convert.hap-missing.vcf.gz | /build/bcftools-1.11/bcftools convert --haplegendsample -,.,. .. ok test_vcf_convert_gvcf: /build/bcftools-1.11/bcftools convert --no-version --gvcf2vcf -i'FILTER="PASS"' -f /build/bcftools-1.11/test/gvcf.fa /tmp/urvXTTg_IK/convert.gvcf.vcf.gz .. ok test_vcf_convert_gvcf: /build/bcftools-1.11/bcftools view -Ob /tmp/urvXTTg_IK/convert.gvcf.vcf.gz | /build/bcftools-1.11/bcftools convert --gvcf2vcf -i'FILTER="PASS"' -f /build/bcftools-1.11/test/gvcf.fa | grep -v ^##bcftools .. ok test_vcf_convert_tsv2vcf: /build/bcftools-1.11/bcftools convert --no-version -c ID,CHROM,POS,AA -s SAMPLE1 -f /build/bcftools-1.11/test/23andme.fa --tsv2vcf /build/bcftools-1.11/test/convert.23andme .. ok test_vcf_convert_tsv2vcf: /build/bcftools-1.11/bcftools convert -Ou -c ID,CHROM,POS,AA -s SAMPLE1 -f /build/bcftools-1.11/test/23andme.fa --tsv2vcf /build/bcftools-1.11/test/convert.23andme | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/urvXTTg_IK/consensus.vcf.gz -f /build/bcftools-1.11/test/consensus.fa -m /build/bcftools-1.11/test/consensus.tab .. ok test_vcf_consensus_chain: /build/bcftools-1.11/bcftools consensus /tmp/urvXTTg_IK/consensus.vcf.gz -f /build/bcftools-1.11/test/consensus.fa -m /build/bcftools-1.11/test/consensus.tab -c /tmp/urvXTTg_IK/consensus.1.chain.new >/dev/null; cat /tmp/urvXTTg_IK/consensus.1.chain.new .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/urvXTTg_IK/consensus.vcf.gz -f /build/bcftools-1.11/test/consensus.fa -H 1 -m /build/bcftools-1.11/test/consensus.tab .. ok test_vcf_consensus_chain: /build/bcftools-1.11/bcftools consensus /tmp/urvXTTg_IK/consensus.vcf.gz -f /build/bcftools-1.11/test/consensus.fa -H 1 -m /build/bcftools-1.11/test/consensus.tab -c /tmp/urvXTTg_IK/consensus.2.chain.new >/dev/null; cat /tmp/urvXTTg_IK/consensus.2.chain.new .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/urvXTTg_IK/consensus.vcf.gz -f /build/bcftools-1.11/test/consensus.fa -I -m /build/bcftools-1.11/test/consensus.tab .. ok test_vcf_consensus_chain: /build/bcftools-1.11/bcftools consensus /tmp/urvXTTg_IK/consensus.vcf.gz -f /build/bcftools-1.11/test/consensus.fa -I -m /build/bcftools-1.11/test/consensus.tab -c /tmp/urvXTTg_IK/consensus.3.chain.new >/dev/null; cat /tmp/urvXTTg_IK/consensus.3.chain.new .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/urvXTTg_IK/consensus.vcf.gz -f /build/bcftools-1.11/test/consensus.fa -H 1 .. ok test_vcf_consensus_chain: /build/bcftools-1.11/bcftools consensus /tmp/urvXTTg_IK/consensus.vcf.gz -f /build/bcftools-1.11/test/consensus.fa -H 1 -c /tmp/urvXTTg_IK/consensus.4.chain.new >/dev/null; cat /tmp/urvXTTg_IK/consensus.4.chain.new .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/urvXTTg_IK/consensus2.vcf.gz -f /build/bcftools-1.11/test/consensus2.fa -H 1 .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/urvXTTg_IK/consensus2.vcf.gz -f /build/bcftools-1.11/test/consensus2.fa -H 2 .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/urvXTTg_IK/empty.vcf.gz -f /build/bcftools-1.11/test/consensus.fa .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/urvXTTg_IK/consensus3.vcf.gz -f /build/bcftools-1.11/test/consensus2.fa -H 2 -M "?" .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/urvXTTg_IK/consensus3.vcf.gz -f /build/bcftools-1.11/test/consensus2.fa -H 2 -M "?" -p xx_ .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/urvXTTg_IK/consensus4.vcf.gz -f /build/bcftools-1.11/test/consensus2.fa .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/urvXTTg_IK/consensus5.vcf.gz -f /build/bcftools-1.11/test/consensus5.fa --haplotype LA .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/urvXTTg_IK/consensus6.vcf.gz -f /build/bcftools-1.11/test/consensus6.fa .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/urvXTTg_IK/consensus7.vcf.gz -f /build/bcftools-1.11/test/consensus7.fa -H 2 .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/urvXTTg_IK/consensus7.vcf.gz -f /build/bcftools-1.11/test/consensus7.fa -H 2pIu .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/urvXTTg_IK/consensus7.vcf.gz -f /build/bcftools-1.11/test/consensus7.fa -H 1 .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/urvXTTg_IK/consensus7.vcf.gz -f /build/bcftools-1.11/test/consensus7.fa -H 1pIu .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/urvXTTg_IK/consensus8.vcf.gz -f /build/bcftools-1.11/test/consensus.fa .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/urvXTTg_IK/consensus8.vcf.gz -f /build/bcftools-1.11/test/consensus.fa -a . .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/urvXTTg_IK/consensus8.vcf.gz -f /build/bcftools-1.11/test/consensus.fa -a . -i 'type="snp" || type="ref"' .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/urvXTTg_IK/consensus8.vcf.gz -f /build/bcftools-1.11/test/consensus.fa -a . -i 'ALT!=""' .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/urvXTTg_IK/consensus8.vcf.gz -f /build/bcftools-1.11/test/consensus.fa -a . -e 'MinDP>15' .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/urvXTTg_IK/consensus8.vcf.gz -f /build/bcftools-1.11/test/consensus.fa -a . -e 'MinDP<15' .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/urvXTTg_IK/consensus.9.vcf.gz -f /build/bcftools-1.11/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/urvXTTg_IK/consensus.9.vcf.gz -f /build/bcftools-1.11/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/urvXTTg_IK/consensus.10.vcf.gz -f /build/bcftools-1.11/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/urvXTTg_IK/consensus.10.vcf.gz -f /build/bcftools-1.11/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/urvXTTg_IK/consensus.11.vcf.gz -f /build/bcftools-1.11/test/consensus.11.fa -s smpl .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/urvXTTg_IK/consensus.11.vcf.gz -f /build/bcftools-1.11/test/consensus.11.fa -s smpl -a N .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/urvXTTg_IK/consensus.12.vcf.gz -f /build/bcftools-1.11/test/consensus.12.fa .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/urvXTTg_IK/consensus.13.vcf.gz -f /build/bcftools-1.11/test/consensus.13.fa .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -r17:100-150 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.1.bam /build/bcftools-1.11/test/mpileup/mpileup.2.bam /build/bcftools-1.11/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -r17:100-150 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.1.bam /build/bcftools-1.11/test/mpileup/mpileup.2.bam /build/bcftools-1.11/test/mpileup/mpileup.3.bam | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -r17:100-150 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -b /tmp/urvXTTg_IK/mpileup.bam.list --no-version | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -r17:100-150 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob -b /tmp/urvXTTg_IK/mpileup.bam.urllist | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -r17:100-150 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.1.cram /build/bcftools-1.11/test/mpileup/mpileup.2.cram /build/bcftools-1.11/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -r17:100-150 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.1.cram /build/bcftools-1.11/test/mpileup/mpileup.2.cram /build/bcftools-1.11/test/mpileup/mpileup.3.cram | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -r17:100-150 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -b /tmp/urvXTTg_IK/mpileup.cram.list --no-version | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -r17:100-150 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob -b /tmp/urvXTTg_IK/mpileup.cram.urllist | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -a DP,DV -r17:100-600 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.1.bam /build/bcftools-1.11/test/mpileup/mpileup.2.bam /build/bcftools-1.11/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -a DP,DV -r17:100-600 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.1.bam /build/bcftools-1.11/test/mpileup/mpileup.2.bam /build/bcftools-1.11/test/mpileup/mpileup.3.bam | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -a DP,DV -r17:100-600 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.1.cram /build/bcftools-1.11/test/mpileup/mpileup.2.cram /build/bcftools-1.11/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -a DP,DV -r17:100-600 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.1.cram /build/bcftools-1.11/test/mpileup/mpileup.2.cram /build/bcftools-1.11/test/mpileup/mpileup.3.cram | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.1.bam | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.1.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.1.cram | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.1.bam /build/bcftools-1.11/test/mpileup/mpileup.2.bam /build/bcftools-1.11/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.1.bam /build/bcftools-1.11/test/mpileup/mpileup.2.bam /build/bcftools-1.11/test/mpileup/mpileup.3.bam | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.1.cram /build/bcftools-1.11/test/mpileup/mpileup.2.cram /build/bcftools-1.11/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.1.cram /build/bcftools-1.11/test/mpileup/mpileup.2.cram /build/bcftools-1.11/test/mpileup/mpileup.3.cram | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.1.bam /build/bcftools-1.11/test/mpileup/mpileup.2.bam /build/bcftools-1.11/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.1.bam /build/bcftools-1.11/test/mpileup/mpileup.2.bam /build/bcftools-1.11/test/mpileup/mpileup.3.bam | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.1.cram /build/bcftools-1.11/test/mpileup/mpileup.2.cram /build/bcftools-1.11/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.1.cram /build/bcftools-1.11/test/mpileup/mpileup.2.cram /build/bcftools-1.11/test/mpileup/mpileup.3.cram | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.1.bam /build/bcftools-1.11/test/mpileup/mpileup.2.bam /build/bcftools-1.11/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.1.bam /build/bcftools-1.11/test/mpileup/mpileup.2.bam /build/bcftools-1.11/test/mpileup/mpileup.3.bam | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.1.cram /build/bcftools-1.11/test/mpileup/mpileup.2.cram /build/bcftools-1.11/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.1.cram /build/bcftools-1.11/test/mpileup/mpileup.2.cram /build/bcftools-1.11/test/mpileup/mpileup.3.cram | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.1.bam /build/bcftools-1.11/test/mpileup/mpileup.2.bam /build/bcftools-1.11/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.1.bam /build/bcftools-1.11/test/mpileup/mpileup.2.bam /build/bcftools-1.11/test/mpileup/mpileup.3.bam | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.1.cram /build/bcftools-1.11/test/mpileup/mpileup.2.cram /build/bcftools-1.11/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.1.cram /build/bcftools-1.11/test/mpileup/mpileup.2.cram /build/bcftools-1.11/test/mpileup/mpileup.3.cram | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.1.bam /build/bcftools-1.11/test/mpileup/mpileup.2.bam /build/bcftools-1.11/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.1.bam /build/bcftools-1.11/test/mpileup/mpileup.2.bam /build/bcftools-1.11/test/mpileup/mpileup.3.bam | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.1.cram /build/bcftools-1.11/test/mpileup/mpileup.2.cram /build/bcftools-1.11/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.1.cram /build/bcftools-1.11/test/mpileup/mpileup.2.cram /build/bcftools-1.11/test/mpileup/mpileup.3.cram | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -r17:100-150 -S /build/bcftools-1.11/test/mplp.samples -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.1.bam /build/bcftools-1.11/test/mpileup/mpileup.2.bam /build/bcftools-1.11/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -r17:100-150 -S /build/bcftools-1.11/test/mplp.samples -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.1.bam /build/bcftools-1.11/test/mpileup/mpileup.2.bam /build/bcftools-1.11/test/mpileup/mpileup.3.bam | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -r17:100-150 -S /build/bcftools-1.11/test/mplp.samples -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.1.cram /build/bcftools-1.11/test/mpileup/mpileup.2.cram /build/bcftools-1.11/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -r17:100-150 -S /build/bcftools-1.11/test/mplp.samples -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.1.cram /build/bcftools-1.11/test/mpileup/mpileup.2.cram /build/bcftools-1.11/test/mpileup/mpileup.3.cram | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.1.bam /build/bcftools-1.11/test/mpileup/mpileup.2.bam /build/bcftools-1.11/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.1.bam /build/bcftools-1.11/test/mpileup/mpileup.2.bam /build/bcftools-1.11/test/mpileup/mpileup.3.bam | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.1.cram /build/bcftools-1.11/test/mpileup/mpileup.2.cram /build/bcftools-1.11/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.1.cram /build/bcftools-1.11/test/mpileup/mpileup.2.cram /build/bcftools-1.11/test/mpileup/mpileup.3.cram | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -r17:100-150 -S ^/build/bcftools-1.11/test/mplp.samples -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.1.bam /build/bcftools-1.11/test/mpileup/mpileup.2.bam /build/bcftools-1.11/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -r17:100-150 -S ^/build/bcftools-1.11/test/mplp.samples -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.1.bam /build/bcftools-1.11/test/mpileup/mpileup.2.bam /build/bcftools-1.11/test/mpileup/mpileup.3.bam | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -r17:100-150 -S ^/build/bcftools-1.11/test/mplp.samples -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.1.cram /build/bcftools-1.11/test/mpileup/mpileup.2.cram /build/bcftools-1.11/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -r17:100-150 -S ^/build/bcftools-1.11/test/mplp.samples -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.1.cram /build/bcftools-1.11/test/mpileup/mpileup.2.cram /build/bcftools-1.11/test/mpileup/mpileup.3.cram | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -t17:100-150 -S /build/bcftools-1.11/test/mplp.9.samples -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.1.bam /build/bcftools-1.11/test/mpileup/mpileup.2.bam /build/bcftools-1.11/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -t17:100-150 -S /build/bcftools-1.11/test/mplp.9.samples -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.1.bam /build/bcftools-1.11/test/mpileup/mpileup.2.bam /build/bcftools-1.11/test/mpileup/mpileup.3.bam | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -t17:100-150 -S /build/bcftools-1.11/test/mplp.9.samples -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.1.cram /build/bcftools-1.11/test/mpileup/mpileup.2.cram /build/bcftools-1.11/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -t17:100-150 -S /build/bcftools-1.11/test/mplp.9.samples -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.1.cram /build/bcftools-1.11/test/mpileup/mpileup.2.cram /build/bcftools-1.11/test/mpileup/mpileup.3.cram | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -t17:100-150 -G /build/bcftools-1.11/test/mplp.10.samples -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.1.bam /build/bcftools-1.11/test/mpileup/mpileup.2.bam /build/bcftools-1.11/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -t17:100-150 -G /build/bcftools-1.11/test/mplp.10.samples -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.1.bam /build/bcftools-1.11/test/mpileup/mpileup.2.bam /build/bcftools-1.11/test/mpileup/mpileup.3.bam | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -t17:100-150 -G /build/bcftools-1.11/test/mplp.10.samples -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.1.cram /build/bcftools-1.11/test/mpileup/mpileup.2.cram /build/bcftools-1.11/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -t17:100-150 -G /build/bcftools-1.11/test/mplp.10.samples -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.1.cram /build/bcftools-1.11/test/mpileup/mpileup.2.cram /build/bcftools-1.11/test/mpileup/mpileup.3.cram | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.3.bam | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.3.cram | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -s HG00102 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.3.bam /build/bcftools-1.11/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -s HG00102 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.3.bam /build/bcftools-1.11/test/mpileup/mpileup.4.bam | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -s HG00102 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.3.cram /build/bcftools-1.11/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -s HG00102 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.3.cram /build/bcftools-1.11/test/mpileup/mpileup.4.cram | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -s ^HG99999 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.3.bam /build/bcftools-1.11/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -s ^HG99999 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.3.bam /build/bcftools-1.11/test/mpileup/mpileup.4.bam | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -s ^HG99999 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.3.cram /build/bcftools-1.11/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -s ^HG99999 -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.3.cram /build/bcftools-1.11/test/mpileup/mpileup.4.cram | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -G /build/bcftools-1.11/test/mplp.11.rgs -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.3.bam /build/bcftools-1.11/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -G /build/bcftools-1.11/test/mplp.11.rgs -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.3.bam /build/bcftools-1.11/test/mpileup/mpileup.4.bam | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -G /build/bcftools-1.11/test/mplp.11.rgs -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.3.cram /build/bcftools-1.11/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -G /build/bcftools-1.11/test/mplp.11.rgs -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.3.cram /build/bcftools-1.11/test/mpileup/mpileup.4.cram | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -G /build/bcftools-1.11/test/mplp.11.rgs -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.3.bam /build/bcftools-1.11/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -G /build/bcftools-1.11/test/mplp.11.rgs -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.3.bam /build/bcftools-1.11/test/mpileup/mpileup.4.bam | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -G /build/bcftools-1.11/test/mplp.11.rgs -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa /build/bcftools-1.11/test/mpileup/mpileup.3.cram /build/bcftools-1.11/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -G /build/bcftools-1.11/test/mplp.11.rgs -f /build/bcftools-1.11/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup.3.cram /build/bcftools-1.11/test/mpileup/mpileup.4.cram | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -a AD -f /build/bcftools-1.11/test/mpileup/indel-AD.1.fa /build/bcftools-1.11/test/mpileup/indel-AD.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -a AD -f /build/bcftools-1.11/test/mpileup/indel-AD.1.fa -Ob /build/bcftools-1.11/test/mpileup/indel-AD.1.bam | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -a AD -f /build/bcftools-1.11/test/mpileup/indel-AD.1.fa /build/bcftools-1.11/test/mpileup/indel-AD.1.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -a AD -f /build/bcftools-1.11/test/mpileup/indel-AD.1.fa -Ob /build/bcftools-1.11/test/mpileup/indel-AD.1.cram | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -a INFO/SCR,FMT/SCR -f /build/bcftools-1.11/test/mpileup/mpileup-SCR.fa /build/bcftools-1.11/test/mpileup/mpileup-SCR.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -a INFO/SCR,FMT/SCR -f /build/bcftools-1.11/test/mpileup/mpileup-SCR.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup-SCR.bam | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -a INFO/SCR,FMT/SCR -f /build/bcftools-1.11/test/mpileup/mpileup-SCR.fa /build/bcftools-1.11/test/mpileup/mpileup-SCR.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-1.11/bcftools mpileup -a INFO/SCR,FMT/SCR -f /build/bcftools-1.11/test/mpileup/mpileup-SCR.fa -Ob /build/bcftools-1.11/test/mpileup/mpileup-SCR.cram | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_csq: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq.fa -g /build/bcftools-1.11/test/csq.gff3 /build/bcftools-1.11/test/csq.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000624631/ENST00000624631.fa -g /build/bcftools-1.11/test/csq/ENST00000624631/ENST00000624631.gff /build/bcftools-1.11/test/csq/ENST00000624631/ambiguous.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000593942/ENST00000593942.fa -g /build/bcftools-1.11/test/csq/ENST00000593942/ENST00000593942.gff /build/bcftools-1.11/test/csq/ENST00000593942/last-codon-deletion.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000573314/ENST00000573314.fa -g /build/bcftools-1.11/test/csq/ENST00000573314/ENST00000573314.gff /build/bcftools-1.11/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -l -f /build/bcftools-1.11/test/csq/ENST00000573314/ENST00000573314.fa -g /build/bcftools-1.11/test/csq/ENST00000573314/ENST00000573314.gff /build/bcftools-1.11/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000557788/ENST00000557788.fa -g /build/bcftools-1.11/test/csq/ENST00000557788/ENST00000557788.gff /build/bcftools-1.11/test/csq/ENST00000557788/long-overlap-del.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000545279/ENST00000545279.fa -g /build/bcftools-1.11/test/csq/ENST00000545279/ENST00000545279.gff /build/bcftools-1.11/test/csq/ENST00000545279/splice-region-insert.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000543077/ENST00000543077.fa -g /build/bcftools-1.11/test/csq/ENST00000543077/ENST00000543077.gff /build/bcftools-1.11/test/csq/ENST00000543077/not-a-start-lost.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -l -f /build/bcftools-1.11/test/csq/ENST00000543077/ENST00000543077.fa -g /build/bcftools-1.11/test/csq/ENST00000543077/ENST00000543077.gff /build/bcftools-1.11/test/csq/ENST00000543077/not-a-start-lost.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000542803/ENST00000542803.fa -g /build/bcftools-1.11/test/csq/ENST00000542803/ENST00000542803.gff /build/bcftools-1.11/test/csq/ENST00000542803/splice-region.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -l -f /build/bcftools-1.11/test/csq/ENST00000542803/ENST00000542803.fa -g /build/bcftools-1.11/test/csq/ENST00000542803/ENST00000542803.gff /build/bcftools-1.11/test/csq/ENST00000542803/splice-region.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000536784/ENST00000536784.fa -g /build/bcftools-1.11/test/csq/ENST00000536784/ENST00000536784.gff /build/bcftools-1.11/test/csq/ENST00000536784/not-a-start-lost.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -l -f /build/bcftools-1.11/test/csq/ENST00000536784/ENST00000536784.fa -g /build/bcftools-1.11/test/csq/ENST00000536784/ENST00000536784.gff /build/bcftools-1.11/test/csq/ENST00000536784/not-a-start-lost.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000528237/ENST00000528237.fa -g /build/bcftools-1.11/test/csq/ENST00000528237/ENST00000528237.gff /build/bcftools-1.11/test/csq/ENST00000528237/retained-stop-incomplete-cds.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000520868/ENST00000520868.fa -g /build/bcftools-1.11/test/csq/ENST00000520868/ENST00000520868.gff /build/bcftools-1.11/test/csq/ENST00000520868/long-deletion.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000520795/ENST00000520795.fa -g /build/bcftools-1.11/test/csq/ENST00000520795/ENST00000520795.gff /build/bcftools-1.11/test/csq/ENST00000520795/long-inside-del.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -l -f /build/bcftools-1.11/test/csq/ENST00000520795/ENST00000520795.fa -g /build/bcftools-1.11/test/csq/ENST00000520795/ENST00000520795.gff /build/bcftools-1.11/test/csq/ENST00000520795/long-inside-del.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000519442/ENST00000519442.fa -g /build/bcftools-1.11/test/csq/ENST00000519442/ENST00000519442.gff /build/bcftools-1.11/test/csq/ENST00000519442/synon-splice-region-del.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000518414/ENST00000518414.fa -g /build/bcftools-1.11/test/csq/ENST00000518414/ENST00000518414.gff /build/bcftools-1.11/test/csq/ENST00000518414/incorrect-inframe-del.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.fa -g /build/bcftools-1.11/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.gff /build/bcftools-1.11/test/csq/ENST00000518414-ENST00000521270/valgrind.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000479739/ENST00000479739.fa -g /build/bcftools-1.11/test/csq/ENST00000479739/ENST00000479739.gff /build/bcftools-1.11/test/csq/ENST00000479739/short-cds-start-lost.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -l -f /build/bcftools-1.11/test/csq/ENST00000479739/ENST00000479739.fa -g /build/bcftools-1.11/test/csq/ENST00000479739/ENST00000479739.gff /build/bcftools-1.11/test/csq/ENST00000479739/short-cds-start-lost.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000448695/ENST00000448695.fa -g /build/bcftools-1.11/test/csq/ENST00000448695/ENST00000448695.gff /build/bcftools-1.11/test/csq/ENST00000448695/syn-and-splice-reg.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000436063/ENST00000436063.fa -g /build/bcftools-1.11/test/csq/ENST00000436063/ENST00000436063.gff /build/bcftools-1.11/test/csq/ENST00000436063/insert-before-utr.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000423372/ENST00000423372.fa -g /build/bcftools-1.11/test/csq/ENST00000423372/ENST00000423372.gff /build/bcftools-1.11/test/csq/ENST00000423372/snps.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -l -f /build/bcftools-1.11/test/csq/ENST00000423372/ENST00000423372.fa -g /build/bcftools-1.11/test/csq/ENST00000423372/ENST00000423372.gff /build/bcftools-1.11/test/csq/ENST00000423372/snps.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000423372/ENST00000423372.fa -g /build/bcftools-1.11/test/csq/ENST00000423372/ENST00000423372.gff /build/bcftools-1.11/test/csq/ENST00000423372/insert3.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -l -f /build/bcftools-1.11/test/csq/ENST00000423372/ENST00000423372.fa -g /build/bcftools-1.11/test/csq/ENST00000423372/ENST00000423372.gff /build/bcftools-1.11/test/csq/ENST00000423372/insert3.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000420670/ENST00000420670.fa -g /build/bcftools-1.11/test/csq/ENST00000420670/ENST00000420670.gff /build/bcftools-1.11/test/csq/ENST00000420670/start-stop-lost.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000420670/ENST00000420670.fa -g /build/bcftools-1.11/test/csq/ENST00000420670/ENST00000420670.gff /build/bcftools-1.11/test/csq/ENST00000420670/segfault.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000420190/ENST00000420190.fa -g /build/bcftools-1.11/test/csq/ENST00000420190/ENST00000420190.gff /build/bcftools-1.11/test/csq/ENST00000420190/abort-in-csq-push.vcf | /build/bcftools-1.11/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000413103/ENST00000413103.fa -g /build/bcftools-1.11/test/csq/ENST00000413103/ENST00000413103.gff /build/bcftools-1.11/test/csq/ENST00000413103/long-deletion.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000410009/ENST00000410009.fa -g /build/bcftools-1.11/test/csq/ENST00000410009/ENST00000410009.gff /build/bcftools-1.11/test/csq/ENST00000410009/frameshift.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /build/bcftools-1.11/test/csq/ENST00000410009 && /build/bcftools-1.11/bcftools csq -lb -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/bcftools-1.11/test/csq/ENST00000410009 && /build/bcftools-1.11/bcftools csq -b -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000409523/ENST00000409523.fa -g /build/bcftools-1.11/test/csq/ENST00000409523/ENST00000409523.gff /build/bcftools-1.11/test/csq/ENST00000409523/long-overlapping-del.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000400151/ENST00000400151.fa -g /build/bcftools-1.11/test/csq/ENST00000400151/ENST00000400151.gff /build/bcftools-1.11/test/csq/ENST00000400151/long-del.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000390520/ENST00000390520.fa -g /build/bcftools-1.11/test/csq/ENST00000390520/ENST00000390520.gff /build/bcftools-1.11/test/csq/ENST00000390520/deletion-overlap.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000382647/ENST00000382647.fa -g /build/bcftools-1.11/test/csq/ENST00000382647/ENST00000382647.gff /build/bcftools-1.11/test/csq/ENST00000382647/synon-splice-region-insert.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000381157/ENST00000381157.fa -g /build/bcftools-1.11/test/csq/ENST00000381157/ENST00000381157.gff /build/bcftools-1.11/test/csq/ENST00000381157/haploid-diploid.vcf | /build/bcftools-1.11/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000378322/ENST00000378322.fa -g /build/bcftools-1.11/test/csq/ENST00000378322/ENST00000378322.gff /build/bcftools-1.11/test/csq/ENST00000378322/end-overlap-tscript.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -l -f /build/bcftools-1.11/test/csq/ENST00000378322/ENST00000378322.fa -g /build/bcftools-1.11/test/csq/ENST00000378322/ENST00000378322.gff /build/bcftools-1.11/test/csq/ENST00000378322/end-overlap-tscript.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000375992/ENST00000375992.fa -g /build/bcftools-1.11/test/csq/ENST00000375992/ENST00000375992.gff /build/bcftools-1.11/test/csq/ENST00000375992/incorrect-synon-del-not-start-lost.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000373833/ENST00000373833.fa -g /build/bcftools-1.11/test/csq/ENST00000373833/ENST00000373833.gff /build/bcftools-1.11/test/csq/ENST00000373833/boundary-insertion.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -l -f /build/bcftools-1.11/test/csq/ENST00000373833/ENST00000373833.fa -g /build/bcftools-1.11/test/csq/ENST00000373833/ENST00000373833.gff /build/bcftools-1.11/test/csq/ENST00000373833/boundary-insertion.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000368801/ENST00000368801.fa -g /build/bcftools-1.11/test/csq/ENST00000368801/ENST00000368801.gff /build/bcftools-1.11/test/csq/ENST00000368801/compound-lost.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000368801.2/ENST00000368801.2.fa -g /build/bcftools-1.11/test/csq/ENST00000368801.2/ENST00000368801.2.gff /build/bcftools-1.11/test/csq/ENST00000368801.2/start-lost.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000357367/ENST00000357367.fa -g /build/bcftools-1.11/test/csq/ENST00000357367/ENST00000357367.gff /build/bcftools-1.11/test/csq/ENST00000357367/stop-retained.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.11/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -l -f /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.11/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.11/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -l -f /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.11/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.11/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -l -f /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.11/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.11/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -l -f /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.11/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.11/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -l -f /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.11/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.11/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -l -f /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.11/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.11/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -l -f /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.11/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.11/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -l -f /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.11/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.11/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -l -f /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.11/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.11/test/csq/ENST00000341065/not-a-start-lost.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -l -f /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.11/test/csq/ENST00000341065/not-a-start-lost.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.11/test/csq/ENST00000341065/frame3.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -l -f /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.11/test/csq/ENST00000341065/frame3.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.11/test/csq/ENST00000341065/frame2.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -l -f /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.11/test/csq/ENST00000341065/frame2.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.11/test/csq/ENST00000341065/frame1.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -l -f /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-1.11/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-1.11/test/csq/ENST00000341065/frame1.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000329454/ENST00000329454.fa -g /build/bcftools-1.11/test/csq/ENST00000329454/ENST00000329454.gff /build/bcftools-1.11/test/csq/ENST00000329454/boundary-deletion.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -l -f /build/bcftools-1.11/test/csq/ENST00000329454/ENST00000329454.fa -g /build/bcftools-1.11/test/csq/ENST00000329454/ENST00000329454.gff /build/bcftools-1.11/test/csq/ENST00000329454/boundary-deletion.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000318249/ENST00000318249.fa -g /build/bcftools-1.11/test/csq/ENST00000318249/ENST00000318249.gff /build/bcftools-1.11/test/csq/ENST00000318249/start-lost.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -l -f /build/bcftools-1.11/test/csq/ENST00000318249/ENST00000318249.fa -g /build/bcftools-1.11/test/csq/ENST00000318249/ENST00000318249.gff /build/bcftools-1.11/test/csq/ENST00000318249/start-lost.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000318249.2/ENST00000318249.2.fa -g /build/bcftools-1.11/test/csq/ENST00000318249.2/ENST00000318249.2.gff /build/bcftools-1.11/test/csq/ENST00000318249.2/synonymous-start-lost.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000303039/ENST00000303039.fa -g /build/bcftools-1.11/test/csq/ENST00000303039/ENST00000303039.gff /build/bcftools-1.11/test/csq/ENST00000303039/not-a-stop.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -l -f /build/bcftools-1.11/test/csq/ENST00000303039/ENST00000303039.fa -g /build/bcftools-1.11/test/csq/ENST00000303039/ENST00000303039.gff /build/bcftools-1.11/test/csq/ENST00000303039/not-a-stop.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000301246/ENST00000301246.fa -g /build/bcftools-1.11/test/csq/ENST00000301246/ENST00000301246.gff /build/bcftools-1.11/test/csq/ENST00000301246/15bp-insert.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000295641/ENST00000295641.fa -g /build/bcftools-1.11/test/csq/ENST00000295641/ENST00000295641.gff /build/bcftools-1.11/test/csq/ENST00000295641/not-a-start-lost.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -l -f /build/bcftools-1.11/test/csq/ENST00000295641/ENST00000295641.fa -g /build/bcftools-1.11/test/csq/ENST00000295641/ENST00000295641.gff /build/bcftools-1.11/test/csq/ENST00000295641/not-a-start-lost.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000294661/ENST00000294661.fa -g /build/bcftools-1.11/test/csq/ENST00000294661/ENST00000294661.gff /build/bcftools-1.11/test/csq/ENST00000294661/non-coding-boundary.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -l -f /build/bcftools-1.11/test/csq/ENST00000294661/ENST00000294661.fa -g /build/bcftools-1.11/test/csq/ENST00000294661/ENST00000294661.gff /build/bcftools-1.11/test/csq/ENST00000294661/non-coding-boundary.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000271583/ENST00000271583.fa -g /build/bcftools-1.11/test/csq/ENST00000271583/ENST00000271583.gff /build/bcftools-1.11/test/csq/ENST00000271583/splice-acceptor.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000263103-INS/ENST00000263103-INS.fa -g /build/bcftools-1.11/test/csq/ENST00000263103-INS/ENST00000263103-INS.gff /build/bcftools-1.11/test/csq/ENST00000263103-INS/insertions.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000256452/ENST00000256452.fa -g /build/bcftools-1.11/test/csq/ENST00000256452/ENST00000256452.gff /build/bcftools-1.11/test/csq/ENST00000256452/intron.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000230048/ENST00000230048.fa -g /build/bcftools-1.11/test/csq/ENST00000230048/ENST00000230048.gff /build/bcftools-1.11/test/csq/ENST00000230048/start-del.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000227471/ENST00000227471.fa -g /build/bcftools-1.11/test/csq/ENST00000227471/ENST00000227471.gff /build/bcftools-1.11/test/csq/ENST00000227471/insert-splice-vs-frameshift.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000218032/ENST00000218032.fa -g /build/bcftools-1.11/test/csq/ENST00000218032/ENST00000218032.gff /build/bcftools-1.11/test/csq/ENST00000218032/start-lost.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -l -f /build/bcftools-1.11/test/csq/ENST00000218032/ENST00000218032.fa -g /build/bcftools-1.11/test/csq/ENST00000218032/ENST00000218032.gff /build/bcftools-1.11/test/csq/ENST00000218032/start-lost.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENST00000218032/ENST00000218032.fa -g /build/bcftools-1.11/test/csq/ENST00000218032/ENST00000218032.gff /build/bcftools-1.11/test/csq/ENST00000218032/start-lost-del.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /build/bcftools-1.11/test/csq/ENSMUST00000133836 && /build/bcftools-1.11/bcftools csq -f ENSMUST00000133836.fa -g ENSMUST00000133836.gff filter-problem.vcf -i 'FILTER="PASS"' --phase m | ../sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/bcftools-1.11/test/csq/ENSMUST00000121418 && /build/bcftools-1.11/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25500' --phase m | ../sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/bcftools-1.11/test/csq/ENSMUST00000121418 && /build/bcftools-1.11/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25496' --phase m | ../sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/bcftools-1.11/test/csq/ENSMUST00000121418 && /build/bcftools-1.11/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25105' --phase m | ../sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/ENSG00000173376/ENSG00000173376.fa -g /build/bcftools-1.11/test/csq/ENSG00000173376/ENSG00000173376.gff /build/bcftools-1.11/test/csq/ENSG00000173376/synon.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /build/bcftools-1.11/test/csq/EMN908947 && /build/bcftools-1.11/bcftools csq -f EMN908947.fa -g simple.gff simple.vcf | ../sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /build/bcftools-1.11/test/csq/EMN908947 && /build/bcftools-1.11/bcftools csq -f EMN908947.fa -g ribosomal-slippage.gff ribosomal-slippage.vcf --force | ../sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/EDUMMY0003/EDUMMY0003.fa -g /build/bcftools-1.11/test/csq/EDUMMY0003/EDUMMY0003.gff /build/bcftools-1.11/test/csq/EDUMMY0003/long-del.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/EDUMMY0002/EDUMMY0002.fa -g /build/bcftools-1.11/test/csq/EDUMMY0002/EDUMMY0002.gff /build/bcftools-1.11/test/csq/EDUMMY0002/boundaries.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -f /build/bcftools-1.11/test/csq/EDUMMY0001/EDUMMY0001.fa -g /build/bcftools-1.11/test/csq/EDUMMY0001/EDUMMY0001.gff /build/bcftools-1.11/test/csq/EDUMMY0001/starts-with-1.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-1.11/bcftools csq -l -f /build/bcftools-1.11/test/csq/EDUMMY0001/EDUMMY0001.fa -g /build/bcftools-1.11/test/csq/EDUMMY0001/EDUMMY0001.gff /build/bcftools-1.11/test/csq/EDUMMY0001/starts-with-1.vcf | /build/bcftools-1.11/test/csq/sort-csq | /build/bcftools-1.11/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_roh: /build/bcftools-1.11/bcftools roh /build/bcftools-1.11/test/roh.1.vcf.gz -Or -G30 --AF-dflt 0.4| grep -v ^# .. ok test_roh: /build/bcftools-1.11/bcftools roh /build/bcftools-1.11/test/roh.1.vcf.gz -Or -G30 --AF-file /build/bcftools-1.11/test/roh.1.tab.gz| grep -v ^# .. ok test_roh: /build/bcftools-1.11/bcftools roh /build/bcftools-1.11/test/roh.1.vcf.gz -Or -G30 --AF-file /build/bcftools-1.11/test/roh.1.tab.gz --ignore-homref| grep -v ^# .. ok test_roh: /build/bcftools-1.11/bcftools roh /build/bcftools-1.11/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245| grep -v ^# .. ok test_roh: /build/bcftools-1.11/bcftools roh /build/bcftools-1.11/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --ignore-homref| grep -v ^# .. ok test_roh: /build/bcftools-1.11/bcftools roh /build/bcftools-1.11/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --ignore-homref --include-noalt| grep -v ^# .. ok test_roh: /build/bcftools-1.11/bcftools roh /build/bcftools-1.11/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --include-noalt| grep -v ^# .. ok test_gtcheck: /build/bcftools-1.11/bcftools gtcheck -e 0 /tmp/urvXTTg_IK/gtcheck.1.vcf.gz -g /tmp/urvXTTg_IK/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.11/bcftools gtcheck -e 0 -u GT,GT /tmp/urvXTTg_IK/gtcheck.1.vcf.gz -g /tmp/urvXTTg_IK/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.11/bcftools gtcheck -e 0 -u GT,PL /tmp/urvXTTg_IK/gtcheck.1.vcf.gz -g /tmp/urvXTTg_IK/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.11/bcftools gtcheck -e 0 -u PL,GT /tmp/urvXTTg_IK/gtcheck.1.vcf.gz -g /tmp/urvXTTg_IK/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.11/bcftools gtcheck -e 0 -u PL,PL /tmp/urvXTTg_IK/gtcheck.1.vcf.gz -g /tmp/urvXTTg_IK/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.11/bcftools gtcheck -e 0 -p s1,s1 /tmp/urvXTTg_IK/gtcheck.1.vcf.gz -g /tmp/urvXTTg_IK/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.11/bcftools gtcheck -e 0 /tmp/urvXTTg_IK/gtcheck.2.vcf.gz -g /tmp/urvXTTg_IK/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.11/bcftools gtcheck -e 0 /tmp/urvXTTg_IK/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.11/bcftools gtcheck -e 0 -p B,A,C,A,C,B,D,A,D,B,D,C,E,A,E,B,E,C,E,D /tmp/urvXTTg_IK/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.11/bcftools gtcheck -e 0 -P /build/bcftools-1.11/test/gtcheck.3.pairs /tmp/urvXTTg_IK/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.11/bcftools gtcheck -e 0 -u PL /tmp/urvXTTg_IK/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.11/bcftools gtcheck -e 0 --n-matches 4 /tmp/urvXTTg_IK/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO | sort .. ok test_gtcheck: /build/bcftools-1.11/bcftools gtcheck -e 0 -s qry:E,D,C /tmp/urvXTTg_IK/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.11/bcftools gtcheck -e 0 -s qry:E,D,C -u PL /tmp/urvXTTg_IK/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.11/bcftools gtcheck -e 0 -s qry:B -s gt:D /tmp/urvXTTg_IK/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.11/bcftools gtcheck -e 0 -s qry:B -s gt:D -u PL /tmp/urvXTTg_IK/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.11/bcftools gtcheck -e 0 -s qry:B -s gt:D,C /tmp/urvXTTg_IK/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.11/bcftools gtcheck -e 0 -p B,C,B,D /tmp/urvXTTg_IK/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.11/bcftools gtcheck -e 0 -u GT,GT -H /tmp/urvXTTg_IK/gtcheck.1.vcf.gz -g /tmp/urvXTTg_IK/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.11/bcftools gtcheck -e 0 -u GT,PL -H /tmp/urvXTTg_IK/gtcheck.1.vcf.gz -g /tmp/urvXTTg_IK/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.11/bcftools gtcheck -e 0 -u PL,GT -H /tmp/urvXTTg_IK/gtcheck.1.vcf.gz -g /tmp/urvXTTg_IK/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.11/bcftools gtcheck -e 0 -u PL,PL -H /tmp/urvXTTg_IK/gtcheck.1.vcf.gz -g /tmp/urvXTTg_IK/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.11/bcftools gtcheck -e 0 -P /build/bcftools-1.11/test/gtcheck.4.pairs --distinctive-sites 3 /tmp/urvXTTg_IK/gtcheck.4.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.11/bcftools gtcheck -e 0 -P /build/bcftools-1.11/test/gtcheck.4.pairs --distinctive-sites 3,1 /tmp/urvXTTg_IK/gtcheck.4.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.11/bcftools gtcheck -u GT -e 30 /tmp/urvXTTg_IK/gtcheck.1.vcf.gz -g /tmp/urvXTTg_IK/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.11/bcftools gtcheck -u GT -e 30 -p s1,s1 /tmp/urvXTTg_IK/gtcheck.1.vcf.gz -g /tmp/urvXTTg_IK/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.11/bcftools gtcheck -u GT -e 300 /tmp/urvXTTg_IK/gtcheck.1.vcf.gz -g /tmp/urvXTTg_IK/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.11/bcftools gtcheck -u PL -e 30 /tmp/urvXTTg_IK/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok Number of tests: total .. 1210 passed .. 1210 failed .. 0 make[2]: Leaving directory '/build/bcftools-1.11' make[1]: Leaving directory '/build/bcftools-1.11' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install make -j8 install DESTDIR=/build/bcftools-1.11/debian/bcftools AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/bcftools-1.11' mkdir -p -m 755 /build/bcftools-1.11/debian/bcftools/usr/bin /build/bcftools-1.11/debian/bcftools/usr/share/man/man1 /build/bcftools-1.11/debian/bcftools/usr/lib/aarch64-linux-gnu/bcftools install -p bcftools /build/bcftools-1.11/debian/bcftools/usr/bin install -p misc/color-chrs.pl misc/gff2gff.py misc/guess-ploidy.py misc/plot-vcfstats misc/plot-roh.py misc/run-roh.pl misc/vcfutils.pl /build/bcftools-1.11/debian/bcftools/usr/bin install -p -m 644 doc/bcftools.1 /build/bcftools-1.11/debian/bcftools/usr/share/man/man1 install -p plugins/*.so /build/bcftools-1.11/debian/bcftools/usr/lib/aarch64-linux-gnu/bcftools make[1]: Leaving directory '/build/bcftools-1.11' debian/rules override_dh_install make[1]: Entering directory '/build/bcftools-1.11' dh_install # Fix Perl interpreter PATH for pscript in `grep -Rl '#!/usr/bin/env \+perl' debian/*` ; do \ sed -i '1s?#!/usr/bin/env \+perl?#!/usr/bin/perl?' ${pscript} ; \ done make[1]: Leaving directory '/build/bcftools-1.11' dh_installdocs dh_installchangelogs debian/rules override_dh_installman make[1]: Entering directory '/build/bcftools-1.11' dh_installman --language=C make[1]: Leaving directory '/build/bcftools-1.11' dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dpkg-gencontrol: warning: package bcftools: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package bcftools: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'bcftools-dbgsym' in '../bcftools-dbgsym_1.11-1_arm64.deb'. dpkg-deb: building package 'bcftools' in '../bcftools_1.11-1_arm64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../bcftools_1.11-1_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: 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/28602 and its subdirectories I: Current time: Mon Aug 29 18:17:02 -12 2022 I: pbuilder-time-stamp: 1661840222 Tue Jul 27 23:54:05 UTC 2021 I: 1st build successful. Starting 2nd build on remote node codethink12-arm64.debian.net. Tue Jul 27 23:54:05 UTC 2021 I: Preparing to do remote build '2' on codethink12-arm64.debian.net. Tue Jul 27 23:57:24 UTC 2021 I: Deleting $TMPDIR on codethink12-arm64.debian.net. Tue Jul 27 23:57:25 UTC 2021 I: bcftools_1.11-1_arm64.changes: Format: 1.8 Date: Thu, 01 Oct 2020 15:43:46 +0200 Source: bcftools Binary: bcftools bcftools-dbgsym Architecture: arm64 Version: 1.11-1 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 (1.11-1) unstable; urgency=medium . * Team upload. * New upstream version * Versioned Build-Depends: libhts-dev (>= 1.11) Checksums-Sha1: de1cb250a0f5612d573eb90ec1b32fa4635a8791 1678428 bcftools-dbgsym_1.11-1_arm64.deb e133da0c0334bb953fa663cb722f6ad13c7449ff 5653 bcftools_1.11-1_arm64.buildinfo db498aff36c014edd5637aca0eef24193927f3a4 563164 bcftools_1.11-1_arm64.deb Checksums-Sha256: 185b9292f68f9f426267cd31b6ddd6b74748c6e8b901c7593fecbb8bc73e69ed 1678428 bcftools-dbgsym_1.11-1_arm64.deb 2c0bb0d2a0081467e7bae4cc27b22888ff1e19e5de51a2c3e490ac28d53f021a 5653 bcftools_1.11-1_arm64.buildinfo 57d17852aa8358981b293eadeb65594cec718fbf11665580b2e2382ac9bdca55 563164 bcftools_1.11-1_arm64.deb Files: 1b1ad714688280288a54156857d62825 1678428 debug optional bcftools-dbgsym_1.11-1_arm64.deb f98e35019bf4e0c47feeb10b158ee388 5653 science optional bcftools_1.11-1_arm64.buildinfo 3568d55cf6424184ea655373168cd741 563164 science optional bcftools_1.11-1_arm64.deb Tue Jul 27 23:57:30 UTC 2021 I: diffoscope 177 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.wrmUl1lcEW/bcftools_1.11-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.wrmUl1lcEW/bcftools_1.11-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.wrmUl1lcEW/bcftools_1.11-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.wrmUl1lcEW/b1/bcftools_1.11-1_arm64.changes /srv/reproducible-results/rbuild-debian/tmp.wrmUl1lcEW/b2/bcftools_1.11-1_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: 0.529s) 0.529s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.058s) 0.057s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Tue Jul 27 23:57:33 UTC 2021 I: diffoscope 177 found no differences in the changes files, and a .buildinfo file also exists. Tue Jul 27 23:57:33 UTC 2021 I: bcftools from bullseye built successfully and reproducibly on arm64. Tue Jul 27 23:57:35 UTC 2021 I: Submitting .buildinfo files to external archives: Tue Jul 27 23:57:35 UTC 2021 I: Submitting 8.0K b1/bcftools_1.11-1_arm64.buildinfo.asc Tue Jul 27 23:57:36 UTC 2021 I: Submitting 8.0K b2/bcftools_1.11-1_arm64.buildinfo.asc Tue Jul 27 23:57:38 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Jul 27 23:57:38 UTC 2021 I: Done submitting .buildinfo files. Tue Jul 27 23:57:38 UTC 2021 I: Removing signed bcftools_1.11-1_arm64.buildinfo.asc files: removed './b1/bcftools_1.11-1_arm64.buildinfo.asc' removed './b2/bcftools_1.11-1_arm64.buildinfo.asc'