Sat Oct 30 23:11:41 UTC 2021 I: starting to build bcftools/bullseye/amd64 on jenkins on '2021-10-30 23:11' Sat Oct 30 23:11:41 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_30/40398/console.log Sat Oct 30 23:11:41 UTC 2021 I: Downloading source for bullseye/bcftools=1.11-1 --2021-10-30 23:11:42-- 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% 157M=0s 2021-10-30 23:11:42 (157 MB/s) - ‘bcftools_1.11-1.dsc’ saved [2109/2109] Sat Oct 30 23:11:42 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----- Sat Oct 30 23:11:42 UTC 2021 I: Checking whether the package is not for us Sat Oct 30 23:11:42 UTC 2021 I: Starting 1st build on remote node ionos5-amd64.debian.net. Sat Oct 30 23:11:42 UTC 2021 I: Preparing to do remote build '1' on ionos5-amd64.debian.net. Sat Oct 30 23:12:57 UTC 2021 I: Deleting $TMPDIR on ionos5-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri Dec 2 17:34:47 -12 2022 I: pbuilder-time-stamp: 1670045687 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.g5SrFDBL/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/1806311/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=16' DISTRIBUTION='' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='90ee784e434349169fba875ed8822aea' 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='1806311' 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.wOChQMYvSj/pbuilderrc_v4LH --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.wOChQMYvSj/b1 --logfile b1/build.log bcftools_1.11-1.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://85.184.249.68:3128' I: uname -a Linux ionos5-amd64 5.14.0-0.bpo.2-amd64 #1 SMP Debian 5.14.9-2~bpo11+1 (2021-10-10) x86_64 GNU/Linux I: ls -l /bin total 5476 -rwxr-xr-x 1 root root 1234376 Aug 4 2021 bash -rwxr-xr-x 3 root root 38984 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 38984 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 38984 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 18424 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 43936 Sep 23 2020 cat -rwxr-xr-x 1 root root 72672 Sep 23 2020 chgrp -rwxr-xr-x 1 root root 64448 Sep 23 2020 chmod -rwxr-xr-x 1 root root 72672 Sep 23 2020 chown -rwxr-xr-x 1 root root 151168 Sep 23 2020 cp -rwxr-xr-x 1 root root 125560 Dec 10 2020 dash -rwxr-xr-x 1 root root 113664 Sep 23 2020 date -rwxr-xr-x 1 root root 80968 Sep 23 2020 dd -rwxr-xr-x 1 root root 93936 Sep 23 2020 df -rwxr-xr-x 1 root root 147176 Sep 23 2020 dir -rwxr-xr-x 1 root root 84440 Jul 28 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 39712 Sep 23 2020 echo -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep -rwxr-xr-x 1 root root 39680 Sep 23 2020 false -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep -rwxr-xr-x 1 root root 69032 Jul 28 2021 findmnt -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount -rwxr-xr-x 1 root root 203072 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 98048 Mar 2 2021 gzip -rwxr-xr-x 1 root root 22600 Nov 6 2019 hostname -rwxr-xr-x 1 root root 72840 Sep 23 2020 ln -rwxr-xr-x 1 root root 56952 Feb 7 2020 login -rwxr-xr-x 1 root root 147176 Sep 23 2020 ls -rwxr-xr-x 1 root root 149736 Jul 28 2021 lsblk -rwxr-xr-x 1 root root 85184 Sep 23 2020 mkdir -rwxr-xr-x 1 root root 76896 Sep 23 2020 mknod -rwxr-xr-x 1 root root 48064 Sep 23 2020 mktemp -rwxr-xr-x 1 root root 59632 Jul 28 2021 more -rwsr-xr-x 1 root root 55528 Jul 28 2021 mount -rwxr-xr-x 1 root root 18664 Jul 28 2021 mountpoint -rwxr-xr-x 1 root root 147080 Sep 23 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 43872 Sep 23 2020 pwd lrwxrwxrwx 1 root root 4 Aug 4 2021 rbash -> bash -rwxr-xr-x 1 root root 52032 Sep 23 2020 readlink -rwxr-xr-x 1 root root 72704 Sep 23 2020 rm -rwxr-xr-x 1 root root 52032 Sep 23 2020 rmdir -rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Nov 23 06:04 sh -> dash -rwxr-xr-x 1 root root 43808 Sep 23 2020 sleep -rwxr-xr-x 1 root root 84928 Sep 23 2020 stty -rwsr-xr-x 1 root root 71912 Jul 28 2021 su -rwxr-xr-x 1 root root 39744 Sep 23 2020 sync -rwxr-xr-x 1 root root 531928 Feb 16 2021 tar -rwxr-xr-x 1 root root 14456 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 101408 Sep 23 2020 touch -rwxr-xr-x 1 root root 39680 Sep 23 2020 true -rwxr-xr-x 1 root root 14328 Feb 26 2021 ulockmgr_server -rwsr-xr-x 1 root root 35040 Jul 28 2021 umount -rwxr-xr-x 1 root root 39744 Sep 23 2020 uname -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress -rwxr-xr-x 1 root root 147176 Sep 23 2020 vdir -rwxr-xr-x 1 root root 63744 Jul 28 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/1806311/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), zlib1g-dev, libbz2-dev, liblzma-dev, libhts-dev (>= 1.11), 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 ... 19655 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 27.4 MB of archives. After unpacking 92.3 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main amd64 bsdextrautils amd64 2.36.1-8 [145 kB] Get: 2 http://deb.debian.org/debian bullseye/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 3 http://deb.debian.org/debian bullseye/main amd64 groff-base amd64 1.22.4-6 [936 kB] Get: 4 http://deb.debian.org/debian bullseye/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB] Get: 5 http://deb.debian.org/debian bullseye/main amd64 man-db amd64 2.9.4-2 [1354 kB] Get: 6 http://deb.debian.org/debian bullseye/main amd64 sensible-utils all 0.0.14 [14.8 kB] Get: 7 http://deb.debian.org/debian bullseye/main amd64 libmagic-mgc amd64 1:5.39-3 [273 kB] Get: 8 http://deb.debian.org/debian bullseye/main amd64 libmagic1 amd64 1:5.39-3 [126 kB] Get: 9 http://deb.debian.org/debian bullseye/main amd64 file amd64 1:5.39-3 [69.1 kB] Get: 10 http://deb.debian.org/debian bullseye/main amd64 gettext-base amd64 0.21-4 [175 kB] Get: 11 http://deb.debian.org/debian bullseye/main amd64 libsigsegv2 amd64 2.13-1 [34.8 kB] Get: 12 http://deb.debian.org/debian bullseye/main amd64 m4 amd64 1.4.18-5 [204 kB] Get: 13 http://deb.debian.org/debian bullseye/main amd64 autoconf all 2.69-14 [313 kB] Get: 14 http://deb.debian.org/debian bullseye/main amd64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 15 http://deb.debian.org/debian bullseye/main amd64 automake all 1:1.16.3-2 [814 kB] Get: 16 http://deb.debian.org/debian bullseye/main amd64 autopoint all 0.21-4 [510 kB] Get: 17 http://deb.debian.org/debian bullseye/main amd64 libdebhelper-perl all 13.3.4 [189 kB] Get: 18 http://deb.debian.org/debian bullseye/main amd64 libtool all 2.4.6-15 [513 kB] Get: 19 http://deb.debian.org/debian bullseye/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian bullseye/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian bullseye/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 22 http://deb.debian.org/debian bullseye/main amd64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 23 http://deb.debian.org/debian bullseye/main amd64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 24 http://deb.debian.org/debian bullseye/main amd64 libelf1 amd64 0.183-1 [165 kB] Get: 25 http://deb.debian.org/debian bullseye/main amd64 dwz amd64 0.13+20210201-1 [175 kB] Get: 26 http://deb.debian.org/debian bullseye/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get: 27 http://deb.debian.org/debian bullseye/main amd64 libxml2 amd64 2.9.10+dfsg-6.7 [693 kB] Get: 28 http://deb.debian.org/debian bullseye/main amd64 gettext amd64 0.21-4 [1311 kB] Get: 29 http://deb.debian.org/debian bullseye/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 30 http://deb.debian.org/debian bullseye/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian bullseye/main amd64 debhelper all 13.3.4 [1049 kB] Get: 32 http://deb.debian.org/debian bullseye/main amd64 libbrotli1 amd64 1.0.9-2+b2 [279 kB] Get: 33 http://deb.debian.org/debian bullseye/main amd64 libbz2-dev amd64 1.0.8-4 [30.1 kB] Get: 34 http://deb.debian.org/debian bullseye/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-2.1 [69.1 kB] Get: 35 http://deb.debian.org/debian bullseye/main amd64 libsasl2-2 amd64 2.1.27+dfsg-2.1 [106 kB] Get: 36 http://deb.debian.org/debian bullseye/main amd64 libldap-2.4-2 amd64 2.4.57+dfsg-3 [232 kB] Get: 37 http://deb.debian.org/debian bullseye/main amd64 libnghttp2-14 amd64 1.43.0-1 [77.1 kB] Get: 38 http://deb.debian.org/debian bullseye/main amd64 libpsl5 amd64 0.21.0-1.2 [57.3 kB] Get: 39 http://deb.debian.org/debian bullseye/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get: 40 http://deb.debian.org/debian bullseye/main amd64 libssh2-1 amd64 1.9.0-2 [156 kB] Get: 41 http://deb.debian.org/debian bullseye/main amd64 libcurl3-gnutls amd64 7.74.0-1.3+b1 [338 kB] Get: 42 http://deb.debian.org/debian bullseye/main amd64 libcurl4-gnutls-dev amd64 7.74.0-1.3+b1 [429 kB] Get: 43 http://deb.debian.org/debian bullseye/main amd64 libdeflate0 amd64 1.7-1 [53.1 kB] Get: 44 http://deb.debian.org/debian bullseye/main amd64 libdeflate-dev amd64 1.7-1 [46.9 kB] Get: 45 http://deb.debian.org/debian bullseye/main amd64 libgslcblas0 amd64 2.6+dfsg-2 [102 kB] Get: 46 http://deb.debian.org/debian bullseye/main amd64 libgsl25 amd64 2.6+dfsg-2 [934 kB] Get: 47 http://deb.debian.org/debian bullseye/main amd64 libgsl-dev amd64 2.6+dfsg-2 [1123 kB] Get: 48 http://deb.debian.org/debian bullseye/main amd64 libhts3 amd64 1.11-4 [378 kB] Get: 49 http://deb.debian.org/debian bullseye/main amd64 liblzma-dev amd64 5.2.5-2 [229 kB] Get: 50 http://deb.debian.org/debian bullseye/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2 [190 kB] Get: 51 http://deb.debian.org/debian bullseye/main amd64 libhts-dev amd64 1.11-4 [3858 kB] Get: 52 http://deb.debian.org/debian bullseye/main amd64 libio-pty-perl amd64 1:1.15-2 [37.0 kB] Get: 53 http://deb.debian.org/debian bullseye/main amd64 tabix amd64 1.11-4 [339 kB] Fetched 27.4 MB in 0s (55.9 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 ... 19655 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-8_amd64.deb ... Unpacking bsdextrautils (2.36.1-8) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../01-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-6_amd64.deb ... 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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 amd64 debian/rules clean rm -f config.mk && touch config.mk dh clean dh_auto_clean make -j16 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/x86_64-linux-gnu/bcftools ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system --enable-gsl --with-cblas=gslcblas --with-bcf-plugin-dir=/usr/lib/x86_64-linux-gnu/bcftools checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether 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 -j16 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/x86_64-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/4fAc0nrnfk/merge.a.vcf.gz 2:3199812-3199812 .. ok test_tabix: /build/bcftools-1.11/bcftools view -H /tmp/4fAc0nrnfk/merge.a.bcf 2:3199812-3199812 .. ok test_tabix: tabix /tmp/4fAc0nrnfk/merge.a.vcf.gz 1:3000151-3000151 .. ok test_tabix: /build/bcftools-1.11/bcftools view -H /tmp/4fAc0nrnfk/merge.a.bcf 1:3000151-3000151 .. ok test_index: /build/bcftools-1.11/bcftools view -H /tmp/4fAc0nrnfk/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /build/bcftools-1.11/bcftools view -H /tmp/4fAc0nrnfk/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/bcftools-1.11/bcftools view -H /tmp/4fAc0nrnfk/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/bcftools-1.11/bcftools view -H /tmp/4fAc0nrnfk/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /build/bcftools-1.11/bcftools view -H /tmp/4fAc0nrnfk/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/bcftools-1.11/bcftools view -H /tmp/4fAc0nrnfk/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /build/bcftools-1.11/bcftools view -H /tmp/4fAc0nrnfk/large_chrom_csi_limit.bcf chr20 .. ok test_index: /build/bcftools-1.11/bcftools view -H /tmp/4fAc0nrnfk/large_chrom_csi_limit.bcf chr20 .. ok test_index: /build/bcftools-1.11/bcftools view -H /tmp/4fAc0nrnfk/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /build/bcftools-1.11/bcftools view -H /tmp/4fAc0nrnfk/large_chrom_csi_limit.bcf chr20 .. ok test_vcf_idxstats: /build/bcftools-1.11/bcftools index -s /tmp/4fAc0nrnfk/idx.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.11/bcftools index -s /tmp/4fAc0nrnfk/idx.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.11/bcftools index -s /tmp/4fAc0nrnfk/idx.bcf .. ok test_vcf_idxstats: /build/bcftools-1.11/bcftools index -n /tmp/4fAc0nrnfk/idx.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.11/bcftools index -n /tmp/4fAc0nrnfk/idx.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.11/bcftools index -n /tmp/4fAc0nrnfk/idx.bcf .. ok test_vcf_idxstats: /build/bcftools-1.11/bcftools index -s /tmp/4fAc0nrnfk/empty.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.11/bcftools index -s /tmp/4fAc0nrnfk/empty.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.11/bcftools index -s /tmp/4fAc0nrnfk/empty.bcf .. ok test_vcf_idxstats: /build/bcftools-1.11/bcftools index -n /tmp/4fAc0nrnfk/empty.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.11/bcftools index -n /tmp/4fAc0nrnfk/empty.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-1.11/bcftools index -n /tmp/4fAc0nrnfk/empty.bcf .. ok test_vcf_check: /build/bcftools-1.11/bcftools stats -s - /tmp/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/check.1.chk /tmp/4fAc0nrnfk/check.2.chk /tmp/4fAc0nrnfk/check.3.chk /tmp/4fAc0nrnfk/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/4fAc0nrnfk/stats.a.vcf.gz /tmp/4fAc0nrnfk/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/bcftools-1.11/bcftools stats -s B /tmp/4fAc0nrnfk/stats.a.vcf.gz /tmp/4fAc0nrnfk/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/bcftools-1.11/bcftools stats -s - /tmp/4fAc0nrnfk/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_isec: /build/bcftools-1.11/bcftools isec -n =2 /tmp/4fAc0nrnfk/isec.a.vcf.gz /tmp/4fAc0nrnfk/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.11/bcftools isec -Ob -n =2 /tmp/4fAc0nrnfk/isec.a.vcf.gz /tmp/4fAc0nrnfk/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.11/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/4fAc0nrnfk/isec.a.vcf.gz /tmp/4fAc0nrnfk/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.11/bcftools isec -Ob -n =2 -i"STRLEN(REF)==2" /tmp/4fAc0nrnfk/isec.a.vcf.gz /tmp/4fAc0nrnfk/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.11/bcftools isec -n =2 -c both /tmp/4fAc0nrnfk/isec.a.vcf.gz /tmp/4fAc0nrnfk/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.11/bcftools isec -Ob -n =2 -c both /tmp/4fAc0nrnfk/isec.a.vcf.gz /tmp/4fAc0nrnfk/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.11/bcftools isec -n =2 -c any /tmp/4fAc0nrnfk/isec.a.vcf.gz /tmp/4fAc0nrnfk/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.11/bcftools isec -Ob -n =2 -c any /tmp/4fAc0nrnfk/isec.a.vcf.gz /tmp/4fAc0nrnfk/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.11/bcftools isec -C -c any /tmp/4fAc0nrnfk/isec.a.vcf.gz /tmp/4fAc0nrnfk/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-1.11/bcftools isec -Ob -C -c any /tmp/4fAc0nrnfk/isec.a.vcf.gz /tmp/4fAc0nrnfk/isec.b.vcf.gz .. ok test_vcf_isec2: /build/bcftools-1.11/bcftools isec --no-version -T /tmp/4fAc0nrnfk/isec.tab.gz /tmp/4fAc0nrnfk/isec.a.vcf.gz .. ok test_vcf_isec2: /build/bcftools-1.11/bcftools isec -Ob -T /tmp/4fAc0nrnfk/isec.tab.gz /tmp/4fAc0nrnfk/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/4fAc0nrnfk/isec-miss.1.1.vcf.gz /tmp/4fAc0nrnfk/isec-miss.1.2.vcf.gz /tmp/4fAc0nrnfk/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/4fAc0nrnfk/isec-miss.1.1.vcf.gz /tmp/4fAc0nrnfk/isec-miss.1.2.vcf.gz /tmp/4fAc0nrnfk/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/4fAc0nrnfk/isec-miss.1.1.vcf.gz /tmp/4fAc0nrnfk/isec-miss.1.2.vcf.gz /tmp/4fAc0nrnfk/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/4fAc0nrnfk/isec-miss.1.1.vcf.gz /tmp/4fAc0nrnfk/isec-miss.1.2.vcf.gz /tmp/4fAc0nrnfk/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/4fAc0nrnfk/isec-miss.2.1.vcf.gz /tmp/4fAc0nrnfk/isec-miss.2.2.vcf.gz /tmp/4fAc0nrnfk/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/4fAc0nrnfk/isec-miss.2.1.vcf.gz /tmp/4fAc0nrnfk/isec-miss.2.2.vcf.gz /tmp/4fAc0nrnfk/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/4fAc0nrnfk/isec-miss.2.1.vcf.gz /tmp/4fAc0nrnfk/isec-miss.2.2.vcf.gz /tmp/4fAc0nrnfk/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/4fAc0nrnfk/isec-miss.2.1.vcf.gz /tmp/4fAc0nrnfk/isec-miss.2.2.vcf.gz /tmp/4fAc0nrnfk/isec-miss.2.3.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge --no-version -i AF:join /tmp/4fAc0nrnfk/merge.join.a.vcf.gz /tmp/4fAc0nrnfk/merge.join.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob -i AF:join /tmp/4fAc0nrnfk/merge.join.a.vcf.gz /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.join.a.bcf /tmp/4fAc0nrnfk/merge.join.b.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob -i AF:join /tmp/4fAc0nrnfk/merge.join.a.bcf /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.LPL.a.vcf.gz /tmp/4fAc0nrnfk/merge.LPL.b.vcf.gz /tmp/4fAc0nrnfk/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples /tmp/4fAc0nrnfk/merge.LPL.a.vcf.gz /tmp/4fAc0nrnfk/merge.LPL.b.vcf.gz /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.LPL.a.bcf /tmp/4fAc0nrnfk/merge.LPL.b.bcf /tmp/4fAc0nrnfk/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples /tmp/4fAc0nrnfk/merge.LPL.a.bcf /tmp/4fAc0nrnfk/merge.LPL.b.bcf /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.LPL.a.vcf.gz /tmp/4fAc0nrnfk/merge.LPL.b.vcf.gz /tmp/4fAc0nrnfk/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -L 1 /tmp/4fAc0nrnfk/merge.LPL.a.vcf.gz /tmp/4fAc0nrnfk/merge.LPL.b.vcf.gz /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.LPL.a.bcf /tmp/4fAc0nrnfk/merge.LPL.b.bcf /tmp/4fAc0nrnfk/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -L 1 /tmp/4fAc0nrnfk/merge.LPL.a.bcf /tmp/4fAc0nrnfk/merge.LPL.b.bcf /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.LPL.a.vcf.gz /tmp/4fAc0nrnfk/merge.LPL.b.vcf.gz /tmp/4fAc0nrnfk/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -L 2 /tmp/4fAc0nrnfk/merge.LPL.a.vcf.gz /tmp/4fAc0nrnfk/merge.LPL.b.vcf.gz /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.LPL.a.bcf /tmp/4fAc0nrnfk/merge.LPL.b.bcf /tmp/4fAc0nrnfk/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -L 2 /tmp/4fAc0nrnfk/merge.LPL.a.bcf /tmp/4fAc0nrnfk/merge.LPL.b.bcf /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.LPL.a.vcf.gz /tmp/4fAc0nrnfk/merge.LPL.b.vcf.gz /tmp/4fAc0nrnfk/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -L 3 /tmp/4fAc0nrnfk/merge.LPL.a.vcf.gz /tmp/4fAc0nrnfk/merge.LPL.b.vcf.gz /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.LPL.a.bcf /tmp/4fAc0nrnfk/merge.LPL.b.bcf /tmp/4fAc0nrnfk/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -L 3 /tmp/4fAc0nrnfk/merge.LPL.a.bcf /tmp/4fAc0nrnfk/merge.LPL.b.bcf /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.LPL.a.vcf.gz /tmp/4fAc0nrnfk/merge.LPL.b.vcf.gz /tmp/4fAc0nrnfk/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -L 4 /tmp/4fAc0nrnfk/merge.LPL.a.vcf.gz /tmp/4fAc0nrnfk/merge.LPL.b.vcf.gz /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.LPL.a.bcf /tmp/4fAc0nrnfk/merge.LPL.b.bcf /tmp/4fAc0nrnfk/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -L 4 /tmp/4fAc0nrnfk/merge.LPL.a.bcf /tmp/4fAc0nrnfk/merge.LPL.b.bcf /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.LPL.a.vcf.gz /tmp/4fAc0nrnfk/merge.LPL.b.vcf.gz /tmp/4fAc0nrnfk/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -L 5 /tmp/4fAc0nrnfk/merge.LPL.a.vcf.gz /tmp/4fAc0nrnfk/merge.LPL.b.vcf.gz /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.LPL.a.bcf /tmp/4fAc0nrnfk/merge.LPL.b.bcf /tmp/4fAc0nrnfk/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -L 5 /tmp/4fAc0nrnfk/merge.LPL.a.bcf /tmp/4fAc0nrnfk/merge.LPL.b.bcf /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.a.vcf.gz /tmp/4fAc0nrnfk/merge.b.vcf.gz /tmp/4fAc0nrnfk/merge.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples /tmp/4fAc0nrnfk/merge.a.vcf.gz /tmp/4fAc0nrnfk/merge.b.vcf.gz /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.a.bcf /tmp/4fAc0nrnfk/merge.b.bcf /tmp/4fAc0nrnfk/merge.c.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples /tmp/4fAc0nrnfk/merge.a.bcf /tmp/4fAc0nrnfk/merge.b.bcf /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.a.vcf.gz /tmp/4fAc0nrnfk/merge.b.vcf.gz /tmp/4fAc0nrnfk/merge.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -Fx /tmp/4fAc0nrnfk/merge.a.vcf.gz /tmp/4fAc0nrnfk/merge.b.vcf.gz /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.a.bcf /tmp/4fAc0nrnfk/merge.b.bcf /tmp/4fAc0nrnfk/merge.c.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -Fx /tmp/4fAc0nrnfk/merge.a.bcf /tmp/4fAc0nrnfk/merge.b.bcf /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.a.vcf.gz /tmp/4fAc0nrnfk/merge.b.vcf.gz /tmp/4fAc0nrnfk/merge.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -0 /tmp/4fAc0nrnfk/merge.a.vcf.gz /tmp/4fAc0nrnfk/merge.b.vcf.gz /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.a.bcf /tmp/4fAc0nrnfk/merge.b.bcf /tmp/4fAc0nrnfk/merge.c.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -0 /tmp/4fAc0nrnfk/merge.a.bcf /tmp/4fAc0nrnfk/merge.b.bcf /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.2.a.vcf.gz /tmp/4fAc0nrnfk/merge.2.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -m none /tmp/4fAc0nrnfk/merge.2.a.vcf.gz /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.2.a.bcf /tmp/4fAc0nrnfk/merge.2.b.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -m none /tmp/4fAc0nrnfk/merge.2.a.bcf /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.2.a.vcf.gz /tmp/4fAc0nrnfk/merge.2.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -m both /tmp/4fAc0nrnfk/merge.2.a.vcf.gz /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.2.a.bcf /tmp/4fAc0nrnfk/merge.2.b.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -m both /tmp/4fAc0nrnfk/merge.2.a.bcf /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.2.a.vcf.gz /tmp/4fAc0nrnfk/merge.2.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -m all /tmp/4fAc0nrnfk/merge.2.a.vcf.gz /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.2.a.bcf /tmp/4fAc0nrnfk/merge.2.b.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -m all /tmp/4fAc0nrnfk/merge.2.a.bcf /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.3.a.vcf.gz /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.3.a.vcf.gz /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.3.a.bcf /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.3.a.bcf /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.4.a.vcf.gz /tmp/4fAc0nrnfk/merge.4.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -m id /tmp/4fAc0nrnfk/merge.4.a.vcf.gz /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.4.a.bcf /tmp/4fAc0nrnfk/merge.4.b.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples -m id /tmp/4fAc0nrnfk/merge.4.a.bcf /tmp/4fAc0nrnfk/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/4fAc0nrnfk/gvcf.merge.1.vcf.gz /tmp/4fAc0nrnfk/gvcf.merge.2.vcf.gz /tmp/4fAc0nrnfk/gvcf.merge.3.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --gvcf - /tmp/4fAc0nrnfk/gvcf.merge.1.vcf.gz /tmp/4fAc0nrnfk/gvcf.merge.2.vcf.gz /tmp/4fAc0nrnfk/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/4fAc0nrnfk/gvcf.merge.1.bcf /tmp/4fAc0nrnfk/gvcf.merge.2.bcf /tmp/4fAc0nrnfk/gvcf.merge.3.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --gvcf - /tmp/4fAc0nrnfk/gvcf.merge.1.bcf /tmp/4fAc0nrnfk/gvcf.merge.2.bcf /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.gvcf.2.a.vcf.gz /tmp/4fAc0nrnfk/merge.gvcf.2.b.vcf.gz /tmp/4fAc0nrnfk/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --gvcf - /tmp/4fAc0nrnfk/merge.gvcf.2.a.vcf.gz /tmp/4fAc0nrnfk/merge.gvcf.2.b.vcf.gz /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.gvcf.3.a.vcf.gz /tmp/4fAc0nrnfk/merge.gvcf.3.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --gvcf - -i SRC:join /tmp/4fAc0nrnfk/merge.gvcf.3.a.vcf.gz /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.gvcf.4.a.vcf.gz /tmp/4fAc0nrnfk/merge.gvcf.4.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --gvcf - /tmp/4fAc0nrnfk/merge.gvcf.4.a.vcf.gz /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.gvcf.4.a.bcf /tmp/4fAc0nrnfk/merge.gvcf.4.b.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --gvcf - /tmp/4fAc0nrnfk/merge.gvcf.4.a.bcf /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.5.a.vcf.gz /tmp/4fAc0nrnfk/merge.5.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob /tmp/4fAc0nrnfk/merge.5.a.vcf.gz /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.5.a.bcf /tmp/4fAc0nrnfk/merge.5.b.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob /tmp/4fAc0nrnfk/merge.5.a.bcf /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.6.a.vcf.gz /tmp/4fAc0nrnfk/merge.6.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob /tmp/4fAc0nrnfk/merge.6.a.vcf.gz /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.6.a.bcf /tmp/4fAc0nrnfk/merge.6.b.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob /tmp/4fAc0nrnfk/merge.6.a.bcf /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.gvcf.7.a.vcf.gz /tmp/4fAc0nrnfk/merge.gvcf.7.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --gvcf - /tmp/4fAc0nrnfk/merge.gvcf.7.a.vcf.gz /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.gvcf.7.a.bcf /tmp/4fAc0nrnfk/merge.gvcf.7.b.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --gvcf - /tmp/4fAc0nrnfk/merge.gvcf.7.a.bcf /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.gvcf.8.a.vcf.gz /tmp/4fAc0nrnfk/merge.gvcf.8.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --gvcf - /tmp/4fAc0nrnfk/merge.gvcf.8.a.vcf.gz /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.gvcf.8.a.bcf /tmp/4fAc0nrnfk/merge.gvcf.8.b.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --gvcf - /tmp/4fAc0nrnfk/merge.gvcf.8.a.bcf /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.7.a.vcf.gz /tmp/4fAc0nrnfk/merge.7.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples /tmp/4fAc0nrnfk/merge.7.a.vcf.gz /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.7.a.bcf /tmp/4fAc0nrnfk/merge.7.b.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --force-samples /tmp/4fAc0nrnfk/merge.7.a.bcf /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.gvcf.9a.vcf.gz /tmp/4fAc0nrnfk/merge.gvcf.9b.vcf.gz /tmp/4fAc0nrnfk/merge.gvcf.9c.vcf.gz /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.gvcf.9a.vcf.gz /tmp/4fAc0nrnfk/merge.gvcf.9b.vcf.gz /tmp/4fAc0nrnfk/merge.gvcf.9c.vcf.gz /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.gvcf.9a.bcf /tmp/4fAc0nrnfk/merge.gvcf.9b.bcf /tmp/4fAc0nrnfk/merge.gvcf.9c.bcf /tmp/4fAc0nrnfk/merge.gvcf.9d.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --gvcf /build/bcftools-1.11/test/gvcf.fa /tmp/4fAc0nrnfk/merge.gvcf.9a.bcf /tmp/4fAc0nrnfk/merge.gvcf.9b.bcf /tmp/4fAc0nrnfk/merge.gvcf.9c.bcf /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.gvcf.9a.vcf.gz /tmp/4fAc0nrnfk/merge.gvcf.9b.vcf.gz /tmp/4fAc0nrnfk/merge.gvcf.9c.vcf.gz /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.gvcf.9a.vcf.gz /tmp/4fAc0nrnfk/merge.gvcf.9b.vcf.gz /tmp/4fAc0nrnfk/merge.gvcf.9c.vcf.gz /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.gvcf.9a.bcf /tmp/4fAc0nrnfk/merge.gvcf.9b.bcf /tmp/4fAc0nrnfk/merge.gvcf.9c.bcf /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.gvcf.9a.bcf /tmp/4fAc0nrnfk/merge.gvcf.9b.bcf /tmp/4fAc0nrnfk/merge.gvcf.9c.bcf /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.gvcf.9a.vcf.gz /tmp/4fAc0nrnfk/merge.gvcf.9b.vcf.gz /tmp/4fAc0nrnfk/merge.gvcf.9c.vcf.gz /tmp/4fAc0nrnfk/merge.gvcf.9d.vcf.gz /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.gvcf.9a.vcf.gz /tmp/4fAc0nrnfk/merge.gvcf.9b.vcf.gz /tmp/4fAc0nrnfk/merge.gvcf.9c.vcf.gz /tmp/4fAc0nrnfk/merge.gvcf.9d.vcf.gz /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.gvcf.9a.bcf /tmp/4fAc0nrnfk/merge.gvcf.9b.bcf /tmp/4fAc0nrnfk/merge.gvcf.9c.bcf /tmp/4fAc0nrnfk/merge.gvcf.9d.bcf /tmp/4fAc0nrnfk/merge.gvcf.9e.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --gvcf /build/bcftools-1.11/test/gvcf.fa /tmp/4fAc0nrnfk/merge.gvcf.9a.bcf /tmp/4fAc0nrnfk/merge.gvcf.9b.bcf /tmp/4fAc0nrnfk/merge.gvcf.9c.bcf /tmp/4fAc0nrnfk/merge.gvcf.9d.bcf /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.gvcf.9a.vcf.gz /tmp/4fAc0nrnfk/merge.gvcf.9b.vcf.gz /tmp/4fAc0nrnfk/merge.gvcf.9c.vcf.gz /tmp/4fAc0nrnfk/merge.gvcf.9d.vcf.gz /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.gvcf.9a.vcf.gz /tmp/4fAc0nrnfk/merge.gvcf.9b.vcf.gz /tmp/4fAc0nrnfk/merge.gvcf.9c.vcf.gz /tmp/4fAc0nrnfk/merge.gvcf.9d.vcf.gz /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.gvcf.9a.bcf /tmp/4fAc0nrnfk/merge.gvcf.9b.bcf /tmp/4fAc0nrnfk/merge.gvcf.9c.bcf /tmp/4fAc0nrnfk/merge.gvcf.9d.bcf /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.gvcf.9a.bcf /tmp/4fAc0nrnfk/merge.gvcf.9b.bcf /tmp/4fAc0nrnfk/merge.gvcf.9c.bcf /tmp/4fAc0nrnfk/merge.gvcf.9d.bcf /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.gvcf.10.a.vcf.gz /tmp/4fAc0nrnfk/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob /tmp/4fAc0nrnfk/merge.gvcf.10.a.vcf.gz /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.gvcf.10.a.bcf /tmp/4fAc0nrnfk/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob /tmp/4fAc0nrnfk/merge.gvcf.10.a.bcf /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.gvcf.10.a.vcf.gz /tmp/4fAc0nrnfk/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob -m none /tmp/4fAc0nrnfk/merge.gvcf.10.a.vcf.gz /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.gvcf.10.a.bcf /tmp/4fAc0nrnfk/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob -m none /tmp/4fAc0nrnfk/merge.gvcf.10.a.bcf /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.gvcf.10.a.vcf.gz /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.gvcf.10.a.vcf.gz /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.gvcf.10.a.bcf /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.gvcf.10.a.bcf /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.gvcf.10.a.vcf.gz /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.gvcf.10.a.vcf.gz /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.gvcf.10.a.bcf /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.gvcf.10.a.bcf /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.gvcf.10.b.vcf.gz /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.gvcf.10.b.vcf.gz /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.gvcf.10.b.bcf /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.gvcf.10.b.bcf /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.gvcf.10.b.vcf.gz /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.gvcf.10.b.vcf.gz /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.gvcf.10.b.bcf /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.gvcf.10.b.bcf /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.noidx.a.vcf.gz /tmp/4fAc0nrnfk/merge.noidx.b.vcf.gz /tmp/4fAc0nrnfk/merge.noidx.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob /tmp/4fAc0nrnfk/merge.noidx.a.vcf.gz /tmp/4fAc0nrnfk/merge.noidx.b.vcf.gz /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.noidx.a.bcf /tmp/4fAc0nrnfk/merge.noidx.b.bcf /tmp/4fAc0nrnfk/merge.noidx.c.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob /tmp/4fAc0nrnfk/merge.noidx.a.bcf /tmp/4fAc0nrnfk/merge.noidx.b.bcf /tmp/4fAc0nrnfk/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/4fAc0nrnfk/merge.noidx.a.bcf /tmp/4fAc0nrnfk/merge.noidx.b.bcf /tmp/4fAc0nrnfk/merge.noidx.c.bcf .. ok test_vcf_merge: /build/bcftools-1.11/bcftools merge -Ob --no-index /tmp/4fAc0nrnfk/merge.noidx.a.bcf /tmp/4fAc0nrnfk/merge.noidx.b.bcf /tmp/4fAc0nrnfk/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/4fAc0nrnfk/query.string.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/query.string.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/query.string.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/query.variantkey.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/view.vectors.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/query.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/query.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/query.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/query.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/query.2.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/filter-missing-floats.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/filter-missing-floats.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/query.filter.2.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/query.filter.3.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/query.filter.3.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/query.filter.3.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/query.filter.4.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/view.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/query.filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/query.filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/query.filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/query.negative.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/query.negative.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/query.negative.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/query.negative.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/query.filter.6.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/query.filter.8.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/query.filter.8.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/query.filter.9.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/query.filter.9.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/query.filter.10.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/query.filter.10.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/query.vcf.gz .. ok test_vcf_query: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/norm.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -cx -f /build/bcftools-1.11/test/norm.fa /tmp/4fAc0nrnfk/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/4fAc0nrnfk/norm.split.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -m- /tmp/4fAc0nrnfk/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/4fAc0nrnfk/norm.split.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -m- /tmp/4fAc0nrnfk/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/4fAc0nrnfk/norm.split.3.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -m- --force /tmp/4fAc0nrnfk/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/4fAc0nrnfk/norm.split.4.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -m- /tmp/4fAc0nrnfk/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/4fAc0nrnfk/norm.split.4.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -m- --keep-sum AD /tmp/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/norm.merge.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -m+ /tmp/4fAc0nrnfk/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/4fAc0nrnfk/norm.merge.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -m+ /tmp/4fAc0nrnfk/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/4fAc0nrnfk/norm.merge.3.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -m+ /tmp/4fAc0nrnfk/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/4fAc0nrnfk/norm.merge.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -m+ -s /tmp/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/norm.telomere.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -f /build/bcftools-1.11/test/norm.fa /tmp/4fAc0nrnfk/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/4fAc0nrnfk/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -d snps /tmp/4fAc0nrnfk/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/4fAc0nrnfk/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -d indels /tmp/4fAc0nrnfk/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/4fAc0nrnfk/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -d both /tmp/4fAc0nrnfk/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/4fAc0nrnfk/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -d all /tmp/4fAc0nrnfk/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/4fAc0nrnfk/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -d none /tmp/4fAc0nrnfk/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/4fAc0nrnfk/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -d exact /tmp/4fAc0nrnfk/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/4fAc0nrnfk/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -d none /tmp/4fAc0nrnfk/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/4fAc0nrnfk/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -d exact /tmp/4fAc0nrnfk/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/4fAc0nrnfk/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -d indels /tmp/4fAc0nrnfk/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/4fAc0nrnfk/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -d any /tmp/4fAc0nrnfk/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/4fAc0nrnfk/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -d both /tmp/4fAc0nrnfk/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/4fAc0nrnfk/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-1.11/bcftools norm -Ob -d snps /tmp/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/4fAc0nrnfk/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/4fAc0nrnfk/view.vcf.gz -r20,Y .. ok test_vcf_view: /build/bcftools-1.11/bcftools view -Ob -f PASS -Xks NA00003 /tmp/4fAc0nrnfk/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/4fAc0nrnfk/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view -Ob -xs NA00003 /tmp/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view -Ob -p /tmp/4fAc0nrnfk/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/4fAc0nrnfk/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view -Ob -P /tmp/4fAc0nrnfk/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/4fAc0nrnfk/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/4fAc0nrnfk/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/4fAc0nrnfk/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -GVsnps /tmp/4fAc0nrnfk/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view -Ob -GVsnps /tmp/4fAc0nrnfk/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/4fAc0nrnfk/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/4fAc0nrnfk/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/4fAc0nrnfk/view.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view -Ob -s ^NA00003 /tmp/4fAc0nrnfk/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/4fAc0nrnfk/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view -Ob -G /tmp/4fAc0nrnfk/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/4fAc0nrnfk/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -a /tmp/4fAc0nrnfk/many.alleles.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view -Ob -a /tmp/4fAc0nrnfk/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/4fAc0nrnfk/view.vectors.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view -Ob -asA /tmp/4fAc0nrnfk/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/4fAc0nrnfk/view.vectors.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view -Ob -asB /tmp/4fAc0nrnfk/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/4fAc0nrnfk/view.vectors.2.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view -Ob -asA /tmp/4fAc0nrnfk/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/4fAc0nrnfk/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -H -i'FMT/FGS[*:2]="C"' /tmp/4fAc0nrnfk/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -H -i'FMT/FGS[*:4]="EE"' /tmp/4fAc0nrnfk/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -H -i'FMT/FRS[*:1]="BB"' /tmp/4fAc0nrnfk/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -H -i'TXT0="text"' /tmp/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/filter.2.vcf.gz 1:3062917-3157410 .. ok test_vcf_view: /build/bcftools-1.11/bcftools view -Ob -i 'POS>=3062917' /tmp/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -H -c6:nonmajor /tmp/4fAc0nrnfk/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -H -q0.3:major /tmp/4fAc0nrnfk/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/4fAc0nrnfk/view.filter.annovar.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -H -i 'Gene.refGene~"NOD"' /tmp/4fAc0nrnfk/view.filter.annovar.vcf.gz .. ok test_vcf_view: /build/bcftools-1.11/bcftools view --no-version -H -i 'LJB2_MutationTaster=="0.291000"' /tmp/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-1.11/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/4fAc0nrnfk/regions.tab.gz /tmp/4fAc0nrnfk/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/regions.vcf.gz | /build/bcftools-1.11/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/4fAc0nrnfk/regions.tab.gz .. ok test_vcf_regions: /build/bcftools-1.11/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/4fAc0nrnfk/regions.tab.gz /tmp/4fAc0nrnfk/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-1.11/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/4fAc0nrnfk/regions.bed /tmp/4fAc0nrnfk/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/regions.vcf.gz | /build/bcftools-1.11/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/4fAc0nrnfk/regions.bed .. ok test_vcf_regions: /build/bcftools-1.11/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/4fAc0nrnfk/regions.bed /tmp/4fAc0nrnfk/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-1.11/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/4fAc0nrnfk/regions.bed.gz /tmp/4fAc0nrnfk/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/regions.vcf.gz | /build/bcftools-1.11/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/4fAc0nrnfk/regions.bed.gz .. ok test_vcf_regions: /build/bcftools-1.11/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/4fAc0nrnfk/regions.bed.gz /tmp/4fAc0nrnfk/regions.vcf.gz .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/4fAc0nrnfk/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/4fAc0nrnfk/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/4fAc0nrnfk/annotate.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/4fAc0nrnfk/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/4fAc0nrnfk/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/4fAc0nrnfk/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/4fAc0nrnfk/annotate2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/4fAc0nrnfk/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/4fAc0nrnfk/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/4fAc0nrnfk/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/4fAc0nrnfk/annotate2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/4fAc0nrnfk/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/4fAc0nrnfk/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/4fAc0nrnfk/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/4fAc0nrnfk/annotate2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/4fAc0nrnfk/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/4fAc0nrnfk/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/4fAc0nrnfk/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/4fAc0nrnfk/annotate2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/4fAc0nrnfk/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/4fAc0nrnfk/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/4fAc0nrnfk/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/4fAc0nrnfk/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/4fAc0nrnfk/annots4.vcf.gz -c +INFO /tmp/4fAc0nrnfk/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/4fAc0nrnfk/annots4.vcf.gz -c +INFO /tmp/4fAc0nrnfk/annotate4.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/4fAc0nrnfk/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/4fAc0nrnfk/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/4fAc0nrnfk/annotate2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/4fAc0nrnfk/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/4fAc0nrnfk/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/4fAc0nrnfk/annotate2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/4fAc0nrnfk/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/4fAc0nrnfk/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/4fAc0nrnfk/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/4fAc0nrnfk/annotate2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/4fAc0nrnfk/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/4fAc0nrnfk/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/4fAc0nrnfk/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/4fAc0nrnfk/annotate2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/4fAc0nrnfk/annots11.vcf.gz -c FMT /tmp/4fAc0nrnfk/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/4fAc0nrnfk/annots11.vcf.gz -c FMT /tmp/4fAc0nrnfk/annotate11.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/4fAc0nrnfk/annots2.vcf.gz -c FMT/newGT:=GT /tmp/4fAc0nrnfk/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/4fAc0nrnfk/annots2.vcf.gz -c FMT/newGT:=GT /tmp/4fAc0nrnfk/annotate2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/4fAc0nrnfk/annots12.vcf.gz -c FMT/GT:=newGT /tmp/4fAc0nrnfk/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/4fAc0nrnfk/annots12.vcf.gz -c FMT/GT:=newGT /tmp/4fAc0nrnfk/annotate2.vcf.gz | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-1.11/bcftools annotate -a /tmp/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/4fAc0nrnfk/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/4fAc0nrnfk/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/4fAc0nrnfk/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/4fAc0nrnfk/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/4fAc0nrnfk/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/4fAc0nrnfk/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/4fAc0nrnfk/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/4fAc0nrnfk/annotate20.src.vcf.gz -c FMT/GT /tmp/4fAc0nrnfk/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/4fAc0nrnfk/annotate20.src.vcf.gz -c FMT/GT /tmp/4fAc0nrnfk/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/4fAc0nrnfk/annotate20.src.vcf.gz -c +FMT/GT /tmp/4fAc0nrnfk/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/4fAc0nrnfk/annotate20.src.vcf.gz -c +FMT/GT /tmp/4fAc0nrnfk/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/4fAc0nrnfk/annotate20.src.vcf.gz -c -FMT/GT /tmp/4fAc0nrnfk/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/4fAc0nrnfk/annotate20.src.vcf.gz -c -FMT/GT /tmp/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/concat.1.a.vcf.gz /tmp/4fAc0nrnfk/concat.1.b.vcf.gz .. ok test_vcf_concat: /build/bcftools-1.11/bcftools concat -Ob /tmp/4fAc0nrnfk/concat.1.a.vcf.gz /tmp/4fAc0nrnfk/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/4fAc0nrnfk/concat.1.a.bcf /tmp/4fAc0nrnfk/concat.1.b.bcf .. ok test_vcf_concat: /build/bcftools-1.11/bcftools concat -Ob /tmp/4fAc0nrnfk/concat.1.a.bcf /tmp/4fAc0nrnfk/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/4fAc0nrnfk/concat.2.a.vcf.gz /tmp/4fAc0nrnfk/concat.2.b.vcf.gz .. ok test_vcf_concat: /build/bcftools-1.11/bcftools concat -Ob -a /tmp/4fAc0nrnfk/concat.2.a.vcf.gz /tmp/4fAc0nrnfk/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/4fAc0nrnfk/concat.2.a.bcf /tmp/4fAc0nrnfk/concat.2.b.bcf .. ok test_vcf_concat: /build/bcftools-1.11/bcftools concat -Ob -a /tmp/4fAc0nrnfk/concat.2.a.bcf /tmp/4fAc0nrnfk/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/4fAc0nrnfk/concat.2.a.vcf.gz /tmp/4fAc0nrnfk/concat.2.b.vcf.gz .. ok test_vcf_concat: /build/bcftools-1.11/bcftools concat -Ob -aD /tmp/4fAc0nrnfk/concat.2.a.vcf.gz /tmp/4fAc0nrnfk/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/4fAc0nrnfk/concat.2.a.bcf /tmp/4fAc0nrnfk/concat.2.b.bcf .. ok test_vcf_concat: /build/bcftools-1.11/bcftools concat -Ob -aD /tmp/4fAc0nrnfk/concat.2.a.bcf /tmp/4fAc0nrnfk/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/4fAc0nrnfk/concat.3.a.vcf.gz /tmp/4fAc0nrnfk/concat.3.b.vcf.gz /tmp/4fAc0nrnfk/concat.3.0.vcf.gz /tmp/4fAc0nrnfk/concat.3.c.vcf.gz /tmp/4fAc0nrnfk/concat.3.d.vcf.gz /tmp/4fAc0nrnfk/concat.3.e.vcf.gz /tmp/4fAc0nrnfk/concat.3.f.vcf.gz .. ok test_vcf_concat: /build/bcftools-1.11/bcftools concat -Ob -l /tmp/4fAc0nrnfk/concat.3.a.vcf.gz /tmp/4fAc0nrnfk/concat.3.b.vcf.gz /tmp/4fAc0nrnfk/concat.3.0.vcf.gz /tmp/4fAc0nrnfk/concat.3.c.vcf.gz /tmp/4fAc0nrnfk/concat.3.d.vcf.gz /tmp/4fAc0nrnfk/concat.3.e.vcf.gz /tmp/4fAc0nrnfk/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/4fAc0nrnfk/concat.3.a.bcf /tmp/4fAc0nrnfk/concat.3.b.bcf /tmp/4fAc0nrnfk/concat.3.0.bcf /tmp/4fAc0nrnfk/concat.3.c.bcf /tmp/4fAc0nrnfk/concat.3.d.bcf /tmp/4fAc0nrnfk/concat.3.e.bcf /tmp/4fAc0nrnfk/concat.3.f.bcf .. ok test_vcf_concat: /build/bcftools-1.11/bcftools concat -Ob -l /tmp/4fAc0nrnfk/concat.3.a.bcf /tmp/4fAc0nrnfk/concat.3.b.bcf /tmp/4fAc0nrnfk/concat.3.0.bcf /tmp/4fAc0nrnfk/concat.3.c.bcf /tmp/4fAc0nrnfk/concat.3.d.bcf /tmp/4fAc0nrnfk/concat.3.e.bcf /tmp/4fAc0nrnfk/concat.3.f.bcf | /build/bcftools-1.11/bcftools view | grep -v ^##bcftools_ Random seed for test_naive_concat: 1708821253 .. ok test_naive_concat: /build/bcftools-1.11/bcftools concat --naive-force /tmp/4fAc0nrnfk/naive_concat.0.bcf /tmp/4fAc0nrnfk/naive_concat.1.bcf /tmp/4fAc0nrnfk/naive_concat.2.bcf /tmp/4fAc0nrnfk/naive_concat.3.bcf /tmp/4fAc0nrnfk/naive_concat.4.bcf /tmp/4fAc0nrnfk/naive_concat.5.bcf /tmp/4fAc0nrnfk/naive_concat.6.bcf /tmp/4fAc0nrnfk/naive_concat.7.bcf /tmp/4fAc0nrnfk/naive_concat.8.bcf /tmp/4fAc0nrnfk/naive_concat.9.bcf | /build/bcftools-1.11/bcftools view -H .. ok test_naive_concat: /build/bcftools-1.11/bcftools concat --naive /tmp/4fAc0nrnfk/naive_concat.0.vcf.gz /tmp/4fAc0nrnfk/naive_concat.1.vcf.gz /tmp/4fAc0nrnfk/naive_concat.2.vcf.gz /tmp/4fAc0nrnfk/naive_concat.3.vcf.gz /tmp/4fAc0nrnfk/naive_concat.4.vcf.gz /tmp/4fAc0nrnfk/naive_concat.5.vcf.gz /tmp/4fAc0nrnfk/naive_concat.6.vcf.gz /tmp/4fAc0nrnfk/naive_concat.7.vcf.gz /tmp/4fAc0nrnfk/naive_concat.8.vcf.gz /tmp/4fAc0nrnfk/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/4fAc0nrnfk/reheader.bcf | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/4fAc0nrnfk/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/4fAc0nrnfk/reheader.vcf.gz | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/4fAc0nrnfk/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/4fAc0nrnfk/reheader.bcf | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/4fAc0nrnfk/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/4fAc0nrnfk/reheader.vcf.gz | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/4fAc0nrnfk/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/4fAc0nrnfk/reheader.bcf | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/4fAc0nrnfk/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/4fAc0nrnfk/reheader.vcf.gz | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/4fAc0nrnfk/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/4fAc0nrnfk/reheader.bcf | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/4fAc0nrnfk/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/4fAc0nrnfk/reheader.vcf.gz | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/4fAc0nrnfk/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/4fAc0nrnfk/reheader.bcf | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/4fAc0nrnfk/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/4fAc0nrnfk/reheader.vcf.gz | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/4fAc0nrnfk/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/4fAc0nrnfk/empty.bcf | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/4fAc0nrnfk/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/4fAc0nrnfk/empty.vcf.gz | /build/bcftools-1.11/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/rename.map -Ov /tmp/4fAc0nrnfk/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/4fAc0nrnfk/rename.map -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/convert.vcf.gz | /build/bcftools-1.11/bcftools convert -g -,. .. ok test_vcf_convert: /build/bcftools-1.11/bcftools convert -g .,- /tmp/4fAc0nrnfk/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/convert.vcf.gz | /build/bcftools-1.11/bcftools convert -g .,- .. ok test_vcf_convert: /build/bcftools-1.11/bcftools convert -g -,. --tag PL /tmp/4fAc0nrnfk/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/check.vcf.gz | /build/bcftools-1.11/bcftools convert -g -,. --chrom .. ok test_vcf_convert: /build/bcftools-1.11/bcftools convert -g .,- --chrom /tmp/4fAc0nrnfk/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/convert.vcf.gz | /build/bcftools-1.11/bcftools convert -h -,.,. .. ok test_vcf_convert: /build/bcftools-1.11/bcftools convert -h .,-,. /tmp/4fAc0nrnfk/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/convert.vcf.gz | /build/bcftools-1.11/bcftools convert -h .,-,. .. ok test_vcf_convert: /build/bcftools-1.11/bcftools convert -h .,.,- /tmp/4fAc0nrnfk/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/convert.vcf.gz | /build/bcftools-1.11/bcftools convert --hapsample -,. .. ok test_vcf_convert: /build/bcftools-1.11/bcftools convert --hapsample .,- /tmp/4fAc0nrnfk/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/convert.vcf.gz | /build/bcftools-1.11/bcftools convert --hapsample .,- .. ok test_vcf_convert: /build/bcftools-1.11/bcftools convert --haplegendsample -,.,. /tmp/4fAc0nrnfk/convert.hap-missing.vcf.gz .. ok test_vcf_convert: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/convert.gvcf.vcf.gz .. ok test_vcf_convert_gvcf: /build/bcftools-1.11/bcftools view -Ob /tmp/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/consensus.vcf.gz -f /build/bcftools-1.11/test/consensus.fa -m /build/bcftools-1.11/test/consensus.tab -c /tmp/4fAc0nrnfk/consensus.1.chain.new >/dev/null; cat /tmp/4fAc0nrnfk/consensus.1.chain.new .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/4fAc0nrnfk/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/4fAc0nrnfk/consensus.vcf.gz -f /build/bcftools-1.11/test/consensus.fa -H 1 -m /build/bcftools-1.11/test/consensus.tab -c /tmp/4fAc0nrnfk/consensus.2.chain.new >/dev/null; cat /tmp/4fAc0nrnfk/consensus.2.chain.new .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/4fAc0nrnfk/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/4fAc0nrnfk/consensus.vcf.gz -f /build/bcftools-1.11/test/consensus.fa -I -m /build/bcftools-1.11/test/consensus.tab -c /tmp/4fAc0nrnfk/consensus.3.chain.new >/dev/null; cat /tmp/4fAc0nrnfk/consensus.3.chain.new .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/4fAc0nrnfk/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/4fAc0nrnfk/consensus.vcf.gz -f /build/bcftools-1.11/test/consensus.fa -H 1 -c /tmp/4fAc0nrnfk/consensus.4.chain.new >/dev/null; cat /tmp/4fAc0nrnfk/consensus.4.chain.new .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/4fAc0nrnfk/consensus2.vcf.gz -f /build/bcftools-1.11/test/consensus2.fa -H 1 .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/4fAc0nrnfk/consensus2.vcf.gz -f /build/bcftools-1.11/test/consensus2.fa -H 2 .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/4fAc0nrnfk/empty.vcf.gz -f /build/bcftools-1.11/test/consensus.fa .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/consensus4.vcf.gz -f /build/bcftools-1.11/test/consensus2.fa .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/4fAc0nrnfk/consensus5.vcf.gz -f /build/bcftools-1.11/test/consensus5.fa --haplotype LA .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/4fAc0nrnfk/consensus6.vcf.gz -f /build/bcftools-1.11/test/consensus6.fa .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/4fAc0nrnfk/consensus7.vcf.gz -f /build/bcftools-1.11/test/consensus7.fa -H 2 .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/4fAc0nrnfk/consensus7.vcf.gz -f /build/bcftools-1.11/test/consensus7.fa -H 2pIu .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/4fAc0nrnfk/consensus7.vcf.gz -f /build/bcftools-1.11/test/consensus7.fa -H 1 .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/4fAc0nrnfk/consensus7.vcf.gz -f /build/bcftools-1.11/test/consensus7.fa -H 1pIu .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/4fAc0nrnfk/consensus8.vcf.gz -f /build/bcftools-1.11/test/consensus.fa .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/4fAc0nrnfk/consensus8.vcf.gz -f /build/bcftools-1.11/test/consensus.fa -a . .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/consensus.12.vcf.gz -f /build/bcftools-1.11/test/consensus.12.fa .. ok test_vcf_consensus: /build/bcftools-1.11/bcftools consensus /tmp/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/gtcheck.1.vcf.gz -g /tmp/4fAc0nrnfk/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/4fAc0nrnfk/gtcheck.1.vcf.gz -g /tmp/4fAc0nrnfk/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/4fAc0nrnfk/gtcheck.1.vcf.gz -g /tmp/4fAc0nrnfk/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/4fAc0nrnfk/gtcheck.1.vcf.gz -g /tmp/4fAc0nrnfk/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/4fAc0nrnfk/gtcheck.1.vcf.gz -g /tmp/4fAc0nrnfk/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/4fAc0nrnfk/gtcheck.1.vcf.gz -g /tmp/4fAc0nrnfk/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.11/bcftools gtcheck -e 0 /tmp/4fAc0nrnfk/gtcheck.2.vcf.gz -g /tmp/4fAc0nrnfk/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.11/bcftools gtcheck -e 0 /tmp/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.11/bcftools gtcheck -e 0 -u PL /tmp/4fAc0nrnfk/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.11/bcftools gtcheck -e 0 --n-matches 4 /tmp/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/gtcheck.1.vcf.gz -g /tmp/4fAc0nrnfk/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/4fAc0nrnfk/gtcheck.1.vcf.gz -g /tmp/4fAc0nrnfk/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/4fAc0nrnfk/gtcheck.1.vcf.gz -g /tmp/4fAc0nrnfk/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/4fAc0nrnfk/gtcheck.1.vcf.gz -g /tmp/4fAc0nrnfk/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/4fAc0nrnfk/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/4fAc0nrnfk/gtcheck.4.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.11/bcftools gtcheck -u GT -e 30 /tmp/4fAc0nrnfk/gtcheck.1.vcf.gz -g /tmp/4fAc0nrnfk/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/4fAc0nrnfk/gtcheck.1.vcf.gz -g /tmp/4fAc0nrnfk/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.11/bcftools gtcheck -u GT -e 300 /tmp/4fAc0nrnfk/gtcheck.1.vcf.gz -g /tmp/4fAc0nrnfk/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-1.11/bcftools gtcheck -u PL -e 30 /tmp/4fAc0nrnfk/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 -j16 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/x86_64-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/x86_64-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_amd64.deb'. dpkg-deb: building package 'bcftools' in '../bcftools_1.11-1_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../bcftools_1.11-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1806311 and its subdirectories I: Current time: Fri Dec 2 17:35:59 -12 2022 I: pbuilder-time-stamp: 1670045759 Sat Oct 30 23:12:57 UTC 2021 I: 1st build successful. Starting 2nd build on remote node ionos11-amd64.debian.net. Sat Oct 30 23:12:57 UTC 2021 I: Preparing to do remote build '2' on ionos11-amd64.debian.net. Sat Oct 30 23:14:59 UTC 2021 I: Deleting $TMPDIR on ionos11-amd64.debian.net. Sat Oct 30 23:14:59 UTC 2021 I: bcftools_1.11-1_amd64.changes: Format: 1.8 Date: Thu, 01 Oct 2020 15:43:46 +0200 Source: bcftools Binary: bcftools bcftools-dbgsym Architecture: amd64 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: 6debb38876c9a510029b3671a4f21dfda3dde8d4 1718416 bcftools-dbgsym_1.11-1_amd64.deb 99675f35c7bf9a290ae490c904405716a538c1b5 5830 bcftools_1.11-1_amd64.buildinfo 94cf000e4ebeec35998ede3b64fee4b179188669 617376 bcftools_1.11-1_amd64.deb Checksums-Sha256: 6325552df5969a12e819fb324004e896cfc25f68297d307367da31885d1204a8 1718416 bcftools-dbgsym_1.11-1_amd64.deb a732b721717b2d587f4e85aaefe85127ea790f0e28fe4c740ec4c46a258237ec 5830 bcftools_1.11-1_amd64.buildinfo 0206a42cabb634c3dbd6fa1358a4c4147121c1b7b709607c294540c278917d0f 617376 bcftools_1.11-1_amd64.deb Files: c601489c976ea7ccd3e58bbe1df1879b 1718416 debug optional bcftools-dbgsym_1.11-1_amd64.deb d00905e5c273c6aae6b6e8fae3275c7b 5830 science optional bcftools_1.11-1_amd64.buildinfo 670f9ee5fb8eab7036412dfac9071d32 617376 science optional bcftools_1.11-1_amd64.deb Sat Oct 30 23:15:02 UTC 2021 I: will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.wOChQMYvSj/bcftools_1.11-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.wOChQMYvSj/bcftools_1.11-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.wOChQMYvSj/bcftools_1.11-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.wOChQMYvSj/b1/bcftools_1.11-1_amd64.changes /srv/reproducible-results/rbuild-debian/tmp.wOChQMYvSj/b2/bcftools_1.11-1_amd64.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: 2.324s) 2.323s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.304s) 0.304s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Sat Oct 30 23:18:02 UTC 2021 I: found no differences in the changes files, and a .buildinfo file also exists. Sat Oct 30 23:18:02 UTC 2021 I: bcftools from bullseye built successfully and reproducibly on amd64. Sat Oct 30 23:18:07 UTC 2021 I: Submitting .buildinfo files to external archives: Sat Oct 30 23:18:07 UTC 2021 I: Submitting 8.0K b1/bcftools_1.11-1_amd64.buildinfo.asc Sat Oct 30 23:18:15 UTC 2021 I: Submitting 8.0K b2/bcftools_1.11-1_amd64.buildinfo.asc Sat Oct 30 23:18:25 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sat Oct 30 23:18:25 UTC 2021 I: Done submitting .buildinfo files. Sat Oct 30 23:18:25 UTC 2021 I: Removing signed bcftools_1.11-1_amd64.buildinfo.asc files: removed './b1/bcftools_1.11-1_amd64.buildinfo.asc' removed './b2/bcftools_1.11-1_amd64.buildinfo.asc'