sbuild (Debian sbuild) 0.89.1 (28 April 2025) on carme.larted.org.uk +==============================================================================+ | bcftools 1.21-1 (amd64) Sun, 17 Aug 2025 08:43:41 +0000 | +==============================================================================+ Package: bcftools Version: 1.21-1 Source Version: 1.21-1 Distribution: perl-5.42-throwaway Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: full I: Setting up the chroot... I: Creating chroot session... I: Setting up log color... +------------------------------------------------------------------------------+ | Chroot Setup Commands Sun, 17 Aug 2025 08:43:42 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup bcftools_1.21-1 perl-5.42-throwaway amd64 ---------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup bcftools_1.21-1 perl-5.42-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: Setting up apt archive... +------------------------------------------------------------------------------+ | Update chroot Sun, 17 Aug 2025 08:43:43 +0000 | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.42 InRelease [3024 B] Get:1 file:/srv/reprepro perl-5.42 InRelease [3024 B] Get:2 file:/srv/reprepro perl-5.42/main amd64 Packages [547 kB] Get:3 http://deb.debian.org/debian unstable InRelease [216 kB] Get:4 http://deb.debian.org/debian sid InRelease [216 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 Packages.diff/Index [63.6 kB] Get:6 http://deb.debian.org/debian sid/main Sources.diff/Index [63.6 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 Packages T-2025-08-17-0805.57-F-2025-08-16-2015.43.pdiff [71.2 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 Packages T-2025-08-17-0805.57-F-2025-08-16-2015.43.pdiff [71.2 kB] Get:8 http://deb.debian.org/debian sid/main Sources T-2025-08-17-0805.57-F-2025-08-16-2015.43.pdiff [56.4 kB] Get:8 http://deb.debian.org/debian sid/main Sources T-2025-08-17-0805.57-F-2025-08-16-2015.43.pdiff [56.4 kB] Fetched 686 kB in 8s (83.1 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: binutils binutils-common binutils-x86-64-linux-gnu init-system-helpers libbinutils libctf-nobfd0 libctf0 libgprofng0 libidn2-0 libldap2 libsframe2 11 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 5687 kB/5881 kB of archives. After this operation, 7168 B of additional disk space will be used. Get:1 file:/srv/reprepro perl-5.42/main amd64 libldap2 amd64 2.6.10+dfsg-1+b1 [194 kB] Get:2 http://deb.debian.org/debian unstable/main amd64 init-system-helpers all 1.69 [39.3 kB] Get:3 http://deb.debian.org/debian unstable/main amd64 libgprofng0 amd64 2.45-4 [810 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 libctf0 amd64 2.45-4 [89.7 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 libctf-nobfd0 amd64 2.45-4 [157 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 binutils-x86-64-linux-gnu amd64 2.45-4 [1042 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 binutils amd64 2.45-4 [266 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 libbinutils amd64 2.45-4 [539 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 binutils-common amd64 2.45-4 [2556 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 libsframe2 amd64 2.45-4 [79.5 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.8-3 [109 kB] Fetched 5687 kB in 0s (61.4 MB/s) (Reading database ... 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(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 ... 14971 files and directories currently installed.) Preparing to unpack .../0-libgprofng0_2.45-4_amd64.deb ... Unpacking libgprofng0:amd64 (2.45-4) over (2.45-3) ... Preparing to unpack .../1-libctf0_2.45-4_amd64.deb ... Unpacking libctf0:amd64 (2.45-4) over (2.45-3) ... Preparing to unpack .../2-libctf-nobfd0_2.45-4_amd64.deb ... Unpacking libctf-nobfd0:amd64 (2.45-4) over (2.45-3) ... Preparing to unpack .../3-binutils-x86-64-linux-gnu_2.45-4_amd64.deb ... Unpacking binutils-x86-64-linux-gnu (2.45-4) over (2.45-3) ... Preparing to unpack .../4-binutils_2.45-4_amd64.deb ... Unpacking binutils (2.45-4) over (2.45-3) ... Preparing to unpack .../5-libbinutils_2.45-4_amd64.deb ... Unpacking libbinutils:amd64 (2.45-4) over (2.45-3) ... Preparing to unpack .../6-binutils-common_2.45-4_amd64.deb ... Unpacking binutils-common:amd64 (2.45-4) over (2.45-3) ... Preparing to unpack .../7-libsframe2_2.45-4_amd64.deb ... Unpacking libsframe2:amd64 (2.45-4) over (2.45-3) ... Preparing to unpack .../8-libidn2-0_2.3.8-3_amd64.deb ... Unpacking libidn2-0:amd64 (2.3.8-3) over (2.3.8-2) ... Preparing to unpack .../9-libldap2_2.6.10+dfsg-1+b1_amd64.deb ... Unpacking libldap2:amd64 (2.6.10+dfsg-1+b1) over (2.6.10+dfsg-1) ... Setting up libsframe2:amd64 (2.45-4) ... Setting up binutils-common:amd64 (2.45-4) ... Setting up libctf-nobfd0:amd64 (2.45-4) ... Setting up libidn2-0:amd64 (2.3.8-3) ... Setting up libbinutils:amd64 (2.45-4) ... Setting up libldap2:amd64 (2.6.10+dfsg-1+b1) ... Setting up libctf0:amd64 (2.45-4) ... Setting up libgprofng0:amd64 (2.45-4) ... Setting up binutils-x86-64-linux-gnu (2.45-4) ... Setting up binutils (2.45-4) ... Processing triggers for libc-bin (2.41-12) ... +------------------------------------------------------------------------------+ | Fetch source files Sun, 17 Aug 2025 08:43:56 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/bcftools_1.21-1.dsc exists in /srv/debomatic/incoming; copying to chroot +------------------------------------------------------------------------------+ | Install package build dependencies Sun, 17 Aug 2025 08:43:57 +0000 | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), zlib1g-dev, libbz2-dev, liblzma-dev, libhts-dev (>= 1.14), libgsl-dev, tabix, libio-pty-perl, build-essential Filtered Build-Depends: debhelper-compat (= 13), zlib1g-dev, libbz2-dev, liblzma-dev, libhts-dev (>= 1.14), libgsl-dev, tabix, libio-pty-perl, build-essential dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/build/bcftools-V6n0z8/resolver-ge7J9t/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/build/bcftools-V6n0z8/resolver-ge7J9t/apt_archive ./ InRelease Get:2 copy:/build/bcftools-V6n0z8/resolver-ge7J9t/apt_archive ./ Release [609 B] Ign:3 copy:/build/bcftools-V6n0z8/resolver-ge7J9t/apt_archive ./ Release.gpg Get:4 copy:/build/bcftools-V6n0z8/resolver-ge7J9t/apt_archive ./ Sources [716 B] Get:5 copy:/build/bcftools-V6n0z8/resolver-ge7J9t/apt_archive ./ Packages [733 B] Fetched 2058 B in 0s (87.1 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils comerr-dev debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian krb5-multidev libarchive-zip-perl libbrotli-dev libbrotli1 libbz2-dev libcom-err2 libcurl3t64-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libelf1t64 libevent-2.1-7t64 libfile-stripnondeterminism-perl libgmp-dev libgmpxx4ldbl libgnutls-dane0t64 libgnutls-openssl27t64 libgnutls28-dev libgsl-dev libgsl28 libgslcblas0 libgssapi-krb5-2 libgssrpc4t64 libhts-dev libhts3t64 libhtscodecs2 libidn2-dev libio-pty-perl libk5crypto3 libkadm5clnt-mit12 libkadm5srv-mit12 libkdb5-10t64 libkeyutils1 libkrb5-3 libkrb5-dev libkrb5support0 libldap-dev liblzma-dev libmagic-mgc libmagic1t64 libnghttp2-14 libnghttp2-dev libnghttp3-9 libnghttp3-dev libngtcp2-16 libngtcp2-crypto-gnutls-dev libngtcp2-crypto-gnutls8 libngtcp2-dev libp11-kit-dev libpipeline1 libpkgconf3 libpsl-dev libpsl5t64 librtmp-dev librtmp1 libssh2-1-dev libssh2-1t64 libssl-dev libtasn1-6-dev libtool libuchardet0 libunbound8 libxml2-16 libzstd-dev m4 man-db nettle-dev pkgconf pkgconf-bin po-debconf sensible-utils tabix zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc doc-base dh-make gettext-doc libasprintf-dev libgettextpo-dev gnulib-l10n groff krb5-doc libcurl4-doc libidn-dev gmp-doc libgmp10-doc libmpfr-dev dns-root-data gnutls-bin gnutls-doc gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html krb5-user liblzma-doc libnghttp2-doc p11-kit-doc libssl-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx bzip2-doc ca-certificates libarchive-cpio-perl krb5-locales publicsuffix libtasn1-doc libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils comerr-dev debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian krb5-multidev libarchive-zip-perl libbrotli-dev libbrotli1 libbz2-dev libcom-err2 libcurl3t64-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libelf1t64 libevent-2.1-7t64 libfile-stripnondeterminism-perl libgmp-dev libgmpxx4ldbl libgnutls-dane0t64 libgnutls-openssl27t64 libgnutls28-dev libgsl-dev libgsl28 libgslcblas0 libgssapi-krb5-2 libgssrpc4t64 libhts-dev libhts3t64 libhtscodecs2 libidn2-dev libio-pty-perl libk5crypto3 libkadm5clnt-mit12 libkadm5srv-mit12 libkdb5-10t64 libkeyutils1 libkrb5-3 libkrb5-dev libkrb5support0 libldap-dev liblzma-dev libmagic-mgc libmagic1t64 libnghttp2-14 libnghttp2-dev libnghttp3-9 libnghttp3-dev libngtcp2-16 libngtcp2-crypto-gnutls-dev libngtcp2-crypto-gnutls8 libngtcp2-dev libp11-kit-dev libpipeline1 libpkgconf3 libpsl-dev libpsl5t64 librtmp-dev librtmp1 libssh2-1-dev libssh2-1t64 libssl-dev libtasn1-6-dev libtool libuchardet0 libunbound8 libxml2-16 libzstd-dev m4 man-db nettle-dev pkgconf pkgconf-bin po-debconf sbuild-build-depends-main-dummy sensible-utils tabix zlib1g-dev 0 upgraded, 90 newly installed, 0 to remove and 0 not upgraded. Need to get 30.6 MB/31.0 MB of archives. After this operation, 115 MB of additional disk space will be used. Get:1 copy:/build/bcftools-V6n0z8/resolver-ge7J9t/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [908 B] Get:2 file:/srv/reprepro perl-5.42/main amd64 libldap-dev amd64 2.6.10+dfsg-1+b1 [312 kB] Get:3 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.25 [25.0 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get:8 file:/srv/reprepro perl-5.42/main amd64 libio-pty-perl amd64 1:1.20-1+b4 [34.5 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41.1-1 [94.7 kB] Get:12 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get:13 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get:14 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-8 [294 kB] Get:15 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get:16 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get:17 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-3+b3 [25.0 kB] Get:20 http://deb.debian.org/debian unstable/main amd64 comerr-dev amd64 2.1-1.47.2-3+b3 [56.7 kB] Get:21 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.25 [91.6 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-4 [539 kB] Get:23 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get:24 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:25 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get:26 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get:27 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get:29 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.1 [640 kB] Get:30 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get:31 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:32 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:33 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.25 [937 kB] Get:34 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get:35 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get:36 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get:37 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get:38 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get:39 http://deb.debian.org/debian unstable/main amd64 libgssrpc4t64 amd64 1.21.3-5 [60.0 kB] Get:40 http://deb.debian.org/debian unstable/main amd64 libkadm5clnt-mit12 amd64 1.21.3-5 [42.5 kB] Get:41 http://deb.debian.org/debian unstable/main amd64 libkdb5-10t64 amd64 1.21.3-5 [42.6 kB] Get:42 http://deb.debian.org/debian unstable/main amd64 libkadm5srv-mit12 amd64 1.21.3-5 [54.2 kB] Get:43 http://deb.debian.org/debian unstable/main amd64 krb5-multidev amd64 1.21.3-5 [126 kB] Get:44 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get:45 http://deb.debian.org/debian unstable/main amd64 libbrotli-dev amd64 1.1.0-2+b7 [316 kB] Get:46 http://deb.debian.org/debian unstable/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Get:47 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1.1+b1 [76.2 kB] Get:48 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.8.0-1 [67.7 kB] Get:49 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.11.0-1 [131 kB] Get:50 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.11.0-1 [29.3 kB] Get:51 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get:52 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-3 [58.3 kB] Get:53 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get:54 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.15.0-1 [385 kB] Get:55 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get:56 http://deb.debian.org/debian unstable/main amd64 libunbound8 amd64 1.22.0-2 [598 kB] Get:57 http://deb.debian.org/debian unstable/main amd64 libgnutls-dane0t64 amd64 3.8.10-2 [458 kB] Get:58 http://deb.debian.org/debian unstable/main amd64 libgnutls-openssl27t64 amd64 3.8.10-2 [458 kB] Get:59 http://deb.debian.org/debian unstable/main amd64 libidn2-dev amd64 2.3.8-3 [103 kB] Get:60 http://deb.debian.org/debian unstable/main amd64 libp11-kit-dev amd64 0.25.5-3 [208 kB] Get:61 http://deb.debian.org/debian unstable/main amd64 libtasn1-6-dev amd64 4.20.0-2 [99.2 kB] Get:62 http://deb.debian.org/debian unstable/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-3 [329 kB] Get:63 http://deb.debian.org/debian unstable/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-3 [642 kB] Get:64 http://deb.debian.org/debian unstable/main amd64 nettle-dev amd64 3.10.1-1 [1318 kB] Get:65 http://deb.debian.org/debian unstable/main amd64 libgnutls28-dev amd64 3.8.10-2 [1423 kB] Get:66 http://deb.debian.org/debian unstable/main amd64 libkrb5-dev amd64 1.21.3-5 [16.1 kB] Get:67 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get:68 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get:69 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get:70 http://deb.debian.org/debian unstable/main amd64 libnghttp2-dev amd64 1.64.0-1.1+b1 [117 kB] Get:71 http://deb.debian.org/debian unstable/main amd64 libnghttp3-dev amd64 1.8.0-1 [91.3 kB] Get:72 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.11.0-1 [34.0 kB] Get:73 http://deb.debian.org/debian unstable/main amd64 libngtcp2-dev amd64 1.11.0-1 [179 kB] Get:74 http://deb.debian.org/debian unstable/main amd64 libpsl-dev amd64 0.21.2-1.1+b1 [77.6 kB] Get:75 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get:76 http://deb.debian.org/debian unstable/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-3 [67.9 kB] Get:77 http://deb.debian.org/debian unstable/main amd64 libssl-dev amd64 3.5.2-1 [2957 kB] Get:78 http://deb.debian.org/debian unstable/main amd64 libssh2-1-dev amd64 1.11.1-1 [393 kB] Get:79 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.7+dfsg-1 [371 kB] Get:80 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls-dev amd64 8.15.0-1 [504 kB] Get:81 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.23-2 [47.3 kB] Get:82 http://deb.debian.org/debian unstable/main amd64 libdeflate-dev amd64 1.23-2 [55.9 kB] Get:83 http://deb.debian.org/debian unstable/main amd64 libgslcblas0 amd64 2.8+dfsg-5 [116 kB] Get:84 http://deb.debian.org/debian unstable/main amd64 libgsl28 amd64 2.8+dfsg-5 [994 kB] Get:85 http://deb.debian.org/debian unstable/main amd64 libgsl-dev amd64 2.8+dfsg-5 [1222 kB] Get:86 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.1-2 [95.8 kB] Get:87 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.21+ds-1 [463 kB] Get:88 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.8.1-1 [348 kB] Get:89 http://deb.debian.org/debian unstable/main amd64 libhts-dev amd64 1.21+ds-1 [1733 kB] Get:90 http://deb.debian.org/debian unstable/main amd64 tabix amd64 1.21+ds-1 [496 kB] Preconfiguring packages ... 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Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-3) ... Setting up libldap-dev:amd64 (2.6.10+dfsg-1+b1) ... Setting up comerr-dev:amd64 (2.1-1.47.2-3+b3) ... Setting up libssl-dev:amd64 (3.5.2-1) ... Setting up autopoint (0.23.1-2) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libk5crypto3:amd64 (1.21.3-5) ... Setting up libidn2-dev:amd64 (2.3.8-3) ... Setting up autoconf (2.72-3.1) ... Setting up libnghttp3-9:amd64 (1.8.0-1) ... Setting up libnghttp3-dev:amd64 (1.8.0-1) ... Setting up liblzma-dev:amd64 (5.8.1-1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.25) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up libngtcp2-16:amd64 (1.11.0-1) ... Setting up libkrb5-3:amd64 (1.21.3-5) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up libgsl28:amd64 (2.8+dfsg-5) ... Setting up libtasn1-6-dev:amd64 (4.20.0-2) ... Setting up libdeflate-dev:amd64 (1.23-2) ... Setting up tabix (1.21+ds-1) ... Setting up libbrotli-dev:amd64 (1.1.0-2+b7) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.11.0-1) ... Setting up libp11-kit-dev:amd64 (0.25.5-3) ... Setting up libbz2-dev:amd64 (1.0.8-6) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up gettext (0.23.1-2+b1) ... Setting up libgsl-dev (2.8+dfsg-5) ... Setting up libgmp-dev:amd64 (2:6.3.0+dfsg-3) ... Setting up nettle-dev:amd64 (3.10.1-1) ... Setting up libtool (2.5.4-4) ... Setting up libngtcp2-crypto-gnutls-dev:amd64 (1.11.0-1) ... Setting up libngtcp2-dev:amd64 (1.11.0-1) ... Setting up pkgconf:amd64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-5) ... Setting up libssh2-1-dev:amd64 (1.11.1-1) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-9) ... Setting up libgnutls28-dev:amd64 (3.8.10-2) ... Setting up libnghttp2-dev:amd64 (1.64.0-1.1+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3t64-gnutls:amd64 (8.15.0-1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libgssrpc4t64:amd64 (1.21.3-5) ... Setting up librtmp-dev:amd64 (2.4+20151223.gitfa8646d.1-3) ... Setting up libhts3t64:amd64 (1.21+ds-1) ... Setting up libkadm5clnt-mit12:amd64 (1.21.3-5) ... Setting up libkdb5-10t64:amd64 (1.21.3-5) ... Setting up debhelper (13.25) ... Setting up libkadm5srv-mit12:amd64 (1.21.3-5) ... Setting up krb5-multidev:amd64 (1.21.3-5) ... Setting up libkrb5-dev:amd64 (1.21.3-5) ... Setting up libcurl4-gnutls-dev:amd64 (8.15.0-1) ... Setting up libhts-dev:amd64 (1.21+ds-1) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.41-12) ... +------------------------------------------------------------------------------+ | Check architectures Sun, 17 Aug 2025 08:44:09 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Build environment Sun, 17 Aug 2025 08:44:09 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 6.12.25-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.25-1 (2025-04-25) amd64 (x86_64) Toolchain package versions: binutils_2.45-4 dpkg-dev_1.22.21 g++-14_14.3.0-5 gcc-14_14.3.0-5 libc6-dev_2.41-12 libstdc++-14-dev_14.3.0-5 libstdc++6_15.2.0-1 linux-libc-dev_6.12.38-1 Package versions: adduser_3.152 apt_3.1.4 autoconf_2.72-3.1 automake_1:1.17-4 autopoint_0.23.1-2 autotools-dev_20240727.1 base-files_14 base-passwd_3.6.7 bash_5.2.37-2+b5 binutils_2.45-4 binutils-common_2.45-4 binutils-gold_2.44-2 binutils-gold-x86-64-linux-gnu_2.44-2 binutils-x86-64-linux-gnu_2.45-4 bsdextrautils_2.41.1-1 bsdutils_1:2.41.1-1 build-essential_12.12 bzip2_1.0.8-6 comerr-dev_2.1-1.47.2-3+b3 coreutils_9.7-3 cpp_4:14.2.0-1 cpp-14_14.3.0-5 cpp-14-x86-64-linux-gnu_14.3.0-5 cpp-x86-64-linux-gnu_4:14.2.0-1 dash_0.5.12-12 debconf_1.5.91 debhelper_13.25 debian-archive-keyring_2025.1 debianutils_5.23.2 dh-autoreconf_20 dh-strip-nondeterminism_1.14.1-2 diffutils_1:3.10-4 dirmngr_2.4.8-2 dpkg_1.22.21 dpkg-dev_1.22.21 dwz_0.15-1+b1 eatmydata_131-2 file_1:5.46-5 findutils_4.10.0-3 g++_4:14.2.0-1 g++-14_14.3.0-5 g++-14-x86-64-linux-gnu_14.3.0-5 g++-x86-64-linux-gnu_4:14.2.0-1 gcc_4:14.2.0-1 gcc-14_14.3.0-5 gcc-14-base_14.3.0-5 gcc-14-x86-64-linux-gnu_14.3.0-5 gcc-15-base_15.2.0-1 gcc-x86-64-linux-gnu_4:14.2.0-1 gettext_0.23.1-2+b1 gettext-base_0.23.1-2+b1 gnupg_2.4.8-2 gnupg-l10n_2.4.8-2 gpg_2.4.8-2 gpg-agent_2.4.8-2 gpgconf_2.4.8-2 gpgsm_2.4.8-2 grep_3.11-4 groff-base_1.23.0-9 gzip_1.13-1 hostname_3.25 init-system-helpers_1.69 intltool-debian_0.35.0+20060710.6 krb5-multidev_1.21.3-5 libacl1_2.3.2-2+b1 libapt-pkg7.0_3.1.4 libarchive-zip-perl_1.68-1 libasan8_15.2.0-1 libassuan9_3.0.2-2 libatomic1_15.2.0-1 libattr1_1:2.5.2-3 libaudit-common_1:4.0.5-1 libaudit1_1:4.0.5-1 libbinutils_2.45-4 libblkid1_2.41.1-1 libbrotli-dev_1.1.0-2+b7 libbrotli1_1.1.0-2+b7 libbsd0_0.12.2-2 libbz2-1.0_1.0.8-6 libbz2-dev_1.0.8-6 libc-bin_2.41-12 libc-dev-bin_2.41-12 libc6_2.41-12 libc6-dev_2.41-12 libcap-ng0_0.8.5-4+b1 libcap2_1:2.75-10+b1 libcc1-0_15.2.0-1 libcom-err2_1.47.2-3+b3 libcrypt-dev_1:4.4.38-1 libcrypt1_1:4.4.38-1 libctf-nobfd0_2.45-4 libctf0_2.45-4 libcurl3t64-gnutls_8.15.0-1 libcurl4-gnutls-dev_8.15.0-1 libdb5.3t64_5.3.28+dfsg2-9 libdebconfclient0_0.280 libdebhelper-perl_13.25 libdeflate-dev_1.23-2 libdeflate0_1.23-2 libdpkg-perl_1.22.21 libeatmydata1_131-2+b1 libelf1t64_0.192-4 libevent-2.1-7t64_2.1.12-stable-10+b1 libffi8_3.4.8-2 libfile-stripnondeterminism-perl_1.14.1-2 libgcc-14-dev_14.3.0-5 libgcc-s1_15.2.0-1 libgcrypt20_1.11.2-2 libgdbm-compat4t64_1.24-2 libgdbm6t64_1.24-2 libgmp-dev_2:6.3.0+dfsg-3 libgmp10_2:6.3.0+dfsg-3 libgmpxx4ldbl_2:6.3.0+dfsg-3 libgnutls-dane0t64_3.8.10-2 libgnutls-openssl27t64_3.8.10-2 libgnutls28-dev_3.8.10-2 libgnutls30t64_3.8.10-2 libgomp1_15.2.0-1 libgpg-error0_1.55-2 libgprofng0_2.45-4 libgsl-dev_2.8+dfsg-5 libgsl28_2.8+dfsg-5 libgslcblas0_2.8+dfsg-5 libgssapi-krb5-2_1.21.3-5 libgssrpc4t64_1.21.3-5 libhogweed6t64_3.10.1-1 libhts-dev_1.21+ds-1 libhts3t64_1.21+ds-1 libhtscodecs2_1.6.1-2 libhwasan0_15.2.0-1 libidn2-0_2.3.8-3 libidn2-dev_2.3.8-3 libio-pty-perl_1:1.20-1+b4 libisl23_0.27-1 libitm1_15.2.0-1 libjansson4_2.14-2+b3 libk5crypto3_1.21.3-5 libkadm5clnt-mit12_1.21.3-5 libkadm5srv-mit12_1.21.3-5 libkdb5-10t64_1.21.3-5 libkeyutils1_1.6.3-6 libkrb5-3_1.21.3-5 libkrb5-dev_1.21.3-5 libkrb5support0_1.21.3-5 libksba8_1.6.7-2+b1 liblastlog2-2_2.41.1-1 libldap-dev_2.6.10+dfsg-1+b1 libldap2_2.6.10+dfsg-1+b1 liblsan0_15.2.0-1 liblz4-1_1.10.0-4 liblzma-dev_5.8.1-1 liblzma5_5.8.1-1 libmagic-mgc_1:5.46-5 libmagic1t64_1:5.46-5 libmd0_1.1.0-2+b1 libmount1_2.41.1-1 libmpc3_1.3.1-1+b3 libmpfr6_4.2.2-1 libncursesw6_6.5+20250216-2 libnettle8t64_3.10.1-1 libnghttp2-14_1.64.0-1.1+b1 libnghttp2-dev_1.64.0-1.1+b1 libnghttp3-9_1.8.0-1 libnghttp3-dev_1.8.0-1 libngtcp2-16_1.11.0-1 libngtcp2-crypto-gnutls-dev_1.11.0-1 libngtcp2-crypto-gnutls8_1.11.0-1 libngtcp2-dev_1.11.0-1 libnpth0t64_1.8-3 libp11-kit-dev_0.25.5-3 libp11-kit0_0.25.5-3 libpam-modules_1.7.0-5 libpam-modules-bin_1.7.0-5 libpam-runtime_1.7.0-5 libpam0g_1.7.0-5 libpcre2-8-0_10.45-1 libperl5.40_5.40.1-6 libperl5.42_5.42.0-1 libpipeline1_1.5.8-1 libpkgconf3_1.8.1-4 libpsl-dev_0.21.2-1.1+b1 libpsl5t64_0.21.2-1.1+b1 libquadmath0_15.2.0-1 libreadline8t64_8.2-6 librtmp-dev_2.4+20151223.gitfa8646d.1-3 librtmp1_2.4+20151223.gitfa8646d.1-3 libsasl2-2_2.1.28+dfsg1-9 libsasl2-modules-db_2.1.28+dfsg1-9 libseccomp2_2.6.0-2 libselinux1_3.8.1-1 libsemanage-common_3.8.1-1 libsemanage2_3.8.1-1 libsepol2_3.8.1-1 libsframe2_2.45-4 libsmartcols1_2.41.1-1 libsqlite3-0_3.46.1-7 libssh2-1-dev_1.11.1-1 libssh2-1t64_1.11.1-1 libssl-dev_3.5.2-1 libssl3t64_3.5.2-1 libstdc++-14-dev_14.3.0-5 libstdc++6_15.2.0-1 libsystemd0_258~rc2-2 libtasn1-6_4.20.0-2 libtasn1-6-dev_4.20.0-2 libtinfo6_6.5+20250216-2 libtool_2.5.4-4 libtsan2_15.2.0-1 libubsan1_15.2.0-1 libuchardet0_0.0.8-1+b2 libudev1_258~rc2-2 libunbound8_1.22.0-2 libunistring5_1.3-2 libuuid1_2.41.1-1 libxml2-16_2.14.5+dfsg-0.1 libxxhash0_0.8.3-2 libzstd-dev_1.5.7+dfsg-1 libzstd1_1.5.7+dfsg-1 linux-libc-dev_6.12.38-1 login.defs_1:4.17.4-2 m4_1.4.19-8 make_4.4.1-2 man-db_2.13.1-1 mawk_1.3.4.20250131-1 ncurses-base_6.5+20250216-2 ncurses-bin_6.5+20250216-2 nettle-dev_3.10.1-1 openssl-provider-legacy_3.5.2-1 passwd_1:4.17.4-2 patch_2.8-2 perl_5.42.0-1 perl-base_5.42.0-1 perl-modules-5.40_5.40.1-6 perl-modules-5.42_5.42.0-1 pinentry-curses_1.3.2-3 pkgconf_1.8.1-4 pkgconf-bin_1.8.1-4 po-debconf_1.0.21+nmu1 readline-common_8.2-6 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.25 sqv_1.3.0-3 sysvinit-utils_3.14-4 tabix_1.21+ds-1 tar_1.35+dfsg-3.1 util-linux_2.41.1-1 xz-utils_5.8.1-1 zlib1g_1:1.3.dfsg+really1.3.1-1+b1 zlib1g-dev_1:1.3.dfsg+really1.3.1-1+b1 +------------------------------------------------------------------------------+ | Build Sun, 17 Aug 2025 08:44:09 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: bcftools Binary: bcftools Architecture: any Version: 1.21-1 Maintainer: Debian Med Packaging Team Uploaders: Michael R. Crusoe , Étienne Mollier Homepage: https://samtools.github.io/bcftools/ Standards-Version: 4.7.0 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 (>= 1.14), libgsl-dev, tabix , libio-pty-perl Package-List: bcftools deb science optional arch=any Checksums-Sha1: 7f367e0f03d4f56ca88d5f3a79435f196591fbce 3665160 bcftools_1.21.orig.tar.gz 5b3b3f9251d64665efa2c5ed61c6e2aef032cde1 7504 bcftools_1.21-1.debian.tar.xz Checksums-Sha256: 7484695c5d833fb1a89c2b886ec302db0514ba3c8e5ef7397b9302fa8bd37f8d 3665160 bcftools_1.21.orig.tar.gz d1332716453f270248afa7476a5a824b0289150a7829442f691559209dcc38cf 7504 bcftools_1.21-1.debian.tar.xz Files: e144a5777c606c69eb643ae8ff613dbb 3665160 bcftools_1.21.orig.tar.gz 756abc1b4df76e455bd705ddf6ef5c9e 7504 bcftools_1.21-1.debian.tar.xz Dgit: 1cbbbd21cccc5d95d73df54271b167d9e450842a debian archive/debian/1.21-1 https://git.dgit.debian.org/bcftools -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmeuYIEUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdpyzRAAlczvukE0/A+j5esHHalBAeaq8nnO SC4BULLNsaVcn31OlRTGS1RXt1zU6u3ise+jLfRMAbhM4Qx57Ek9S+2+uvX2M5lh 6Wlz3M6DvyTEXN0MZTztIinmdxODYf/IiD8d4qDf8KYZNBeKE+spfINNeRiWyl6e /QXwVTUB0jRc5ZBqsOONR4uOliMKk3LWUy3xwM3YzUKhVlFQpf2OJXk5bQSew6NM PIwjBLcHdDE42tplpMuRjT0FdWk4i8EeZlR8oIdBwoVc1ffNqRpWbz77OJouDhe8 dz7kPHok/2DEBod4k3yeIZH0deK+G47sycXhhSOA7IS+43opAYIHFscpHZMdnoaA lQjIMES546gBHagarHdb5dbHKcvWuq2aQdsuyc0Z2kOnS4Kaop/YugT14ba0pu73 50x5eyPJL2LgnFDb+36HygKNL0CCA6v6EOC7qEU5zzqkmXYXBWEKGxht4KvXbdtc NAvxqxbw2AtQF1kRH6dur00lo9ZCjVq+wa5NnQHZh+BILAIrdo8lpM5Gm6yCifwE 9HU+bY2IaF3LMMgTxvRVyT8yeu65YtA6FbZjnYW6Y0ZeVlQLFvn+830b4L4fWlt3 waTPrdRQcvexseaLFmxuZY2igfMRPtzyf3UXQaomDkitd4jC0WhH+Tg6OoTD88Fa IFTp1pvu+xmgjw4= =1qOu -----END PGP SIGNATURE----- dpkg-source: warning: cannot verify inline signature for ./bcftools_1.21-1.dsc: no acceptable signature found dpkg-source: info: extracting bcftools in /build/bcftools-V6n0z8/bcftools-1.21 dpkg-source: info: unpacking bcftools_1.21.orig.tar.gz dpkg-source: info: unpacking bcftools_1.21-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying skip_new_test_failing_on_32bit.patch dpkg-source: info: applying 2to3.patch Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Timed Build Commands Sun, 17 Aug 2025 08:44:11 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network bcftools_1.21-1 perl-5.42-throwaway amd64 ---------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network bcftools_1.21-1 perl-5.42-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LC_ALL=C.UTF-8 LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so LOGNAME=debomatic PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games PWD=/build/bcftools-V6n0z8/bcftools-1.21 SCHROOT_ALIAS_NAME=perl-5.42-throwaway-amd64-debomatic SCHROOT_CHROOT_NAME=perl-5.42-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=110 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=perl-5.42-amd64-debomatic-183268cc-e311-4772-bb61-0ced52aae463 SCHROOT_UID=1002 SCHROOT_USER=debomatic SHELL=/bin/sh USER=debomatic dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -Zxz dpkg-buildpackage: info: source package bcftools dpkg-buildpackage: info: source version 1.21-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source -Zxz --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean rm -f config.mk && touch config.mk dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/bcftools-V6n0z8/bcftools-1.21' dh_auto_clean make -j2 distclean make[2]: Entering directory '/build/bcftools-V6n0z8/bcftools-1.21' rm -f test/*.o test/*.fa.fai test/*~ test/test-rbuf test/test-regidx rm -f plugins/*.so plugins/*.P rm -f test/*.unsorted.hex test/*.unsorted.tsv rm -rf plugins/*.dSYM rm -f gmon.out *.o *.a *~ bcftools version.h rm -rf *.dSYM test/*.dSYM rm -f config.cache config.h config.log config.mk config.status rm -rf autom4te.cache rm -f TAGS make[2]: Leaving directory '/build/bcftools-V6n0z8/bcftools-1.21' rm -f test/mpileup/indel-AD.1.out.new test/view-t.1.out.new test/view-t.2.out.new make[1]: Leaving directory '/build/bcftools-V6n0z8/bcftools-1.21' dh_clean dpkg-source -Zxz -b . dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building bcftools using existing ./bcftools_1.21.orig.tar.gz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: building bcftools in bcftools_1.21-1.debian.tar.xz dpkg-source: info: building bcftools in bcftools_1.21-1.dsc debian/rules binary dh binary dh_update_autotools_config debian/rules override_dh_autoreconf make[1]: Entering directory '/build/bcftools-V6n0z8/bcftools-1.21' rm -f config.mk && touch config.mk export MAKEFLAGS="-s"; dh_autoreconf configure.ac:94: warning: _AC_CONFIG_SUBDIRS: you should use literals ./lib/autoconf/status.m4:1096: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:94: the top level make[1]: Leaving directory '/build/bcftools-V6n0z8/bcftools-1.21' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/bcftools-V6n0z8/bcftools-1.21' 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 the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking for -Wdate-time -D_FORTIFY_SOURCE=2 option for large files... none needed checking for htslib/sam.h... yes checking for hts_version in -lhts... yes checking shared library type... plain .so checking for library containing dlopen... none required checking if the compiler accepts -rdynamic... yes checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing regcomp... none required configure: creating ./config.status config.status: creating config.mk config.status: creating config.h make[1]: Leaving directory '/build/bcftools-V6n0z8/bcftools-1.21' dh_auto_build make -j2 make[1]: Entering directory '/build/bcftools-V6n0z8/bcftools-1.21' echo '#define BCFTOOLS_VERSION "1.21"' > version.h gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-V6n0z8/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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-D_FORTIFY_SOURCE=2 -c -o HMM.o HMM.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-V6n0z8/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o consensus.o consensus.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-V6n0z8/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ploidy.o ploidy.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-V6n0z8/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bin.o bin.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-V6n0z8/bcftools-1.21=. -fstack-protector-strong 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-D_FORTIFY_SOURCE=2 -DPLUGINPATH='"/usr/lib/x86_64-linux-gnu/bcftools"' -c -o vcfplugin.o vcfplugin.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-V6n0z8/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-rbuf.o test/test-rbuf.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-V6n0z8/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-regidx.o test/test-regidx.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-V6n0z8/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/GTisec.so version.c plugins/GTisec.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-V6n0z8/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/GTsubset.so version.c plugins/GTsubset.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-V6n0z8/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/ad-bias.so convert.c version.c plugins/ad-bias.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-V6n0z8/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/add-variantkey.so version.c plugins/add-variantkey.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-V6n0z8/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/af-dist.so bin.c version.c plugins/af-dist.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-V6n0z8/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/allele-length.so version.c plugins/allele-length.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-V6n0z8/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/check-ploidy.so version.c plugins/check-ploidy.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-V6n0z8/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/check-sparsity.so version.c plugins/check-sparsity.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-V6n0z8/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/color-chrs.so HMM.c version.c plugins/color-chrs.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-V6n0z8/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/contrast.so version.c plugins/contrast.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-V6n0z8/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/counts.so version.c plugins/counts.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-V6n0z8/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/dosage.so version.c plugins/dosage.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-V6n0z8/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/fill-AN-AC.so version.c plugins/fill-AN-AC.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-V6n0z8/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/fill-from-fasta.so filter.c version.c plugins/fill-from-fasta.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-V6n0z8/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/fill-tags.so version.c plugins/fill-tags.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-V6n0z8/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/fixploidy.so ploidy.c regidx.c version.c plugins/fixploidy.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-V6n0z8/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/fixref.so version.c plugins/fixref.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-V6n0z8/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/frameshifts.so version.c plugins/frameshifts.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-V6n0z8/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/guess-ploidy.so version.c plugins/guess-ploidy.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-V6n0z8/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/gvcfz.so version.c plugins/gvcfz.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-V6n0z8/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/impute-info.so version.c plugins/impute-info.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-V6n0z8/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/indel-stats.so version.c plugins/indel-stats.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-V6n0z8/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/isecGT.so smpl_ilist.c version.c plugins/isecGT.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-V6n0z8/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/mendelian2.so version.c plugins/mendelian2.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-V6n0z8/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/missing2ref.so version.c plugins/missing2ref.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-V6n0z8/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/parental-origin.so version.c plugins/parental-origin.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-V6n0z8/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/prune.so version.c plugins/prune.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-V6n0z8/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/remove-overlaps.so version.c plugins/remove-overlaps.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-V6n0z8/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/scatter.so version.c plugins/scatter.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-V6n0z8/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/setGT.so version.c plugins/setGT.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-V6n0z8/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/smpl-stats.so version.c plugins/smpl-stats.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-V6n0z8/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/split-vep.so version.c plugins/split-vep.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-V6n0z8/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/split.so version.c plugins/split.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-V6n0z8/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/tag2tag.so version.c plugins/tag2tag.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-V6n0z8/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/trio-dnm2.so version.c plugins/trio-dnm2.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-V6n0z8/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/trio-stats.so version.c plugins/trio-stats.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-V6n0z8/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/trio-switch-rate.so version.c plugins/trio-switch-rate.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-V6n0z8/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/variant-distance.so version.c plugins/variant-distance.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-V6n0z8/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/variantkey-hex.so version.c plugins/variantkey-hex.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-V6n0z8/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o main.o main.c gcc -Wl,-z,relro -Wl,-z,now -o test/test-rbuf test/test-rbuf.o -lz gcc -Wl,-z,relro -Wl,-z,now -o test/test-regidx test/test-regidx.o regidx.o -lhts -lpthread -lz gcc -rdynamic -Wl,-z,relro -Wl,-z,now -o bcftools main.o vcfindex.o tabix.o vcfstats.o vcfisec.o vcfmerge.o vcfquery.o vcffilter.o filter.o vcfsom.o vcfnorm.o vcfgtcheck.o vcfview.o vcfannotate.o vcfroh.o vcfconcat.o vcfcall.o mcall.o vcmp.o gvcf.o reheader.o convert.o vcfconvert.o tsv2vcf.o vcfcnv.o vcfhead.o HMM.o consensus.o ploidy.o bin.o hclust.o version.o regidx.o smpl_ilist.o csq.o vcfbuf.o mpileup.o bam2bcf.o bam2bcf_indel.o bam2bcf_iaux.o bam2bcf_edlib.o read_consensus.o bam_sample.o vcfsort.o cols.o extsort.o dist.o abuf.o ccall.o em.o prob1.o kmin.o str_finder.o gff.o edlib.o vcfplugin.o -lhts -lm -lz -lpthread make[1]: Leaving directory '/build/bcftools-V6n0z8/bcftools-1.21' debian/rules override_dh_auto_test make[1]: Entering directory '/build/bcftools-V6n0z8/bcftools-1.21' make test-no-plugins VERBOSE=1 make[2]: Entering directory '/build/bcftools-V6n0z8/bcftools-1.21' ./test/test-rbuf Inserted 1-9 starting at offset 5: 5 6 7 8 9 0 1 2 3 1 2 3 4 5 6 7 8 9 4th is 4 Deleting 1-2: 7 8 9 0 1 2 3 3 4 5 6 7 8 9 Prepending 0-8: 8 9 0 1 2 3 4 5 6 7 8 7 6 5 4 3 2 1 0 3 Expanding: 8 9 10 11 12 13 14 15 16 17 8 7 6 5 4 3 2 1 0 3 ./test/test-regidx REF_PATH=: ./test/test.pl --exec bgzip= --exec tabix= --htsdir= ${TEST_OPTS:-} test_usage: bcftools .. ok test_usage_subcommand: bcftools index .. ok test_usage_subcommand: bcftools annotate .. ok test_usage_subcommand: bcftools concat .. ok test_usage_subcommand: bcftools convert .. ok test_usage_subcommand: bcftools head .. ok test_usage_subcommand: bcftools isec .. ok test_usage_subcommand: bcftools merge .. ok test_usage_subcommand: bcftools norm .. ok test_usage_subcommand: bcftools plugin .. ok test_usage_subcommand: bcftools query .. ok test_usage_subcommand: bcftools reheader .. ok test_usage_subcommand: bcftools sort .. ok test_usage_subcommand: bcftools view .. ok test_usage_subcommand: bcftools call .. ok test_usage_subcommand: bcftools consensus .. ok test_usage_subcommand: bcftools cnv .. ok test_usage_subcommand: bcftools csq .. ok test_usage_subcommand: bcftools filter .. ok test_usage_subcommand: bcftools gtcheck .. ok test_usage_subcommand: bcftools mpileup .. ok test_usage_subcommand: bcftools roh .. ok test_usage_subcommand: bcftools stats .. ok test_tabix: tabix /tmp/w22ChRBs6d/merge.a.vcf.gz 2:3199812-3199812 .. ok test_tabix: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -H /tmp/w22ChRBs6d/merge.a.bcf 2:3199812-3199812 .. ok test_tabix: tabix /tmp/w22ChRBs6d/merge.a.vcf.gz 1:3000151-3000151 .. ok test_tabix: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -H /tmp/w22ChRBs6d/merge.a.bcf 1:3000151-3000151 .. ok test_index: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -H /tmp/w22ChRBs6d/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -H /tmp/w22ChRBs6d/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -H /tmp/w22ChRBs6d/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -H /tmp/w22ChRBs6d/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -H /tmp/w22ChRBs6d/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -H /tmp/w22ChRBs6d/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -H /tmp/w22ChRBs6d/large_chrom_csi_limit.bcf chr20 .. ok test_index: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -H /tmp/w22ChRBs6d/large_chrom_csi_limit.bcf chr20 .. ok test_index: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -H /tmp/w22ChRBs6d/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -H /tmp/w22ChRBs6d/large_chrom_csi_limit.bcf chr20 .. ok test_vcf_idxstats: /build/bcftools-V6n0z8/bcftools-1.21/bcftools index -s /tmp/w22ChRBs6d/idx.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-V6n0z8/bcftools-1.21/bcftools index -s /tmp/w22ChRBs6d/idx.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-V6n0z8/bcftools-1.21/bcftools index -s /tmp/w22ChRBs6d/idx.bcf .. ok test_vcf_idxstats: /build/bcftools-V6n0z8/bcftools-1.21/bcftools index -n /tmp/w22ChRBs6d/idx.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-V6n0z8/bcftools-1.21/bcftools index -n /tmp/w22ChRBs6d/idx.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-V6n0z8/bcftools-1.21/bcftools index -n /tmp/w22ChRBs6d/idx.vcf.gz.csi .. ok test_vcf_idxstats: /build/bcftools-V6n0z8/bcftools-1.21/bcftools index -n /tmp/w22ChRBs6d/idx.bcf .. ok test_vcf_idxstats: /build/bcftools-V6n0z8/bcftools-1.21/bcftools index -n /tmp/w22ChRBs6d/idx.bcf.csi .. ok test_vcf_idxstats: /build/bcftools-V6n0z8/bcftools-1.21/bcftools index -s /tmp/w22ChRBs6d/empty.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-V6n0z8/bcftools-1.21/bcftools index -s /tmp/w22ChRBs6d/empty.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-V6n0z8/bcftools-1.21/bcftools index -s /tmp/w22ChRBs6d/empty.bcf .. ok test_vcf_idxstats: /build/bcftools-V6n0z8/bcftools-1.21/bcftools index -n /tmp/w22ChRBs6d/empty.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-V6n0z8/bcftools-1.21/bcftools index -n /tmp/w22ChRBs6d/empty.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-V6n0z8/bcftools-1.21/bcftools index -n /tmp/w22ChRBs6d/empty.vcf.gz.csi .. ok test_vcf_idxstats: /build/bcftools-V6n0z8/bcftools-1.21/bcftools index -n /tmp/w22ChRBs6d/empty.bcf .. ok test_vcf_idxstats: /build/bcftools-V6n0z8/bcftools-1.21/bcftools index -n /tmp/w22ChRBs6d/empty.bcf.csi .. ok test_vcf_check: /build/bcftools-V6n0z8/bcftools-1.21/bcftools stats -s - /tmp/w22ChRBs6d/check.vcf.gz | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/check.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools stats -s - | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check_merge: /build/bcftools-V6n0z8/bcftools-1.21/misc/plot-vcfstats -m /tmp/w22ChRBs6d/check.1.chk /tmp/w22ChRBs6d/check.2.chk /tmp/w22ChRBs6d/check.3.chk /tmp/w22ChRBs6d/check.4.chk | grep -v 'plot-vcfstats' | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_stats: /build/bcftools-V6n0z8/bcftools-1.21/bcftools stats -s - /tmp/w22ChRBs6d/stats.a.vcf.gz /tmp/w22ChRBs6d/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/bcftools-V6n0z8/bcftools-1.21/bcftools stats -s B /tmp/w22ChRBs6d/stats.a.vcf.gz /tmp/w22ChRBs6d/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/bcftools-V6n0z8/bcftools-1.21/bcftools stats -s - /tmp/w22ChRBs6d/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/bcftools-V6n0z8/bcftools-1.21/bcftools stats -s - -i 'type="snp"' /tmp/w22ChRBs6d/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/bcftools-V6n0z8/bcftools-1.21/bcftools stats -s - /tmp/w22ChRBs6d/stats.vaf.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_isec: /build/bcftools-V6n0z8/bcftools-1.21/bcftools isec -n =2 /tmp/w22ChRBs6d/isec.a.vcf.gz /tmp/w22ChRBs6d/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-V6n0z8/bcftools-1.21/bcftools isec -Ob -n =2 /tmp/w22ChRBs6d/isec.a.vcf.gz /tmp/w22ChRBs6d/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-V6n0z8/bcftools-1.21/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/w22ChRBs6d/isec.a.vcf.gz /tmp/w22ChRBs6d/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-V6n0z8/bcftools-1.21/bcftools isec -Ob -n =2 -i"STRLEN(REF)==2" /tmp/w22ChRBs6d/isec.a.vcf.gz /tmp/w22ChRBs6d/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-V6n0z8/bcftools-1.21/bcftools isec -n =2 -c both /tmp/w22ChRBs6d/isec.a.vcf.gz /tmp/w22ChRBs6d/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-V6n0z8/bcftools-1.21/bcftools isec -Ob -n =2 -c both /tmp/w22ChRBs6d/isec.a.vcf.gz /tmp/w22ChRBs6d/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-V6n0z8/bcftools-1.21/bcftools isec -n =2 -c any /tmp/w22ChRBs6d/isec.a.vcf.gz /tmp/w22ChRBs6d/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-V6n0z8/bcftools-1.21/bcftools isec -Ob -n =2 -c any /tmp/w22ChRBs6d/isec.a.vcf.gz /tmp/w22ChRBs6d/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-V6n0z8/bcftools-1.21/bcftools isec -C -c any /tmp/w22ChRBs6d/isec.a.vcf.gz /tmp/w22ChRBs6d/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-V6n0z8/bcftools-1.21/bcftools isec -Ob -C -c any /tmp/w22ChRBs6d/isec.a.vcf.gz /tmp/w22ChRBs6d/isec.b.vcf.gz .. ok test_vcf_isec2: /build/bcftools-V6n0z8/bcftools-1.21/bcftools isec --no-version -T /tmp/w22ChRBs6d/isec.tab.gz /tmp/w22ChRBs6d/isec.a.vcf.gz .. ok test_vcf_isec2: /build/bcftools-V6n0z8/bcftools-1.21/bcftools isec -Ob -T /tmp/w22ChRBs6d/isec.tab.gz /tmp/w22ChRBs6d/isec.a.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_isec: /build/bcftools-V6n0z8/bcftools-1.21/bcftools isec -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/w22ChRBs6d/isec-miss.1.1.vcf.gz /tmp/w22ChRBs6d/isec-miss.1.2.vcf.gz /tmp/w22ChRBs6d/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /build/bcftools-V6n0z8/bcftools-1.21/bcftools isec -Ob -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/w22ChRBs6d/isec-miss.1.1.vcf.gz /tmp/w22ChRBs6d/isec-miss.1.2.vcf.gz /tmp/w22ChRBs6d/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /build/bcftools-V6n0z8/bcftools-1.21/bcftools isec -R /build/bcftools-V6n0z8/bcftools-1.21/test/isec-miss.1.regs.txt -n +1 /tmp/w22ChRBs6d/isec-miss.1.1.vcf.gz /tmp/w22ChRBs6d/isec-miss.1.2.vcf.gz /tmp/w22ChRBs6d/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /build/bcftools-V6n0z8/bcftools-1.21/bcftools isec -Ob -R /build/bcftools-V6n0z8/bcftools-1.21/test/isec-miss.1.regs.txt -n +1 /tmp/w22ChRBs6d/isec-miss.1.1.vcf.gz /tmp/w22ChRBs6d/isec-miss.1.2.vcf.gz /tmp/w22ChRBs6d/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /build/bcftools-V6n0z8/bcftools-1.21/bcftools isec -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/w22ChRBs6d/isec-miss.2.1.vcf.gz /tmp/w22ChRBs6d/isec-miss.2.2.vcf.gz /tmp/w22ChRBs6d/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /build/bcftools-V6n0z8/bcftools-1.21/bcftools isec -Ob -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/w22ChRBs6d/isec-miss.2.1.vcf.gz /tmp/w22ChRBs6d/isec-miss.2.2.vcf.gz /tmp/w22ChRBs6d/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /build/bcftools-V6n0z8/bcftools-1.21/bcftools isec -R /build/bcftools-V6n0z8/bcftools-1.21/test/isec-miss.1.regs.txt -n +1 /tmp/w22ChRBs6d/isec-miss.2.1.vcf.gz /tmp/w22ChRBs6d/isec-miss.2.2.vcf.gz /tmp/w22ChRBs6d/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /build/bcftools-V6n0z8/bcftools-1.21/bcftools isec -Ob -R /build/bcftools-V6n0z8/bcftools-1.21/test/isec-miss.1.regs.txt -n +1 /tmp/w22ChRBs6d/isec-miss.2.1.vcf.gz /tmp/w22ChRBs6d/isec-miss.2.2.vcf.gz /tmp/w22ChRBs6d/isec-miss.2.3.vcf.gz .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version /tmp/w22ChRBs6d/merge.11.a.vcf.gz /tmp/w22ChRBs6d/merge.11.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob /tmp/w22ChRBs6d/merge.11.a.vcf.gz /tmp/w22ChRBs6d/merge.11.b.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version /tmp/w22ChRBs6d/merge.11.a.bcf /tmp/w22ChRBs6d/merge.11.b.bcf .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob /tmp/w22ChRBs6d/merge.11.a.bcf /tmp/w22ChRBs6d/merge.11.b.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -i AF:join /tmp/w22ChRBs6d/merge.join.a.vcf.gz /tmp/w22ChRBs6d/merge.join.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob -i AF:join /tmp/w22ChRBs6d/merge.join.a.vcf.gz /tmp/w22ChRBs6d/merge.join.b.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -i AF:join /tmp/w22ChRBs6d/merge.join.a.bcf /tmp/w22ChRBs6d/merge.join.b.bcf .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob -i AF:join /tmp/w22ChRBs6d/merge.join.a.bcf /tmp/w22ChRBs6d/merge.join.b.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version --force-single /tmp/w22ChRBs6d/merge.LPL.a.vcf.gz .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob --force-single /tmp/w22ChRBs6d/merge.LPL.a.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version --force-single /tmp/w22ChRBs6d/merge.LPL.a.bcf .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob --force-single /tmp/w22ChRBs6d/merge.LPL.a.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version --force-samples /tmp/w22ChRBs6d/merge.LPL.a.vcf.gz /tmp/w22ChRBs6d/merge.LPL.b.vcf.gz /tmp/w22ChRBs6d/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/w22ChRBs6d/merge.LPL.a.vcf.gz /tmp/w22ChRBs6d/merge.LPL.b.vcf.gz /tmp/w22ChRBs6d/merge.LPL.c.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version --force-samples /tmp/w22ChRBs6d/merge.LPL.a.bcf /tmp/w22ChRBs6d/merge.LPL.b.bcf /tmp/w22ChRBs6d/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/w22ChRBs6d/merge.LPL.a.bcf /tmp/w22ChRBs6d/merge.LPL.b.bcf /tmp/w22ChRBs6d/merge.LPL.c.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version --force-samples -L 1 /tmp/w22ChRBs6d/merge.LPL.a.vcf.gz /tmp/w22ChRBs6d/merge.LPL.b.vcf.gz /tmp/w22ChRBs6d/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 1 /tmp/w22ChRBs6d/merge.LPL.a.vcf.gz /tmp/w22ChRBs6d/merge.LPL.b.vcf.gz /tmp/w22ChRBs6d/merge.LPL.c.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version --force-samples -L 1 /tmp/w22ChRBs6d/merge.LPL.a.bcf /tmp/w22ChRBs6d/merge.LPL.b.bcf /tmp/w22ChRBs6d/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 1 /tmp/w22ChRBs6d/merge.LPL.a.bcf /tmp/w22ChRBs6d/merge.LPL.b.bcf /tmp/w22ChRBs6d/merge.LPL.c.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version --force-samples -L 2 /tmp/w22ChRBs6d/merge.LPL.a.vcf.gz /tmp/w22ChRBs6d/merge.LPL.b.vcf.gz /tmp/w22ChRBs6d/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 2 /tmp/w22ChRBs6d/merge.LPL.a.vcf.gz /tmp/w22ChRBs6d/merge.LPL.b.vcf.gz /tmp/w22ChRBs6d/merge.LPL.c.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version --force-samples -L 2 /tmp/w22ChRBs6d/merge.LPL.a.bcf /tmp/w22ChRBs6d/merge.LPL.b.bcf /tmp/w22ChRBs6d/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 2 /tmp/w22ChRBs6d/merge.LPL.a.bcf /tmp/w22ChRBs6d/merge.LPL.b.bcf /tmp/w22ChRBs6d/merge.LPL.c.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version --force-samples -L 3 /tmp/w22ChRBs6d/merge.LPL.a.vcf.gz /tmp/w22ChRBs6d/merge.LPL.b.vcf.gz /tmp/w22ChRBs6d/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 3 /tmp/w22ChRBs6d/merge.LPL.a.vcf.gz /tmp/w22ChRBs6d/merge.LPL.b.vcf.gz /tmp/w22ChRBs6d/merge.LPL.c.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version --force-samples -L 3 /tmp/w22ChRBs6d/merge.LPL.a.bcf /tmp/w22ChRBs6d/merge.LPL.b.bcf /tmp/w22ChRBs6d/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 3 /tmp/w22ChRBs6d/merge.LPL.a.bcf /tmp/w22ChRBs6d/merge.LPL.b.bcf /tmp/w22ChRBs6d/merge.LPL.c.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version --force-samples -L 4 /tmp/w22ChRBs6d/merge.LPL.a.vcf.gz /tmp/w22ChRBs6d/merge.LPL.b.vcf.gz /tmp/w22ChRBs6d/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 4 /tmp/w22ChRBs6d/merge.LPL.a.vcf.gz /tmp/w22ChRBs6d/merge.LPL.b.vcf.gz /tmp/w22ChRBs6d/merge.LPL.c.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version --force-samples -L 4 /tmp/w22ChRBs6d/merge.LPL.a.bcf /tmp/w22ChRBs6d/merge.LPL.b.bcf /tmp/w22ChRBs6d/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 4 /tmp/w22ChRBs6d/merge.LPL.a.bcf /tmp/w22ChRBs6d/merge.LPL.b.bcf /tmp/w22ChRBs6d/merge.LPL.c.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version --force-samples -L 5 /tmp/w22ChRBs6d/merge.LPL.a.vcf.gz /tmp/w22ChRBs6d/merge.LPL.b.vcf.gz /tmp/w22ChRBs6d/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 5 /tmp/w22ChRBs6d/merge.LPL.a.vcf.gz /tmp/w22ChRBs6d/merge.LPL.b.vcf.gz /tmp/w22ChRBs6d/merge.LPL.c.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version --force-samples -L 5 /tmp/w22ChRBs6d/merge.LPL.a.bcf /tmp/w22ChRBs6d/merge.LPL.b.bcf /tmp/w22ChRBs6d/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 5 /tmp/w22ChRBs6d/merge.LPL.a.bcf /tmp/w22ChRBs6d/merge.LPL.b.bcf /tmp/w22ChRBs6d/merge.LPL.c.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version --force-samples /tmp/w22ChRBs6d/merge.a.vcf.gz /tmp/w22ChRBs6d/merge.b.vcf.gz /tmp/w22ChRBs6d/merge.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/w22ChRBs6d/merge.a.vcf.gz /tmp/w22ChRBs6d/merge.b.vcf.gz /tmp/w22ChRBs6d/merge.c.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version --force-samples /tmp/w22ChRBs6d/merge.a.bcf /tmp/w22ChRBs6d/merge.b.bcf /tmp/w22ChRBs6d/merge.c.bcf .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/w22ChRBs6d/merge.a.bcf /tmp/w22ChRBs6d/merge.b.bcf /tmp/w22ChRBs6d/merge.c.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version --force-samples -Fx /tmp/w22ChRBs6d/merge.a.vcf.gz /tmp/w22ChRBs6d/merge.b.vcf.gz /tmp/w22ChRBs6d/merge.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -Fx /tmp/w22ChRBs6d/merge.a.vcf.gz /tmp/w22ChRBs6d/merge.b.vcf.gz /tmp/w22ChRBs6d/merge.c.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version --force-samples -Fx /tmp/w22ChRBs6d/merge.a.bcf /tmp/w22ChRBs6d/merge.b.bcf /tmp/w22ChRBs6d/merge.c.bcf .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -Fx /tmp/w22ChRBs6d/merge.a.bcf /tmp/w22ChRBs6d/merge.b.bcf /tmp/w22ChRBs6d/merge.c.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version --force-samples -0 /tmp/w22ChRBs6d/merge.a.vcf.gz /tmp/w22ChRBs6d/merge.b.vcf.gz /tmp/w22ChRBs6d/merge.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -0 /tmp/w22ChRBs6d/merge.a.vcf.gz /tmp/w22ChRBs6d/merge.b.vcf.gz /tmp/w22ChRBs6d/merge.c.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version --force-samples -0 /tmp/w22ChRBs6d/merge.a.bcf /tmp/w22ChRBs6d/merge.b.bcf /tmp/w22ChRBs6d/merge.c.bcf .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -0 /tmp/w22ChRBs6d/merge.a.bcf /tmp/w22ChRBs6d/merge.b.bcf /tmp/w22ChRBs6d/merge.c.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version --force-samples -m none /tmp/w22ChRBs6d/merge.2.a.vcf.gz /tmp/w22ChRBs6d/merge.2.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m none /tmp/w22ChRBs6d/merge.2.a.vcf.gz /tmp/w22ChRBs6d/merge.2.b.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version --force-samples -m none /tmp/w22ChRBs6d/merge.2.a.bcf /tmp/w22ChRBs6d/merge.2.b.bcf .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m none /tmp/w22ChRBs6d/merge.2.a.bcf /tmp/w22ChRBs6d/merge.2.b.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version --force-samples -m both /tmp/w22ChRBs6d/merge.2.a.vcf.gz /tmp/w22ChRBs6d/merge.2.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m both /tmp/w22ChRBs6d/merge.2.a.vcf.gz /tmp/w22ChRBs6d/merge.2.b.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version --force-samples -m both /tmp/w22ChRBs6d/merge.2.a.bcf /tmp/w22ChRBs6d/merge.2.b.bcf .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m both /tmp/w22ChRBs6d/merge.2.a.bcf /tmp/w22ChRBs6d/merge.2.b.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version --force-samples -m all /tmp/w22ChRBs6d/merge.2.a.vcf.gz /tmp/w22ChRBs6d/merge.2.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m all /tmp/w22ChRBs6d/merge.2.a.vcf.gz /tmp/w22ChRBs6d/merge.2.b.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version --force-samples -m all /tmp/w22ChRBs6d/merge.2.a.bcf /tmp/w22ChRBs6d/merge.2.b.bcf .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m all /tmp/w22ChRBs6d/merge.2.a.bcf /tmp/w22ChRBs6d/merge.2.b.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/w22ChRBs6d/merge.3.a.vcf.gz /tmp/w22ChRBs6d/merge.3.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/w22ChRBs6d/merge.3.a.vcf.gz /tmp/w22ChRBs6d/merge.3.b.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/w22ChRBs6d/merge.3.a.bcf /tmp/w22ChRBs6d/merge.3.b.bcf .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/w22ChRBs6d/merge.3.a.bcf /tmp/w22ChRBs6d/merge.3.b.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version --force-samples -m id /tmp/w22ChRBs6d/merge.4.a.vcf.gz /tmp/w22ChRBs6d/merge.4.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m id /tmp/w22ChRBs6d/merge.4.a.vcf.gz /tmp/w22ChRBs6d/merge.4.b.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version --force-samples -m id /tmp/w22ChRBs6d/merge.4.a.bcf /tmp/w22ChRBs6d/merge.4.b.bcf .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m id /tmp/w22ChRBs6d/merge.4.a.bcf /tmp/w22ChRBs6d/merge.4.b.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/w22ChRBs6d/gvcf.merge.1.vcf.gz /tmp/w22ChRBs6d/gvcf.merge.2.vcf.gz /tmp/w22ChRBs6d/gvcf.merge.3.vcf.gz .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/w22ChRBs6d/gvcf.merge.1.vcf.gz /tmp/w22ChRBs6d/gvcf.merge.2.vcf.gz /tmp/w22ChRBs6d/gvcf.merge.3.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/w22ChRBs6d/gvcf.merge.1.bcf /tmp/w22ChRBs6d/gvcf.merge.2.bcf /tmp/w22ChRBs6d/gvcf.merge.3.bcf .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/w22ChRBs6d/gvcf.merge.1.bcf /tmp/w22ChRBs6d/gvcf.merge.2.bcf /tmp/w22ChRBs6d/gvcf.merge.3.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/w22ChRBs6d/merge.gvcf.2.a.vcf.gz /tmp/w22ChRBs6d/merge.gvcf.2.b.vcf.gz /tmp/w22ChRBs6d/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/w22ChRBs6d/merge.gvcf.2.a.vcf.gz /tmp/w22ChRBs6d/merge.gvcf.2.b.vcf.gz /tmp/w22ChRBs6d/merge.gvcf.2.c.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version --gvcf - -m both,* /tmp/w22ChRBs6d/merge.gvcf.2.a.vcf.gz /tmp/w22ChRBs6d/merge.gvcf.2.b.vcf.gz /tmp/w22ChRBs6d/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - -m both,* /tmp/w22ChRBs6d/merge.gvcf.2.a.vcf.gz /tmp/w22ChRBs6d/merge.gvcf.2.b.vcf.gz /tmp/w22ChRBs6d/merge.gvcf.2.c.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version --gvcf - -m both,** /tmp/w22ChRBs6d/merge.gvcf.2.a.vcf.gz /tmp/w22ChRBs6d/merge.gvcf.2.b.vcf.gz /tmp/w22ChRBs6d/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - -m both,** /tmp/w22ChRBs6d/merge.gvcf.2.a.vcf.gz /tmp/w22ChRBs6d/merge.gvcf.2.b.vcf.gz /tmp/w22ChRBs6d/merge.gvcf.2.c.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version --gvcf - -i SRC:join /tmp/w22ChRBs6d/merge.gvcf.3.a.vcf.gz /tmp/w22ChRBs6d/merge.gvcf.3.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - -i SRC:join /tmp/w22ChRBs6d/merge.gvcf.3.a.vcf.gz /tmp/w22ChRBs6d/merge.gvcf.3.b.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/w22ChRBs6d/merge.gvcf.4.a.vcf.gz /tmp/w22ChRBs6d/merge.gvcf.4.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/w22ChRBs6d/merge.gvcf.4.a.vcf.gz /tmp/w22ChRBs6d/merge.gvcf.4.b.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/w22ChRBs6d/merge.gvcf.4.a.bcf /tmp/w22ChRBs6d/merge.gvcf.4.b.bcf .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/w22ChRBs6d/merge.gvcf.4.a.bcf /tmp/w22ChRBs6d/merge.gvcf.4.b.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version /tmp/w22ChRBs6d/merge.5.a.vcf.gz /tmp/w22ChRBs6d/merge.5.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob /tmp/w22ChRBs6d/merge.5.a.vcf.gz /tmp/w22ChRBs6d/merge.5.b.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version /tmp/w22ChRBs6d/merge.5.a.bcf /tmp/w22ChRBs6d/merge.5.b.bcf .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob /tmp/w22ChRBs6d/merge.5.a.bcf /tmp/w22ChRBs6d/merge.5.b.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version /tmp/w22ChRBs6d/merge.6.a.vcf.gz /tmp/w22ChRBs6d/merge.6.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob /tmp/w22ChRBs6d/merge.6.a.vcf.gz /tmp/w22ChRBs6d/merge.6.b.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version /tmp/w22ChRBs6d/merge.6.a.bcf /tmp/w22ChRBs6d/merge.6.b.bcf .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob /tmp/w22ChRBs6d/merge.6.a.bcf /tmp/w22ChRBs6d/merge.6.b.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/w22ChRBs6d/merge.gvcf.7.a.vcf.gz /tmp/w22ChRBs6d/merge.gvcf.7.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/w22ChRBs6d/merge.gvcf.7.a.vcf.gz /tmp/w22ChRBs6d/merge.gvcf.7.b.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/w22ChRBs6d/merge.gvcf.7.a.bcf /tmp/w22ChRBs6d/merge.gvcf.7.b.bcf .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/w22ChRBs6d/merge.gvcf.7.a.bcf /tmp/w22ChRBs6d/merge.gvcf.7.b.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/w22ChRBs6d/merge.gvcf.8.a.vcf.gz /tmp/w22ChRBs6d/merge.gvcf.8.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/w22ChRBs6d/merge.gvcf.8.a.vcf.gz /tmp/w22ChRBs6d/merge.gvcf.8.b.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/w22ChRBs6d/merge.gvcf.8.a.bcf /tmp/w22ChRBs6d/merge.gvcf.8.b.bcf .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/w22ChRBs6d/merge.gvcf.8.a.bcf /tmp/w22ChRBs6d/merge.gvcf.8.b.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version --force-samples /tmp/w22ChRBs6d/merge.7.a.vcf.gz /tmp/w22ChRBs6d/merge.7.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/w22ChRBs6d/merge.7.a.vcf.gz /tmp/w22ChRBs6d/merge.7.b.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version --force-samples /tmp/w22ChRBs6d/merge.7.a.bcf /tmp/w22ChRBs6d/merge.7.b.bcf .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/w22ChRBs6d/merge.7.a.bcf /tmp/w22ChRBs6d/merge.7.b.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version --gvcf /build/bcftools-V6n0z8/bcftools-1.21/test/gvcf.fa /tmp/w22ChRBs6d/merge.gvcf.9a.vcf.gz /tmp/w22ChRBs6d/merge.gvcf.9b.vcf.gz /tmp/w22ChRBs6d/merge.gvcf.9c.vcf.gz /tmp/w22ChRBs6d/merge.gvcf.9d.vcf.gz .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob --gvcf /build/bcftools-V6n0z8/bcftools-1.21/test/gvcf.fa /tmp/w22ChRBs6d/merge.gvcf.9a.vcf.gz /tmp/w22ChRBs6d/merge.gvcf.9b.vcf.gz /tmp/w22ChRBs6d/merge.gvcf.9c.vcf.gz /tmp/w22ChRBs6d/merge.gvcf.9d.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version --gvcf /build/bcftools-V6n0z8/bcftools-1.21/test/gvcf.fa /tmp/w22ChRBs6d/merge.gvcf.9a.bcf /tmp/w22ChRBs6d/merge.gvcf.9b.bcf /tmp/w22ChRBs6d/merge.gvcf.9c.bcf /tmp/w22ChRBs6d/merge.gvcf.9d.bcf .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob --gvcf /build/bcftools-V6n0z8/bcftools-1.21/test/gvcf.fa /tmp/w22ChRBs6d/merge.gvcf.9a.bcf /tmp/w22ChRBs6d/merge.gvcf.9b.bcf /tmp/w22ChRBs6d/merge.gvcf.9c.bcf /tmp/w22ChRBs6d/merge.gvcf.9d.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version --gvcf /build/bcftools-V6n0z8/bcftools-1.21/test/gvcf.fa -r 22:21-23 /tmp/w22ChRBs6d/merge.gvcf.9a.vcf.gz /tmp/w22ChRBs6d/merge.gvcf.9b.vcf.gz /tmp/w22ChRBs6d/merge.gvcf.9c.vcf.gz /tmp/w22ChRBs6d/merge.gvcf.9d.vcf.gz .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob --gvcf /build/bcftools-V6n0z8/bcftools-1.21/test/gvcf.fa -r 22:21-23 /tmp/w22ChRBs6d/merge.gvcf.9a.vcf.gz /tmp/w22ChRBs6d/merge.gvcf.9b.vcf.gz /tmp/w22ChRBs6d/merge.gvcf.9c.vcf.gz /tmp/w22ChRBs6d/merge.gvcf.9d.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version --gvcf /build/bcftools-V6n0z8/bcftools-1.21/test/gvcf.fa -r 22:21-23 /tmp/w22ChRBs6d/merge.gvcf.9a.bcf /tmp/w22ChRBs6d/merge.gvcf.9b.bcf /tmp/w22ChRBs6d/merge.gvcf.9c.bcf /tmp/w22ChRBs6d/merge.gvcf.9d.bcf .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob --gvcf /build/bcftools-V6n0z8/bcftools-1.21/test/gvcf.fa -r 22:21-23 /tmp/w22ChRBs6d/merge.gvcf.9a.bcf /tmp/w22ChRBs6d/merge.gvcf.9b.bcf /tmp/w22ChRBs6d/merge.gvcf.9c.bcf /tmp/w22ChRBs6d/merge.gvcf.9d.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version --gvcf /build/bcftools-V6n0z8/bcftools-1.21/test/gvcf.fa /tmp/w22ChRBs6d/merge.gvcf.9a.vcf.gz /tmp/w22ChRBs6d/merge.gvcf.9b.vcf.gz /tmp/w22ChRBs6d/merge.gvcf.9c.vcf.gz /tmp/w22ChRBs6d/merge.gvcf.9d.vcf.gz /tmp/w22ChRBs6d/merge.gvcf.9e.vcf.gz .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob --gvcf /build/bcftools-V6n0z8/bcftools-1.21/test/gvcf.fa /tmp/w22ChRBs6d/merge.gvcf.9a.vcf.gz /tmp/w22ChRBs6d/merge.gvcf.9b.vcf.gz /tmp/w22ChRBs6d/merge.gvcf.9c.vcf.gz /tmp/w22ChRBs6d/merge.gvcf.9d.vcf.gz /tmp/w22ChRBs6d/merge.gvcf.9e.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version --gvcf /build/bcftools-V6n0z8/bcftools-1.21/test/gvcf.fa /tmp/w22ChRBs6d/merge.gvcf.9a.bcf /tmp/w22ChRBs6d/merge.gvcf.9b.bcf /tmp/w22ChRBs6d/merge.gvcf.9c.bcf /tmp/w22ChRBs6d/merge.gvcf.9d.bcf /tmp/w22ChRBs6d/merge.gvcf.9e.bcf .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob --gvcf /build/bcftools-V6n0z8/bcftools-1.21/test/gvcf.fa /tmp/w22ChRBs6d/merge.gvcf.9a.bcf /tmp/w22ChRBs6d/merge.gvcf.9b.bcf /tmp/w22ChRBs6d/merge.gvcf.9c.bcf /tmp/w22ChRBs6d/merge.gvcf.9d.bcf /tmp/w22ChRBs6d/merge.gvcf.9e.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version --gvcf /build/bcftools-V6n0z8/bcftools-1.21/test/gvcf.fa -r 22:21-23 /tmp/w22ChRBs6d/merge.gvcf.9a.vcf.gz /tmp/w22ChRBs6d/merge.gvcf.9b.vcf.gz /tmp/w22ChRBs6d/merge.gvcf.9c.vcf.gz /tmp/w22ChRBs6d/merge.gvcf.9d.vcf.gz /tmp/w22ChRBs6d/merge.gvcf.9e.vcf.gz .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob --gvcf /build/bcftools-V6n0z8/bcftools-1.21/test/gvcf.fa -r 22:21-23 /tmp/w22ChRBs6d/merge.gvcf.9a.vcf.gz /tmp/w22ChRBs6d/merge.gvcf.9b.vcf.gz /tmp/w22ChRBs6d/merge.gvcf.9c.vcf.gz /tmp/w22ChRBs6d/merge.gvcf.9d.vcf.gz /tmp/w22ChRBs6d/merge.gvcf.9e.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version --gvcf /build/bcftools-V6n0z8/bcftools-1.21/test/gvcf.fa -r 22:21-23 /tmp/w22ChRBs6d/merge.gvcf.9a.bcf /tmp/w22ChRBs6d/merge.gvcf.9b.bcf /tmp/w22ChRBs6d/merge.gvcf.9c.bcf /tmp/w22ChRBs6d/merge.gvcf.9d.bcf /tmp/w22ChRBs6d/merge.gvcf.9e.bcf .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob --gvcf /build/bcftools-V6n0z8/bcftools-1.21/test/gvcf.fa -r 22:21-23 /tmp/w22ChRBs6d/merge.gvcf.9a.bcf /tmp/w22ChRBs6d/merge.gvcf.9b.bcf /tmp/w22ChRBs6d/merge.gvcf.9c.bcf /tmp/w22ChRBs6d/merge.gvcf.9d.bcf /tmp/w22ChRBs6d/merge.gvcf.9e.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version /tmp/w22ChRBs6d/merge.gvcf.10.a.vcf.gz /tmp/w22ChRBs6d/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob /tmp/w22ChRBs6d/merge.gvcf.10.a.vcf.gz /tmp/w22ChRBs6d/merge.gvcf.10.b.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version /tmp/w22ChRBs6d/merge.gvcf.10.a.bcf /tmp/w22ChRBs6d/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob /tmp/w22ChRBs6d/merge.gvcf.10.a.bcf /tmp/w22ChRBs6d/merge.gvcf.10.b.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -m none /tmp/w22ChRBs6d/merge.gvcf.10.a.vcf.gz /tmp/w22ChRBs6d/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob -m none /tmp/w22ChRBs6d/merge.gvcf.10.a.vcf.gz /tmp/w22ChRBs6d/merge.gvcf.10.b.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -m none /tmp/w22ChRBs6d/merge.gvcf.10.a.bcf /tmp/w22ChRBs6d/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob -m none /tmp/w22ChRBs6d/merge.gvcf.10.a.bcf /tmp/w22ChRBs6d/merge.gvcf.10.b.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -g /build/bcftools-V6n0z8/bcftools-1.21/test/merge.gvcf.10.fa /tmp/w22ChRBs6d/merge.gvcf.10.a.vcf.gz /tmp/w22ChRBs6d/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob -g /build/bcftools-V6n0z8/bcftools-1.21/test/merge.gvcf.10.fa /tmp/w22ChRBs6d/merge.gvcf.10.a.vcf.gz /tmp/w22ChRBs6d/merge.gvcf.10.b.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -g /build/bcftools-V6n0z8/bcftools-1.21/test/merge.gvcf.10.fa /tmp/w22ChRBs6d/merge.gvcf.10.a.bcf /tmp/w22ChRBs6d/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob -g /build/bcftools-V6n0z8/bcftools-1.21/test/merge.gvcf.10.fa /tmp/w22ChRBs6d/merge.gvcf.10.a.bcf /tmp/w22ChRBs6d/merge.gvcf.10.b.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -g /build/bcftools-V6n0z8/bcftools-1.21/test/merge.gvcf.10.fa -m none /tmp/w22ChRBs6d/merge.gvcf.10.a.vcf.gz /tmp/w22ChRBs6d/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob -g /build/bcftools-V6n0z8/bcftools-1.21/test/merge.gvcf.10.fa -m none /tmp/w22ChRBs6d/merge.gvcf.10.a.vcf.gz /tmp/w22ChRBs6d/merge.gvcf.10.b.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -g /build/bcftools-V6n0z8/bcftools-1.21/test/merge.gvcf.10.fa -m none /tmp/w22ChRBs6d/merge.gvcf.10.a.bcf /tmp/w22ChRBs6d/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob -g /build/bcftools-V6n0z8/bcftools-1.21/test/merge.gvcf.10.fa -m none /tmp/w22ChRBs6d/merge.gvcf.10.a.bcf /tmp/w22ChRBs6d/merge.gvcf.10.b.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version /tmp/w22ChRBs6d/merge.noidx.a.vcf.gz /tmp/w22ChRBs6d/merge.noidx.b.vcf.gz /tmp/w22ChRBs6d/merge.noidx.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob /tmp/w22ChRBs6d/merge.noidx.a.vcf.gz /tmp/w22ChRBs6d/merge.noidx.b.vcf.gz /tmp/w22ChRBs6d/merge.noidx.c.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version /tmp/w22ChRBs6d/merge.noidx.a.bcf /tmp/w22ChRBs6d/merge.noidx.b.bcf /tmp/w22ChRBs6d/merge.noidx.c.bcf .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob /tmp/w22ChRBs6d/merge.noidx.a.bcf /tmp/w22ChRBs6d/merge.noidx.b.bcf /tmp/w22ChRBs6d/merge.noidx.c.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version --no-index /build/bcftools-V6n0z8/bcftools-1.21/test/merge.noidx.a.vcf /build/bcftools-V6n0z8/bcftools-1.21/test/merge.noidx.b.vcf /build/bcftools-V6n0z8/bcftools-1.21/test/merge.noidx.c.vcf .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob --no-index /build/bcftools-V6n0z8/bcftools-1.21/test/merge.noidx.a.vcf /build/bcftools-V6n0z8/bcftools-1.21/test/merge.noidx.b.vcf /build/bcftools-V6n0z8/bcftools-1.21/test/merge.noidx.c.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version --no-index /tmp/w22ChRBs6d/merge.noidx.a.bcf /tmp/w22ChRBs6d/merge.noidx.b.bcf /tmp/w22ChRBs6d/merge.noidx.c.bcf .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob --no-index /tmp/w22ChRBs6d/merge.noidx.a.bcf /tmp/w22ChRBs6d/merge.noidx.b.bcf /tmp/w22ChRBs6d/merge.noidx.c.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version /tmp/w22ChRBs6d/merge.8.a.vcf.gz /tmp/w22ChRBs6d/merge.8.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob /tmp/w22ChRBs6d/merge.8.a.vcf.gz /tmp/w22ChRBs6d/merge.8.b.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version /tmp/w22ChRBs6d/merge.8.a.bcf /tmp/w22ChRBs6d/merge.8.b.bcf .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob /tmp/w22ChRBs6d/merge.8.a.bcf /tmp/w22ChRBs6d/merge.8.b.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -i AN:sum,AC:sum /tmp/w22ChRBs6d/merge.8.a.vcf.gz /tmp/w22ChRBs6d/merge.8.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/w22ChRBs6d/merge.8.a.vcf.gz /tmp/w22ChRBs6d/merge.8.b.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -i AN:sum,AC:sum /tmp/w22ChRBs6d/merge.8.a.bcf /tmp/w22ChRBs6d/merge.8.b.bcf .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/w22ChRBs6d/merge.8.a.bcf /tmp/w22ChRBs6d/merge.8.b.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version /tmp/w22ChRBs6d/merge.9.a.vcf.gz /tmp/w22ChRBs6d/merge.9.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob /tmp/w22ChRBs6d/merge.9.a.vcf.gz /tmp/w22ChRBs6d/merge.9.b.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version /tmp/w22ChRBs6d/merge.9.a.bcf /tmp/w22ChRBs6d/merge.9.b.bcf .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob /tmp/w22ChRBs6d/merge.9.a.bcf /tmp/w22ChRBs6d/merge.9.b.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -i AN:sum,AC:sum /tmp/w22ChRBs6d/merge.9.a.vcf.gz /tmp/w22ChRBs6d/merge.9.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/w22ChRBs6d/merge.9.a.vcf.gz /tmp/w22ChRBs6d/merge.9.b.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -i AN:sum,AC:sum /tmp/w22ChRBs6d/merge.9.a.bcf /tmp/w22ChRBs6d/merge.9.b.bcf .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/w22ChRBs6d/merge.9.a.bcf /tmp/w22ChRBs6d/merge.9.b.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -m none /tmp/w22ChRBs6d/merge.10.a.vcf.gz /tmp/w22ChRBs6d/merge.10.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob -m none /tmp/w22ChRBs6d/merge.10.a.vcf.gz /tmp/w22ChRBs6d/merge.10.b.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -m none /tmp/w22ChRBs6d/merge.10.a.bcf /tmp/w22ChRBs6d/merge.10.b.bcf .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob -m none /tmp/w22ChRBs6d/merge.10.a.bcf /tmp/w22ChRBs6d/merge.10.b.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -m both /tmp/w22ChRBs6d/merge.10.a.vcf.gz /tmp/w22ChRBs6d/merge.10.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob -m both /tmp/w22ChRBs6d/merge.10.a.vcf.gz /tmp/w22ChRBs6d/merge.10.b.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -m both /tmp/w22ChRBs6d/merge.10.a.bcf /tmp/w22ChRBs6d/merge.10.b.bcf .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob -m both /tmp/w22ChRBs6d/merge.10.a.bcf /tmp/w22ChRBs6d/merge.10.b.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -m snp-ins-del /tmp/w22ChRBs6d/merge.10.a.vcf.gz /tmp/w22ChRBs6d/merge.10.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob -m snp-ins-del /tmp/w22ChRBs6d/merge.10.a.vcf.gz /tmp/w22ChRBs6d/merge.10.b.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -m snp-ins-del /tmp/w22ChRBs6d/merge.10.a.bcf /tmp/w22ChRBs6d/merge.10.b.bcf .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob -m snp-ins-del /tmp/w22ChRBs6d/merge.10.a.bcf /tmp/w22ChRBs6d/merge.10.b.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/w22ChRBs6d/merge.mrules.1.a.vcf.gz /tmp/w22ChRBs6d/merge.mrules.1.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/w22ChRBs6d/merge.mrules.1.a.vcf.gz /tmp/w22ChRBs6d/merge.mrules.1.b.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/w22ChRBs6d/merge.mrules.1.a.bcf /tmp/w22ChRBs6d/merge.mrules.1.b.bcf .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/w22ChRBs6d/merge.mrules.1.a.bcf /tmp/w22ChRBs6d/merge.mrules.1.b.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version --gvcf - -M AD:.,PL:. /tmp/w22ChRBs6d/merge.mrules.1.a.vcf.gz /tmp/w22ChRBs6d/merge.mrules.1.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - -M AD:.,PL:. /tmp/w22ChRBs6d/merge.mrules.1.a.vcf.gz /tmp/w22ChRBs6d/merge.mrules.1.b.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version --gvcf - -M AD:.,PL:. /tmp/w22ChRBs6d/merge.mrules.1.a.bcf /tmp/w22ChRBs6d/merge.mrules.1.b.bcf .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - -M AD:.,PL:. /tmp/w22ChRBs6d/merge.mrules.1.a.bcf /tmp/w22ChRBs6d/merge.mrules.1.b.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/w22ChRBs6d/merge.gvcf.5.a.vcf.gz /tmp/w22ChRBs6d/merge.gvcf.5.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/w22ChRBs6d/merge.gvcf.5.a.vcf.gz /tmp/w22ChRBs6d/merge.gvcf.5.b.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/w22ChRBs6d/merge.gvcf.5.a.bcf /tmp/w22ChRBs6d/merge.gvcf.5.b.bcf .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/w22ChRBs6d/merge.gvcf.5.a.bcf /tmp/w22ChRBs6d/merge.gvcf.5.b.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version --gvcf - --merge none /tmp/w22ChRBs6d/merge.gvcf.5.a.vcf.gz /tmp/w22ChRBs6d/merge.gvcf.5.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - --merge none /tmp/w22ChRBs6d/merge.gvcf.5.a.vcf.gz /tmp/w22ChRBs6d/merge.gvcf.5.b.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version --gvcf - --merge none /tmp/w22ChRBs6d/merge.gvcf.5.a.bcf /tmp/w22ChRBs6d/merge.gvcf.5.b.bcf .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - --merge none /tmp/w22ChRBs6d/merge.gvcf.5.a.bcf /tmp/w22ChRBs6d/merge.gvcf.5.b.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/w22ChRBs6d/merge.gvcf.11.a.vcf.gz /tmp/w22ChRBs6d/merge.gvcf.11.b.vcf.gz /tmp/w22ChRBs6d/merge.gvcf.11.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/w22ChRBs6d/merge.gvcf.11.a.vcf.gz /tmp/w22ChRBs6d/merge.gvcf.11.b.vcf.gz /tmp/w22ChRBs6d/merge.gvcf.11.c.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/w22ChRBs6d/merge.gvcf.11.a.bcf /tmp/w22ChRBs6d/merge.gvcf.11.b.bcf /tmp/w22ChRBs6d/merge.gvcf.11.c.bcf .. ok test_vcf_merge: /build/bcftools-V6n0z8/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/w22ChRBs6d/merge.gvcf.11.a.bcf /tmp/w22ChRBs6d/merge.gvcf.11.b.bcf /tmp/w22ChRBs6d/merge.gvcf.11.c.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided,_conflicting_interpretations"' /tmp/w22ChRBs6d/query.string.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.string.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided,_conflicting_interpretations"' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" || CLNREVSTAT="_conflicting_interpretations"' /tmp/w22ChRBs6d/query.string.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.string.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" || CLNREVSTAT="_conflicting_interpretations"' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" && CLNREVSTAT="_conflicting_interpretations"' /tmp/w22ChRBs6d/query.string.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.string.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" && CLNREVSTAT="_conflicting_interpretations"' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%INFO/STR\n' -i'INFO/STR=@/build/bcftools-V6n0z8/bcftools-1.21/test/query.string.2.1.txt' /tmp/w22ChRBs6d/query.string.2.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.string.2.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%INFO/STR\n' -i'INFO/STR=@/build/bcftools-V6n0z8/bcftools-1.21/test/query.string.2.1.txt' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%CHROM\t%POS[\t%STR]\n' -i'FMT/STR=@/build/bcftools-V6n0z8/bcftools-1.21/test/query.string.2.2.txt' /tmp/w22ChRBs6d/query.string.2.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.string.2.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%CHROM\t%POS[\t%STR]\n' -i'FMT/STR=@/build/bcftools-V6n0z8/bcftools-1.21/test/query.string.2.2.txt' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' /tmp/w22ChRBs6d/query.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/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-V6n0z8/bcftools-1.21/bcftools query -f '%RSX\t%VKX\n' /tmp/w22ChRBs6d/query.variantkey.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.variantkey.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%RSX\t%VKX\n' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%XRI\n' -i'XRI[*]>1111' /tmp/w22ChRBs6d/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/view.filter.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%XRI\n' -i'XRI[*]>1111' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' /tmp/w22ChRBs6d/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/view.filter.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' /tmp/w22ChRBs6d/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/view.filter.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' /tmp/w22ChRBs6d/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/view.filter.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' /tmp/w22ChRBs6d/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/view.filter.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' /tmp/w22ChRBs6d/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/view.filter.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' /tmp/w22ChRBs6d/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/view.filter.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' /tmp/w22ChRBs6d/query.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' /tmp/w22ChRBs6d/query.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' /tmp/w22ChRBs6d/query.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' /tmp/w22ChRBs6d/query.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' /tmp/w22ChRBs6d/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/view.filter.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' /tmp/w22ChRBs6d/query.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' /tmp/w22ChRBs6d/query.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' /tmp/w22ChRBs6d/query.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' /tmp/w22ChRBs6d/query.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/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/w22ChRBs6d/view.vectors.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/view.vectors.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/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-V6n0z8/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' /tmp/w22ChRBs6d/query.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.filter.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' /tmp/w22ChRBs6d/query.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.filter.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' /tmp/w22ChRBs6d/query.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.filter.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' /tmp/w22ChRBs6d/query.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.filter.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' /tmp/w22ChRBs6d/query.2.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.2.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -i'IINT="."' -f'%POS %IINT\n' /tmp/w22ChRBs6d/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/missing.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -i'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -i'IINT!="."' -f'%POS %IINT\n' /tmp/w22ChRBs6d/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/missing.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -i'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -e'IINT!="."' -f'%POS %IINT\n' /tmp/w22ChRBs6d/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/missing.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -e'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -e'IINT="."' -f'%POS %IINT\n' /tmp/w22ChRBs6d/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/missing.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -e'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' /tmp/w22ChRBs6d/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/missing.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' /tmp/w22ChRBs6d/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/missing.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' /tmp/w22ChRBs6d/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/missing.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' /tmp/w22ChRBs6d/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/missing.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' /tmp/w22ChRBs6d/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/missing.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' /tmp/w22ChRBs6d/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/missing.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' /tmp/w22ChRBs6d/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/missing.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' /tmp/w22ChRBs6d/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/missing.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' /tmp/w22ChRBs6d/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/missing.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -i'FILTER="A"' -f'%POS %FILTER\n' /tmp/w22ChRBs6d/filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/filter.11.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -i'FILTER="A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -i'FILTER!="A"' -f'%POS %FILTER\n' /tmp/w22ChRBs6d/filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/filter.11.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -i'FILTER!="A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -i'FILTER~"A"' -f'%POS %FILTER\n' /tmp/w22ChRBs6d/filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/filter.11.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -i'FILTER~"A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n' /tmp/w22ChRBs6d/filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/filter.11.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%LINE' /tmp/w22ChRBs6d/query.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%LINE' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' /tmp/w22ChRBs6d/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.filter-type.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' /tmp/w22ChRBs6d/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.filter-type.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' /tmp/w22ChRBs6d/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.filter-type.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' /tmp/w22ChRBs6d/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.filter-type.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'INFO/TYPE="xxx"' /tmp/w22ChRBs6d/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.filter-type.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'INFO/TYPE="xxx"' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/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/w22ChRBs6d/filter-missing-floats.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/filter-missing-floats.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/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-V6n0z8/bcftools-1.21/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/w22ChRBs6d/filter-missing-floats.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/filter-missing-floats.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/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-V6n0z8/bcftools-1.21/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' /tmp/w22ChRBs6d/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/missing.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' /tmp/w22ChRBs6d/query.filter.2.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.filter.2.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' /tmp/w22ChRBs6d/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/view.filter.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' /tmp/w22ChRBs6d/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/view.filter.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' /tmp/w22ChRBs6d/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/view.filter.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' /tmp/w22ChRBs6d/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/view.filter.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' /tmp/w22ChRBs6d/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/view.filter.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' /tmp/w22ChRBs6d/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/view.filter.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' /tmp/w22ChRBs6d/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/view.filter.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' /tmp/w22ChRBs6d/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/view.filter.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' /tmp/w22ChRBs6d/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/view.filter.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' /tmp/w22ChRBs6d/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/view.filter.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' /tmp/w22ChRBs6d/filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/filter.5.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' /tmp/w22ChRBs6d/filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/filter.5.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' /tmp/w22ChRBs6d/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/view.filter.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' /tmp/w22ChRBs6d/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/view.filter.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' /tmp/w22ChRBs6d/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/view.filter.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' /tmp/w22ChRBs6d/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/view.filter.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' /tmp/w22ChRBs6d/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/view.filter.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 & FMT/GQ=589' /tmp/w22ChRBs6d/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/view.filter.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 & FMT/GQ=589' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' /tmp/w22ChRBs6d/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/view.filter.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' /tmp/w22ChRBs6d/query.filter.3.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.filter.3.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"' /tmp/w22ChRBs6d/query.filter.3.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.filter.3.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' /tmp/w22ChRBs6d/query.filter.3.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.filter.3.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %AD\n]\n' -i'AD[:0]+AD[:1] > 12' /tmp/w22ChRBs6d/filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/filter.5.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %AD\n]\n' -i'AD[:0]+AD[:1] > 12' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' /tmp/w22ChRBs6d/query.filter.4.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.filter.4.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%ID\n' -i 'ID=@/build/bcftools-V6n0z8/bcftools-1.21/test/query.56.out' /tmp/w22ChRBs6d/view.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/view.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%ID\n' -i 'ID=@/build/bcftools-V6n0z8/bcftools-1.21/test/query.56.out' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD)>0.01' /tmp/w22ChRBs6d/query.filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.filter.5.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/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-V6n0z8/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD[:0],FMT/AD[:1])>0.01' /tmp/w22ChRBs6d/query.filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.filter.5.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/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-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%AD\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01' /tmp/w22ChRBs6d/query.filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.filter.5.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%AD\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[GT]==10' /tmp/w22ChRBs6d/query.filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.filter.5.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[GT]==10' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'sSUM(FMT/AD[GT])==210' /tmp/w22ChRBs6d/query.filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.filter.5.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'sSUM(FMT/AD[GT])==210' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[0:GT]==30' /tmp/w22ChRBs6d/query.filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.filter.5.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[0:GT]==30' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TF[:GT]==1 && FMT/TF[:GT]==2' /tmp/w22ChRBs6d/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.gtidx.1.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TF[:GT]==1 && FMT/TF[:GT]==2' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TI[:GT]==1 && FMT/TF[:GT]==2' /tmp/w22ChRBs6d/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.gtidx.1.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TI[:GT]==1 && FMT/TF[:GT]==2' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TS[:GT]=="BB" && FMT/TS[:GT]=="CC"' /tmp/w22ChRBs6d/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.gtidx.1.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TS[:GT]=="BB" && FMT/TS[:GT]=="CC"' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TC[:GT]=="B" && FMT/TC[:GT]=="C"' /tmp/w22ChRBs6d/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.gtidx.1.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TC[:GT]=="B" && FMT/TC[:GT]=="C"' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%GT %TI\n]' -i'FMT/TI[:GT]=="."' /tmp/w22ChRBs6d/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.gtidx.1.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%GT %TI\n]' -i'FMT/TI[:GT]=="."' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%CHROM %POS\n' -i'CHROM="4"' /tmp/w22ChRBs6d/query.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%CHROM %POS\n' -i'CHROM="4"' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%TAG1\n' -i'(TAG1>=-129 && TAG1<=-120) || (TAG1>=-32769 && TAG1<=-32760)' /tmp/w22ChRBs6d/query.negative.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.negative.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%TAG1\n' -i'(TAG1>=-129 && TAG1<=-120) || (TAG1>=-32769 && TAG1<=-32760)' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%TAGV1\n' -i'(TAGV1>=-129 && TAGV1<=-120) || (TAGV1>=-32769 && TAGV1<=-32760)' /tmp/w22ChRBs6d/query.negative.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.negative.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%TAGV1\n' -i'(TAGV1>=-129 && TAGV1<=-120) || (TAGV1>=-32769 && TAGV1<=-32760)' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%TAG2\n' -i'(TAG2>=-129 && TAG2<=-120) || (TAG2>=-32769 && TAG2<=-32760)' /tmp/w22ChRBs6d/query.negative.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.negative.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%TAG2\n' -i'(TAG2>=-129 && TAG2<=-120) || (TAG2>=-32769 && TAG2<=-32760)' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%TAGV2\n' -i'(TAGV2>=-129 && TAGV2<=-120) || (TAGV2>=-32769 && TAGV2<=-32760)' /tmp/w22ChRBs6d/query.negative.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.negative.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%TAGV2\n' -i'(TAGV2>=-129 && TAGV2<=-120) || (TAGV2>=-32769 && TAGV2<=-32760)' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GQ\n]' -i'N_PASS(GQ<20)==1' /tmp/w22ChRBs6d/query.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GQ\n]' -i'N_PASS(GQ<20)==1' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")==1' /tmp/w22ChRBs6d/query.filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.filter.11.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")==1' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")!=1' /tmp/w22ChRBs6d/query.filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.filter.11.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")!=1' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")==1' /tmp/w22ChRBs6d/query.filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.filter.11.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")==1' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")!=1' /tmp/w22ChRBs6d/query.filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.filter.11.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")!=1' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%CHROM\t%POS\t%INFO\t%FORMAT\n' -s D,C /tmp/w22ChRBs6d/query.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%CHROM\t%POS\t%INFO\t%FORMAT\n' -s D,C .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\n' -i'POS==16777217 || POS==33554432 || POS=118673904' /tmp/w22ChRBs6d/query.filter.6.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.filter.6.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\n' -i'POS==16777217 || POS==33554432 || POS=118673904' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(II)==6' /tmp/w22ChRBs6d/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.filter.7.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(II)==6' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(FORMAT/FI)==7' /tmp/w22ChRBs6d/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.filter.7.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(FORMAT/FI)==7' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(II)==2' /tmp/w22ChRBs6d/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.filter.7.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(II)==2' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(FORMAT/FI)==1.75' /tmp/w22ChRBs6d/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.filter.7.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(FORMAT/FI)==1.75' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(II)==2' /tmp/w22ChRBs6d/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.filter.7.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(II)==2' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(FORMAT/FI)==1.75' /tmp/w22ChRBs6d/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.filter.7.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(FORMAT/FI)==1.75' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(II)==2' /tmp/w22ChRBs6d/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.filter.7.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(II)==2' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(FORMAT/FI)==1.5' /tmp/w22ChRBs6d/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.filter.7.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(FORMAT/FI)==1.5' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'%ILEN==1' /tmp/w22ChRBs6d/query.filter.8.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.filter.8.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'%ILEN==1' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'ILEN==1' /tmp/w22ChRBs6d/query.filter.8.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.filter.8.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'ILEN==1' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] < FMT/AD[:1]' /tmp/w22ChRBs6d/query.filter.9.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.filter.9.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] < FMT/AD[:1]' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] > FMT/AD[:1]' /tmp/w22ChRBs6d/query.filter.9.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.filter.9.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] > FMT/AD[:1]' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[ %AD\n]' -i'AD[:1] / sum(AD[*]) > 0.5' /tmp/w22ChRBs6d/query.filter.13.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.filter.13.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[ %AD\n]' -i'AD[:1] / sum(AD[*]) > 0.5' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS %NUM_TAG\n' -i'COUNT(INFO/NUM_TAG)=2' /tmp/w22ChRBs6d/query.filter.10.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.filter.10.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS %NUM_TAG\n' -i'COUNT(INFO/NUM_TAG)=2' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2' /tmp/w22ChRBs6d/query.filter.10.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.filter.10.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%CHROM:%POS\t%N_PASS(GT="alt" & GQ>110)\t[\t%GT]\t[\t%GQ]\n' /tmp/w22ChRBs6d/query.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%CHROM:%POS\t%N_PASS(GT="alt" & GQ>110)\t[\t%GT]\t[\t%GQ]\n' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 1,3,0 /tmp/w22ChRBs6d/query.filter.12.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.filter.12.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 1,3,0 .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 0,1,3 /tmp/w22ChRBs6d/query.filter.12.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.filter.12.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 0,1,3 .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f "[%SAMPLE %GT\n]" -S /build/bcftools-V6n0z8/bcftools-1.21/test/query.smpl.11.txt /tmp/w22ChRBs6d/query.smpl.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.smpl.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f "[%SAMPLE %GT\n]" -S /build/bcftools-V6n0z8/bcftools-1.21/test/query.smpl.11.txt .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -l -S /build/bcftools-V6n0z8/bcftools-1.21/test/query.smpl.11.txt /tmp/w22ChRBs6d/query.smpl.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.smpl.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -l -S /build/bcftools-V6n0z8/bcftools-1.21/test/query.smpl.11.txt .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f "[%SAMPLE %GT\n]" -S ^/build/bcftools-V6n0z8/bcftools-1.21/test/query.smpl.11.txt /tmp/w22ChRBs6d/query.smpl.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.smpl.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f "[%SAMPLE %GT\n]" -S ^/build/bcftools-V6n0z8/bcftools-1.21/test/query.smpl.11.txt .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -l -S ^/build/bcftools-V6n0z8/bcftools-1.21/test/query.smpl.11.txt /tmp/w22ChRBs6d/query.smpl.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.smpl.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -l -S ^/build/bcftools-V6n0z8/bcftools-1.21/test/query.smpl.11.txt .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f "[%SAMPLE %GT\n]" -S /build/bcftools-V6n0z8/bcftools-1.21/test/query.smpl.txt /tmp/w22ChRBs6d/query.smpl.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.smpl.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f "[%SAMPLE %GT\n]" -S /build/bcftools-V6n0z8/bcftools-1.21/test/query.smpl.txt .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -l -S /build/bcftools-V6n0z8/bcftools-1.21/test/query.smpl.txt /tmp/w22ChRBs6d/query.smpl.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.smpl.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -l -S /build/bcftools-V6n0z8/bcftools-1.21/test/query.smpl.txt .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%ID\n' -i'ID~"s12"' /tmp/w22ChRBs6d/query.filter.id.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.filter.id.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%ID\n' -i'ID~"s12"' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%ID\n' -i'ID="rs123"' /tmp/w22ChRBs6d/query.filter.id.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.filter.id.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%ID\n' -i'ID="rs123"' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%ID\n' -i'ID="abc"' /tmp/w22ChRBs6d/query.filter.id.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.filter.id.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%ID\n' -i'ID="abc"' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%ID\n' -i'ID=@/build/bcftools-V6n0z8/bcftools-1.21/test/query.filter.id.3.txt' /tmp/w22ChRBs6d/query.filter.id.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.filter.id.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%ID\n' -i'ID=@/build/bcftools-V6n0z8/bcftools-1.21/test/query.filter.id.3.txt' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%ID\n' -i'ID!="abc"' /tmp/w22ChRBs6d/query.filter.id.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.filter.id.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%ID\n' -i'ID!="abc"' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%ID\n' -i'ID!=@/build/bcftools-V6n0z8/bcftools-1.21/test/query.filter.id.3.txt' /tmp/w22ChRBs6d/query.filter.id.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.filter.id.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%ID\n' -i'ID!=@/build/bcftools-V6n0z8/bcftools-1.21/test/query.filter.id.3.txt' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -i'FILTER="A"' -f'%FILTER\n' /tmp/w22ChRBs6d/filter.12.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/filter.12.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -i'FILTER="A"' -f'%FILTER\n' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -i'FILTER~"A"' -f'%FILTER\n' /tmp/w22ChRBs6d/filter.12.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/filter.12.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -i'FILTER~"A"' -f'%FILTER\n' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -i'FILTER="A;B"' -f'%FILTER\n' /tmp/w22ChRBs6d/filter.12.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/filter.12.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -i'FILTER="A;B"' -f'%FILTER\n' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -i'FILTER!="A;B"' -f'%FILTER\n' /tmp/w22ChRBs6d/filter.12.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/filter.12.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -i'FILTER!="A;B"' -f'%FILTER\n' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -i'FILTER~"A;B"' -f'%FILTER\n' /tmp/w22ChRBs6d/filter.12.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/filter.12.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -i'FILTER~"A;B"' -f'%FILTER\n' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -i'FILTER!~"A;B"' -f'%FILTER\n' /tmp/w22ChRBs6d/filter.12.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/filter.12.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -i'FILTER!~"A;B"' -f'%FILTER\n' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -i'DP%10==2' -f'[ %DP]\n' /tmp/w22ChRBs6d/filter.10.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/filter.10.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -i'DP%10==2' -f'[ %DP]\n' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -i'REF="N"' -f'%CHROM %POS %REF %ALT %QUAL\n' /tmp/w22ChRBs6d/filter.13.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/filter.13.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -i'REF="N"' -f'%CHROM %POS %REF %ALT %QUAL\n' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -H -f'[%CHROM %POS %SAMPLE %DP %GT\n]' /tmp/w22ChRBs6d/query.header.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.header.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -H -f'[%CHROM %POS %SAMPLE %DP %GT\n]' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -H -f'[%CHROM %POS %SAMPLE %DP %GT\t]\n' /tmp/w22ChRBs6d/query.header.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.header.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -H -f'[%CHROM %POS %SAMPLE %DP %GT\t]\n' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]\n' /tmp/w22ChRBs6d/query.header.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.header.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]\n' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]' /tmp/w22ChRBs6d/query.header.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.header.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]\n' /tmp/w22ChRBs6d/query.header.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.header.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]\n' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]' /tmp/w22ChRBs6d/query.header.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.header.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -HH -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]' /tmp/w22ChRBs6d/query.header.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.header.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -HH -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%SAMPLE %DP\n]' -i'DP=1 || DP=2' /tmp/w22ChRBs6d/query.filter-or.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.filter-or.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%SAMPLE %DP\n]' -i'DP=1 || DP=2' .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%SAMPLE %DP\n]' -i'DP=1 | DP=2' /tmp/w22ChRBs6d/query.filter-or.vcf.gz .. ok test_vcf_query: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/query.filter-or.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%SAMPLE %DP\n]' -i'DP=1 | DP=2' .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m - /tmp/w22ChRBs6d/norm.sort.vcf.gz .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m - /tmp/w22ChRBs6d/norm.sort.vcf.gz -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m - -S lex /tmp/w22ChRBs6d/norm.sort.vcf.gz .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m - -S lex /tmp/w22ChRBs6d/norm.sort.vcf.gz -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m +both /tmp/w22ChRBs6d/norm.join-missing-ploidy.vcf.gz .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m +both /tmp/w22ChRBs6d/norm.join-missing-ploidy.vcf.gz -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m - --multi-overlaps . /tmp/w22ChRBs6d/norm.split.5.vcf.gz .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m - --multi-overlaps . /tmp/w22ChRBs6d/norm.split.5.vcf.gz -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version /tmp/w22ChRBs6d/norm.symbolic.3.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/norm.symbolic.3.fa .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version /tmp/w22ChRBs6d/norm.symbolic.3.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/norm.symbolic.3.fa -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -cx /tmp/w22ChRBs6d/norm.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/norm.fa .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -cx /tmp/w22ChRBs6d/norm.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/norm.fa -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m- /tmp/w22ChRBs6d/norm.split.vcf.gz .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m- /tmp/w22ChRBs6d/norm.split.vcf.gz -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m- /tmp/w22ChRBs6d/norm.split.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m- /tmp/w22ChRBs6d/norm.split.2.vcf.gz -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m- --force /tmp/w22ChRBs6d/norm.split.3.vcf.gz .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m- --force /tmp/w22ChRBs6d/norm.split.3.vcf.gz -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m- /tmp/w22ChRBs6d/norm.split.4.vcf.gz .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m- /tmp/w22ChRBs6d/norm.split.4.vcf.gz -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m- --keep-sum AD /tmp/w22ChRBs6d/norm.split.4.vcf.gz .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m- --keep-sum AD /tmp/w22ChRBs6d/norm.split.4.vcf.gz -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m- /tmp/w22ChRBs6d/norm.split.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/norm.fa .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m- /tmp/w22ChRBs6d/norm.split.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/norm.fa -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m+ /tmp/w22ChRBs6d/norm.merge.vcf.gz .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m+ /tmp/w22ChRBs6d/norm.merge.vcf.gz -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m+ /tmp/w22ChRBs6d/norm.merge.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m+ /tmp/w22ChRBs6d/norm.merge.2.vcf.gz -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m+ /tmp/w22ChRBs6d/norm.merge.3.vcf.gz .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m+ /tmp/w22ChRBs6d/norm.merge.3.vcf.gz -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m+ -s /tmp/w22ChRBs6d/norm.merge.vcf.gz .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m+ -s /tmp/w22ChRBs6d/norm.merge.vcf.gz -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -Nc s /tmp/w22ChRBs6d/norm.setref.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/norm.fa .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -Nc s /tmp/w22ChRBs6d/norm.setref.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/norm.fa -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version /tmp/w22ChRBs6d/norm.telomere.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/norm.fa .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version /tmp/w22ChRBs6d/norm.telomere.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/norm.fa -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -d snps /tmp/w22ChRBs6d/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -d snps /tmp/w22ChRBs6d/norm.rmdup.vcf.gz -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -d indels /tmp/w22ChRBs6d/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -d indels /tmp/w22ChRBs6d/norm.rmdup.vcf.gz -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -d both /tmp/w22ChRBs6d/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -d both /tmp/w22ChRBs6d/norm.rmdup.vcf.gz -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -d all /tmp/w22ChRBs6d/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -d all /tmp/w22ChRBs6d/norm.rmdup.vcf.gz -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -d none /tmp/w22ChRBs6d/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -d none /tmp/w22ChRBs6d/norm.rmdup.vcf.gz -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -d exact /tmp/w22ChRBs6d/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -d exact /tmp/w22ChRBs6d/norm.rmdup.vcf.gz -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -d none /tmp/w22ChRBs6d/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -d none /tmp/w22ChRBs6d/norm.rmdup.2.vcf.gz -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -d exact /tmp/w22ChRBs6d/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -d exact /tmp/w22ChRBs6d/norm.rmdup.2.vcf.gz -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -d indels /tmp/w22ChRBs6d/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -d indels /tmp/w22ChRBs6d/norm.rmdup.2.vcf.gz -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -d any /tmp/w22ChRBs6d/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -d any /tmp/w22ChRBs6d/norm.rmdup.2.vcf.gz -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -d both /tmp/w22ChRBs6d/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -d both /tmp/w22ChRBs6d/norm.rmdup.2.vcf.gz -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -d snps /tmp/w22ChRBs6d/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -d snps /tmp/w22ChRBs6d/norm.rmdup.2.vcf.gz -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -d exact /tmp/w22ChRBs6d/norm.rmdup.3.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/norm.rmdup.3.fa .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -d exact /tmp/w22ChRBs6d/norm.rmdup.3.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/norm.rmdup.3.fa -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -d all /tmp/w22ChRBs6d/norm.rmdup.3.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/norm.rmdup.3.fa .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -d all /tmp/w22ChRBs6d/norm.rmdup.3.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/norm.rmdup.3.fa -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -c s -a /tmp/w22ChRBs6d/norm.2.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/norm.2.fa .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -c s -a /tmp/w22ChRBs6d/norm.2.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/norm.2.fa -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -c s /tmp/w22ChRBs6d/norm.iupac.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/norm.iupac.fa .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -c s /tmp/w22ChRBs6d/norm.iupac.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/norm.iupac.fa -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -c s /tmp/w22ChRBs6d/norm.3.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/norm.3.fa .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -c s /tmp/w22ChRBs6d/norm.3.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/norm.3.fa -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -c s -i'alt="N"' /tmp/w22ChRBs6d/norm.3.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/norm.3.fa .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -c s -i'alt="N"' /tmp/w22ChRBs6d/norm.3.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/norm.3.fa -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -a --old-rec-tag OLD_REC /tmp/w22ChRBs6d/atomize.split.1.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m -any --force .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -a --old-rec-tag OLD_REC /tmp/w22ChRBs6d/atomize.split.1.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m -any --force -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m -any --old-rec-tag OLD_REC --force /tmp/w22ChRBs6d/atomize.split.1.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -a .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m -any --old-rec-tag OLD_REC --force /tmp/w22ChRBs6d/atomize.split.1.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -a -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m -any --old-rec-tag OLD_REC --force -a /tmp/w22ChRBs6d/atomize.split.1.vcf.gz .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m -any --old-rec-tag OLD_REC --force -a /tmp/w22ChRBs6d/atomize.split.1.vcf.gz -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/w22ChRBs6d/atomize.split.1.vcf.gz .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/w22ChRBs6d/atomize.split.1.vcf.gz -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/w22ChRBs6d/atomize.split.1.vcf.gz .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/w22ChRBs6d/atomize.split.1.vcf.gz -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/w22ChRBs6d/atomize.split.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/w22ChRBs6d/atomize.split.2.vcf.gz -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/w22ChRBs6d/atomize.split.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/w22ChRBs6d/atomize.split.2.vcf.gz -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . /tmp/w22ChRBs6d/atomize.split.3.vcf.gz .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . /tmp/w22ChRBs6d/atomize.split.3.vcf.gz -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/w22ChRBs6d/atomize.split.4.vcf.gz .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/w22ChRBs6d/atomize.split.4.vcf.gz -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC -i 'ILEN=0' /tmp/w22ChRBs6d/atomize.split.4.vcf.gz .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC -i 'ILEN=0' /tmp/w22ChRBs6d/atomize.split.4.vcf.gz -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version --atomize --old-rec-tag OLD_REC --atom-overlaps . /tmp/w22ChRBs6d/atomize.split.5.vcf.gz .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version --atomize --old-rec-tag OLD_REC --atom-overlaps . /tmp/w22ChRBs6d/atomize.split.5.vcf.gz -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/w22ChRBs6d/atomize.split.5.vcf.gz .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/w22ChRBs6d/atomize.split.5.vcf.gz -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m +both /tmp/w22ChRBs6d/norm.4.vcf.gz .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m +both /tmp/w22ChRBs6d/norm.4.vcf.gz -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m +any /tmp/w22ChRBs6d/norm.4.vcf.gz .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m +any /tmp/w22ChRBs6d/norm.4.vcf.gz -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m - --multi-overlaps 0 /tmp/w22ChRBs6d/norm.5.vcf.gz .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m - --multi-overlaps 0 /tmp/w22ChRBs6d/norm.5.vcf.gz -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m - --multi-overlaps . /tmp/w22ChRBs6d/norm.5.vcf.gz .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m - --multi-overlaps . /tmp/w22ChRBs6d/norm.5.vcf.gz -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m -any /tmp/w22ChRBs6d/norm.m-any.vcf.gz .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m -any /tmp/w22ChRBs6d/norm.m-any.vcf.gz -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m -any /tmp/w22ChRBs6d/norm.phased-split.vcf.gz .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m -any /tmp/w22ChRBs6d/norm.phased-split.vcf.gz -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m +any /tmp/w22ChRBs6d/norm.phased-join.vcf.gz .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m +any /tmp/w22ChRBs6d/norm.phased-join.vcf.gz -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI /tmp/w22ChRBs6d/norm.symbolic.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/norm.symbolic.fa .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI /tmp/w22ChRBs6d/norm.symbolic.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/norm.symbolic.fa -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI /tmp/w22ChRBs6d/norm.symbolic.2.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/norm.symbolic.fa .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI /tmp/w22ChRBs6d/norm.symbolic.2.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/norm.symbolic.fa -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI /tmp/w22ChRBs6d/norm.right-align.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/norm.right-align.fa .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI /tmp/w22ChRBs6d/norm.right-align.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/norm.right-align.fa -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI -g /build/bcftools-V6n0z8/bcftools-1.21/test/norm.right-align.gff /tmp/w22ChRBs6d/norm.right-align.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/norm.right-align.fa .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI -g /build/bcftools-V6n0z8/bcftools-1.21/test/norm.right-align.gff /tmp/w22ChRBs6d/norm.right-align.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/norm.right-align.fa -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI -a -m -any /tmp/w22ChRBs6d/norm.atom-split-norm.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/norm.atom-split-norm.fa .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI -a -m -any /tmp/w22ChRBs6d/norm.atom-split-norm.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/norm.atom-split-norm.fa -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m -any /tmp/w22ChRBs6d/norm.string-tags.vcf.gz .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m -any /tmp/w22ChRBs6d/norm.string-tags.vcf.gz -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m - /tmp/w22ChRBs6d/norm.split.merge.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m +both .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m - /tmp/w22ChRBs6d/norm.split.merge.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m +both -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m - /tmp/w22ChRBs6d/norm.split.merge.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m +indels .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m - /tmp/w22ChRBs6d/norm.split.merge.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m +indels -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m - /tmp/w22ChRBs6d/norm.split.merge.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m +snps .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m - /tmp/w22ChRBs6d/norm.split.merge.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m +snps -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m - /tmp/w22ChRBs6d/norm.split.merge.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m +snps .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m - /tmp/w22ChRBs6d/norm.split.merge.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m +snps -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m - /tmp/w22ChRBs6d/norm.split.merge.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m +any .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m - /tmp/w22ChRBs6d/norm.split.merge.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m +any -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m - -i 'type="snp"' /tmp/w22ChRBs6d/norm.split.merge.vcf.gz .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m - -i 'type="snp"' /tmp/w22ChRBs6d/norm.split.merge.vcf.gz -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m +any /tmp/w22ChRBs6d/norm.merge.4.vcf.gz .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m +any /tmp/w22ChRBs6d/norm.merge.4.vcf.gz -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m +both /tmp/w22ChRBs6d/norm.merge.4.vcf.gz .. ok test_vcf_norm: /build/bcftools-V6n0z8/bcftools-1.21/bcftools norm --no-version -m +both /tmp/w22ChRBs6d/norm.merge.4.vcf.gz -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version -i 'INFO/TAG=@/build/bcftools-V6n0z8/bcftools-1.21/test/filter.string.1.txt' /tmp/w22ChRBs6d/filter.string.1.vcf.gz .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob -i 'INFO/TAG=@/build/bcftools-V6n0z8/bcftools-1.21/test/filter.string.1.txt' /tmp/w22ChRBs6d/filter.string.1.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version -i 'FMT/TAG=@/build/bcftools-V6n0z8/bcftools-1.21/test/filter.string.1.txt' /tmp/w22ChRBs6d/filter.string.1.vcf.gz .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob -i 'FMT/TAG=@/build/bcftools-V6n0z8/bcftools-1.21/test/filter.string.1.txt' /tmp/w22ChRBs6d/filter.string.1.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version -HA /tmp/w22ChRBs6d/merge.gvcf.2.a.vcf.gz .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version -HAA /tmp/w22ChRBs6d/merge.gvcf.2.a.vcf.gz .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version /tmp/w22ChRBs6d/weird-chr-names.vcf.gz -r 1 .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/weird-chr-names.vcf.gz -r 1 | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version /tmp/w22ChRBs6d/weird-chr-names.vcf.gz -r 1:1-2 .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/weird-chr-names.vcf.gz -r 1:1-2 | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version /tmp/w22ChRBs6d/weird-chr-names.vcf.gz -r 1:1,1:2 .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/weird-chr-names.vcf.gz -r 1:1,1:2 | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version /tmp/w22ChRBs6d/weird-chr-names.vcf.gz -r 1:1-1 .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/weird-chr-names.vcf.gz -r 1:1-1 | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version /tmp/w22ChRBs6d/weird-chr-names.vcf.gz -r {1:1} .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/weird-chr-names.vcf.gz -r {1:1} | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version /tmp/w22ChRBs6d/weird-chr-names.vcf.gz -r {1:1}:1-2 .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/weird-chr-names.vcf.gz -r {1:1}:1-2 | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version /tmp/w22ChRBs6d/weird-chr-names.vcf.gz -r {1:1}:1,{1:1}:2 .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/weird-chr-names.vcf.gz -r {1:1}:1,{1:1}:2 | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version /tmp/w22ChRBs6d/weird-chr-names.vcf.gz -r {1:1}:1-1 .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/weird-chr-names.vcf.gz -r {1:1}:1-1 | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version /tmp/w22ChRBs6d/weird-chr-names.vcf.gz -r {1:1-1} .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/weird-chr-names.vcf.gz -r {1:1-1} | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version /tmp/w22ChRBs6d/weird-chr-names.vcf.gz -r {1:1-1}:1-2 .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/weird-chr-names.vcf.gz -r {1:1-1}:1-2 | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version /tmp/w22ChRBs6d/weird-chr-names.vcf.gz -r {1:1-1}:1,{1:1-1}:2 .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/weird-chr-names.vcf.gz -r {1:1-1}:1,{1:1-1}:2 | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version /tmp/w22ChRBs6d/weird-chr-names.vcf.gz -r {1:1-1}:1-1 .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/weird-chr-names.vcf.gz -r {1:1-1}:1-1 | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version /tmp/w22ChRBs6d/weird-chr-names.vcf.gz -r {1:1-1}-2 .. ok, expected non-zero status test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/weird-chr-names.vcf.gz -r {1:1-1}-2 | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok, expected non-zero status test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version -aUc1 -C1 -s NA00002 -v snps /tmp/w22ChRBs6d/view.vcf.gz .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/w22ChRBs6d/view.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version -f PASS -Xks NA00003 /tmp/w22ChRBs6d/view.vcf.gz -r20,Y .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob -f PASS -Xks NA00003 /tmp/w22ChRBs6d/view.vcf.gz -r20,Y | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version -xs NA00003 /tmp/w22ChRBs6d/view.vcf.gz .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob -xs NA00003 /tmp/w22ChRBs6d/view.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/w22ChRBs6d/view.vcf.gz .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/w22ChRBs6d/view.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version -p /tmp/w22ChRBs6d/view.vcf.gz .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob -p /tmp/w22ChRBs6d/view.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version -P /tmp/w22ChRBs6d/view.vcf.gz .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob -P /tmp/w22ChRBs6d/view.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version -hm2 -M2 -q0.3 -Q0.7 /tmp/w22ChRBs6d/view.vcf.gz .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/w22ChRBs6d/view.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version -Hu /tmp/w22ChRBs6d/view.vcf.gz .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version -GVsnps /tmp/w22ChRBs6d/view.vcf.gz .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob -GVsnps /tmp/w22ChRBs6d/view.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version -ne 'INDEL=1 || PV4[0]<0.006' /tmp/w22ChRBs6d/view.vcf.gz .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/w22ChRBs6d/view.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version -s ^NA00003 /tmp/w22ChRBs6d/view.vcf.gz .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob -s ^NA00003 /tmp/w22ChRBs6d/view.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version /tmp/w22ChRBs6d/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/view.omitgenotypes.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version -G /tmp/w22ChRBs6d/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob -G /tmp/w22ChRBs6d/view.omitgenotypes.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version -HG /tmp/w22ChRBs6d/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version -a /tmp/w22ChRBs6d/many.alleles.vcf.gz .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob -a /tmp/w22ChRBs6d/many.alleles.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version -asA /tmp/w22ChRBs6d/view.vectors.vcf.gz .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob -asA /tmp/w22ChRBs6d/view.vectors.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version -asB /tmp/w22ChRBs6d/view.vectors.vcf.gz .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob -asB /tmp/w22ChRBs6d/view.vectors.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version -asA /tmp/w22ChRBs6d/view.vectors.2.vcf.gz .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob -asA /tmp/w22ChRBs6d/view.vectors.2.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version -H -i'FMT/FGS[*:0]="AAAAAA"' /tmp/w22ChRBs6d/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version -H -i'FMT/FGS[*:2]="C"' /tmp/w22ChRBs6d/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version -H -i'FMT/FGS[*:4]="EE"' /tmp/w22ChRBs6d/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version -H -i'FMT/FRS[*:1]="BB"' /tmp/w22ChRBs6d/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version -H -i'TXT0="text"' /tmp/w22ChRBs6d/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version -T /build/bcftools-V6n0z8/bcftools-1.21/test/view.chrs.tab /tmp/w22ChRBs6d/view.chrs.vcf.gz .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob -T /build/bcftools-V6n0z8/bcftools-1.21/test/view.chrs.tab /tmp/w22ChRBs6d/view.chrs.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version -i 'POS>=3062917' /tmp/w22ChRBs6d/filter.2.vcf.gz 1:3062917-3157410 .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob -i 'POS>=3062917' /tmp/w22ChRBs6d/filter.2.vcf.gz 1:3062917-3157410 | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version -H -r 1:10,1:12,1:10 /tmp/w22ChRBs6d/idx.1.vcf.gz .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version -H -r 1:1172777-1172804,1:1172806-1172808 /tmp/w22ChRBs6d/idx.2.vcf.gz .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version -H -R /build/bcftools-V6n0z8/bcftools-1.21/test/idx.2.bed /tmp/w22ChRBs6d/idx.2.vcf.gz .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version -H -R /build/bcftools-V6n0z8/bcftools-1.21/test/idx.3.bed /tmp/w22ChRBs6d/idx.3.vcf.gz .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version -H -R /build/bcftools-V6n0z8/bcftools-1.21/test/idx.4.bed /tmp/w22ChRBs6d/idx.4.vcf.gz .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version -Ht 2 /tmp/w22ChRBs6d/view-t.vcf.gz .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version -Ht 3 /tmp/w22ChRBs6d/view-t.vcf.gz .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 0 /tmp/w22ChRBs6d/overlap.vcf.gz .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 1 /tmp/w22ChRBs6d/overlap.vcf.gz .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 2 /tmp/w22ChRBs6d/overlap.vcf.gz .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 0 /tmp/w22ChRBs6d/overlap.vcf.gz .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 1 /tmp/w22ChRBs6d/overlap.vcf.gz .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 2 /tmp/w22ChRBs6d/overlap.vcf.gz .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 0 /tmp/w22ChRBs6d/overlap.vcf.gz .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 1 /tmp/w22ChRBs6d/overlap.vcf.gz .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 2 /tmp/w22ChRBs6d/overlap.vcf.gz .. ok test_vcf_64bit: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view /build/bcftools-V6n0z8/bcftools-1.21/test/view64bit.1.vcf -H .. ok test_vcf_64bit: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view /build/bcftools-V6n0z8/bcftools-1.21/test/view64bit.1.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view /build/bcftools-V6n0z8/bcftools-1.21/test/view64bit.1.vcf -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view /build/bcftools-V6n0z8/bcftools-1.21/test/view64bit.2.vcf -H .. ok test_vcf_64bit: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view /build/bcftools-V6n0z8/bcftools-1.21/test/view64bit.2.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view /build/bcftools-V6n0z8/bcftools-1.21/test/view64bit.2.vcf -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view /build/bcftools-V6n0z8/bcftools-1.21/test/view64bit.3.vcf -H .. ok test_vcf_64bit: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view /build/bcftools-V6n0z8/bcftools-1.21/test/view64bit.3.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view /build/bcftools-V6n0z8/bcftools-1.21/test/view64bit.4.vcf -H .. ok test_vcf_64bit: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view /build/bcftools-V6n0z8/bcftools-1.21/test/view64bit.4.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view /build/bcftools-V6n0z8/bcftools-1.21/test/view64bit.4.vcf -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view /build/bcftools-V6n0z8/bcftools-1.21/test/view64bit.5.vcf -H .. ok test_vcf_64bit: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view /build/bcftools-V6n0z8/bcftools-1.21/test/view64bit.5.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view /build/bcftools-V6n0z8/bcftools-1.21/test/view64bit.5.vcf -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -H .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version -H -C5:nonmajor /tmp/w22ChRBs6d/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version -H -c6:nonmajor /tmp/w22ChRBs6d/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version -H -q0.3:major /tmp/w22ChRBs6d/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/w22ChRBs6d/view.filter.annovar.vcf.gz .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version -H -i 'Gene.refGene~"NOD"' /tmp/w22ChRBs6d/view.filter.annovar.vcf.gz .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version -H -i 'LJB2_MutationTaster=="0.291000"' /tmp/w22ChRBs6d/view.filter.annovar.vcf.gz .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version -H -a /tmp/w22ChRBs6d/view-a.vcf.gz .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version -T /build/bcftools-V6n0z8/bcftools-1.21/test/view.sites.txt /tmp/w22ChRBs6d/view.sites.vcf.gz .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob -T /build/bcftools-V6n0z8/bcftools-1.21/test/view.sites.txt /tmp/w22ChRBs6d/view.sites.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version -T /build/bcftools-V6n0z8/bcftools-1.21/test/view.sites.txt.gz /tmp/w22ChRBs6d/view.sites.vcf.gz .. ok test_vcf_view: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob -T /build/bcftools-V6n0z8/bcftools-1.21/test/view.sites.txt.gz /tmp/w22ChRBs6d/view.sites.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_head: /build/bcftools-V6n0z8/bcftools-1.21/bcftools head /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_head: /build/bcftools-V6n0z8/bcftools-1.21/bcftools head -h 0 /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_head: /build/bcftools-V6n0z8/bcftools-1.21/bcftools head -h 1 /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_head: /build/bcftools-V6n0z8/bcftools-1.21/bcftools head -h 5 /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_head: /build/bcftools-V6n0z8/bcftools-1.21/bcftools head -h 22 /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_head: /build/bcftools-V6n0z8/bcftools-1.21/bcftools head -h 23 /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_head: /build/bcftools-V6n0z8/bcftools-1.21/bcftools head -n 0 /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_head: /build/bcftools-V6n0z8/bcftools-1.21/bcftools head -n 1 /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_head: /build/bcftools-V6n0z8/bcftools-1.21/bcftools head -n 5 /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_head: /build/bcftools-V6n0z8/bcftools-1.21/bcftools head -h 5 -n 5 < /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_head2: /build/bcftools-V6n0z8/bcftools-1.21/bcftools head -s0 /tmp/w22ChRBs6d/mpileup.2.vcf.gz .. ok test_vcf_head2: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version -Ob /tmp/w22ChRBs6d/mpileup.2.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools head -s0 .. ok test_vcf_head2: /build/bcftools-V6n0z8/bcftools-1.21/bcftools head -s1 /tmp/w22ChRBs6d/mpileup.2.vcf.gz .. ok test_vcf_head2: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version -Ob /tmp/w22ChRBs6d/mpileup.2.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools head -s1 .. ok test_vcf_head2: /build/bcftools-V6n0z8/bcftools-1.21/bcftools head -s2 -h2 /tmp/w22ChRBs6d/mpileup.2.vcf.gz .. ok test_vcf_head2: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version -Ob /tmp/w22ChRBs6d/mpileup.2.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools head -s2 -h2 .. ok test_vcf_call: /build/bcftools-V6n0z8/bcftools-1.21/bcftools call --no-version -mv /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.vcf .. ok test_vcf_call: /build/bcftools-V6n0z8/bcftools-1.21/bcftools call -Ob -mv /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-V6n0z8/bcftools-1.21/bcftools call --no-version -mg0 /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.vcf .. ok test_vcf_call: /build/bcftools-V6n0z8/bcftools-1.21/bcftools call -Ob -mg0 /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-V6n0z8/bcftools-1.21/bcftools call --no-version -mv -S /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.3.samples /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.vcf .. ok test_vcf_call: /build/bcftools-V6n0z8/bcftools-1.21/bcftools call -Ob -mv -S /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.3.samples /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-V6n0z8/bcftools-1.21/bcftools call --no-version -mv -S /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.4.samples /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.vcf .. ok test_vcf_call: /build/bcftools-V6n0z8/bcftools-1.21/bcftools call -Ob -mv -S /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.4.samples /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-V6n0z8/bcftools-1.21/bcftools call --no-version -mv -S /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.5.samples /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.vcf .. ok test_vcf_call: /build/bcftools-V6n0z8/bcftools-1.21/bcftools call -Ob -mv -S /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.5.samples /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-V6n0z8/bcftools-1.21/bcftools call --no-version -mv --ploidy-file /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.ploidy -S /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.samples /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.X.vcf .. ok test_vcf_call: /build/bcftools-V6n0z8/bcftools-1.21/bcftools call -Ob -mv --ploidy-file /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.ploidy -S /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.samples /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.X.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-V6n0z8/bcftools-1.21/bcftools call --no-version -mv --ploidy-file /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.ploidy -S /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.ped /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.X.vcf .. ok test_vcf_call: /build/bcftools-V6n0z8/bcftools-1.21/bcftools call -Ob -mv --ploidy-file /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.ploidy -S /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.ped /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.X.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-V6n0z8/bcftools-1.21/bcftools call --no-version -mv --ploidy-file /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.ploidy -S /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.2.samples /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.X.vcf .. ok test_vcf_call: /build/bcftools-V6n0z8/bcftools-1.21/bcftools call -Ob -mv --ploidy-file /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.ploidy -S /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.2.samples /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.X.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-V6n0z8/bcftools-1.21/bcftools call --no-version -mv /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.NA19213.NA19129.vcf .. ok test_vcf_call: /build/bcftools-V6n0z8/bcftools-1.21/bcftools call -Ob -mv /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.NA19213.NA19129.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-V6n0z8/bcftools-1.21/bcftools call --no-version -mv -G - --group-samples-tag AD /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.NA19213.NA19129.vcf .. ok test_vcf_call: /build/bcftools-V6n0z8/bcftools-1.21/bcftools call -Ob -mv -G - --group-samples-tag AD /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.NA19213.NA19129.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-V6n0z8/bcftools-1.21/bcftools call --no-version -mv /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.hwe.vcf .. ok test_vcf_call: /build/bcftools-V6n0z8/bcftools-1.21/bcftools call -Ob -mv /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.hwe.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-V6n0z8/bcftools-1.21/bcftools call --no-version -mv -G - --group-samples-tag AD /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.hwe.vcf .. ok test_vcf_call: /build/bcftools-V6n0z8/bcftools-1.21/bcftools call -Ob -mv -G - --group-samples-tag AD /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.hwe.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-V6n0z8/bcftools-1.21/bcftools call --no-version -mv -G /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.hwe.samples --group-samples-tag AD /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.hwe.vcf .. ok test_vcf_call: /build/bcftools-V6n0z8/bcftools-1.21/bcftools call -Ob -mv -G /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.hwe.samples --group-samples-tag AD /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.hwe.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-V6n0z8/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/w22ChRBs6d/mpileup.tab.gz /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.vcf .. ok test_vcf_call_cAls: /build/bcftools-V6n0z8/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/w22ChRBs6d/mpileup.tab.gz /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-V6n0z8/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/w22ChRBs6d/mpileup.2.tab.gz /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_call_cAls: /build/bcftools-V6n0z8/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/w22ChRBs6d/mpileup.2.tab.gz /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.2.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-V6n0z8/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/w22ChRBs6d/mpileup.3.tab.gz -i /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /build/bcftools-V6n0z8/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/w22ChRBs6d/mpileup.3.tab.gz -i /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.3.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-V6n0z8/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/w22ChRBs6d/mpileup.4.tab.gz -i /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /build/bcftools-V6n0z8/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/w22ChRBs6d/mpileup.4.tab.gz -i /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.3.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-V6n0z8/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/w22ChRBs6d/mpileup.5.tab.gz -i /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /build/bcftools-V6n0z8/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/w22ChRBs6d/mpileup.5.tab.gz -i /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.3.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-V6n0z8/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/w22ChRBs6d/mpileup.6.tab.gz -i /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.4.vcf .. ok test_vcf_call_cAls: /build/bcftools-V6n0z8/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/w22ChRBs6d/mpileup.6.tab.gz -i /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.4.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-V6n0z8/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/w22ChRBs6d/mpileup.7.tab.gz -i /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.5.vcf .. ok test_vcf_call_cAls: /build/bcftools-V6n0z8/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/w22ChRBs6d/mpileup.7.tab.gz -i /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.5.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-V6n0z8/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/w22ChRBs6d/mpileup.cals.1.tab.gz /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.cals.1.vcf .. ok test_vcf_call_cAls: /build/bcftools-V6n0z8/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/w22ChRBs6d/mpileup.cals.1.tab.gz /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.cals.1.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-V6n0z8/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/w22ChRBs6d/mpileup.cals.2.tab.gz /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.cals.2.vcf .. ok test_vcf_call_cAls: /build/bcftools-V6n0z8/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/w22ChRBs6d/mpileup.cals.2.tab.gz /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.cals.2.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-V6n0z8/bcftools-1.21/bcftools call --no-version -cv /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.c.vcf .. ok test_vcf_call: /build/bcftools-V6n0z8/bcftools-1.21/bcftools call -Ob -cv /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.c.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-V6n0z8/bcftools-1.21/bcftools call --no-version -cv --ploidy-file /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.ploidy -S /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.samples /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.c.X.vcf .. ok test_vcf_call: /build/bcftools-V6n0z8/bcftools-1.21/bcftools call -Ob -cv --ploidy-file /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.ploidy -S /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.samples /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.c.X.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-V6n0z8/bcftools-1.21/bcftools call --no-version -cv --ploidy-file /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.ploidy -S /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.ped /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.c.X.vcf .. ok test_vcf_call: /build/bcftools-V6n0z8/bcftools-1.21/bcftools call -Ob -cv --ploidy-file /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.ploidy -S /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.ped /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.c.X.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-V6n0z8/bcftools-1.21/bcftools call --no-version -cv --ploidy-file /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.ploidy -S /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.2.samples /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.c.X.vcf .. ok test_vcf_call: /build/bcftools-V6n0z8/bcftools-1.21/bcftools call -Ob -cv --ploidy-file /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.ploidy -S /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.2.samples /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup.c.X.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-V6n0z8/bcftools-1.21/bcftools call --no-version -mv /build/bcftools-V6n0z8/bcftools-1.21/test/call-G.vcf .. ok test_vcf_call: /build/bcftools-V6n0z8/bcftools-1.21/bcftools call -Ob -mv /build/bcftools-V6n0z8/bcftools-1.21/test/call-G.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-V6n0z8/bcftools-1.21/bcftools call --no-version -mv -G - --group-samples-tag AD /build/bcftools-V6n0z8/bcftools-1.21/test/call-G.vcf .. ok test_vcf_call: /build/bcftools-V6n0z8/bcftools-1.21/bcftools call -Ob -mv -G - --group-samples-tag AD /build/bcftools-V6n0z8/bcftools-1.21/test/call-G.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-V6n0z8/bcftools-1.21/bcftools call --no-version -mv -F AN_POP,AC_POP /build/bcftools-V6n0z8/bcftools-1.21/test/call-G.2.vcf .. ok test_vcf_call: /build/bcftools-V6n0z8/bcftools-1.21/bcftools call -Ob -mv -F AN_POP,AC_POP /build/bcftools-V6n0z8/bcftools-1.21/test/call-G.2.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-V6n0z8/bcftools-1.21/bcftools call --no-version -m /build/bcftools-V6n0z8/bcftools-1.21/test/call.af-fixation.vcf .. ok test_vcf_call: /build/bcftools-V6n0z8/bcftools-1.21/bcftools call -Ob -m /build/bcftools-V6n0z8/bcftools-1.21/test/call.af-fixation.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-V6n0z8/bcftools-1.21/bcftools call --no-version -m -G /build/bcftools-V6n0z8/bcftools-1.21/test/call.af-fixation.txt /build/bcftools-V6n0z8/bcftools-1.21/test/call.af-fixation.vcf .. ok test_vcf_call: /build/bcftools-V6n0z8/bcftools-1.21/bcftools call -Ob -m -G /build/bcftools-V6n0z8/bcftools-1.21/test/call.af-fixation.txt /build/bcftools-V6n0z8/bcftools-1.21/test/call.af-fixation.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-V6n0z8/bcftools-1.21/bcftools call --no-version -m -G /build/bcftools-V6n0z8/bcftools-1.21/test/call.af-fixation.txt -a GP,GQ /build/bcftools-V6n0z8/bcftools-1.21/test/call.af-fixation.vcf .. ok test_vcf_call: /build/bcftools-V6n0z8/bcftools-1.21/bcftools call -Ob -m -G /build/bcftools-V6n0z8/bcftools-1.21/test/call.af-fixation.txt -a GP,GQ /build/bcftools-V6n0z8/bcftools-1.21/test/call.af-fixation.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -S. -e'TXT0="text"' /build/bcftools-V6n0z8/bcftools-1.21/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -S. -e'TXT0="text"' /build/bcftools-V6n0z8/bcftools-1.21/test/view.filter.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -S. -e'FMT/FRS[*:1]="BB"' /build/bcftools-V6n0z8/bcftools-1.21/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -S. -e'FMT/FRS[*:1]="BB"' /build/bcftools-V6n0z8/bcftools-1.21/test/view.filter.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -S. -e'FMT/FGS[*:0]="AAAAAA"' /build/bcftools-V6n0z8/bcftools-1.21/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -S. -e'FMT/FGS[*:0]="AAAAAA"' /build/bcftools-V6n0z8/bcftools-1.21/test/view.filter.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -S. -e'FMT/FGS[*:1]="BBB"' /build/bcftools-V6n0z8/bcftools-1.21/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -S. -e'FMT/FGS[*:1]="BBB"' /build/bcftools-V6n0z8/bcftools-1.21/test/view.filter.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -S. -e'FMT/FGS[*:4]="EE"' /build/bcftools-V6n0z8/bcftools-1.21/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -S. -e'FMT/FGS[*:4]="EE"' /build/bcftools-V6n0z8/bcftools-1.21/test/view.filter.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -S. -e'FMT/STR="XX"' /build/bcftools-V6n0z8/bcftools-1.21/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -S. -e'FMT/STR="XX"' /build/bcftools-V6n0z8/bcftools-1.21/test/view.filter.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -S. -e'FMT/FILTER="aaa"' /build/bcftools-V6n0z8/bcftools-1.21/test/view.filter.2.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -S. -e'FMT/FILTER="aaa"' /build/bcftools-V6n0z8/bcftools-1.21/test/view.filter.2.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -mx -g2 -G2 /build/bcftools-V6n0z8/bcftools-1.21/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -mx -g2 -G2 /build/bcftools-V6n0z8/bcftools-1.21/test/filter.1.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /build/bcftools-V6n0z8/bcftools-1.21/test/filter.2.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /build/bcftools-V6n0z8/bcftools-1.21/test/filter.2.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -e'INFO/DP=19' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.3.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -e'INFO/DP=19' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.3.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -e'INFO/DP=19' -s XX /build/bcftools-V6n0z8/bcftools-1.21/test/filter.3.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -e'INFO/DP=19' -s XX /build/bcftools-V6n0z8/bcftools-1.21/test/filter.3.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -e'INFO/DP=19' -s XX -m+ /build/bcftools-V6n0z8/bcftools-1.21/test/filter.3.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+ /build/bcftools-V6n0z8/bcftools-1.21/test/filter.3.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -e'INFO/DP=19' -s XX -mx /build/bcftools-V6n0z8/bcftools-1.21/test/filter.3.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -e'INFO/DP=19' -s XX -mx /build/bcftools-V6n0z8/bcftools-1.21/test/filter.3.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -e'INFO/DP=19' -s XX -m+x /build/bcftools-V6n0z8/bcftools-1.21/test/filter.3.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+x /build/bcftools-V6n0z8/bcftools-1.21/test/filter.3.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -e'FMT/GT="0/2"' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.3.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -e'FMT/GT="0/2"' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.3.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -e'FMT/GT="0/2"' -s XX /build/bcftools-V6n0z8/bcftools-1.21/test/filter.3.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX /build/bcftools-V6n0z8/bcftools-1.21/test/filter.3.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -e'FMT/GT="0/2"' -s XX -m+ /build/bcftools-V6n0z8/bcftools-1.21/test/filter.3.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+ /build/bcftools-V6n0z8/bcftools-1.21/test/filter.3.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -e'FMT/GT="0/2"' -s XX -mx /build/bcftools-V6n0z8/bcftools-1.21/test/filter.3.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -mx /build/bcftools-V6n0z8/bcftools-1.21/test/filter.3.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -e'FMT/GT="0/2"' -s XX -m+x /build/bcftools-V6n0z8/bcftools-1.21/test/filter.3.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+x /build/bcftools-V6n0z8/bcftools-1.21/test/filter.3.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -i'FMT/GT="0/0" && AC[*]=2' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.2.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -i'FMT/GT="0/0" && AC[*]=2' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.2.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -i'AC[*]=2 && FMT/GT="0/0"' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.2.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -i'AC[*]=2 && FMT/GT="0/0"' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.2.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -i'ALT="."' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.2.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -i'ALT="."' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.2.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -S . -i 'FORMAT/TEST3<25' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.4.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -S . -i 'FORMAT/TEST3<25' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.4.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -S . -i 'FORMAT/TEST4<25' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.4.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -S . -i 'FORMAT/TEST4<25' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.4.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -i'GT="A"' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.2.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -i'GT="A"' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.2.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -i'GT="RR"' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.2.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -i'GT="RR"' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.2.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -i'GT="RA"' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.2.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -i'GT="RA"' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.2.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -i'GT="AR"' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.2.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -i'GT="AR"' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.2.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -i'GT="AA"' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.2.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -i'GT="AA"' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.2.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -i'GT="aA"' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.2.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -i'GT="aA"' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.2.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -i'GT="Aa"' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.2.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -i'GT="Aa"' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.2.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -i'GT="HOM"' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.2.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -i'GT="HOM"' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.2.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -i'GT="HET"' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.2.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -i'GT="HET"' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.2.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -i'GT="HAP"' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.2.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -i'GT="HAP"' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.2.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -i'AD[:1]=11' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.5.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -i'AD[:1]=11' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.5.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -i'AD[1:]=11' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.5.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -i'AD[1:]=11' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.5.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -i'FR[0:1]=11' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.5.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS[\t%FR]\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -i'FR[0:1]=11' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.5.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS[\t%FR]\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -i'AD[*]="."' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.5.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -i'AD[*]="."' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.5.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -i'AD[0:0]=="."' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.5.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -i'AD[0:0]=="."' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.5.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -i'AD[0:0]!="."' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.5.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -i'AD[0:0]!="."' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.5.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -i'QUAL=="."' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.5.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS\t%QUAL\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -i'QUAL=="."' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.5.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS\t%QUAL\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -i'N_PASS(DP>32)=1' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.2.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -i'N_PASS(DP>32)=1' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.2.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -i'F_PASS(DP>32)=0.5' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.2.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -i'F_PASS(DP>32)=0.5' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.2.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -i'F_MISSING>=1/5' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.6.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -i'F_MISSING>=1/5' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.6.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -i'F_MISSING>=0.2' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.6.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -i'F_MISSING>=0.2' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.6.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -i'F_PASS(GT=="mis")>=1/5' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.6.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -i'F_PASS(GT=="mis")>=1/5' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.6.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -i'F_PASS(GT=="mis")>=0.2' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.6.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -i'F_PASS(GT=="mis")>=0.2' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.6.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -mx -s + -g2:mnp,indel,other /build/bcftools-V6n0z8/bcftools-1.21/test/filter.7.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -mx -s + -g2:mnp,indel,other /build/bcftools-V6n0z8/bcftools-1.21/test/filter.7.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -S . -e 'FORMAT/AO==4' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -S . -e 'FORMAT/AO==4' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.8.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -S . -e 'MAX(FORMAT/AO[0:])==4' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -S . -e 'MAX(FORMAT/AO[0:])==4' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.8.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -S . -e 'MAX(FORMAT/AO)==4' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -S . -e 'MAX(FORMAT/AO)==4' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.8.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -S . -e 'MIN(FORMAT/AO[0:])==3' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO[0:])==3' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.8.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -S . -e 'MIN(FORMAT/AO)==2' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO)==2' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.8.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -S . -e 'MIN(FORMAT/AO[0:])==3' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO[0:])==3' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.8.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -S . -e 'AVG(FORMAT/AO[2:])==4' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -S . -e 'AVG(FORMAT/AO[2:])==4' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.8.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -S . -e 'MEDIAN(FORMAT/AO[2:])==4' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -S . -e 'MEDIAN(FORMAT/AO[2:])==4' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.8.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -S . -e 'STDEV(FORMAT/AO[0:])=0.5' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -S . -e 'STDEV(FORMAT/AO[0:])=0.5' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.8.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -S . -e 'SUM(FORMAT/AO[0:])=7' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -S . -e 'SUM(FORMAT/AO[0:])=7' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.8.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -S . -e 'SMPL_MAX(FORMAT/AO)==4' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -S . -e 'SMPL_MAX(FORMAT/AO)==4' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.8.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -S . -e 'sMIN(FORMAT/AO)==2' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -S . -e 'sMIN(FORMAT/AO)==2' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.8.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -S . -e 'ABS(sAVG(FORMAT/AO)-3.66666)<1e-5' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -S . -e 'ABS(sAVG(FORMAT/AO)-3.66666)<1e-5' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.8.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -S . -e 'sMEDIAN(FORMAT/AO)==4' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -S . -e 'sMEDIAN(FORMAT/AO)==4' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.8.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -S . -e 'ABS(sSTDEV(FORMAT/AO)-1.2472191)<1e-5' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -S . -e 'ABS(sSTDEV(FORMAT/AO)-1.2472191)<1e-5' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.8.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -S . -e 'sSUM(FORMAT/AO)==11' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -S . -e 'sSUM(FORMAT/AO)==11' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.8.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -i 'QUAL/FMT/AD==55' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.9.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -i 'QUAL/FMT/AD==55' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.9.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -i 'QUAL/INFO/AD==10' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.9.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -i 'QUAL/INFO/AD==10' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.9.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -S . -e 'ABS(SMPL_MAX(FORMAT/AO))=5' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -S . -e 'ABS(SMPL_MAX(FORMAT/AO))=5' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.8.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -S . -e 'PHRED(AO[1:])>-4' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -S . -e 'PHRED(AO[1:])>-4' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.8.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -S . -e 'ABS(AO[1:])==2' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -S . -e 'ABS(AO[1:])==2' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.8.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -i 'sum(AD[*]) > FORMAT/DP' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -i 'sum(AD[*]) > FORMAT/DP' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.10.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -i 'FORMAT/DP < sum(AD[*])' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -i 'FORMAT/DP < sum(AD[*])' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.10.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -i 'sum(AD[*]) < FORMAT/DP' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -i 'sum(AD[*]) < FORMAT/DP' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.10.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -i 'FORMAT/DP > sum(AD[*])' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob -i 'FORMAT/DP > sum(AD[*])' /build/bcftools-V6n0z8/bcftools-1.21/test/filter.10.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 0 /build/bcftools-V6n0z8/bcftools-1.21/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 0 /build/bcftools-V6n0z8/bcftools-1.21/test/filter.1.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 1 /build/bcftools-V6n0z8/bcftools-1.21/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 1 /build/bcftools-V6n0z8/bcftools-1.21/test/filter.1.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 2 /build/bcftools-V6n0z8/bcftools-1.21/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 2 /build/bcftools-V6n0z8/bcftools-1.21/test/filter.1.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter --soft-filter xxx --mask ^2:1005-1008 /build/bcftools-V6n0z8/bcftools-1.21/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-V6n0z8/bcftools-1.21/bcftools filter -Ob --soft-filter xxx --mask ^2:1005-1008 /build/bcftools-V6n0z8/bcftools-1.21/test/filter.1.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_sort: /build/bcftools-V6n0z8/bcftools-1.21/bcftools sort -m 0 /build/bcftools-V6n0z8/bcftools-1.21/test/sort.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /build/bcftools-V6n0z8/bcftools-1.21/bcftools sort -Ob -m 0 /build/bcftools-V6n0z8/bcftools-1.21/test/sort.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /build/bcftools-V6n0z8/bcftools-1.21/bcftools sort -m 1000 /build/bcftools-V6n0z8/bcftools-1.21/test/sort.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /build/bcftools-V6n0z8/bcftools-1.21/bcftools sort -Ob -m 1000 /build/bcftools-V6n0z8/bcftools-1.21/test/sort.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_regions: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /build/bcftools-V6n0z8/bcftools-1.21/test/regions.tab /tmp/w22ChRBs6d/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/regions.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /build/bcftools-V6n0z8/bcftools-1.21/test/regions.tab .. ok test_vcf_regions: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /build/bcftools-V6n0z8/bcftools-1.21/test/regions.tab /tmp/w22ChRBs6d/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/w22ChRBs6d/regions.tab.gz /tmp/w22ChRBs6d/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/regions.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/w22ChRBs6d/regions.tab.gz .. ok test_vcf_regions: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/w22ChRBs6d/regions.tab.gz /tmp/w22ChRBs6d/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/w22ChRBs6d/regions.bed /tmp/w22ChRBs6d/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/regions.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/w22ChRBs6d/regions.bed .. ok test_vcf_regions: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/w22ChRBs6d/regions.bed /tmp/w22ChRBs6d/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/w22ChRBs6d/regions.bed.gz /tmp/w22ChRBs6d/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/regions.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/w22ChRBs6d/regions.bed.gz .. ok test_vcf_regions: /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/w22ChRBs6d/regions.bed.gz /tmp/w22ChRBs6d/regions.vcf.gz .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annotate.escape.1.tab.gz -c CHROM,POS,ISTR,FMT/FSTR /build/bcftools-V6n0z8/bcftools-1.21/test/annotate.escape.1.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annotate.escape.1.tab.gz -c CHROM,POS,ISTR,FMT/FSTR /build/bcftools-V6n0z8/bcftools-1.21/test/annotate.escape.1.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annotate.match.1.tab.gz -c CHROM,POS,-,-,SCORE,~X,-,- -i'STR={X}' /build/bcftools-V6n0z8/bcftools-1.21/test/annotate.match.1.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annotate.match.1.tab.gz -c CHROM,POS,-,-,SCORE,~X,-,- -i'STR={X}' /build/bcftools-V6n0z8/bcftools-1.21/test/annotate.match.1.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annotate.match.1.tab.gz -c CHROM,POS,REF,ALT,SCORE,-,~X,- -i'INT={X}' /build/bcftools-V6n0z8/bcftools-1.21/test/annotate.match.1.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annotate.match.1.tab.gz -c CHROM,POS,REF,ALT,SCORE,-,~X,- -i'INT={X}' /build/bcftools-V6n0z8/bcftools-1.21/test/annotate.match.1.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annotate.match.1.tab.gz -c CHROM,POS,REF,ALT,SCORE,-,-,~X -i'FLT={X}' /build/bcftools-V6n0z8/bcftools-1.21/test/annotate.match.1.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annotate.match.1.tab.gz -c CHROM,POS,REF,ALT,SCORE,-,-,~X -i'FLT={X}' /build/bcftools-V6n0z8/bcftools-1.21/test/annotate.match.1.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annotate.tab.gz -h /build/bcftools-V6n0z8/bcftools-1.21/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /build/bcftools-V6n0z8/bcftools-1.21/test/annotate.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annotate.tab.gz -h /build/bcftools-V6n0z8/bcftools-1.21/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /build/bcftools-V6n0z8/bcftools-1.21/test/annotate.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annotate2.tab.gz -h /build/bcftools-V6n0z8/bcftools-1.21/test/annotate.hdr -c CHROM,POS,-,T_STR /build/bcftools-V6n0z8/bcftools-1.21/test/annotate.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annotate2.tab.gz -h /build/bcftools-V6n0z8/bcftools-1.21/test/annotate.hdr -c CHROM,POS,-,T_STR /build/bcftools-V6n0z8/bcftools-1.21/test/annotate.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annotate2.tab.gz -h /build/bcftools-V6n0z8/bcftools-1.21/test/annotate.hdr -c CHROM,FROM,TO,T_STR /build/bcftools-V6n0z8/bcftools-1.21/test/annotate.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annotate2.tab.gz -h /build/bcftools-V6n0z8/bcftools-1.21/test/annotate.hdr -c CHROM,FROM,TO,T_STR /build/bcftools-V6n0z8/bcftools-1.21/test/annotate.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/w22ChRBs6d/annotate.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/w22ChRBs6d/annotate.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/w22ChRBs6d/annotate2.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/w22ChRBs6d/annotate2.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/w22ChRBs6d/annotate2.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/w22ChRBs6d/annotate2.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/w22ChRBs6d/annotate2.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/w22ChRBs6d/annotate2.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/w22ChRBs6d/annotate2.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/w22ChRBs6d/annotate2.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/w22ChRBs6d/annotate2.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/w22ChRBs6d/annotate2.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /build/bcftools-V6n0z8/bcftools-1.21/test/annotate3.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /build/bcftools-V6n0z8/bcftools-1.21/test/annotate3.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -x FORMAT /build/bcftools-V6n0z8/bcftools-1.21/test/annotate3.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -x FORMAT /build/bcftools-V6n0z8/bcftools-1.21/test/annotate3.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annots4.vcf.gz -c +INFO /tmp/w22ChRBs6d/annotate4.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annots4.vcf.gz -c +INFO /tmp/w22ChRBs6d/annotate4.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annots4.tab.gz -h /build/bcftools-V6n0z8/bcftools-1.21/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /build/bcftools-V6n0z8/bcftools-1.21/test/annotate4.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annots4.tab.gz -h /build/bcftools-V6n0z8/bcftools-1.21/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /build/bcftools-V6n0z8/bcftools-1.21/test/annotate4.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annots10.tab.gz -h /build/bcftools-V6n0z8/bcftools-1.21/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /build/bcftools-V6n0z8/bcftools-1.21/test/annotate10.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annots10.tab.gz -h /build/bcftools-V6n0z8/bcftools-1.21/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /build/bcftools-V6n0z8/bcftools-1.21/test/annotate10.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/w22ChRBs6d/annotate2.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/w22ChRBs6d/annotate2.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /build/bcftools-V6n0z8/bcftools-1.21/test/annotate2.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /build/bcftools-V6n0z8/bcftools-1.21/test/annotate2.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/w22ChRBs6d/annotate2.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/w22ChRBs6d/annotate2.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/w22ChRBs6d/annotate2.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/w22ChRBs6d/annotate2.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/w22ChRBs6d/annotate2.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/w22ChRBs6d/annotate2.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annots11.vcf.gz -c FMT /tmp/w22ChRBs6d/annotate11.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annots11.vcf.gz -c FMT /tmp/w22ChRBs6d/annotate11.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annots2.vcf.gz -c FMT/newGT:=GT /tmp/w22ChRBs6d/annotate2.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annots2.vcf.gz -c FMT/newGT:=GT /tmp/w22ChRBs6d/annotate2.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annots12.vcf.gz -c FMT/GT:=newGT /tmp/w22ChRBs6d/annotate2.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annots12.vcf.gz -c FMT/GT:=newGT /tmp/w22ChRBs6d/annotate2.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annots13.tab.gz -h /build/bcftools-V6n0z8/bcftools-1.21/test/annotate13.hdr -c CHROM,BEG,END,ABC /build/bcftools-V6n0z8/bcftools-1.21/test/annotate13.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annots13.tab.gz -h /build/bcftools-V6n0z8/bcftools-1.21/test/annotate13.hdr -c CHROM,BEG,END,ABC /build/bcftools-V6n0z8/bcftools-1.21/test/annotate13.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annots13.tab.gz -h /build/bcftools-V6n0z8/bcftools-1.21/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:append /build/bcftools-V6n0z8/bcftools-1.21/test/annotate13.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annots13.tab.gz -h /build/bcftools-V6n0z8/bcftools-1.21/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:append /build/bcftools-V6n0z8/bcftools-1.21/test/annotate13.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annots13.tab.gz -h /build/bcftools-V6n0z8/bcftools-1.21/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:unique /build/bcftools-V6n0z8/bcftools-1.21/test/annotate13.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annots13.tab.gz -h /build/bcftools-V6n0z8/bcftools-1.21/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:unique /build/bcftools-V6n0z8/bcftools-1.21/test/annotate13.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -x FILTER/XX,INFO/XX --force /build/bcftools-V6n0z8/bcftools-1.21/test/annotate14.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -x FILTER/XX,INFO/XX --force /build/bcftools-V6n0z8/bcftools-1.21/test/annotate14.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annotate15.tab.gz -h /build/bcftools-V6n0z8/bcftools-1.21/test/annotate15.hdr -s SAMPLE1 -c CHROM,FROM,TO,FMT/FOO,BAR /build/bcftools-V6n0z8/bcftools-1.21/test/annotate15.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annotate15.tab.gz -h /build/bcftools-V6n0z8/bcftools-1.21/test/annotate15.hdr -s SAMPLE1 -c CHROM,FROM,TO,FMT/FOO,BAR /build/bcftools-V6n0z8/bcftools-1.21/test/annotate15.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annotate15.tab.gz -h /build/bcftools-V6n0z8/bcftools-1.21/test/annotate15.hdr -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR /build/bcftools-V6n0z8/bcftools-1.21/test/annotate15.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annotate15.tab.gz -h /build/bcftools-V6n0z8/bcftools-1.21/test/annotate15.hdr -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR /build/bcftools-V6n0z8/bcftools-1.21/test/annotate15.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annotate15.tab.gz -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR -H '##FORMAT=' -H '##INFO=' /build/bcftools-V6n0z8/bcftools-1.21/test/annotate15.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annotate15.tab.gz -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR -H '##FORMAT=' -H '##INFO=' /build/bcftools-V6n0z8/bcftools-1.21/test/annotate15.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -x FILTER /build/bcftools-V6n0z8/bcftools-1.21/test/annotate16.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -x FILTER /build/bcftools-V6n0z8/bcftools-1.21/test/annotate16.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/bcftools-V6n0z8/bcftools-1.21/test/annotate17.1.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/bcftools-V6n0z8/bcftools-1.21/test/annotate17.1.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/bcftools-V6n0z8/bcftools-1.21/test/annotate17.2.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/bcftools-V6n0z8/bcftools-1.21/test/annotate17.2.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annotate17.3.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/bcftools-V6n0z8/bcftools-1.21/test/annotate17.3.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annotate17.3.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/bcftools-V6n0z8/bcftools-1.21/test/annotate17.3.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/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-V6n0z8/bcftools-1.21/test/annotate18.1.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/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-V6n0z8/bcftools-1.21/test/annotate18.1.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/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-V6n0z8/bcftools-1.21/test/annotate18.2.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/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-V6n0z8/bcftools-1.21/test/annotate18.2.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/w22ChRBs6d/annotate19.dst.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/w22ChRBs6d/annotate19.dst.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/w22ChRBs6d/annotate19.dst.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/w22ChRBs6d/annotate19.dst.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/w22ChRBs6d/annotate19.dst.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/w22ChRBs6d/annotate19.dst.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -c INFO/FILTER:=FILTER /build/bcftools-V6n0z8/bcftools-1.21/test/annotate19.dst.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -c INFO/FILTER:=FILTER /build/bcftools-V6n0z8/bcftools-1.21/test/annotate19.dst.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER /tmp/w22ChRBs6d/annotate19.dst.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER /tmp/w22ChRBs6d/annotate19.dst.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER /tmp/w22ChRBs6d/annotate19.dst.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER /tmp/w22ChRBs6d/annotate19.dst.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER,FILTER /tmp/w22ChRBs6d/annotate19.dst.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER,FILTER /tmp/w22ChRBs6d/annotate19.dst.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=./FILTER /tmp/w22ChRBs6d/annotate19.dst.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=./FILTER /tmp/w22ChRBs6d/annotate19.dst.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annotate20.src.vcf.gz -c FMT/GT /tmp/w22ChRBs6d/annotate20.dst.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annotate20.src.vcf.gz -c FMT/GT /tmp/w22ChRBs6d/annotate20.dst.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annotate20.src.vcf.gz -c +FMT/GT /tmp/w22ChRBs6d/annotate20.dst.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annotate20.src.vcf.gz -c +FMT/GT /tmp/w22ChRBs6d/annotate20.dst.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annotate20.src.vcf.gz -c -FMT/GT /tmp/w22ChRBs6d/annotate20.dst.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annotate20.src.vcf.gz -c -FMT/GT /tmp/w22ChRBs6d/annotate20.dst.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annotate.multi.tab.gz -c CHROM,POS,REF,ALT,ANN -l ANN:append /build/bcftools-V6n0z8/bcftools-1.21/test/annotate.multi.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annotate.multi.tab.gz -c CHROM,POS,REF,ALT,ANN -l ANN:append /build/bcftools-V6n0z8/bcftools-1.21/test/annotate.multi.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annotate.missing-append.tab.gz -c CHROM,POS,REF,ALT,STR,INT,FLT -l STR:append-missing,INT:append-missing,FLT:append-missing /build/bcftools-V6n0z8/bcftools-1.21/test/annotate.missing-append.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annotate.missing-append.tab.gz -c CHROM,POS,REF,ALT,STR,INT,FLT -l STR:append-missing,INT:append-missing,FLT:append-missing /build/bcftools-V6n0z8/bcftools-1.21/test/annotate.missing-append.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /build/bcftools-V6n0z8/bcftools-1.21/test/annotate9.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /build/bcftools-V6n0z8/bcftools-1.21/test/annotate9.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate --rename-annots /build/bcftools-V6n0z8/bcftools-1.21/test/annotate21.txt /build/bcftools-V6n0z8/bcftools-1.21/test/annotate21.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob --rename-annots /build/bcftools-V6n0z8/bcftools-1.21/test/annotate21.txt /build/bcftools-V6n0z8/bcftools-1.21/test/annotate21.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -c XX:=FORMAT/X-X,YY:=FORMAT/Y-Y,AA:=FORMAT/A-A,AA:=INFO/A-A,BB:=INFO/B-B,XX:=INFO/X-X,YY:=INFO/Y-Y,fltA:=FILTER/flt-A,fltB:=FILTER/flt-B,fltX:=FILTER/flt-X,fltY:=FILTER/flt-Y /build/bcftools-V6n0z8/bcftools-1.21/test/annotate21.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -c XX:=FORMAT/X-X,YY:=FORMAT/Y-Y,AA:=FORMAT/A-A,AA:=INFO/A-A,BB:=INFO/B-B,XX:=INFO/X-X,YY:=INFO/Y-Y,fltA:=FILTER/flt-A,fltB:=FILTER/flt-B,fltX:=FILTER/flt-X,fltY:=FILTER/flt-Y /build/bcftools-V6n0z8/bcftools-1.21/test/annotate21.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/w22ChRBs6d/annotate22.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/w22ChRBs6d/annotate22.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annotate23.tab.gz -c CHROM,POS,~ID,REF,ALT,INFO/END /build/bcftools-V6n0z8/bcftools-1.21/test/annotate23.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annotate23.tab.gz -c CHROM,POS,~ID,REF,ALT,INFO/END /build/bcftools-V6n0z8/bcftools-1.21/test/annotate23.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annotate24.src.vcf.gz -c XX /tmp/w22ChRBs6d/annotate24.dst.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annotate24.src.vcf.gz -c XX /tmp/w22ChRBs6d/annotate24.dst.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annotate25.tab.gz -c CHROM,POS,ID,REF,ALT,~INFO/END /build/bcftools-V6n0z8/bcftools-1.21/test/annotate25.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annotate25.tab.gz -c CHROM,POS,ID,REF,ALT,~INFO/END /build/bcftools-V6n0z8/bcftools-1.21/test/annotate25.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annotate26.tab.gz -c CHROM,POS,-POS /build/bcftools-V6n0z8/bcftools-1.21/test/annotate26.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annotate26.tab.gz -c CHROM,POS,-POS /build/bcftools-V6n0z8/bcftools-1.21/test/annotate26.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,TSTR,TFLT,TINT /build/bcftools-V6n0z8/bcftools-1.21/test/annotate.missing.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,TSTR,TFLT,TINT /build/bcftools-V6n0z8/bcftools-1.21/test/annotate.missing.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.TSTR,.TFLT,.TINT /build/bcftools-V6n0z8/bcftools-1.21/test/annotate.missing.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.TSTR,.TFLT,.TINT /build/bcftools-V6n0z8/bcftools-1.21/test/annotate.missing.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.+TSTR,.+TFLT,.+TINT /build/bcftools-V6n0z8/bcftools-1.21/test/annotate.missing.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.+TSTR,.+TFLT,.+TINT /build/bcftools-V6n0z8/bcftools-1.21/test/annotate.missing.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,+TSTR,+TFLT,+TINT /build/bcftools-V6n0z8/bcftools-1.21/test/annotate.missing.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,+TSTR,+TFLT,+TINT /build/bcftools-V6n0z8/bcftools-1.21/test/annotate.missing.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.=TSTR,.=TFLT,.=TINT /build/bcftools-V6n0z8/bcftools-1.21/test/annotate.missing.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.=TSTR,.=TFLT,.=TINT /build/bcftools-V6n0z8/bcftools-1.21/test/annotate.missing.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,=TSTR,=TFLT,=TINT /build/bcftools-V6n0z8/bcftools-1.21/test/annotate.missing.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,=TSTR,=TFLT,=TINT /build/bcftools-V6n0z8/bcftools-1.21/test/annotate.missing.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique /build/bcftools-V6n0z8/bcftools-1.21/test/annotate.olap.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique /build/bcftools-V6n0z8/bcftools-1.21/test/annotate.olap.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique --min-overlap 0.4:0.5 -m XXX /build/bcftools-V6n0z8/bcftools-1.21/test/annotate.olap.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique --min-overlap 0.4:0.5 -m XXX /build/bcftools-V6n0z8/bcftools-1.21/test/annotate.olap.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annots.id.vcf.gz -c ALT /tmp/w22ChRBs6d/annotate.id.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annots.id.vcf.gz -c ALT /tmp/w22ChRBs6d/annotate.id.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annots.id.vcf.gz -c +ALT /tmp/w22ChRBs6d/annotate.id.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annots.id.vcf.gz -c +ALT /tmp/w22ChRBs6d/annotate.id.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annots.id.2.vcf.gz --pair-logic some -c +ID /tmp/w22ChRBs6d/annotate.id.2.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annots.id.2.vcf.gz --pair-logic some -c +ID /tmp/w22ChRBs6d/annotate.id.2.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annots.id.2.vcf.gz --pair-logic any -c +ID /tmp/w22ChRBs6d/annotate.id.2.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annots.id.2.vcf.gz --pair-logic any -c +ID /tmp/w22ChRBs6d/annotate.id.2.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annotate27.tab.gz -c CHROM,POS,REF,ALT,EVIDENCE /build/bcftools-V6n0z8/bcftools-1.21/test/annotate27.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annotate27.tab.gz -c CHROM,POS,REF,ALT,EVIDENCE /build/bcftools-V6n0z8/bcftools-1.21/test/annotate27.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1,smpl2 /build/bcftools-V6n0z8/bcftools-1.21/test/annotate28.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1,smpl2 /build/bcftools-V6n0z8/bcftools-1.21/test/annotate28.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2,smpl1 /build/bcftools-V6n0z8/bcftools-1.21/test/annotate28.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2,smpl1 /build/bcftools-V6n0z8/bcftools-1.21/test/annotate28.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1 /build/bcftools-V6n0z8/bcftools-1.21/test/annotate28.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1 /build/bcftools-V6n0z8/bcftools-1.21/test/annotate28.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2 /build/bcftools-V6n0z8/bcftools-1.21/test/annotate28.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2 /build/bcftools-V6n0z8/bcftools-1.21/test/annotate28.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -m XXX /build/bcftools-V6n0z8/bcftools-1.21/test/annotate.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -m XXX /build/bcftools-V6n0z8/bcftools-1.21/test/annotate.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annots34.tab.gz -c CHROM,FROM,TO,INFO/END -H '##INFO=' /build/bcftools-V6n0z8/bcftools-1.21/test/annotate34.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annots34.tab.gz -c CHROM,FROM,TO,INFO/END -H '##INFO=' /build/bcftools-V6n0z8/bcftools-1.21/test/annotate34.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -a /tmp/w22ChRBs6d/annots-mark.bed.gz -c CHROM,FROM,TO -m TAG /build/bcftools-V6n0z8/bcftools-1.21/test/annots-mark.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate -Ob -a /tmp/w22ChRBs6d/annots-mark.bed.gz -c CHROM,FROM,TO -m TAG /build/bcftools-V6n0z8/bcftools-1.21/test/annots-mark.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-V6n0z8/bcftools-1.21/bcftools concat --no-version /tmp/w22ChRBs6d/concat.1.a.vcf.gz /tmp/w22ChRBs6d/concat.1.b.vcf.gz .. ok test_vcf_concat: /build/bcftools-V6n0z8/bcftools-1.21/bcftools concat -Ob /tmp/w22ChRBs6d/concat.1.a.vcf.gz /tmp/w22ChRBs6d/concat.1.b.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-V6n0z8/bcftools-1.21/bcftools concat --no-version /tmp/w22ChRBs6d/concat.1.a.bcf /tmp/w22ChRBs6d/concat.1.b.bcf .. ok test_vcf_concat: /build/bcftools-V6n0z8/bcftools-1.21/bcftools concat -Ob /tmp/w22ChRBs6d/concat.1.a.bcf /tmp/w22ChRBs6d/concat.1.b.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-V6n0z8/bcftools-1.21/bcftools concat --no-version -a /tmp/w22ChRBs6d/concat.2.a.vcf.gz /tmp/w22ChRBs6d/concat.2.b.vcf.gz .. ok test_vcf_concat: /build/bcftools-V6n0z8/bcftools-1.21/bcftools concat -Ob -a /tmp/w22ChRBs6d/concat.2.a.vcf.gz /tmp/w22ChRBs6d/concat.2.b.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-V6n0z8/bcftools-1.21/bcftools concat --no-version -a /tmp/w22ChRBs6d/concat.2.a.bcf /tmp/w22ChRBs6d/concat.2.b.bcf .. ok test_vcf_concat: /build/bcftools-V6n0z8/bcftools-1.21/bcftools concat -Ob -a /tmp/w22ChRBs6d/concat.2.a.bcf /tmp/w22ChRBs6d/concat.2.b.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-V6n0z8/bcftools-1.21/bcftools concat --no-version -aD /tmp/w22ChRBs6d/concat.2.a.vcf.gz /tmp/w22ChRBs6d/concat.2.b.vcf.gz .. ok test_vcf_concat: /build/bcftools-V6n0z8/bcftools-1.21/bcftools concat -Ob -aD /tmp/w22ChRBs6d/concat.2.a.vcf.gz /tmp/w22ChRBs6d/concat.2.b.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-V6n0z8/bcftools-1.21/bcftools concat --no-version -aD /tmp/w22ChRBs6d/concat.2.a.bcf /tmp/w22ChRBs6d/concat.2.b.bcf .. ok test_vcf_concat: /build/bcftools-V6n0z8/bcftools-1.21/bcftools concat -Ob -aD /tmp/w22ChRBs6d/concat.2.a.bcf /tmp/w22ChRBs6d/concat.2.b.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-V6n0z8/bcftools-1.21/bcftools concat --no-version -l --ligate-warn /tmp/w22ChRBs6d/concat.3.a.vcf.gz /tmp/w22ChRBs6d/concat.3.b.vcf.gz /tmp/w22ChRBs6d/concat.3.0.vcf.gz /tmp/w22ChRBs6d/concat.3.c.vcf.gz /tmp/w22ChRBs6d/concat.3.d.vcf.gz /tmp/w22ChRBs6d/concat.3.e.vcf.gz /tmp/w22ChRBs6d/concat.3.f.vcf.gz .. ok test_vcf_concat: /build/bcftools-V6n0z8/bcftools-1.21/bcftools concat -Ob -l --ligate-warn /tmp/w22ChRBs6d/concat.3.a.vcf.gz /tmp/w22ChRBs6d/concat.3.b.vcf.gz /tmp/w22ChRBs6d/concat.3.0.vcf.gz /tmp/w22ChRBs6d/concat.3.c.vcf.gz /tmp/w22ChRBs6d/concat.3.d.vcf.gz /tmp/w22ChRBs6d/concat.3.e.vcf.gz /tmp/w22ChRBs6d/concat.3.f.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-V6n0z8/bcftools-1.21/bcftools concat --no-version -l --ligate-warn /tmp/w22ChRBs6d/concat.3.a.bcf /tmp/w22ChRBs6d/concat.3.b.bcf /tmp/w22ChRBs6d/concat.3.0.bcf /tmp/w22ChRBs6d/concat.3.c.bcf /tmp/w22ChRBs6d/concat.3.d.bcf /tmp/w22ChRBs6d/concat.3.e.bcf /tmp/w22ChRBs6d/concat.3.f.bcf .. ok test_vcf_concat: /build/bcftools-V6n0z8/bcftools-1.21/bcftools concat -Ob -l --ligate-warn /tmp/w22ChRBs6d/concat.3.a.bcf /tmp/w22ChRBs6d/concat.3.b.bcf /tmp/w22ChRBs6d/concat.3.0.bcf /tmp/w22ChRBs6d/concat.3.c.bcf /tmp/w22ChRBs6d/concat.3.d.bcf /tmp/w22ChRBs6d/concat.3.e.bcf /tmp/w22ChRBs6d/concat.3.f.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ Random seed for test_naive_concat: 362955497 .. ok test_naive_concat: /build/bcftools-V6n0z8/bcftools-1.21/bcftools concat --naive-force /tmp/w22ChRBs6d/naive_concat.0.bcf /tmp/w22ChRBs6d/naive_concat.1.bcf /tmp/w22ChRBs6d/naive_concat.2.bcf /tmp/w22ChRBs6d/naive_concat.3.bcf /tmp/w22ChRBs6d/naive_concat.4.bcf /tmp/w22ChRBs6d/naive_concat.5.bcf /tmp/w22ChRBs6d/naive_concat.6.bcf /tmp/w22ChRBs6d/naive_concat.7.bcf /tmp/w22ChRBs6d/naive_concat.8.bcf /tmp/w22ChRBs6d/naive_concat.9.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -H .. ok test_naive_concat: /build/bcftools-V6n0z8/bcftools-1.21/bcftools concat --naive /tmp/w22ChRBs6d/naive_concat.0.vcf.gz /tmp/w22ChRBs6d/naive_concat.1.vcf.gz /tmp/w22ChRBs6d/naive_concat.2.vcf.gz /tmp/w22ChRBs6d/naive_concat.3.vcf.gz /tmp/w22ChRBs6d/naive_concat.4.vcf.gz /tmp/w22ChRBs6d/naive_concat.5.vcf.gz /tmp/w22ChRBs6d/naive_concat.6.vcf.gz /tmp/w22ChRBs6d/naive_concat.7.vcf.gz /tmp/w22ChRBs6d/naive_concat.8.vcf.gz /tmp/w22ChRBs6d/naive_concat.9.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -H .. ok test_vcf_concat: /build/bcftools-V6n0z8/bcftools-1.21/bcftools concat --no-version -l /tmp/w22ChRBs6d/concat.4.a.vcf.gz /tmp/w22ChRBs6d/concat.4.b.vcf.gz .. ok test_vcf_concat: /build/bcftools-V6n0z8/bcftools-1.21/bcftools concat -Ob -l /tmp/w22ChRBs6d/concat.4.a.vcf.gz /tmp/w22ChRBs6d/concat.4.b.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-V6n0z8/bcftools-1.21/bcftools concat --no-version -l /tmp/w22ChRBs6d/concat.4.a.bcf /tmp/w22ChRBs6d/concat.4.b.bcf .. ok test_vcf_concat: /build/bcftools-V6n0z8/bcftools-1.21/bcftools concat -Ob -l /tmp/w22ChRBs6d/concat.4.a.bcf /tmp/w22ChRBs6d/concat.4.b.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-V6n0z8/bcftools-1.21/bcftools concat --no-version -l --ligate-warn /tmp/w22ChRBs6d/concat.5.a.vcf.gz /tmp/w22ChRBs6d/concat.5.b.vcf.gz /tmp/w22ChRBs6d/concat.5.c.vcf.gz .. ok test_vcf_concat: /build/bcftools-V6n0z8/bcftools-1.21/bcftools concat -Ob -l --ligate-warn /tmp/w22ChRBs6d/concat.5.a.vcf.gz /tmp/w22ChRBs6d/concat.5.b.vcf.gz /tmp/w22ChRBs6d/concat.5.c.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-V6n0z8/bcftools-1.21/bcftools concat --no-version -l --ligate-warn /tmp/w22ChRBs6d/concat.5.a.bcf /tmp/w22ChRBs6d/concat.5.b.bcf /tmp/w22ChRBs6d/concat.5.c.bcf .. ok test_vcf_concat: /build/bcftools-V6n0z8/bcftools-1.21/bcftools concat -Ob -l --ligate-warn /tmp/w22ChRBs6d/concat.5.a.bcf /tmp/w22ChRBs6d/concat.5.b.bcf /tmp/w22ChRBs6d/concat.5.c.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-V6n0z8/bcftools-1.21/bcftools concat --no-version -l --ligate-force /tmp/w22ChRBs6d/concat.5.a.bcf /tmp/w22ChRBs6d/concat.5.b.bcf /tmp/w22ChRBs6d/concat.5.c.bcf .. ok test_vcf_concat: /build/bcftools-V6n0z8/bcftools-1.21/bcftools concat -Ob -l --ligate-force /tmp/w22ChRBs6d/concat.5.a.bcf /tmp/w22ChRBs6d/concat.5.b.bcf /tmp/w22ChRBs6d/concat.5.c.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-V6n0z8/bcftools-1.21/bcftools concat --no-version -G -a -D /tmp/w22ChRBs6d/concat.5.a.vcf.gz /tmp/w22ChRBs6d/concat.5.b.vcf.gz /tmp/w22ChRBs6d/concat.5.c.vcf.gz .. ok test_vcf_concat: /build/bcftools-V6n0z8/bcftools-1.21/bcftools concat -Ob -G -a -D /tmp/w22ChRBs6d/concat.5.a.vcf.gz /tmp/w22ChRBs6d/concat.5.b.vcf.gz /tmp/w22ChRBs6d/concat.5.c.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-V6n0z8/bcftools-1.21/bcftools concat --no-version -G -a -D /tmp/w22ChRBs6d/concat.5.a.bcf /tmp/w22ChRBs6d/concat.5.b.bcf /tmp/w22ChRBs6d/concat.5.c.bcf .. ok test_vcf_concat: /build/bcftools-V6n0z8/bcftools-1.21/bcftools concat -Ob -G -a -D /tmp/w22ChRBs6d/concat.5.a.bcf /tmp/w22ChRBs6d/concat.5.b.bcf /tmp/w22ChRBs6d/concat.5.c.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_reheader: /build/bcftools-V6n0z8/bcftools-1.21/bcftools reheader -h /build/bcftools-V6n0z8/bcftools-1.21/test/reheader.hdr /build/bcftools-V6n0z8/bcftools-1.21/test/reheader.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-V6n0z8/bcftools-1.21/test/reheader.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools reheader -h /build/bcftools-V6n0z8/bcftools-1.21/test/reheader.hdr | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-V6n0z8/bcftools-1.21/bcftools reheader -h /build/bcftools-V6n0z8/bcftools-1.21/test/reheader.hdr /tmp/w22ChRBs6d/reheader.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/w22ChRBs6d/reheader.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools reheader -h /build/bcftools-V6n0z8/bcftools-1.21/test/reheader.hdr | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-V6n0z8/bcftools-1.21/bcftools reheader -h /build/bcftools-V6n0z8/bcftools-1.21/test/reheader.hdr /tmp/w22ChRBs6d/reheader.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/w22ChRBs6d/reheader.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools reheader -h /build/bcftools-V6n0z8/bcftools-1.21/test/reheader.hdr | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-V6n0z8/bcftools-1.21/bcftools reheader -s /build/bcftools-V6n0z8/bcftools-1.21/test/reheader.samples /build/bcftools-V6n0z8/bcftools-1.21/test/reheader.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-V6n0z8/bcftools-1.21/test/reheader.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools reheader -s /build/bcftools-V6n0z8/bcftools-1.21/test/reheader.samples | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-V6n0z8/bcftools-1.21/bcftools reheader -s /build/bcftools-V6n0z8/bcftools-1.21/test/reheader.samples /tmp/w22ChRBs6d/reheader.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/w22ChRBs6d/reheader.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools reheader -s /build/bcftools-V6n0z8/bcftools-1.21/test/reheader.samples | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-V6n0z8/bcftools-1.21/bcftools reheader -s /build/bcftools-V6n0z8/bcftools-1.21/test/reheader.samples /tmp/w22ChRBs6d/reheader.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/w22ChRBs6d/reheader.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools reheader -s /build/bcftools-V6n0z8/bcftools-1.21/test/reheader.samples | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-V6n0z8/bcftools-1.21/bcftools reheader -s /build/bcftools-V6n0z8/bcftools-1.21/test/reheader.samples2 /build/bcftools-V6n0z8/bcftools-1.21/test/reheader.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-V6n0z8/bcftools-1.21/test/reheader.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools reheader -s /build/bcftools-V6n0z8/bcftools-1.21/test/reheader.samples2 | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-V6n0z8/bcftools-1.21/bcftools reheader -s /build/bcftools-V6n0z8/bcftools-1.21/test/reheader.samples2 /tmp/w22ChRBs6d/reheader.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/w22ChRBs6d/reheader.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools reheader -s /build/bcftools-V6n0z8/bcftools-1.21/test/reheader.samples2 | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-V6n0z8/bcftools-1.21/bcftools reheader -s /build/bcftools-V6n0z8/bcftools-1.21/test/reheader.samples2 /tmp/w22ChRBs6d/reheader.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/w22ChRBs6d/reheader.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools reheader -s /build/bcftools-V6n0z8/bcftools-1.21/test/reheader.samples2 | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-V6n0z8/bcftools-1.21/bcftools reheader -s /build/bcftools-V6n0z8/bcftools-1.21/test/reheader.samples3 /build/bcftools-V6n0z8/bcftools-1.21/test/reheader.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-V6n0z8/bcftools-1.21/test/reheader.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools reheader -s /build/bcftools-V6n0z8/bcftools-1.21/test/reheader.samples3 | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-V6n0z8/bcftools-1.21/bcftools reheader -s /build/bcftools-V6n0z8/bcftools-1.21/test/reheader.samples3 /tmp/w22ChRBs6d/reheader.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/w22ChRBs6d/reheader.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools reheader -s /build/bcftools-V6n0z8/bcftools-1.21/test/reheader.samples3 | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-V6n0z8/bcftools-1.21/bcftools reheader -s /build/bcftools-V6n0z8/bcftools-1.21/test/reheader.samples3 /tmp/w22ChRBs6d/reheader.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/w22ChRBs6d/reheader.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools reheader -s /build/bcftools-V6n0z8/bcftools-1.21/test/reheader.samples3 | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-V6n0z8/bcftools-1.21/bcftools reheader -s /build/bcftools-V6n0z8/bcftools-1.21/test/reheader.samples4 /build/bcftools-V6n0z8/bcftools-1.21/test/reheader.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-V6n0z8/bcftools-1.21/test/reheader.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools reheader -s /build/bcftools-V6n0z8/bcftools-1.21/test/reheader.samples4 | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-V6n0z8/bcftools-1.21/bcftools reheader -s /build/bcftools-V6n0z8/bcftools-1.21/test/reheader.samples4 /tmp/w22ChRBs6d/reheader.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/w22ChRBs6d/reheader.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools reheader -s /build/bcftools-V6n0z8/bcftools-1.21/test/reheader.samples4 | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-V6n0z8/bcftools-1.21/bcftools reheader -s /build/bcftools-V6n0z8/bcftools-1.21/test/reheader.samples4 /tmp/w22ChRBs6d/reheader.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/w22ChRBs6d/reheader.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools reheader -s /build/bcftools-V6n0z8/bcftools-1.21/test/reheader.samples4 | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-V6n0z8/bcftools-1.21/bcftools reheader -h /build/bcftools-V6n0z8/bcftools-1.21/test/reheader.empty.hdr /build/bcftools-V6n0z8/bcftools-1.21/test/empty.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-V6n0z8/bcftools-1.21/test/empty.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools reheader -h /build/bcftools-V6n0z8/bcftools-1.21/test/reheader.empty.hdr | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-V6n0z8/bcftools-1.21/bcftools reheader -h /build/bcftools-V6n0z8/bcftools-1.21/test/reheader.empty.hdr /tmp/w22ChRBs6d/empty.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/w22ChRBs6d/empty.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools reheader -h /build/bcftools-V6n0z8/bcftools-1.21/test/reheader.empty.hdr | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-V6n0z8/bcftools-1.21/bcftools reheader -h /build/bcftools-V6n0z8/bcftools-1.21/test/reheader.empty.hdr /tmp/w22ChRBs6d/empty.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/w22ChRBs6d/empty.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools reheader -h /build/bcftools-V6n0z8/bcftools-1.21/test/reheader.empty.hdr | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-V6n0z8/bcftools-1.21/bcftools reheader -f /build/bcftools-V6n0z8/bcftools-1.21/test/reheader.fai /build/bcftools-V6n0z8/bcftools-1.21/test/reheader.2.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-V6n0z8/bcftools-1.21/bcftools reheader -f /build/bcftools-V6n0z8/bcftools-1.21/test/reheader.fai /tmp/w22ChRBs6d/reheader.2.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-V6n0z8/bcftools-1.21/bcftools reheader -f /build/bcftools-V6n0z8/bcftools-1.21/test/reheader.fai /tmp/w22ChRBs6d/reheader.2.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-V6n0z8/bcftools-1.21/bcftools reheader -h /build/bcftools-V6n0z8/bcftools-1.21/test/reheader.2.hdr -f /build/bcftools-V6n0z8/bcftools-1.21/test/reheader.fai /build/bcftools-V6n0z8/bcftools-1.21/test/reheader.2.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-V6n0z8/bcftools-1.21/bcftools reheader -h /build/bcftools-V6n0z8/bcftools-1.21/test/reheader.2.hdr -f /build/bcftools-V6n0z8/bcftools-1.21/test/reheader.fai /tmp/w22ChRBs6d/reheader.2.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-V6n0z8/bcftools-1.21/bcftools reheader -h /build/bcftools-V6n0z8/bcftools-1.21/test/reheader.2.hdr -f /build/bcftools-V6n0z8/bcftools-1.21/test/reheader.fai /tmp/w22ChRBs6d/reheader.2.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-V6n0z8/bcftools-1.21/bcftools reheader -f /build/bcftools-V6n0z8/bcftools-1.21/test/reheader.3.fai /build/bcftools-V6n0z8/bcftools-1.21/test/reheader.3.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-V6n0z8/bcftools-1.21/bcftools reheader -f /build/bcftools-V6n0z8/bcftools-1.21/test/reheader.3.fai /tmp/w22ChRBs6d/reheader.3.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-V6n0z8/bcftools-1.21/bcftools reheader -f /build/bcftools-V6n0z8/bcftools-1.21/test/reheader.3.fai /tmp/w22ChRBs6d/reheader.3.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view --no-version .. ok test_rename_chrs: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate --rename-chrs /tmp/w22ChRBs6d/rename.map -Ov /tmp/w22ChRBs6d/annotate.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate --rename-chrs /tmp/w22ChRBs6d/rename.map -Ob /tmp/w22ChRBs6d/annotate.bcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate --rename-chrs /tmp/w22ChRBs6d/rename.map -Ov /build/bcftools-V6n0z8/bcftools-1.21/test/annotate.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /build/bcftools-V6n0z8/bcftools-1.21/bcftools annotate --rename-chrs /tmp/w22ChRBs6d/rename.map -Ob /build/bcftools-V6n0z8/bcftools-1.21/test/annotate.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%CHROM\t%POS\n' .. ok test_vcf_convert: /build/bcftools-V6n0z8/bcftools-1.21/bcftools convert -g -,. /tmp/w22ChRBs6d/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/convert.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools convert -g -,. .. ok test_vcf_convert: /build/bcftools-V6n0z8/bcftools-1.21/bcftools convert -g -,. --vcf-ids /tmp/w22ChRBs6d/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/convert.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools convert -g -,. --vcf-ids .. ok test_vcf_convert: /build/bcftools-V6n0z8/bcftools-1.21/bcftools convert -g -,. --vcf-ids --3N6 /tmp/w22ChRBs6d/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/convert.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools convert -g -,. --vcf-ids --3N6 .. ok test_vcf_convert: /build/bcftools-V6n0z8/bcftools-1.21/bcftools convert -g .,- /tmp/w22ChRBs6d/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/convert.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools convert -g .,- .. ok test_vcf_convert_hs2vcf: /build/bcftools-V6n0z8/bcftools-1.21/bcftools convert --vcf-ids -G /build/bcftools-V6n0z8/bcftools-1.21/test/convert.gs.gt.ids.gen,/build/bcftools-V6n0z8/bcftools-1.21/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-V6n0z8/bcftools-1.21/bcftools convert --vcf-ids -G /build/bcftools-V6n0z8/bcftools-1.21/test/convert.gs.gt.ids.gen,/build/bcftools-V6n0z8/bcftools-1.21/test/convert.gs.gt.samples -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-V6n0z8/bcftools-1.21/bcftools convert -G /build/bcftools-V6n0z8/bcftools-1.21/test/convert.gs.gt.ids.gen,/build/bcftools-V6n0z8/bcftools-1.21/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-V6n0z8/bcftools-1.21/bcftools convert -G /build/bcftools-V6n0z8/bcftools-1.21/test/convert.gs.gt.ids.gen,/build/bcftools-V6n0z8/bcftools-1.21/test/convert.gs.gt.samples -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-V6n0z8/bcftools-1.21/bcftools convert --3N6 -G /build/bcftools-V6n0z8/bcftools-1.21/test/convert.gs.gt.ids.3N6.gen,/build/bcftools-V6n0z8/bcftools-1.21/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-V6n0z8/bcftools-1.21/bcftools convert --3N6 -G /build/bcftools-V6n0z8/bcftools-1.21/test/convert.gs.gt.ids.3N6.gen,/build/bcftools-V6n0z8/bcftools-1.21/test/convert.gs.gt.samples -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-V6n0z8/bcftools-1.21/bcftools convert --vcf-ids -G /build/bcftools-V6n0z8/bcftools-1.21/test/convert.gs.gt.ids.gen.rev,/build/bcftools-V6n0z8/bcftools-1.21/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-V6n0z8/bcftools-1.21/bcftools convert --vcf-ids -G /build/bcftools-V6n0z8/bcftools-1.21/test/convert.gs.gt.ids.gen.rev,/build/bcftools-V6n0z8/bcftools-1.21/test/convert.gs.gt.samples -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-V6n0z8/bcftools-1.21/bcftools convert -G /build/bcftools-V6n0z8/bcftools-1.21/test/convert.gs.gt.ids.gen.rev,/build/bcftools-V6n0z8/bcftools-1.21/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-V6n0z8/bcftools-1.21/bcftools convert -G /build/bcftools-V6n0z8/bcftools-1.21/test/convert.gs.gt.ids.gen.rev,/build/bcftools-V6n0z8/bcftools-1.21/test/convert.gs.gt.samples -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^## .. ok test_vcf_convert: /build/bcftools-V6n0z8/bcftools-1.21/bcftools convert -g -,. --tag PL /tmp/w22ChRBs6d/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/convert.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools convert -g -,. --tag PL .. ok test_vcf_convert: /build/bcftools-V6n0z8/bcftools-1.21/bcftools convert -g .,- --tag PL /tmp/w22ChRBs6d/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/convert.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools convert -g .,- --tag PL .. ok test_vcf_convert: /build/bcftools-V6n0z8/bcftools-1.21/bcftools convert -g -,. --vcf-ids /tmp/w22ChRBs6d/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/check.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools convert -g -,. --vcf-ids .. ok test_vcf_convert: /build/bcftools-V6n0z8/bcftools-1.21/bcftools convert -g .,- --vcf-ids /tmp/w22ChRBs6d/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/check.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools convert -g .,- --vcf-ids .. ok test_vcf_convert: /build/bcftools-V6n0z8/bcftools-1.21/bcftools convert -g -,. --3N6 /tmp/w22ChRBs6d/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/check.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools convert -g -,. --3N6 .. ok test_vcf_convert: /build/bcftools-V6n0z8/bcftools-1.21/bcftools convert -g .,- --3N6 /tmp/w22ChRBs6d/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/check.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools convert -g .,- --3N6 .. ok test_vcf_convert: /build/bcftools-V6n0z8/bcftools-1.21/bcftools convert -g -,. --3N6 --vcf-ids /tmp/w22ChRBs6d/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/check.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools convert -g -,. --3N6 --vcf-ids .. ok test_vcf_convert: /build/bcftools-V6n0z8/bcftools-1.21/bcftools convert -g .,- --3N6 --vcf-ids /tmp/w22ChRBs6d/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/check.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools convert -g .,- --3N6 --vcf-ids .. ok test_vcf_convert: /build/bcftools-V6n0z8/bcftools-1.21/bcftools convert -h -,.,. /tmp/w22ChRBs6d/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/convert.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools convert -h -,.,. .. ok test_vcf_convert: /build/bcftools-V6n0z8/bcftools-1.21/bcftools convert -h .,-,. /tmp/w22ChRBs6d/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/convert.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools convert -h .,-,. .. ok test_vcf_convert: /build/bcftools-V6n0z8/bcftools-1.21/bcftools convert -h .,-,. --vcf-ids /tmp/w22ChRBs6d/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/convert.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools convert -h .,-,. --vcf-ids .. ok test_vcf_convert: /build/bcftools-V6n0z8/bcftools-1.21/bcftools convert -h .,.,- /tmp/w22ChRBs6d/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/convert.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools convert -h .,.,- .. ok test_vcf_convert_hls2vcf: /build/bcftools-V6n0z8/bcftools-1.21/bcftools convert -H /build/bcftools-V6n0z8/bcftools-1.21/test/convert.hls.gt.hap,/build/bcftools-V6n0z8/bcftools-1.21/test/convert.hls.gt.legend,/build/bcftools-V6n0z8/bcftools-1.21/test/convert.hls.gt.samples | grep -v ^## .. ok test_vcf_convert_hls2vcf: /build/bcftools-V6n0z8/bcftools-1.21/bcftools convert -H /build/bcftools-V6n0z8/bcftools-1.21/test/convert.hls.gt.hap,/build/bcftools-V6n0z8/bcftools-1.21/test/convert.hls.gt.legend,/build/bcftools-V6n0z8/bcftools-1.21/test/convert.hls.gt.samples -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^## .. ok test_vcf_convert: /build/bcftools-V6n0z8/bcftools-1.21/bcftools convert --haplegendsample -,.,. /tmp/w22ChRBs6d/convert.hap-missing.vcf.gz .. ok test_vcf_convert: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/convert.hap-missing.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools convert --haplegendsample -,.,. .. ok test_vcf_convert: /build/bcftools-V6n0z8/bcftools-1.21/bcftools convert --hapsample -,. /tmp/w22ChRBs6d/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/convert.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools convert --hapsample -,. .. ok test_vcf_convert: /build/bcftools-V6n0z8/bcftools-1.21/bcftools convert --hapsample -,. --vcf-ids /tmp/w22ChRBs6d/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/convert.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools convert --hapsample -,. --vcf-ids .. ok test_vcf_convert: /build/bcftools-V6n0z8/bcftools-1.21/bcftools convert --hapsample .,- /tmp/w22ChRBs6d/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/convert.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools convert --hapsample .,- .. ok test_vcf_convert_hs2vcf: /build/bcftools-V6n0z8/bcftools-1.21/bcftools convert --hapsample2vcf /build/bcftools-V6n0z8/bcftools-1.21/test/convert.hs.gt.hap,/build/bcftools-V6n0z8/bcftools-1.21/test/convert.hs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-V6n0z8/bcftools-1.21/bcftools convert --hapsample2vcf /build/bcftools-V6n0z8/bcftools-1.21/test/convert.hs.gt.hap,/build/bcftools-V6n0z8/bcftools-1.21/test/convert.hs.gt.samples -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-V6n0z8/bcftools-1.21/bcftools convert --vcf-ids --hapsample2vcf /build/bcftools-V6n0z8/bcftools-1.21/test/convert.hs.gt.ids.hap,/build/bcftools-V6n0z8/bcftools-1.21/test/convert.hs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-V6n0z8/bcftools-1.21/bcftools convert --vcf-ids --hapsample2vcf /build/bcftools-V6n0z8/bcftools-1.21/test/convert.hs.gt.ids.hap,/build/bcftools-V6n0z8/bcftools-1.21/test/convert.hs.gt.samples -Ou | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^## .. ok test_vcf_convert_gvcf: /build/bcftools-V6n0z8/bcftools-1.21/bcftools convert --no-version --gvcf2vcf -i'FILTER="PASS"' -f /build/bcftools-V6n0z8/bcftools-1.21/test/gvcf.fa /tmp/w22ChRBs6d/convert.gvcf.vcf.gz .. ok test_vcf_convert_gvcf: /build/bcftools-V6n0z8/bcftools-1.21/bcftools view -Ob /tmp/w22ChRBs6d/convert.gvcf.vcf.gz | /build/bcftools-V6n0z8/bcftools-1.21/bcftools convert --gvcf2vcf -i'FILTER="PASS"' -f /build/bcftools-V6n0z8/bcftools-1.21/test/gvcf.fa | grep -v ^##bcftools .. ok test_vcf_convert_tsv2vcf: /build/bcftools-V6n0z8/bcftools-1.21/bcftools convert --no-version -c ID,CHROM,POS,AA -s SAMPLE1 -f /build/bcftools-V6n0z8/bcftools-1.21/test/23andme.fa --tsv2vcf /build/bcftools-V6n0z8/bcftools-1.21/test/convert.23andme .. ok test_vcf_convert_tsv2vcf: /build/bcftools-V6n0z8/bcftools-1.21/bcftools convert -Ou -c ID,CHROM,POS,AA -s SAMPLE1 -f /build/bcftools-V6n0z8/bcftools-1.21/test/23andme.fa --tsv2vcf /build/bcftools-V6n0z8/bcftools-1.21/test/convert.23andme | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_convert_tsv2vcf: /build/bcftools-V6n0z8/bcftools-1.21/bcftools convert --no-version -c -,CHROM,POS,REF,ALT -f /build/bcftools-V6n0z8/bcftools-1.21/test/23andme.fa --tsv2vcf /build/bcftools-V6n0z8/bcftools-1.21/test/convert.tsv .. ok test_vcf_convert_tsv2vcf: /build/bcftools-V6n0z8/bcftools-1.21/bcftools convert -Ou -c -,CHROM,POS,REF,ALT -f /build/bcftools-V6n0z8/bcftools-1.21/test/23andme.fa --tsv2vcf /build/bcftools-V6n0z8/bcftools-1.21/test/convert.tsv | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.overlaps.1.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.overlaps.1.fa -s A .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.overlaps.1.bcf -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.overlaps.1.fa -s A .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.overlaps.1.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.overlaps.1.fa -s B .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.overlaps.1.bcf -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.overlaps.1.fa -s B .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.overlaps.1.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.overlaps.1.fa -s A -a N .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.overlaps.1.bcf -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.overlaps.1.fa -s A -a N .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.overlaps.1.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.overlaps.1.fa -s B -a N .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.overlaps.1.bcf -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.overlaps.1.fa -s B -a N .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.beyond.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.beyond.fa .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.beyond.bcf -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.beyond.fa .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.fa -s - -m /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.tab .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.bcf -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.fa -s - -m /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.tab .. ok test_vcf_consensus_chain: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.fa -s - -m /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.tab -c /tmp/w22ChRBs6d/consensus.1.chain.new >/dev/null; cat /tmp/w22ChRBs6d/consensus.1.chain.new .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.fa -H 1 -m /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.tab .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.bcf -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.fa -H 1 -m /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.tab .. ok test_vcf_consensus_chain: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.fa -H 1 -m /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.tab -c /tmp/w22ChRBs6d/consensus.2.chain.new >/dev/null; cat /tmp/w22ChRBs6d/consensus.2.chain.new .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.fa -I -s - -m /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.tab .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.bcf -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.fa -I -s - -m /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.tab .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.fa -s - -I -m /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.tab --mask-with X -m /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.tab --mask-with lc .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.bcf -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.fa -s - -I -m /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.tab --mask-with X -m /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.tab --mask-with lc .. ok test_vcf_consensus_chain: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.fa -I -m /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.tab -c /tmp/w22ChRBs6d/consensus.3.chain.new >/dev/null; cat /tmp/w22ChRBs6d/consensus.3.chain.new .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.fa -H 1 .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.bcf -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.fa -H 1 .. ok test_vcf_consensus_chain: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.fa -H 1 -c /tmp/w22ChRBs6d/consensus.4.chain.new >/dev/null; cat /tmp/w22ChRBs6d/consensus.4.chain.new .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus2.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus2.fa -H 1 .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus2.bcf -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus2.fa -H 1 .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus2.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus2.fa -H 2 .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus2.bcf -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus2.fa -H 2 .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/empty.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.fa -s - .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/empty.bcf -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.fa -s - .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus3.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus2.fa -H 2 -M "?" .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus3.bcf -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus2.fa -H 2 -M "?" .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus3.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus2.fa -H 2 -M "?" -p xx_ .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus3.bcf -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus2.fa -H 2 -M "?" -p xx_ .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus4.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus2.fa -s - .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus4.bcf -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus2.fa -s - .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus5.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus5.fa --haplotype LA .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus5.bcf -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus5.fa --haplotype LA .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus6.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus6.fa -s - .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus6.bcf -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus6.fa -s - .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus7.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus7.fa -H 2 .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus7.bcf -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus7.fa -H 2 .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus7.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus7.fa -H 4 .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus7.bcf -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus7.fa -H 4 .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus7.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus7.fa -H 2pIu .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus7.bcf -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus7.fa -H 2pIu .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus7.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus7.fa -H 4pIu .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus7.bcf -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus7.fa -H 4pIu .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus7.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus7.fa -H 1 .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus7.bcf -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus7.fa -H 1 .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus7.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus7.fa -H 3 .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus7.bcf -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus7.fa -H 3 .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus7.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus7.fa -H 1pIu .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus7.bcf -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus7.fa -H 1pIu .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus7.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus7.fa -H 3pIu .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus7.bcf -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus7.fa -H 3pIu .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus8.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.fa -s - .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus8.bcf -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.fa -s - .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus8.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.fa -s - -a . .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus8.bcf -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.fa -s - -a . .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus8.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.fa -s - -a . -i 'type="snp" || type="ref"' .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus8.bcf -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.fa -s - -a . -i 'type="snp" || type="ref"' .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus8.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.fa -s - -a . -i 'ALT!=""' .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus8.bcf -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.fa -s - -a . -i 'ALT!=""' .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus8.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.fa -s - -a . -e 'MinDP>15' .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus8.bcf -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.fa -s - -a . -e 'MinDP>15' .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus8.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.fa -s - -a . -e 'MinDP<15' .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus8.bcf -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.fa -s - -a . -e 'MinDP<15' .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.9.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.9.bcf -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.9.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.9.bcf -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.10.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.10.bcf -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.10.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.10.bcf -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.11.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.11.fa -s smpl .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.11.bcf -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.11.fa -s smpl .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.11.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.11.fa -s smpl -a N .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.11.bcf -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.11.fa -s smpl -a N .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.12.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.12.fa -s - .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.12.bcf -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.12.fa -s - .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.13.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.13.fa -s - .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.13.bcf -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.13.fa -s - .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.14.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.14.fa -s - .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.14.bcf -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.14.fa -s - .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.12.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.12.fa -s - --mark-del - --mark-ins uc --mark-snv uc .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.12.bcf -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.12.fa -s - --mark-del - --mark-ins uc --mark-snv uc .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.12.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.12.fa -s - --mark-del - --mark-ins + --mark-snv : .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.12.bcf -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.12.fa -s - --mark-del - --mark-ins + --mark-snv : .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.15.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.15.fa -H I --mark-ins lc --mark-snv lc .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.15.bcf -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.15.fa -H I --mark-ins lc --mark-snv lc .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.16.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.fa -s - -I .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.16.bcf -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.fa -s - -I .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.16.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.fa -H I .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.16.bcf -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.fa -H I .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.17.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus2.fa -s - -M N -m /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.17.bed .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.17.bcf -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus2.fa -s - -M N -m /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.17.bed .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.18.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.18.fa -s - .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.18.bcf -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.18.fa -s - .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.19.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.19.fa -s - .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.19.bcf -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.19.fa -s - .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.20.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.20.fa -s - .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.20.bcf -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.20.fa -s - .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.20.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.20.fa .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.20.bcf -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.20.fa .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.20.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.20.fa -M . -s b .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.20.bcf -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.20.fa -M . -s b .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.20.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.20.fa -M . -s a .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.20.bcf -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.20.fa -M . -s a .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.21.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.21.fa .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.21.bcf -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.21.fa .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.22.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.22.fa --regions-overlap 0 --mark-del . .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.22.bcf -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.22.fa --regions-overlap 0 --mark-del . .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.22.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.22.fa --regions-overlap 1 --mark-del . .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.22.bcf -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.22.fa --regions-overlap 1 --mark-del . .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.22.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.22.fa --regions-overlap 2 --mark-del . .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.22.bcf -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.22.fa --regions-overlap 2 --mark-del . .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.22.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.22.fa --regions-overlap 0 .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.22.bcf -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.22.fa --regions-overlap 0 .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.22.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.22.fa --regions-overlap 1 .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.22.bcf -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.22.fa --regions-overlap 1 .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.22.vcf.gz -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.22.fa --regions-overlap 2 .. ok test_vcf_consensus: /build/bcftools-V6n0z8/bcftools-1.21/bcftools consensus /tmp/w22ChRBs6d/consensus.22.bcf -f /build/bcftools-V6n0z8/bcftools-1.21/test/consensus.22.fa --regions-overlap 2 .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -r17:100-150 -a -AD -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.1.bam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.2.bam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -r17:100-150 -a -AD -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.1.bam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.2.bam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -r17:100-150 -a -AD -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa -b /tmp/w22ChRBs6d/mpileup.bam.list --no-version | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -r17:100-150 -a -AD -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob -b /tmp/w22ChRBs6d/mpileup.bam.urllist | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -r17:100-150 -a -AD -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.1.cram /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.2.cram /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -r17:100-150 -a -AD -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.1.cram /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.2.cram /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -r17:100-150 -a -AD -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa -b /tmp/w22ChRBs6d/mpileup.cram.list --no-version | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -r17:100-150 -a -AD -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob -b /tmp/w22ChRBs6d/mpileup.cram.urllist | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a DP,DV -r17:100-600 -a -AD -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.1.bam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.2.bam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a DP,DV -r17:100-600 -a -AD -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.1.bam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.2.bam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a DP,DV -r17:100-600 -a -AD -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.1.cram /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.2.cram /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a DP,DV -r17:100-600 -a -AD -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.1.cram /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.2.cram /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -a -AD -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -a -AD -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.1.bam | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -a -AD -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.1.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -a -AD -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.1.cram | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP,-AD -r17:100-600 -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.1.bam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.2.bam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP,-AD -r17:100-600 -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.1.bam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.2.bam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP,-AD -r17:100-600 -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.1.cram /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.2.cram /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP,-AD -r17:100-600 -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.1.cram /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.2.cram /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.1.bam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.2.bam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.1.bam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.2.bam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.1.cram /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.2.cram /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.1.cram /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.2.cram /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a DP,DV,-AD -r17:100-600 --gvcf 0,2,5 -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.1.bam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.2.bam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a DP,DV,-AD -r17:100-600 --gvcf 0,2,5 -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.1.bam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.2.bam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a DP,DV,-AD -r17:100-600 --gvcf 0,2,5 -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.1.cram /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.2.cram /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a DP,DV,-AD -r17:100-600 --gvcf 0,2,5 -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.1.cram /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.2.cram /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a DP,DV,-AD -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.1.bam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.2.bam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a DP,DV,-AD -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.1.bam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.2.bam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a DP,DV,-AD -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.1.cram /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.2.cram /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a DP,DV,-AD -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.1.cram /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.2.cram /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -s HG00101,HG00102 -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.1.bam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.2.bam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -s HG00101,HG00102 -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.1.bam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.2.bam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -s HG00101,HG00102 -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.1.cram /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.2.cram /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -s HG00101,HG00102 -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.1.cram /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.2.cram /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -S /build/bcftools-V6n0z8/bcftools-1.21/test/mplp.samples -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.1.bam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.2.bam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -S /build/bcftools-V6n0z8/bcftools-1.21/test/mplp.samples -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.1.bam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.2.bam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -S /build/bcftools-V6n0z8/bcftools-1.21/test/mplp.samples -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.1.cram /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.2.cram /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -S /build/bcftools-V6n0z8/bcftools-1.21/test/mplp.samples -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.1.cram /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.2.cram /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -s ^HG00101,HG00102 -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.1.bam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.2.bam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -s ^HG00101,HG00102 -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.1.bam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.2.bam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -s ^HG00101,HG00102 -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.1.cram /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.2.cram /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -s ^HG00101,HG00102 -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.1.cram /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.2.cram /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -S ^/build/bcftools-V6n0z8/bcftools-1.21/test/mplp.samples -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.1.bam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.2.bam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -S ^/build/bcftools-V6n0z8/bcftools-1.21/test/mplp.samples -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.1.bam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.2.bam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -S ^/build/bcftools-V6n0z8/bcftools-1.21/test/mplp.samples -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.1.cram /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.2.cram /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -S ^/build/bcftools-V6n0z8/bcftools-1.21/test/mplp.samples -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.1.cram /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.2.cram /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -S /build/bcftools-V6n0z8/bcftools-1.21/test/mplp.9.samples -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.1.sam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.2.sam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -S /build/bcftools-V6n0z8/bcftools-1.21/test/mplp.9.samples -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.1.sam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.2.sam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.sam | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -S /build/bcftools-V6n0z8/bcftools-1.21/test/mplp.9.samples -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.1.bam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.2.bam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -S /build/bcftools-V6n0z8/bcftools-1.21/test/mplp.9.samples -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.1.bam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.2.bam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -S /build/bcftools-V6n0z8/bcftools-1.21/test/mplp.9.samples -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.1.cram /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.2.cram /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -S /build/bcftools-V6n0z8/bcftools-1.21/test/mplp.9.samples -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.1.cram /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.2.cram /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -G /build/bcftools-V6n0z8/bcftools-1.21/test/mplp.10.samples -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.1.sam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.2.sam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -G /build/bcftools-V6n0z8/bcftools-1.21/test/mplp.10.samples -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.1.sam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.2.sam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.sam | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -G /build/bcftools-V6n0z8/bcftools-1.21/test/mplp.10.samples -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.1.bam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.2.bam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -G /build/bcftools-V6n0z8/bcftools-1.21/test/mplp.10.samples -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.1.bam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.2.bam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -G /build/bcftools-V6n0z8/bcftools-1.21/test/mplp.10.samples -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.1.cram /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.2.cram /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -G /build/bcftools-V6n0z8/bcftools-1.21/test/mplp.10.samples -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.1.cram /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.2.cram /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.sam | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -s HG00102 -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.sam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -s HG00102 -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.sam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.4.sam | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -s HG00102 -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.bam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -s HG00102 -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.bam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.4.bam | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -s HG00102 -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.cram /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -s HG00102 -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.cram /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.4.cram | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -s ^HG99999 -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.sam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -s ^HG99999 -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.sam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.4.sam | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -s ^HG99999 -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.bam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -s ^HG99999 -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.bam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.4.bam | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -s ^HG99999 -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.cram /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -s ^HG99999 -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.cram /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.4.cram | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -G /build/bcftools-V6n0z8/bcftools-1.21/test/mplp.11.rgs -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.sam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -G /build/bcftools-V6n0z8/bcftools-1.21/test/mplp.11.rgs -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.sam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.4.sam | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -G /build/bcftools-V6n0z8/bcftools-1.21/test/mplp.11.rgs -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.bam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -G /build/bcftools-V6n0z8/bcftools-1.21/test/mplp.11.rgs -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.bam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.4.bam | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -G /build/bcftools-V6n0z8/bcftools-1.21/test/mplp.11.rgs -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.cram /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -G /build/bcftools-V6n0z8/bcftools-1.21/test/mplp.11.rgs -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.cram /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.4.cram | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -G /build/bcftools-V6n0z8/bcftools-1.21/test/mplp.11.rgs -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.sam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -G /build/bcftools-V6n0z8/bcftools-1.21/test/mplp.11.rgs -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.sam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.4.sam | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -G /build/bcftools-V6n0z8/bcftools-1.21/test/mplp.11.rgs -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.bam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -G /build/bcftools-V6n0z8/bcftools-1.21/test/mplp.11.rgs -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.bam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.4.bam | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -G /build/bcftools-V6n0z8/bcftools-1.21/test/mplp.11.rgs -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.cram /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -G /build/bcftools-V6n0z8/bcftools-1.21/test/mplp.11.rgs -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.3.cram /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup.4.cram | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a AD -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/indel-AD.1.fa /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/indel-AD.1.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a AD -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/indel-AD.1.fa -Ob /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/indel-AD.1.sam | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a AD -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/indel-AD.1.fa /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/indel-AD.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a AD -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/indel-AD.1.fa -Ob /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/indel-AD.1.bam | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a AD -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/indel-AD.1.fa /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/indel-AD.1.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a AD -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/indel-AD.1.fa -Ob /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/indel-AD.1.cram | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a AD --indels-cns -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/indel-AD.1.fa /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/indel-AD.1.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a AD --indels-cns -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/indel-AD.1.fa -Ob /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/indel-AD.1.sam | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a AD --indels-cns -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/indel-AD.1.fa /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/indel-AD.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a AD --indels-cns -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/indel-AD.1.fa -Ob /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/indel-AD.1.bam | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a AD --indels-cns -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/indel-AD.1.fa /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/indel-AD.1.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a AD --indels-cns -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/indel-AD.1.fa -Ob /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/indel-AD.1.cram | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a AD -r 11:75 -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/indel-AD.2.fa /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a AD -r 11:75 -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/indel-AD.2.fa -Ob /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/indel-AD.2.bam | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a AD -r 11:75 -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/indel-AD.2.fa /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a AD -r 11:75 -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/indel-AD.2.fa -Ob /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/indel-AD.2.cram | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/indel-AD.2.fa /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/indel-AD.2.fa -Ob /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/indel-AD.2.bam | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/indel-AD.2.fa /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/indel-AD.2.fa -Ob /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/indel-AD.2.cram | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/indel-AD.2.fa /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/indel-AD.2.fa -Ob /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/indel-AD.2.bam | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/indel-AD.2.fa /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/indel-AD.2.fa -Ob /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/indel-AD.2.cram | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD,INFO/SCR,FMT/SCR -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup-SCR.fa /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup-SCR.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD,INFO/SCR,FMT/SCR -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup-SCR.fa -Ob /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup-SCR.bam | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD,INFO/SCR,FMT/SCR -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup-SCR.fa /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup-SCR.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD,INFO/SCR,FMT/SCR -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup-SCR.fa -Ob /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup-SCR.cram | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -t 1:100 --skip-all-set PAIRED,PROPER_PAIR,MREVERSE -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup-SCR.fa /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -t 1:100 --skip-all-set PAIRED,PROPER_PAIR,MREVERSE -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup-SCR.fa -Ob /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup-filter.sam | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -t 1:100 --skip-any-set READ1 -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup-SCR.fa /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -t 1:100 --skip-any-set READ1 -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup-SCR.fa -Ob /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup-filter.sam | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -t 1:100 --skip-all-unset READ1 -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup-SCR.fa /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -t 1:100 --skip-all-unset READ1 -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup-SCR.fa -Ob /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup-filter.sam | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -t 1:100 --skip-any-unset READ1 -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup-SCR.fa /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD -t 1:100 --skip-any-unset READ1 -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup-SCR.fa -Ob /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/mpileup-filter.sam | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD,INFO/NMBZ -r chr19:69-99 -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/annot-NMBZ.1.fa /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/annot-NMBZ.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD,INFO/NMBZ -r chr19:69-99 -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/annot-NMBZ.1.fa -Ob /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/annot-NMBZ.1.bam | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD,INFO/NMBZ -r chr6:75 -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/annot-NMBZ.2.fa /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/annot-NMBZ.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD,INFO/NMBZ -r chr6:75 -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/annot-NMBZ.2.fa -Ob /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/annot-NMBZ.2.bam | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD,INFO/NMBZ -r chr16:75 -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/annot-NMBZ.3.fa /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/annot-NMBZ.3.1.bam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/annot-NMBZ.3.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-V6n0z8/bcftools-1.21/bcftools mpileup -a -AD,INFO/NMBZ -r chr16:75 -f /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/annot-NMBZ.3.fa -Ob /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/annot-NMBZ.3.1.bam /build/bcftools-V6n0z8/bcftools-1.21/test/mpileup/annot-NMBZ.3.2.bam | /build/bcftools-V6n0z8/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_csq: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq.gff3 /build/bcftools-V6n0z8/bcftools-1.21/test/csq.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq.chr.gff3 /build/bcftools-V6n0z8/bcftools-1.21/test/csq.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq.2.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq.2.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq.2.gff --ncsq 64 /build/bcftools-V6n0z8/bcftools-1.21/test/csq.2.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq.nchr.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq.nchr.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq.nchr.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq.ychr.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq.nchr.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq.nchr.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq.nchr.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq.ychr.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq.nchr.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq.ychr.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq.ychr.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq.nchr.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq.ychr.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq.ychr.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq.ychr.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq.ychr.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq.nchr.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq.ychr.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq.nchr.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq.ychr.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq.ychr.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq.nchr.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq.nchr.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq.ychr.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000373833/ENST00000373833.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000373833/ENST00000373833.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000373833/boundary-insertion.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -l -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000373833/ENST00000373833.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000373833/ENST00000373833.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000373833/boundary-insertion.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/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-V6n0z8/bcftools-1.21/test/csq/ENST00000422159 && /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f ENST00000422159.fa -g ENST00000422159.gff multiallelic.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS\t%REF\t%ALT\t%GT\t%TBCSQ\n]' | ../sort-csq -q ; echo ; /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f ENST00000422159.fa -g short.gff multiallelic.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS\t%REF\t%ALT\t%GT\t%TBCSQ\n]' | ../sort-csq -q .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000378322/ENST00000378322.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000378322/ENST00000378322.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000378322/end-overlap-tscript.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -l -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000378322/ENST00000378322.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000378322/ENST00000378322.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000378322/end-overlap-tscript.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000263103-INS/ENST00000263103-INS.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000263103-INS/ENST00000263103-INS.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000263103-INS/insertions.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000269081/ENST00000269081.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000269081/ENST00000269081.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000269081/stop-gained-not-inframe-insertion.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000420190/ENST00000420190.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000420190/ENST00000420190.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000420190/abort-in-csq-push.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000329454/ENST00000329454.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000329454/ENST00000329454.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000329454/boundary-deletion.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -l -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000329454/ENST00000329454.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000329454/ENST00000329454.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000329454/boundary-deletion.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000294661/ENST00000294661.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000294661/ENST00000294661.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000294661/non-coding-boundary.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -l -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000294661/ENST00000294661.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000294661/ENST00000294661.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000294661/non-coding-boundary.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000285021/ENST00000285021.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000285021/ENST00000285021.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000285021/stop-gained-inframe-indel.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000381157/ENST00000381157.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000381157/ENST00000381157.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000381157/haploid-diploid.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n' .. ok test_csq_real: cd /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000410009 && /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -lb -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000410009 && /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -B 5 -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000410009 && /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -b -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000410009/ENST00000410009.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000410009/ENST00000410009.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000410009/frameshift.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/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-V6n0z8/bcftools-1.21/test/csq/ENSMUST00000133836 && /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f ENSMUST00000133836.fa -g ENSMUST00000133836.gff filter-problem.vcf -i 'FILTER="PASS"' --phase m | ../sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/bcftools-V6n0z8/bcftools-1.21/test/csq/EMN908947 && /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f EMN908947.fa -g ribosomal-slippage.gff ribosomal-slippage.vcf --force | ../sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/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-V6n0z8/bcftools-1.21/test/csq/EMN908947 && /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f EMN908947.fa -g simple.gff simple.vcf | ../sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000519442/ENST00000519442.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000519442/ENST00000519442.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000519442/synon-splice-region-del.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000557788/ENST00000557788.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000557788/ENST00000557788.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000557788/long-overlap-del.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/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-V6n0z8/bcftools-1.21/test/csq/ENSMUST00000121418 && /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25105' --phase m | ../sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENSMUST00000121418 && /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25500' --phase m | ../sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENSMUST00000121418 && /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25496' --phase m | ../sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000420670/ENST00000420670.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000420670/ENST00000420670.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000420670/start-stop-lost.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000420670/ENST00000420670.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000420670/ENST00000420670.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000420670/segfault.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000409523/ENST00000409523.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000409523/ENST00000409523.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000409523/long-overlapping-del.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000520795/ENST00000520795.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000520795/ENST00000520795.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000520795/long-inside-del.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -l -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000520795/ENST00000520795.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000520795/ENST00000520795.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000520795/long-inside-del.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000382647/ENST00000382647.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000382647/ENST00000382647.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000382647/synon-splice-region-insert.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000545279/ENST00000545279.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000545279/ENST00000545279.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000545279/splice-region-insert.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000528237/ENST00000528237.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000528237/ENST00000528237.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000528237/retained-stop-incomplete-cds.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/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-V6n0z8/bcftools-1.21/test/csq/ENST00000379416 && /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.del-snp.vcf | ../sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-del.vcf | ../sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-ins.vcf | ../sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-snp.vcf | ../sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff single.vcf | ../sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000400151/ENST00000400151.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000400151/ENST00000400151.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000400151/long-del.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000624631/ENST00000624631.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000624631/ENST00000624631.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000624631/ambiguous.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000218032/ENST00000218032.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000218032/ENST00000218032.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000218032/start-lost-del.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000218032/ENST00000218032.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000218032/ENST00000218032.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000218032/start-lost.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -l -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000218032/ENST00000218032.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000218032/ENST00000218032.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000218032/start-lost.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000542803/ENST00000542803.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000542803/ENST00000542803.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000542803/splice-region.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -l -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000542803/ENST00000542803.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000542803/ENST00000542803.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000542803/splice-region.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000543077/ENST00000543077.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000543077/ENST00000543077.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000543077/not-a-start-lost.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -l -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000543077/ENST00000543077.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000543077/ENST00000543077.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000543077/not-a-start-lost.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -l -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -l -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -l -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/frame3.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -l -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/frame3.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -l -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -l -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -l -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/frame2.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -l -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/frame2.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/not-a-start-lost.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -l -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/not-a-start-lost.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/frame1.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -l -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/frame1.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -l -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -l -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -l -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000536784/ENST00000536784.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000536784/ENST00000536784.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000536784/not-a-start-lost.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -l -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000536784/ENST00000536784.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000536784/ENST00000536784.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000536784/not-a-start-lost.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/EDUMMY0003/EDUMMY0003.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/EDUMMY0003/EDUMMY0003.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/EDUMMY0003/long-del.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/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-V6n0z8/bcftools-1.21/test/csq/ENST00000000000 && /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -p a -f ENST00000000000.fa -g ENST00000000000.gff upstream-stop.vcf | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'[%POS\t%REF\t%ALT\t%SAMPLE\t%GT\t%TBCSQ\n]' | ../sort-csq -q .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000448695/ENST00000448695.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000448695/ENST00000448695.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000448695/syn-and-splice-reg.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/EDUMMY0002/EDUMMY0002.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/EDUMMY0002/EDUMMY0002.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/EDUMMY0002/boundaries.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000318249/ENST00000318249.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000318249/ENST00000318249.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000318249/start-lost.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -l -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000318249/ENST00000318249.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000318249/ENST00000318249.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000318249/start-lost.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/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-V6n0z8/bcftools-1.21/test/csq/ENST00000580206 && /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.ins-snv.vcf | ../sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g short.gff compound.ins-snv.vcf | ../sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff single.ins-snv.vcf | ../sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g short.gff single.ins-snv.vcf | ../sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.del-snv.vcf | ../sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g short.gff compound.del-snv.vcf | ../sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g short.gff single.del-snv.vcf | ../sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.del-ins.vcf | ../sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g short.gff compound.del-ins.vcf | ../sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g short.gff single.del-ins.vcf | ../sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000520868/ENST00000520868.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000520868/ENST00000520868.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000520868/long-deletion.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000413103/ENST00000413103.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000413103/ENST00000413103.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000413103/long-deletion.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENSG00000173376/ENSG00000173376.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENSG00000173376/ENSG00000173376.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENSG00000173376/synon.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000571540/ENST00000571540.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000571540/ENST00000571540.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000571540/nmd.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000227471/ENST00000227471.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000227471/ENST00000227471.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000227471/insert-splice-vs-frameshift.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000271583/ENST00000271583.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000271583/ENST00000271583.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000271583/splice-acceptor.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000368801/ENST00000368801.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000368801/ENST00000368801.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000368801/compound-lost.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000301246/ENST00000301246.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000301246/ENST00000301246.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000301246/15bp-insert.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000318249.2/ENST00000318249.2.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000318249.2/ENST00000318249.2.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000318249.2/synonymous-start-lost.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/EDUMMY0001/EDUMMY0001.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/EDUMMY0001/EDUMMY0001.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/EDUMMY0001/starts-with-1.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -l -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/EDUMMY0001/EDUMMY0001.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/EDUMMY0001/EDUMMY0001.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/EDUMMY0001/starts-with-1.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000295641/ENST00000295641.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000295641/ENST00000295641.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000295641/not-a-start-lost.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -l -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000295641/ENST00000295641.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000295641/ENST00000295641.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000295641/not-a-start-lost.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000479739/ENST00000479739.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000479739/ENST00000479739.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000479739/short-cds-start-lost.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -l -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000479739/ENST00000479739.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000479739/ENST00000479739.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000479739/short-cds-start-lost.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000436063/ENST00000436063.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000436063/ENST00000436063.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000436063/insert-before-utr.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000573035-bt2212/ENST00000573035-bt2212.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000573035-bt2212/ENST00000573035-bt2212.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000573035-bt2212/complex-event.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000518414/ENST00000518414.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000518414/ENST00000518414.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000518414/incorrect-inframe-del.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000368801.2/ENST00000368801.2.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000368801.2/ENST00000368801.2.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000368801.2/start-lost.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000518414-ENST00000521270/valgrind.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000423372/snps.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -l -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000423372/snps.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000423372/insert3.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -l -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000423372/insert3.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000303039/ENST00000303039.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000303039/ENST00000303039.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000303039/not-a-stop.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -l -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000303039/ENST00000303039.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000303039/ENST00000303039.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000303039/not-a-stop.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000256452/ENST00000256452.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000256452/ENST00000256452.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000256452/intron.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000357367/ENST00000357367.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000357367/ENST00000357367.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000357367/stop-retained.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000375992/ENST00000375992.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000375992/ENST00000375992.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000375992/incorrect-synon-del-not-start-lost.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000593942/ENST00000593942.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000593942/ENST00000593942.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000593942/last-codon-deletion.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000360372/ENST00000360372.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000360372/ENST00000360372.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000360372/mnp.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000230048/ENST00000230048.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000230048/ENST00000230048.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000230048/start-del.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000573314/ENST00000573314.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000573314/ENST00000573314.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -l -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000573314/ENST00000573314.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000573314/ENST00000573314.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-V6n0z8/bcftools-1.21/bcftools csq -f /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000390520/ENST00000390520.fa -g /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000390520/ENST00000390520.gff /build/bcftools-V6n0z8/bcftools-1.21/test/csq/ENST00000390520/deletion-overlap.vcf | /build/bcftools-V6n0z8/bcftools-1.21/test/csq/sort-csq | /build/bcftools-V6n0z8/bcftools-1.21/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-V6n0z8/bcftools-1.21/bcftools roh /build/bcftools-V6n0z8/bcftools-1.21/test/roh.1.vcf.gz -Or -G30 --AF-dflt 0.4| grep -v ^# .. ok test_roh: /build/bcftools-V6n0z8/bcftools-1.21/bcftools roh /build/bcftools-V6n0z8/bcftools-1.21/test/roh.1.vcf.gz -Or -G30 --AF-file /build/bcftools-V6n0z8/bcftools-1.21/test/roh.1.tab.gz| grep -v ^# .. ok test_roh: /build/bcftools-V6n0z8/bcftools-1.21/bcftools roh /build/bcftools-V6n0z8/bcftools-1.21/test/roh.1.vcf.gz -Or -G30 --AF-file /build/bcftools-V6n0z8/bcftools-1.21/test/roh.1.tab.gz --ignore-homref| grep -v ^# .. ok test_roh: /build/bcftools-V6n0z8/bcftools-1.21/bcftools roh /build/bcftools-V6n0z8/bcftools-1.21/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245| grep -v ^# .. ok test_roh: /build/bcftools-V6n0z8/bcftools-1.21/bcftools roh /build/bcftools-V6n0z8/bcftools-1.21/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --ignore-homref| grep -v ^# .. ok test_roh: /build/bcftools-V6n0z8/bcftools-1.21/bcftools roh /build/bcftools-V6n0z8/bcftools-1.21/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-V6n0z8/bcftools-1.21/bcftools roh /build/bcftools-V6n0z8/bcftools-1.21/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --include-noalt| grep -v ^# .. ok test_gtcheck: /build/bcftools-V6n0z8/bcftools-1.21/bcftools gtcheck -e 0 --no-HWE-prob /tmp/w22ChRBs6d/gtcheck.1.vcf.gz -g /tmp/w22ChRBs6d/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-V6n0z8/bcftools-1.21/bcftools gtcheck -e 0 /tmp/w22ChRBs6d/gtcheck.1.vcf.gz -g /tmp/w22ChRBs6d/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-V6n0z8/bcftools-1.21/bcftools gtcheck -e 0 -u GT,GT /tmp/w22ChRBs6d/gtcheck.1.vcf.gz -g /tmp/w22ChRBs6d/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-V6n0z8/bcftools-1.21/bcftools gtcheck -e 0 -u GT,PL /tmp/w22ChRBs6d/gtcheck.1.vcf.gz -g /tmp/w22ChRBs6d/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-V6n0z8/bcftools-1.21/bcftools gtcheck -e 0 -u PL,GT /tmp/w22ChRBs6d/gtcheck.1.vcf.gz -g /tmp/w22ChRBs6d/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-V6n0z8/bcftools-1.21/bcftools gtcheck -e 0 -u PL,PL /tmp/w22ChRBs6d/gtcheck.1.vcf.gz -g /tmp/w22ChRBs6d/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-V6n0z8/bcftools-1.21/bcftools gtcheck -e 0 -p s1,s1 /tmp/w22ChRBs6d/gtcheck.1.vcf.gz -g /tmp/w22ChRBs6d/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-V6n0z8/bcftools-1.21/bcftools gtcheck -e 0 /tmp/w22ChRBs6d/gtcheck.2.vcf.gz -g /tmp/w22ChRBs6d/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-V6n0z8/bcftools-1.21/bcftools gtcheck -e 0 /tmp/w22ChRBs6d/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-V6n0z8/bcftools-1.21/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/w22ChRBs6d/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-V6n0z8/bcftools-1.21/bcftools gtcheck -e 0 -P /build/bcftools-V6n0z8/bcftools-1.21/test/gtcheck.3.pairs /tmp/w22ChRBs6d/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-V6n0z8/bcftools-1.21/bcftools gtcheck -e 0 -u PL /tmp/w22ChRBs6d/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-V6n0z8/bcftools-1.21/bcftools gtcheck -e 0 --n-matches 4 /tmp/w22ChRBs6d/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO | sort .. ok test_gtcheck: /build/bcftools-V6n0z8/bcftools-1.21/bcftools gtcheck -e 0 -s qry:E,D,C /tmp/w22ChRBs6d/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-V6n0z8/bcftools-1.21/bcftools gtcheck -e 0 -s qry:E,D,C -u PL /tmp/w22ChRBs6d/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-V6n0z8/bcftools-1.21/bcftools gtcheck -e 0 -s qry:B -s gt:D /tmp/w22ChRBs6d/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-V6n0z8/bcftools-1.21/bcftools gtcheck -e 0 -s qry:B -s gt:D -u PL /tmp/w22ChRBs6d/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-V6n0z8/bcftools-1.21/bcftools gtcheck -e 0 -s qry:B -s gt:D,C /tmp/w22ChRBs6d/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-V6n0z8/bcftools-1.21/bcftools gtcheck -e 0 -p B,C,B,D /tmp/w22ChRBs6d/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-V6n0z8/bcftools-1.21/bcftools gtcheck -e 0 -u GT,GT -H /tmp/w22ChRBs6d/gtcheck.1.vcf.gz -g /tmp/w22ChRBs6d/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-V6n0z8/bcftools-1.21/bcftools gtcheck -e 0 -u GT,PL -H /tmp/w22ChRBs6d/gtcheck.1.vcf.gz -g /tmp/w22ChRBs6d/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-V6n0z8/bcftools-1.21/bcftools gtcheck -e 0 -u PL,GT -H /tmp/w22ChRBs6d/gtcheck.1.vcf.gz -g /tmp/w22ChRBs6d/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-V6n0z8/bcftools-1.21/bcftools gtcheck -e 0 -u PL,PL -H /tmp/w22ChRBs6d/gtcheck.1.vcf.gz -g /tmp/w22ChRBs6d/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-V6n0z8/bcftools-1.21/bcftools gtcheck -e 0 -P /build/bcftools-V6n0z8/bcftools-1.21/test/gtcheck.4.pairs --distinctive-sites 3 /tmp/w22ChRBs6d/gtcheck.4.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-V6n0z8/bcftools-1.21/bcftools gtcheck -e 0 -P /build/bcftools-V6n0z8/bcftools-1.21/test/gtcheck.4.pairs --distinctive-sites 3,1 /tmp/w22ChRBs6d/gtcheck.4.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-V6n0z8/bcftools-1.21/bcftools gtcheck -u GT -e 30 /tmp/w22ChRBs6d/gtcheck.1.vcf.gz -g /tmp/w22ChRBs6d/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-V6n0z8/bcftools-1.21/bcftools gtcheck -u GT -e 30 -p s1,s1 /tmp/w22ChRBs6d/gtcheck.1.vcf.gz -g /tmp/w22ChRBs6d/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-V6n0z8/bcftools-1.21/bcftools gtcheck -u GT -e 300 /tmp/w22ChRBs6d/gtcheck.1.vcf.gz -g /tmp/w22ChRBs6d/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-V6n0z8/bcftools-1.21/bcftools gtcheck -u PL -e 30 /tmp/w22ChRBs6d/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-V6n0z8/bcftools-1.21/bcftools gtcheck /tmp/w22ChRBs6d/gtcheck.ntop.vcf.gz -g /tmp/w22ChRBs6d/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-V6n0z8/bcftools-1.21/bcftools gtcheck --n-matches 2 /tmp/w22ChRBs6d/gtcheck.ntop.vcf.gz -g /tmp/w22ChRBs6d/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-V6n0z8/bcftools-1.21/bcftools gtcheck /tmp/w22ChRBs6d/gtcheck.5.vcf.gz -g /tmp/w22ChRBs6d/gtcheck.5.gts.vcf.gz | grep -v ^# | grep -v Time .. ok test_gtcheck: /build/bcftools-V6n0z8/bcftools-1.21/bcftools gtcheck -p A,B,B,C /tmp/w22ChRBs6d/gtcheck.6.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-V6n0z8/bcftools-1.21/bcftools gtcheck -t 11:33 -p A,D,A,E,D,E -u GT -e 10 /tmp/w22ChRBs6d/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok Number of tests: total .. 1805 passed .. 1805 failed .. 0 make[2]: Leaving directory '/build/bcftools-V6n0z8/bcftools-1.21' make[1]: Leaving directory '/build/bcftools-V6n0z8/bcftools-1.21' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/bcftools/ make -j2 install DESTDIR=/build/bcftools-V6n0z8/bcftools-1.21/debian/bcftools AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/bcftools-V6n0z8/bcftools-1.21' mkdir -p -m 755 /build/bcftools-V6n0z8/bcftools-1.21/debian/bcftools/usr/bin /build/bcftools-V6n0z8/bcftools-1.21/debian/bcftools/usr/share/man/man1 /build/bcftools-V6n0z8/bcftools-1.21/debian/bcftools/usr/lib/x86_64-linux-gnu/bcftools install -p bcftools /build/bcftools-V6n0z8/bcftools-1.21/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-V6n0z8/bcftools-1.21/debian/bcftools/usr/bin install -p -m 644 doc/bcftools.1 /build/bcftools-V6n0z8/bcftools-1.21/debian/bcftools/usr/share/man/man1 install -p plugins/*.so /build/bcftools-V6n0z8/bcftools-1.21/debian/bcftools/usr/lib/x86_64-linux-gnu/bcftools make[1]: Leaving directory '/build/bcftools-V6n0z8/bcftools-1.21' debian/rules override_dh_install make[1]: Entering directory '/build/bcftools-V6n0z8/bcftools-1.21' 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-V6n0z8/bcftools-1.21' dh_installdocs dh_installchangelogs debian/rules override_dh_installman make[1]: Entering directory '/build/bcftools-V6n0z8/bcftools-1.21' dh_installman --language=C make[1]: Leaving directory '/build/bcftools-V6n0z8/bcftools-1.21' dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dpkg-gencontrol: warning: package bcftools: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package bcftools: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'bcftools-dbgsym' in '../bcftools-dbgsym_1.21-1_amd64.deb'. dpkg-deb: building package 'bcftools' in '../bcftools_1.21-1_amd64.deb'. dpkg-genbuildinfo -O../bcftools_1.21-1_amd64.buildinfo dpkg-genchanges -O../bcftools_1.21-1_amd64.changes dpkg-genchanges: info: including full source code in upload dpkg-source -Zxz --after-build . dpkg-buildpackage: info: full upload (original source is included) -------------------------------------------------------------------------------- Build finished at 2025-08-17T08:46:44Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Sun, 17 Aug 2025 08:46:44 +0000 | +------------------------------------------------------------------------------+ bcftools_1.21-1_amd64.changes: ------------------------------ Format: 1.8 Date: Thu, 13 Feb 2025 21:42:57 +0100 Source: bcftools Binary: bcftools bcftools-dbgsym Architecture: source amd64 Version: 1.21-1 Distribution: perl-5.42-throwaway Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: bcftools - genomic variant calling and manipulation of VCF/BCF files Changes: bcftools (1.21-1) unstable; urgency=medium . * New upstream version 1.21 * d/copyright: update copyright year. * skip_new_test_failing_on_32bit.patch: unfuzz. * tests-pluginpath.patch: delete: hunk inhibited upstream. * d/patches/*: normalise Last-Update timestamp. * d/rules: activate hardening. Checksums-Sha1: 6a38e1e0014f7bc1196c43da01b74b14098a91ce 1242 bcftools_1.21-1.dsc 7f367e0f03d4f56ca88d5f3a79435f196591fbce 3665160 bcftools_1.21.orig.tar.gz 4df0cc69dacce808b43d3516e542197da60ab309 7500 bcftools_1.21-1.debian.tar.xz 8f28782b098da1ebf8d5f622ebdf9eca543a4148 2228696 bcftools-dbgsym_1.21-1_amd64.deb 09e9399af6a4c72ced4543f2d275cbe7b2e2a6fd 7272 bcftools_1.21-1_amd64.buildinfo d7fffa6c61e0449369421adbbc5924be89e37804 783660 bcftools_1.21-1_amd64.deb Checksums-Sha256: 51dd5c18612732034ef2be5bd19f48fdc697412bff52e4a24a58a36c2cd42e94 1242 bcftools_1.21-1.dsc 7484695c5d833fb1a89c2b886ec302db0514ba3c8e5ef7397b9302fa8bd37f8d 3665160 bcftools_1.21.orig.tar.gz 10b8964c10a3a4d8bd65d0e568eeb6fe7040e1fd33e0ac2bf5012670aed5a39e 7500 bcftools_1.21-1.debian.tar.xz d67902f95331d103017cea6bca55ef0b30b451f57f4c56f80f741931fc103593 2228696 bcftools-dbgsym_1.21-1_amd64.deb 6a576f540737ac529d3f85682e4e9df1205df18b052aab858a90893116371f71 7272 bcftools_1.21-1_amd64.buildinfo 0b2e012dc91b1acd404a38ae2d5e04971a9215287c1e3ced8e4e381152fe3fcf 783660 bcftools_1.21-1_amd64.deb Files: 6835b0b13b376ba4edc1a14e1764b90a 1242 science optional bcftools_1.21-1.dsc e144a5777c606c69eb643ae8ff613dbb 3665160 science optional bcftools_1.21.orig.tar.gz d02793361bfdb9a259bf61335780f39c 7500 science optional bcftools_1.21-1.debian.tar.xz 91cada3630a48e27e069495a876e6439 2228696 debug optional bcftools-dbgsym_1.21-1_amd64.deb fea74ad407376ffbc85c8e5dc5242be9 7272 science optional bcftools_1.21-1_amd64.buildinfo 9df1879a3e52ac8d931d76621b615113 783660 science optional bcftools_1.21-1_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo Sun, 17 Aug 2025 08:46:44 +0000 | +------------------------------------------------------------------------------+ Format: 1.0 Source: bcftools Binary: bcftools bcftools-dbgsym Architecture: amd64 source Version: 1.21-1 Checksums-Md5: 6835b0b13b376ba4edc1a14e1764b90a 1242 bcftools_1.21-1.dsc 91cada3630a48e27e069495a876e6439 2228696 bcftools-dbgsym_1.21-1_amd64.deb 9df1879a3e52ac8d931d76621b615113 783660 bcftools_1.21-1_amd64.deb Checksums-Sha1: 6a38e1e0014f7bc1196c43da01b74b14098a91ce 1242 bcftools_1.21-1.dsc 8f28782b098da1ebf8d5f622ebdf9eca543a4148 2228696 bcftools-dbgsym_1.21-1_amd64.deb d7fffa6c61e0449369421adbbc5924be89e37804 783660 bcftools_1.21-1_amd64.deb Checksums-Sha256: 51dd5c18612732034ef2be5bd19f48fdc697412bff52e4a24a58a36c2cd42e94 1242 bcftools_1.21-1.dsc d67902f95331d103017cea6bca55ef0b30b451f57f4c56f80f741931fc103593 2228696 bcftools-dbgsym_1.21-1_amd64.deb 0b2e012dc91b1acd404a38ae2d5e04971a9215287c1e3ced8e4e381152fe3fcf 783660 bcftools_1.21-1_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Sun, 17 Aug 2025 08:46:43 +0000 Build-Path: /build/bcftools-V6n0z8/bcftools-1.21 Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: autoconf (= 2.72-3.1), automake (= 1:1.17-4), autopoint (= 0.23.1-2), autotools-dev (= 20240727.1), base-files (= 14), base-passwd (= 3.6.7), bash (= 5.2.37-2+b5), binutils (= 2.45-4), binutils-common (= 2.45-4), binutils-x86-64-linux-gnu (= 2.45-4), bsdextrautils (= 2.41.1-1), bsdutils (= 1:2.41.1-1), build-essential (= 12.12), bzip2 (= 1.0.8-6), comerr-dev (= 2.1-1.47.2-3+b3), coreutils (= 9.7-3), cpp (= 4:14.2.0-1), cpp-14 (= 14.3.0-5), cpp-14-x86-64-linux-gnu (= 14.3.0-5), cpp-x86-64-linux-gnu (= 4:14.2.0-1), dash (= 0.5.12-12), debconf (= 1.5.91), debhelper (= 13.25), debianutils (= 5.23.2), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.14.1-2), diffutils (= 1:3.10-4), dpkg (= 1.22.21), dpkg-dev (= 1.22.21), dwz (= 0.15-1+b1), file (= 1:5.46-5), findutils (= 4.10.0-3), g++ (= 4:14.2.0-1), g++-14 (= 14.3.0-5), g++-14-x86-64-linux-gnu (= 14.3.0-5), g++-x86-64-linux-gnu (= 4:14.2.0-1), gcc (= 4:14.2.0-1), gcc-14 (= 14.3.0-5), gcc-14-base (= 14.3.0-5), gcc-14-x86-64-linux-gnu (= 14.3.0-5), gcc-15-base (= 15.2.0-1), gcc-x86-64-linux-gnu (= 4:14.2.0-1), gettext (= 0.23.1-2+b1), gettext-base (= 0.23.1-2+b1), grep (= 3.11-4), groff-base (= 1.23.0-9), gzip (= 1.13-1), hostname (= 3.25), init-system-helpers (= 1.69), intltool-debian (= 0.35.0+20060710.6), krb5-multidev (= 1.21.3-5), libacl1 (= 2.3.2-2+b1), libarchive-zip-perl (= 1.68-1), libasan8 (= 15.2.0-1), libatomic1 (= 15.2.0-1), libattr1 (= 1:2.5.2-3), libaudit-common (= 1:4.0.5-1), libaudit1 (= 1:4.0.5-1), libbinutils (= 2.45-4), libblkid1 (= 2.41.1-1), libbrotli-dev (= 1.1.0-2+b7), libbrotli1 (= 1.1.0-2+b7), libbz2-1.0 (= 1.0.8-6), libbz2-dev (= 1.0.8-6), libc-bin (= 2.41-12), libc-dev-bin (= 2.41-12), libc6 (= 2.41-12), libc6-dev (= 2.41-12), libcap-ng0 (= 0.8.5-4+b1), libcap2 (= 1:2.75-10+b1), libcc1-0 (= 15.2.0-1), libcom-err2 (= 1.47.2-3+b3), libcrypt-dev (= 1:4.4.38-1), libcrypt1 (= 1:4.4.38-1), libctf-nobfd0 (= 2.45-4), libctf0 (= 2.45-4), libcurl3t64-gnutls (= 8.15.0-1), libcurl4-gnutls-dev (= 8.15.0-1), libdb5.3t64 (= 5.3.28+dfsg2-9), libdebconfclient0 (= 0.280), libdebhelper-perl (= 13.25), libdeflate-dev (= 1.23-2), libdeflate0 (= 1.23-2), libdpkg-perl (= 1.22.21), libelf1t64 (= 0.192-4), libevent-2.1-7t64 (= 2.1.12-stable-10+b1), libffi8 (= 3.4.8-2), libfile-stripnondeterminism-perl (= 1.14.1-2), libgcc-14-dev (= 14.3.0-5), libgcc-s1 (= 15.2.0-1), libgdbm-compat4t64 (= 1.24-2), libgdbm6t64 (= 1.24-2), libgmp-dev (= 2:6.3.0+dfsg-3), libgmp10 (= 2:6.3.0+dfsg-3), libgmpxx4ldbl (= 2:6.3.0+dfsg-3), libgnutls-dane0t64 (= 3.8.10-2), libgnutls-openssl27t64 (= 3.8.10-2), libgnutls28-dev (= 3.8.10-2), libgnutls30t64 (= 3.8.10-2), libgomp1 (= 15.2.0-1), libgprofng0 (= 2.45-4), libgsl-dev (= 2.8+dfsg-5), libgsl28 (= 2.8+dfsg-5), libgslcblas0 (= 2.8+dfsg-5), libgssapi-krb5-2 (= 1.21.3-5), libgssrpc4t64 (= 1.21.3-5), libhogweed6t64 (= 3.10.1-1), libhts-dev (= 1.21+ds-1), libhts3t64 (= 1.21+ds-1), libhtscodecs2 (= 1.6.1-2), libhwasan0 (= 15.2.0-1), libidn2-0 (= 2.3.8-3), libidn2-dev (= 2.3.8-3), libio-pty-perl (= 1:1.20-1+b4), libisl23 (= 0.27-1), libitm1 (= 15.2.0-1), libjansson4 (= 2.14-2+b3), libk5crypto3 (= 1.21.3-5), libkadm5clnt-mit12 (= 1.21.3-5), libkadm5srv-mit12 (= 1.21.3-5), libkdb5-10t64 (= 1.21.3-5), libkeyutils1 (= 1.6.3-6), libkrb5-3 (= 1.21.3-5), libkrb5-dev (= 1.21.3-5), libkrb5support0 (= 1.21.3-5), liblastlog2-2 (= 2.41.1-1), libldap-dev (= 2.6.10+dfsg-1+b1), libldap2 (= 2.6.10+dfsg-1+b1), liblsan0 (= 15.2.0-1), liblzma-dev (= 5.8.1-1), liblzma5 (= 5.8.1-1), libmagic-mgc (= 1:5.46-5), libmagic1t64 (= 1:5.46-5), libmd0 (= 1.1.0-2+b1), libmount1 (= 2.41.1-1), libmpc3 (= 1.3.1-1+b3), libmpfr6 (= 4.2.2-1), libnettle8t64 (= 3.10.1-1), libnghttp2-14 (= 1.64.0-1.1+b1), libnghttp2-dev (= 1.64.0-1.1+b1), libnghttp3-9 (= 1.8.0-1), libnghttp3-dev (= 1.8.0-1), libngtcp2-16 (= 1.11.0-1), libngtcp2-crypto-gnutls-dev (= 1.11.0-1), libngtcp2-crypto-gnutls8 (= 1.11.0-1), libngtcp2-dev (= 1.11.0-1), libp11-kit-dev (= 0.25.5-3), libp11-kit0 (= 0.25.5-3), libpam-modules (= 1.7.0-5), libpam-modules-bin (= 1.7.0-5), libpam-runtime (= 1.7.0-5), libpam0g (= 1.7.0-5), libpcre2-8-0 (= 10.45-1), libperl5.42 (= 5.42.0-1), libpipeline1 (= 1.5.8-1), libpkgconf3 (= 1.8.1-4), libpsl-dev (= 0.21.2-1.1+b1), libpsl5t64 (= 0.21.2-1.1+b1), libquadmath0 (= 15.2.0-1), librtmp-dev (= 2.4+20151223.gitfa8646d.1-3), librtmp1 (= 2.4+20151223.gitfa8646d.1-3), libsasl2-2 (= 2.1.28+dfsg1-9), libsasl2-modules-db (= 2.1.28+dfsg1-9), libseccomp2 (= 2.6.0-2), libselinux1 (= 3.8.1-1), libsframe2 (= 2.45-4), libsmartcols1 (= 2.41.1-1), libsqlite3-0 (= 3.46.1-7), libssh2-1-dev (= 1.11.1-1), libssh2-1t64 (= 1.11.1-1), libssl-dev (= 3.5.2-1), libssl3t64 (= 3.5.2-1), libstdc++-14-dev (= 14.3.0-5), libstdc++6 (= 15.2.0-1), libsystemd0 (= 258~rc2-2), libtasn1-6 (= 4.20.0-2), libtasn1-6-dev (= 4.20.0-2), libtinfo6 (= 6.5+20250216-2), libtool (= 2.5.4-4), libtsan2 (= 15.2.0-1), libubsan1 (= 15.2.0-1), libuchardet0 (= 0.0.8-1+b2), libudev1 (= 258~rc2-2), libunbound8 (= 1.22.0-2), libunistring5 (= 1.3-2), libuuid1 (= 2.41.1-1), libxml2-16 (= 2.14.5+dfsg-0.1), libzstd-dev (= 1.5.7+dfsg-1), libzstd1 (= 1.5.7+dfsg-1), linux-libc-dev (= 6.12.38-1), m4 (= 1.4.19-8), make (= 4.4.1-2), man-db (= 2.13.1-1), mawk (= 1.3.4.20250131-1), ncurses-base (= 6.5+20250216-2), ncurses-bin (= 6.5+20250216-2), nettle-dev (= 3.10.1-1), openssl-provider-legacy (= 3.5.2-1), patch (= 2.8-2), perl (= 5.42.0-1), perl-base (= 5.42.0-1), perl-modules-5.42 (= 5.42.0-1), pkgconf (= 1.8.1-4), pkgconf-bin (= 1.8.1-4), po-debconf (= 1.0.21+nmu1), rpcsvc-proto (= 1.4.3-1), sed (= 4.9-2), sensible-utils (= 0.0.25), sysvinit-utils (= 3.14-4), tabix (= 1.21+ds-1), tar (= 1.35+dfsg-3.1), util-linux (= 2.41.1-1), xz-utils (= 5.8.1-1), zlib1g (= 1:1.3.dfsg+really1.3.1-1+b1), zlib1g-dev (= 1:1.3.dfsg+really1.3.1-1+b1) Environment: DEB_BUILD_OPTIONS="parallel=2" LANG="C.UTF-8" LC_COLLATE="C.UTF-8" LC_CTYPE="C.UTF-8" LD_LIBRARY_PATH="/usr/lib/libeatmydata" SOURCE_DATE_EPOCH="1739479377" +------------------------------------------------------------------------------+ | Package contents Sun, 17 Aug 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variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. 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+------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup Sun, 17 Aug 2025 08:46:45 +0000 | +------------------------------------------------------------------------------+ Purging /build/bcftools-V6n0z8 Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Sun, 17 Aug 2025 08:46:46 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 52772 Build-Time: 153 Distribution: perl-5.42-throwaway Host Architecture: amd64 Install-Time: 12 Job: /srv/debomatic/incoming/bcftools_1.21-1.dsc Machine Architecture: amd64 Package: bcftools Package-Time: 183 Source-Version: 1.21-1 Space: 52772 Status: successful Version: 1.21-1 -------------------------------------------------------------------------------- Finished at 2025-08-17T08:46:44Z Build needed 00:03:03, 52772k disk space