sbuild (Debian sbuild) 0.91.10 (27 June 2026) on carme.larted.org.uk +==============================================================================+ | bcftools 1.22-1 (amd64) Thu, 09 Jul 2026 03:54:46 +0000 | +==============================================================================+ Package: bcftools Version: 1.22-1 Source Version: 1.22-1 Distribution: perl-5.44-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 Thu, 09 Jul 2026 03:54:48 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup bcftools_1.22-1 perl-5.44-throwaway amd64 ---------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup bcftools_1.22-1 perl-5.44-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: Setting up apt archive... +------------------------------------------------------------------------------+ | Update chroot Thu, 09 Jul 2026 03:54:48 +0000 | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.44 InRelease [3039 B] Hit:2 http://deb.debian.org/debian unstable InRelease Hit:3 http://deb.debian.org/debian sid InRelease Get:1 file:/srv/reprepro perl-5.44 InRelease [3039 B] Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files Thu, 09 Jul 2026 03:54:51 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/bcftools_1.22-1.dsc exists in /srv/debomatic/incoming; copying to chroot +------------------------------------------------------------------------------+ | Install package build dependencies Thu, 09 Jul 2026 03:54:51 +0000 | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), zlib1g-dev, libbz2-dev, liblzma-dev, libhts-dev (>= 1.22), libgsl-dev, tabix, libio-pty-perl, build-essential Filtered Build-Depends: debhelper-compat (= 13), zlib1g-dev, libbz2-dev, liblzma-dev, libhts-dev (>= 1.22), libgsl-dev, tabix, libio-pty-perl, build-essential dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/build/bcftools-TfJ6sU/resolver-sJLaN5/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/build/bcftools-TfJ6sU/resolver-sJLaN5/apt_archive ./ InRelease Get:2 copy:/build/bcftools-TfJ6sU/resolver-sJLaN5/apt_archive ./ Release [609 B] Ign:3 copy:/build/bcftools-TfJ6sU/resolver-sJLaN5/apt_archive ./ Release.gpg Get:4 copy:/build/bcftools-TfJ6sU/resolver-sJLaN5/apt_archive ./ Sources [716 B] Get:5 copy:/build/bcftools-TfJ6sU/resolver-sJLaN5/apt_archive ./ Packages [733 B] Fetched 2058 B in 0s (0 B/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... Solving dependencies... 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 libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libelf1t64 libevent-2.1-7t64 libfile-stripnondeterminism-perl libgmp-dev libgmpxx4ldbl libgnutls-dane0t64 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 libpkgconf7 libpsl-dev libpsl5t64 librtmp-dev librtmp1 libssh2-1-dev libssh2-1t64 libssl-dev libtasn1-6-dev libtool libuchardet0 libunbound8 libunistring-dev 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 m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx python3:any 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 libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libelf1t64 libevent-2.1-7t64 libfile-stripnondeterminism-perl libgmp-dev libgmpxx4ldbl libgnutls-dane0t64 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 libpkgconf7 libpsl-dev libpsl5t64 librtmp-dev librtmp1 libssh2-1-dev libssh2-1t64 libssl-dev libtasn1-6-dev libtool libuchardet0 libunbound8 libunistring-dev 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, 91 newly installed, 0 to remove and 0 not upgraded. Need to get 32.4 MB/32.8 MB of archives. After this operation, 134 MB of additional disk space will be used. Get:1 file:/srv/reprepro perl-5.44/main amd64 libldap-dev amd64 2.6.13+dfsg-1+b1 [308 kB] Get:2 copy:/build/bcftools-TfJ6sU/resolver-sJLaN5/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [908 B] Get:3 file:/srv/reprepro perl-5.44/main amd64 libio-pty-perl amd64 1:1.31-1+b1 [38.4 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.47-4 [345 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.47-4 [111 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.47-4 [43.0 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 1.0-3 [332 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2+b2 [69.0 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.24.1-1 [1336 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.42.2-1 [100.0 kB] Get:12 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-3 [49.2 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 1.4.21-1 [332 kB] Get:15 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.73-2 [516 kB] Get:16 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1+nmu1 [60.0 kB] Get:17 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.18.1-4 [877 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 autopoint all 1.0-3 [820 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.4-1 [19.2 kB] Get:20 http://deb.debian.org/debian unstable/main amd64 comerr-dev amd64 2.1-1.47.4-1 [50.9 kB] Get:21 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 14.3 [77.3 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-11 [539 kB] Get:23 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 22 [12.2 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 1.15.1-1 [17.1 kB] Get:26 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.1-1 [6020 B] Get:27 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.195-1 [58.1 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-4 [108 kB] Get:29 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.15.3+dfsg-1 [642 kB] Get:30 http://deb.debian.org/debian unstable/main amd64 gettext amd64 1.0-3 [2658 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 1.0.22 [216 kB] Get:33 http://deb.debian.org/debian unstable/main amd64 debhelper all 14.3 [934 kB] Get:34 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.22.1-3 [31.1 kB] Get:35 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.22.1-3 [79.0 kB] Get:36 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6+b2 [9348 B] Get:37 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.22.1-3 [335 kB] Get:38 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.22.1-3 [137 kB] Get:39 http://deb.debian.org/debian unstable/main amd64 libgssrpc4t64 amd64 1.22.1-3 [58.3 kB] Get:40 http://deb.debian.org/debian unstable/main amd64 libkadm5clnt-mit12 amd64 1.22.1-3 [40.3 kB] Get:41 http://deb.debian.org/debian unstable/main amd64 libkdb5-10t64 amd64 1.22.1-3 [41.3 kB] Get:42 http://deb.debian.org/debian unstable/main amd64 libkadm5srv-mit12 amd64 1.22.1-3 [54.1 kB] Get:43 http://deb.debian.org/debian unstable/main amd64 krb5-multidev amd64 1.22.1-3 [125 kB] Get:44 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.2.0-3 [320 kB] Get:45 http://deb.debian.org/debian unstable/main amd64 libbrotli-dev amd64 1.2.0-3 [324 kB] Get:46 http://deb.debian.org/debian unstable/main amd64 libbz2-dev amd64 1.0.8-6+b2 [33.6 kB] Get:47 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.15.0-1 [67.2 kB] Get:48 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.22.1-1 [133 kB] Get:49 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.69.0-1 [89.0 kB] Get:50 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.22.1-1 [20.8 kB] Get:51 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.22.0-1 [60.7 kB] Get:52 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-4 [244 kB] Get:53 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls amd64 8.21.0-2 [416 kB] Get:54 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.21.0-2 [17.0 kB] Get:55 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.13-stable-1 [183 kB] Get:56 http://deb.debian.org/debian unstable/main amd64 libunbound8 amd64 1.25.1-1+b1 [619 kB] Get:57 http://deb.debian.org/debian unstable/main amd64 libgnutls-dane0t64 amd64 3.8.13-1 [496 kB] Get:58 http://deb.debian.org/debian unstable/main amd64 libidn2-dev amd64 2.3.8-5 [102 kB] Get:59 http://deb.debian.org/debian unstable/main amd64 libp11-kit-dev amd64 0.26.2-3 [222 kB] Get:60 http://deb.debian.org/debian unstable/main amd64 libtasn1-6-dev amd64 4.21.0-2+b1 [98.6 kB] Get:61 http://deb.debian.org/debian unstable/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-5+b2 [328 kB] Get:62 http://deb.debian.org/debian unstable/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-5+b2 [641 kB] Get:63 http://deb.debian.org/debian unstable/main amd64 nettle-dev amd64 3.10.2-1+b1 [1321 kB] Get:64 http://deb.debian.org/debian unstable/main amd64 libgnutls28-dev amd64 3.8.13-1 [1479 kB] Get:65 http://deb.debian.org/debian unstable/main amd64 libkrb5-dev amd64 1.22.1-3 [14.0 kB] Get:66 http://deb.debian.org/debian unstable/main amd64 libpkgconf7 amd64 2.5.1-4 [47.8 kB] Get:67 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 2.5.1-4 [35.9 kB] Get:68 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 2.5.1-4 [33.6 kB] Get:69 http://deb.debian.org/debian unstable/main amd64 libnghttp2-dev amd64 1.69.0-1 [128 kB] Get:70 http://deb.debian.org/debian unstable/main amd64 libnghttp3-dev amd64 1.15.0-1 [94.5 kB] Get:71 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.22.1-1 [20.9 kB] Get:72 http://deb.debian.org/debian unstable/main amd64 libngtcp2-dev amd64 1.22.1-1 [192 kB] Get:73 http://deb.debian.org/debian unstable/main amd64 libunistring-dev amd64 1.4.2-1 [651 kB] Get:74 http://deb.debian.org/debian unstable/main amd64 libpsl-dev amd64 0.22.0-1 [29.8 kB] Get:75 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.6-1 [60.3 kB] Get:76 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.2-3 [918 kB] Get:77 http://deb.debian.org/debian unstable/main amd64 librtmp-dev amd64 2.6-1 [69.7 kB] Get:78 http://deb.debian.org/debian unstable/main amd64 libssl-dev amd64 3.6.3-1 [3025 kB] Get:79 http://deb.debian.org/debian unstable/main amd64 libssh2-1-dev amd64 1.11.1-4 [393 kB] Get:80 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.7+dfsg-3+b2 [372 kB] Get:81 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls-dev amd64 8.21.0-2 [546 kB] Get:82 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.25-1 [48.0 kB] Get:83 http://deb.debian.org/debian unstable/main amd64 libdeflate-dev amd64 1.25-1 [56.7 kB] Get:84 http://deb.debian.org/debian unstable/main amd64 libgslcblas0 amd64 2.8+dfsg-6+b1 [131 kB] Get:85 http://deb.debian.org/debian unstable/main amd64 libgsl28 amd64 2.8+dfsg-6+b1 [1002 kB] Get:86 http://deb.debian.org/debian unstable/main amd64 libgsl-dev amd64 2.8+dfsg-6+b1 [1248 kB] Get:87 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.6-1 [101 kB] Get:88 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.22.1+ds2-1+b2 [475 kB] Get:89 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.8.3-1 [369 kB] Get:90 http://deb.debian.org/debian unstable/main amd64 libhts-dev amd64 1.22.1+ds2-1+b2 [1784 kB] Get:91 http://deb.debian.org/debian unstable/main amd64 tabix amd64 1.22.1+ds2-1+b2 [507 kB] Preconfiguring packages ... Fetched 32.4 MB in 0s (99.5 MB/s) Selecting previously unselected package sensible-utils. (Reading database ... 14518 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.47-4_amd64.deb ... Unpacking libmagic-mgc (1:5.47-4) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.47-4_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.47-4) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.47-4_amd64.deb ... Unpacking file (1:5.47-4) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_1.0-3_amd64.deb ... Unpacking gettext-base (1.0-3) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-2+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-2+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.24.1-1_amd64.deb ... Unpacking groff-base (1.24.1-1) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.42.2-1_amd64.deb ... Unpacking bsdextrautils (2.42.2-1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.8-3_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-3) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.1-1_amd64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.21-1_amd64.deb ... Unpacking m4 (1.4.21-1) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.73-2_all.deb ... Unpacking autoconf (2.73-2) ... Selecting previously unselected package autotools-dev. 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Setting up libgmpxx4ldbl:amd64 (2:6.3.0+dfsg-5+b2) ... Setting up libgnutls-dane0t64:amd64 (3.8.13-1) ... Setting up librtmp1:amd64 (2.6-1) ... Setting up libldap-dev:amd64 (2.6.13+dfsg-1+b1) ... Setting up comerr-dev:amd64 (2.1-1.47.4-1) ... Setting up libssl-dev:amd64 (3.6.3-1) ... Setting up autopoint (1.0-3) ... Setting up pkgconf-bin (2.5.1-4) ... Setting up libk5crypto3:amd64 (1.22.1-3) ... Setting up libidn2-dev:amd64 (2.3.8-5) ... Setting up autoconf (2.73-2) ... Setting up libnghttp3-9:amd64 (1.15.0-1) ... Setting up libnghttp3-dev:amd64 (1.15.0-1) ... Setting up liblzma-dev:amd64 (5.8.3-1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.2-3) ... Setting up dwz (0.16-4) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:amd64 (0.0.8-2+b2) ... Setting up libngtcp2-16:amd64 (1.22.1-1) ... Setting up libkrb5-3:amd64 (1.22.1-3) ... Setting up libssh2-1t64:amd64 (1.11.1-4) ... Setting up libgsl28:amd64 (2.8+dfsg-6+b1) ... Setting up libtasn1-6-dev:amd64 (4.21.0-2+b1) ... Setting up libdeflate-dev:amd64 (1.25-1) ... Setting up tabix (1.22.1+ds2-1+b2) ... Setting up libbrotli-dev:amd64 (1.2.0-3) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.22.1-1) ... Setting up libp11-kit-dev:amd64 (0.26.2-3) ... Setting up libbz2-dev:amd64 (1.0.8-6+b2) ... Setting up automake (1:1.18.1-4) ... update-alternatives: using /usr/bin/automake-1.18 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.1-1) ... Setting up gettext (1.0-3) ... Setting up libgsl-dev (2.8+dfsg-6+b1) ... Setting up libgmp-dev:amd64 (2:6.3.0+dfsg-5+b2) ... Setting up nettle-dev:amd64 (3.10.2-1+b1) ... Setting up libtool (2.5.4-11) ... Setting up libngtcp2-crypto-gnutls-dev:amd64 (1.22.1-1) ... Setting up libngtcp2-dev:amd64 (1.22.1-1) ... Setting up pkgconf:amd64 (2.5.1-4) ... Setting up libpsl-dev:amd64 (0.22.0-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (22) ... Setting up libgssapi-krb5-2:amd64 (1.22.1-3) ... Setting up libssh2-1-dev:amd64 (1.11.1-4) ... Setting up dh-strip-nondeterminism (1.15.1-1) ... Setting up groff-base (1.24.1-1) ... Setting up libgnutls28-dev:amd64 (3.8.13-1) ... Setting up libcurl4-gnutls:amd64 (8.21.0-2) ... Setting up libnghttp2-dev:amd64 (1.69.0-1) ... Setting up po-debconf (1.0.22) ... Setting up libcurl3t64-gnutls:amd64 (8.21.0-2) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libgssrpc4t64:amd64 (1.22.1-3) ... Setting up librtmp-dev:amd64 (2.6-1) ... Setting up libhts3t64:amd64 (1.22.1+ds2-1+b2) ... Setting up libkadm5clnt-mit12:amd64 (1.22.1-3) ... Setting up libkdb5-10t64:amd64 (1.22.1-3) ... Setting up debhelper (14.3) ... Setting up libkadm5srv-mit12:amd64 (1.22.1-3) ... Setting up krb5-multidev:amd64 (1.22.1-3) ... Setting up libkrb5-dev:amd64 (1.22.1-3) ... Setting up libcurl4-gnutls-dev:amd64 (8.21.0-2) ... Setting up libhts-dev:amd64 (1.22.1+ds2-1+b2) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.42-17) ... +------------------------------------------------------------------------------+ | Check architectures Thu, 09 Jul 2026 03:55:03 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Build environment Thu, 09 Jul 2026 03:55:03 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 7.0.10+deb14-amd64 #1 SMP PREEMPT_DYNAMIC Debian 7.0.10-1 (2026-05-27) amd64 (x86_64) Toolchain package versions: binutils_2.46.50.20260617-1 dpkg-dev_1.23.7 g++-15_15.3.0-1 gcc-15_15.3.0-1 libc6-dev_2.42-17 libstdc++-15-dev_15.3.0-1 libstdc++6_16.1.0-2 linux-libc-dev_7.1.3-1 Package versions: apt_3.3.1 autoconf_2.73-2 automake_1:1.18.1-4 autopoint_1.0-3 autotools-dev_20240727.1+nmu1 base-files_14.2 base-passwd_3.6.8 bash_5.3-3 binutils_2.46.50.20260617-1 binutils-common_2.46.50.20260617-1 binutils-x86-64-linux-gnu_2.46.50.20260617-1 bsdextrautils_2.42.2-1 build-essential_12.12 bzip2_1.0.8-6+b2 comerr-dev_2.1-1.47.4-1 coreutils_9.10-1 cpp_4:15.2.0-5+b1 cpp-15_15.3.0-1 cpp-15-x86-64-linux-gnu_15.3.0-1 cpp-x86-64-linux-gnu_4:15.2.0-5+b1 dash_0.5.12-12 debconf_1.5.92 debhelper_14.3 debian-archive-keyring_2025.1 debianutils_5.23.2 dh-autoreconf_22 dh-strip-nondeterminism_1.15.1-1 diffutils_1:3.12-1 dirmngr_2.4.9-5 dpkg_1.23.7 dpkg-dev_1.23.7 dwz_0.16-4 eatmydata_131-2 file_1:5.47-4 findutils_4.10.0-4 g++_4:15.2.0-5+b1 g++-15_15.3.0-1 g++-15-x86-64-linux-gnu_15.3.0-1 g++-x86-64-linux-gnu_4:15.2.0-5+b1 gcc_4:15.2.0-5+b1 gcc-15_15.3.0-1 gcc-15-base_15.3.0-1 gcc-15-x86-64-linux-gnu_15.3.0-1 gcc-16-base_16.1.0-2 gcc-x86-64-linux-gnu_4:15.2.0-5+b1 gettext_1.0-3 gettext-base_1.0-3 gnupg_2.4.9-5 gnupg-l10n_2.4.9-5 gpg_2.4.9-5 gpg-agent_2.4.9-5 gpgconf_2.4.9-5 gpgsm_2.4.9-5 grep_3.12-1 groff-base_1.24.1-1 gzip_1.13-1 hostname_3.25 init-system-helpers_1.69 intltool-debian_0.35.0+20060710.6 krb5-multidev_1.22.1-3 libacl1_2.4.0-1 libapt-pkg7.0_3.3.1 libarchive-zip-perl_1.68-1 libasan8_16.1.0-2 libassuan9_3.0.2-2+b2 libatomic1_16.1.0-2 libattr1_1:2.6.0-1 libaudit-common_1:4.1.2-1 libaudit1_1:4.1.2-1+b1 libbinutils_2.46.50.20260617-1 libblkid1_2.42.2-1 libbrotli-dev_1.2.0-3 libbrotli1_1.2.0-3 libbz2-1.0_1.0.8-6+b2 libbz2-dev_1.0.8-6+b2 libc-bin_2.42-17 libc-dev-bin_2.42-17 libc-gconv-modules-extra_2.42-17 libc6_2.42-17 libc6-dev_2.42-17 libcap-ng0_0.9.3-1+b1 libcc1-0_16.1.0-2 libcom-err2_1.47.4-1 libcrypt1_1:4.5.1-1+b1 libctf-nobfd0_2.46.50.20260617-1 libctf0_2.46.50.20260617-1 libcurl3t64-gnutls_8.21.0-2 libcurl4-gnutls_8.21.0-2 libcurl4-gnutls-dev_8.21.0-2 libdb5.3t64_5.3.28+dfsg2-11+b1 libdebconfclient0_0.283 libdebhelper-perl_14.3 libdeflate-dev_1.25-1 libdeflate0_1.25-1 libdpkg-perl_1.23.7 libeatmydata1_131-2+b2 libelf1t64_0.195-1 libevent-2.1-7t64_2.1.13-stable-1 libffi8_3.5.2-4 libfile-stripnondeterminism-perl_1.15.1-1 libgcc-15-dev_15.3.0-1 libgcc-s1_16.1.0-2 libgcrypt20_1.12.2-1 libgdbm-compat4t64_1.26-1+b2 libgdbm6t64_1.26-1+b2 libgmp-dev_2:6.3.0+dfsg-5+b2 libgmp10_2:6.3.0+dfsg-5+b2 libgmpxx4ldbl_2:6.3.0+dfsg-5+b2 libgnutls-dane0t64_3.8.13-1 libgnutls28-dev_3.8.13-1 libgnutls30t64_3.8.13-1 libgomp1_16.1.0-2 libgpg-error0_1.61-3 libgprofng0_2.46.50.20260617-1 libgsl-dev_2.8+dfsg-6+b1 libgsl28_2.8+dfsg-6+b1 libgslcblas0_2.8+dfsg-6+b1 libgssapi-krb5-2_1.22.1-3 libgssrpc4t64_1.22.1-3 libhogweed6t64_3.10.2-1+b1 libhts-dev_1.22.1+ds2-1+b2 libhts3t64_1.22.1+ds2-1+b2 libhtscodecs2_1.6.6-1 libhwasan0_16.1.0-2 libidn2-0_2.3.8-5 libidn2-dev_2.3.8-5 libio-pty-perl_1:1.31-1+b1 libisl23_0.27-2 libitm1_16.1.0-2 libjansson4_2.15.1-1 libk5crypto3_1.22.1-3 libkadm5clnt-mit12_1.22.1-3 libkadm5srv-mit12_1.22.1-3 libkdb5-10t64_1.22.1-3 libkeyutils1_1.6.3-6+b2 libkrb5-3_1.22.1-3 libkrb5-dev_1.22.1-3 libkrb5support0_1.22.1-3 libksba8_1.8.0-3 libldap-dev_2.6.13+dfsg-1+b1 libldap2_2.6.13+dfsg-1+b1 liblsan0_16.1.0-2 liblz4-1_1.10.0-10 liblzma-dev_5.8.3-1 liblzma5_5.8.3-1 libmagic-mgc_1:5.47-4 libmagic1t64_1:5.47-4 libmd0_1.2.0-2 libmount1_2.42.2-1 libmpc3_1.3.1-3 libmpfr6_4.2.2-3 libncursesw6_6.6+20260608-2 libnettle8t64_3.10.2-1+b1 libnghttp2-14_1.69.0-1 libnghttp2-dev_1.69.0-1 libnghttp3-9_1.15.0-1 libnghttp3-dev_1.15.0-1 libngtcp2-16_1.22.1-1 libngtcp2-crypto-gnutls-dev_1.22.1-1 libngtcp2-crypto-gnutls8_1.22.1-1 libngtcp2-dev_1.22.1-1 libnpth0t64_1.8-3+b2 libp11-kit-dev_0.26.2-3 libp11-kit0_0.26.2-3 libpam-modules_1.7.0-8 libpam-modules-bin_1.7.0-8 libpam-runtime_1.7.0-8 libpam0g_1.7.0-8 libpcre2-8-0_10.46-1+b2 libperl5.40_5.40.1-8 libperl5.44_5.44.0~rc2-1 libpipeline1_1.5.8-3 libpkgconf7_2.5.1-4 libpsl-dev_0.22.0-1 libpsl5t64_0.22.0-1 libquadmath0_16.1.0-2 libreadline8t64_8.3-4 librtmp-dev_2.6-1 librtmp1_2.6-1 libsasl2-2_2.1.28+dfsg1-11 libsasl2-modules-db_2.1.28+dfsg1-11 libseccomp2_2.6.0-2+b1 libselinux1_3.10-1 libsframe3_2.46.50.20260617-1 libsmartcols1_2.42.2-1 libsqlite3-0_3.53.3-1 libssh2-1-dev_1.11.1-4 libssh2-1t64_1.11.1-4 libssl-dev_3.6.3-1 libssl3t64_3.6.3-1 libstdc++-15-dev_15.3.0-1 libstdc++6_16.1.0-2 libsystemd0_261.1-2 libtasn1-6_4.21.0-2+b1 libtasn1-6-dev_4.21.0-2+b1 libtinfo6_6.6+20260608-2 libtool_2.5.4-11 libtsan2_16.1.0-2 libubsan1_16.1.0-2 libuchardet0_0.0.8-2+b2 libudev1_261.1-2 libunbound8_1.25.1-1+b1 libunistring-dev_1.4.2-1 libunistring5_1.4.2-1 libuuid1_2.42.2-1 libxml2-16_2.15.3+dfsg-1 libxxhash0_0.8.3-2+b2 libzstd-dev_1.5.7+dfsg-3+b2 libzstd1_1.5.7+dfsg-3+b2 linux-libc-dev_7.1.3-1 m4_1.4.21-1 make_4.4.1-3 man-db_2.13.1-1 mawk_1.3.4.20260302-1 ncurses-base_6.6+20260608-2 ncurses-bin_6.6+20260608-2 nettle-dev_3.10.2-1+b1 openssl-provider-legacy_3.6.3-1 patch_2.8-2 perl_5.44.0~rc2-1 perl-base_5.44.0~rc2-1 perl-modules-5.40_5.40.1-8 perl-modules-5.44_5.44.0~rc2-1 pinentry-curses_1.3.2-4 pkgconf_2.5.1-4 pkgconf-bin_2.5.1-4 po-debconf_1.0.22 readline-common_8.3-4 rpcsvc-proto_1.4.4-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-3 sensible-utils_0.0.26 sqv_1.4.0-1 sysvinit-utils_3.18-1 tabix_1.22.1+ds2-1+b2 tar_1.35+dfsg-4 util-linux_2.42.2-1 xz-utils_5.8.3-1 zlib1g_1:1.3.dfsg+really1.3.2-3 zlib1g-dev_1:1.3.dfsg+really1.3.2-3 +------------------------------------------------------------------------------+ | Build Thu, 09 Jul 2026 03:55:03 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: bcftools Binary: bcftools Architecture: any Version: 1.22-1 Maintainer: Debian Med Packaging Team Uploaders: Michael R. Crusoe , Étienne Mollier Homepage: https://samtools.github.io/bcftools/ Standards-Version: 4.7.2 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 (>= 1.22), libgsl-dev, tabix , libio-pty-perl Package-List: bcftools deb science optional arch=any Checksums-Sha1: 3fbdc981589442ae1fe328b815544a6b95141e6b 3751342 bcftools_1.22.orig.tar.gz fa886e276d8817623fda074235a8ca68c8fa886d 7552 bcftools_1.22-1.debian.tar.xz Checksums-Sha256: 1608e547daf7bd5ab7d52dea57019f57da3fdfb29bc26dece1e8d01a999a9a2d 3751342 bcftools_1.22.orig.tar.gz bae79924e69dfd47b3d27e8384352924c4cc637e6723b356d82e7babf62d6391 7552 bcftools_1.22-1.debian.tar.xz Files: 2323653f1a21855c1659789d65b1f10c 3751342 bcftools_1.22.orig.tar.gz 3c27e445f5544a940da1ea9224367b32 7552 bcftools_1.22-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEE3z4uQkp+J5wuSwI6ucKa7rL0UKcFAmiiP2MACgkQucKa7rL0 UKeSDQ/+OJWQM6ioS0lvaXR8EeDeIDgwDtaWSoTnzKHiRUJofyvHvpQW6cWkG1UM EJx4ngtfiI0l0qrSr9N3t9jEI2OJBageX5KxDXgAqPdeZL1aQmDKiOhJV062pyw6 1wL52QMqEuH5dy9wjDL+9tHlHkYjS2wFLbg8g1zvVhWO6IgcXpAuNWmzcKuFCJBe bqvfnJ0RR3m+72ewiKvGswvStBXtSSUclcLGV+l1J/zpwFqaXdsVKqvwxfe1tnyk C629xucSZqlAGueplvYqEfnJPQHYjsJaeon8aXFKjxEstZhSX8dwVt3d/lJ80CsI 4dh18T2Qt/HmAGTAu5CW/ar/duOwzK9D2QV/jWsmHJdR6A8PxMKp8uVaWQS5Za8G 0bG178qGMM6YO0IvvMoFAdwVP353GCbuZuZHjQXEXhxvm+E/DORf5J4bIbdqDQgx xH83L4FU53LBtRQtdPNSE07Is4Jjn3cF+itaZL/vArg3TAZfj0QOExqyfx7LnCUZ lwVFSfYB1Vxm5RoYBHyxUt5YEX9+Fx93UJFWUvBNcPwNKOTQ5idAVJ16bSRYHhIb mNV1IVSO92qUchILNzLgGfIDpS4Jvl1JL7gvluwmSBe89+mY9/PakORYqrXHJZNQ ml0Z1kAXGnAWfzRvv8B/7cfw52Zj2cnKB4YHVmxJmeBItgb5iz0= =UAwZ -----END PGP SIGNATURE----- dpkg-source: warning: cannot verify inline signature for ./bcftools_1.22-1.dsc: missing OpenPGP keyrings dpkg-source: info: verifying ./bcftools_1.22-1.dsc dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-keyring.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-tag2upload.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-nonupload.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-maintainers.pgp dpkg-source: info: extracting bcftools in /build/bcftools-TfJ6sU/bcftools-1.22 dpkg-source: info: unpacking bcftools_1.22.orig.tar.gz dpkg-source: info: unpacking bcftools_1.22-1.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 clean up apt cache ------------------ Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Time Build Commands Thu, 09 Jul 2026 03:55:04 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network bcftools_1.22-1 perl-5.44-throwaway amd64 ---------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network bcftools_1.22-1 perl-5.44-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANGUAGE=en_GB:en 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-TfJ6sU/bcftools-1.22 SCHROOT_ALIAS_NAME=perl-5.44-throwaway-amd64-debomatic SCHROOT_CHROOT_NAME=perl-5.44-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=110 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=perl-5.44-amd64-debomatic-463cdd20-2f83-4552-a857-8931d3f82248 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 1.22-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Steffen Möller 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-TfJ6sU/bcftools-1.22' dh_auto_clean make -j2 distclean make[2]: Entering directory '/build/bcftools-TfJ6sU/bcftools-1.22' rm -f test/*.o test/*.fa.fai test/*~ test/test-rbuf test/test-regidx rm -f plugins/*.so plugins/*.P rm -rf plugins/*.dSYM rm -f test/*.unsorted.hex test/*.unsorted.tsv rm -f gmon.out *.o mpileup2/*.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-TfJ6sU/bcftools-1.22' 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-TfJ6sU/bcftools-1.22' dh_clean dpkg-source -Zxz -b . dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building bcftools using existing ../bcftools_1.22.orig.tar.gz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: building bcftools in ../bcftools_1.22-1.debian.tar.xz dpkg-source: info: building bcftools in ../bcftools_1.22-1.dsc debian/rules binary dh binary dh_update_autotools_config debian/rules override_dh_autoreconf make[1]: Entering directory '/build/bcftools-TfJ6sU/bcftools-1.22' rm -f config.mk && touch config.mk export MAKEFLAGS="-s"; dh_autoreconf autoreconf: export WARNINGS= autoreconf: Entering directory '.' autoreconf: configure.ac: no obvious need to run autopoint autoreconf: running: aclocal --force autoreconf: configure.ac: tracing autoreconf: configure.ac: subdirectory $HTSDIR not present autoreconf: configure.ac: not using Libtool autoreconf: configure.ac: not using Intltool autoreconf: configure.ac: not using Gtkdoc autoreconf: configure.ac: no need to run autopoint (confirmed) autoreconf: running: /usr/bin/autoconf --force configure.ac:94: warning: _AC_CONFIG_SUBDIRS: you should use literals ./lib/autoconf/status.m4:1100: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:94: the top level autoreconf: running: /usr/bin/autoheader --force autoreconf: configure.ac: not using Automake autoreconf: configure.ac: not running make: --make not given autoreconf: Leaving directory '.' make[1]: Leaving directory '/build/bcftools-TfJ6sU/bcftools-1.22' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/bcftools-TfJ6sU/bcftools-1.22' 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... x86_64-linux-gnu-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 x86_64-linux-gnu-gcc accepts -g... yes checking for x86_64-linux-gnu-gcc option to enable C23 features... none needed checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking for x86_64-linux-gnu-gcc option to support 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-TfJ6sU/bcftools-1.22' dh_auto_build make -j2 make[1]: Entering directory '/build/bcftools-TfJ6sU/bcftools-1.22' echo '#define BCFTOOLS_VERSION "1.22"' > version.h x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-TfJ6sU/bcftools-1.22=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfindex.o vcfindex.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-TfJ6sU/bcftools-1.22=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tabix.o tabix.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-TfJ6sU/bcftools-1.22=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfstats.o vcfstats.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-TfJ6sU/bcftools-1.22=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfisec.o vcfisec.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-TfJ6sU/bcftools-1.22=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfmerge.o vcfmerge.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-TfJ6sU/bcftools-1.22=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfquery.o vcfquery.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-TfJ6sU/bcftools-1.22=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcffilter.o vcffilter.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-TfJ6sU/bcftools-1.22=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o filter.o filter.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-TfJ6sU/bcftools-1.22=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfsom.o vcfsom.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-TfJ6sU/bcftools-1.22=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfnorm.o vcfnorm.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-TfJ6sU/bcftools-1.22=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfgtcheck.o vcfgtcheck.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-TfJ6sU/bcftools-1.22=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-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 x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-TfJ6sU/bcftools-1.22=. -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 x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-TfJ6sU/bcftools-1.22=. -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 x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-TfJ6sU/bcftools-1.22=. -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 x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-TfJ6sU/bcftools-1.22=. -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 x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-TfJ6sU/bcftools-1.22=. -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 x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-TfJ6sU/bcftools-1.22=. -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 x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-TfJ6sU/bcftools-1.22=. -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 x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-TfJ6sU/bcftools-1.22=. -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 x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-TfJ6sU/bcftools-1.22=. -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 x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-TfJ6sU/bcftools-1.22=. -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 x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-TfJ6sU/bcftools-1.22=. -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 x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-TfJ6sU/bcftools-1.22=. -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 x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-TfJ6sU/bcftools-1.22=. -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 x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-TfJ6sU/bcftools-1.22=. -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 x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-TfJ6sU/bcftools-1.22=. -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 x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-TfJ6sU/bcftools-1.22=. -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 x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-TfJ6sU/bcftools-1.22=. -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 x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-TfJ6sU/bcftools-1.22=. -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 x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-TfJ6sU/bcftools-1.22=. -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 x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-TfJ6sU/bcftools-1.22=. -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 x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-TfJ6sU/bcftools-1.22=. -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 x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-TfJ6sU/bcftools-1.22=. -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 x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-TfJ6sU/bcftools-1.22=. -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 x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-TfJ6sU/bcftools-1.22=. -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 x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-TfJ6sU/bcftools-1.22=. -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 x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-TfJ6sU/bcftools-1.22=. -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 x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-TfJ6sU/bcftools-1.22=. -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 x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-TfJ6sU/bcftools-1.22=. -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 x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-TfJ6sU/bcftools-1.22=. -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 x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-TfJ6sU/bcftools-1.22=. -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 x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-TfJ6sU/bcftools-1.22=. -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 x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-TfJ6sU/bcftools-1.22=. -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 x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-TfJ6sU/bcftools-1.22=. -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 x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-TfJ6sU/bcftools-1.22=. -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 x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-TfJ6sU/bcftools-1.22=. -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 x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-TfJ6sU/bcftools-1.22=. -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/vcf2table.so version.c plugins/vcf2table.c x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-TfJ6sU/bcftools-1.22=. -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/vrfs.so version.c plugins/vrfs.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-TfJ6sU/bcftools-1.22=. -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 x86_64-linux-gnu-gcc -Wl,-z,relro -Wl,-z,now -o test/test-rbuf test/test-rbuf.o -lz x86_64-linux-gnu-gcc -Wl,-z,relro -Wl,-z,now -o test/test-regidx test/test-regidx.o regidx.o -lhts -lpthread -lz x86_64-linux-gnu-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 mpileup2/mpileup.o vcfplugin.o -lhts -lm -lz -lpthread make[1]: Leaving directory '/build/bcftools-TfJ6sU/bcftools-1.22' debian/rules override_dh_auto_test make[1]: Entering directory '/build/bcftools-TfJ6sU/bcftools-1.22' make test-no-plugins VERBOSE=1 make[2]: Entering directory '/build/bcftools-TfJ6sU/bcftools-1.22' ./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/4gcls0ICvB/merge.a.vcf.gz 2:3199812-3199812 .. ok test_tabix: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -H /tmp/4gcls0ICvB/merge.a.bcf 2:3199812-3199812 .. ok test_tabix: tabix /tmp/4gcls0ICvB/merge.a.vcf.gz 1:3000151-3000151 .. ok test_tabix: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -H /tmp/4gcls0ICvB/merge.a.bcf 1:3000151-3000151 .. ok test_index: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -H /tmp/4gcls0ICvB/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -H /tmp/4gcls0ICvB/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -H /tmp/4gcls0ICvB/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -H /tmp/4gcls0ICvB/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -H /tmp/4gcls0ICvB/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -H /tmp/4gcls0ICvB/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -H /tmp/4gcls0ICvB/large_chrom_csi_limit.bcf chr20 .. ok test_index: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -H /tmp/4gcls0ICvB/large_chrom_csi_limit.bcf chr20 .. ok test_index: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -H /tmp/4gcls0ICvB/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -H /tmp/4gcls0ICvB/large_chrom_csi_limit.bcf chr20 .. ok test_vcf_idxstats: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools index -s /tmp/4gcls0ICvB/idx.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools index -s /tmp/4gcls0ICvB/idx.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools index -s /tmp/4gcls0ICvB/idx.bcf .. ok test_vcf_idxstats: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools index -n /tmp/4gcls0ICvB/idx.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools index -n /tmp/4gcls0ICvB/idx.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools index -n /tmp/4gcls0ICvB/idx.vcf.gz.csi .. ok test_vcf_idxstats: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools index -n /tmp/4gcls0ICvB/idx.bcf .. ok test_vcf_idxstats: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools index -n /tmp/4gcls0ICvB/idx.bcf.csi .. ok test_vcf_idxstats: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools index -s /tmp/4gcls0ICvB/empty.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools index -s /tmp/4gcls0ICvB/empty.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools index -s /tmp/4gcls0ICvB/empty.bcf .. ok test_vcf_idxstats: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools index -n /tmp/4gcls0ICvB/empty.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools index -n /tmp/4gcls0ICvB/empty.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools index -n /tmp/4gcls0ICvB/empty.vcf.gz.csi .. ok test_vcf_idxstats: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools index -n /tmp/4gcls0ICvB/empty.bcf .. ok test_vcf_idxstats: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools index -n /tmp/4gcls0ICvB/empty.bcf.csi .. ok test_vcf_check: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools stats -s - /tmp/4gcls0ICvB/check.vcf.gz | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/check.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools stats -s - | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check_merge: /build/bcftools-TfJ6sU/bcftools-1.22/misc/plot-vcfstats -m /tmp/4gcls0ICvB/check.1.chk /tmp/4gcls0ICvB/check.2.chk /tmp/4gcls0ICvB/check.3.chk /tmp/4gcls0ICvB/check.4.chk | grep -v 'plot-vcfstats' | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_stats: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools stats -s - /tmp/4gcls0ICvB/stats.a.vcf.gz /tmp/4gcls0ICvB/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools stats -s B /tmp/4gcls0ICvB/stats.a.vcf.gz /tmp/4gcls0ICvB/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools stats -s - /tmp/4gcls0ICvB/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools stats -s - -i 'type="snp"' /tmp/4gcls0ICvB/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools stats -s - /tmp/4gcls0ICvB/stats.vaf.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_isec: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools isec -n =2 -w 2 --no-version /tmp/4gcls0ICvB/isec.match-id.1.1.vcf.gz /tmp/4gcls0ICvB/isec.match-id.1.2.vcf.gz .. ok test_vcf_isec: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools isec -n =2 -w 2 -c id --no-version /tmp/4gcls0ICvB/isec.match-id.1.1.vcf.gz /tmp/4gcls0ICvB/isec.match-id.1.2.vcf.gz .. ok test_vcf_isec: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools isec -n =2 /tmp/4gcls0ICvB/isec.a.vcf.gz /tmp/4gcls0ICvB/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/4gcls0ICvB/isec.a.vcf.gz /tmp/4gcls0ICvB/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools isec -n =2 -c both /tmp/4gcls0ICvB/isec.a.vcf.gz /tmp/4gcls0ICvB/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools isec -n =2 -c any /tmp/4gcls0ICvB/isec.a.vcf.gz /tmp/4gcls0ICvB/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools isec -C -c any /tmp/4gcls0ICvB/isec.a.vcf.gz /tmp/4gcls0ICvB/isec.b.vcf.gz .. ok test_vcf_isec2: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools isec --no-version -T /tmp/4gcls0ICvB/isec.tab.gz /tmp/4gcls0ICvB/isec.a.vcf.gz .. ok test_vcf_isec2: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools isec -Ob -T /tmp/4gcls0ICvB/isec.tab.gz /tmp/4gcls0ICvB/isec.a.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_isec: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools isec -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/4gcls0ICvB/isec-miss.1.1.vcf.gz /tmp/4gcls0ICvB/isec-miss.1.2.vcf.gz /tmp/4gcls0ICvB/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools isec -R /build/bcftools-TfJ6sU/bcftools-1.22/test/isec-miss.1.regs.txt -n +1 /tmp/4gcls0ICvB/isec-miss.1.1.vcf.gz /tmp/4gcls0ICvB/isec-miss.1.2.vcf.gz /tmp/4gcls0ICvB/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools isec -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/4gcls0ICvB/isec-miss.2.1.vcf.gz /tmp/4gcls0ICvB/isec-miss.2.2.vcf.gz /tmp/4gcls0ICvB/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools isec -R /build/bcftools-TfJ6sU/bcftools-1.22/test/isec-miss.1.regs.txt -n +1 /tmp/4gcls0ICvB/isec-miss.2.1.vcf.gz /tmp/4gcls0ICvB/isec-miss.2.2.vcf.gz /tmp/4gcls0ICvB/isec-miss.2.3.vcf.gz .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version /tmp/4gcls0ICvB/merge.broken-gvcf.a.vcf.gz /tmp/4gcls0ICvB/merge.broken-gvcf.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob /tmp/4gcls0ICvB/merge.broken-gvcf.a.vcf.gz /tmp/4gcls0ICvB/merge.broken-gvcf.b.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version /tmp/4gcls0ICvB/merge.broken-gvcf.a.bcf /tmp/4gcls0ICvB/merge.broken-gvcf.b.bcf .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob /tmp/4gcls0ICvB/merge.broken-gvcf.a.bcf /tmp/4gcls0ICvB/merge.broken-gvcf.b.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version /tmp/4gcls0ICvB/merge.symbolic.1.a.vcf.gz /tmp/4gcls0ICvB/merge.symbolic.1.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob /tmp/4gcls0ICvB/merge.symbolic.1.a.vcf.gz /tmp/4gcls0ICvB/merge.symbolic.1.b.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version /tmp/4gcls0ICvB/merge.symbolic.1.a.bcf /tmp/4gcls0ICvB/merge.symbolic.1.b.bcf .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob /tmp/4gcls0ICvB/merge.symbolic.1.a.bcf /tmp/4gcls0ICvB/merge.symbolic.1.b.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --merge none /tmp/4gcls0ICvB/merge.multiallelics.1.a.vcf.gz /tmp/4gcls0ICvB/merge.multiallelics.1.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --merge none /tmp/4gcls0ICvB/merge.multiallelics.1.a.vcf.gz /tmp/4gcls0ICvB/merge.multiallelics.1.b.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --merge none /tmp/4gcls0ICvB/merge.multiallelics.1.a.bcf /tmp/4gcls0ICvB/merge.multiallelics.1.b.bcf .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --merge none /tmp/4gcls0ICvB/merge.multiallelics.1.a.bcf /tmp/4gcls0ICvB/merge.multiallelics.1.b.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --merge both /tmp/4gcls0ICvB/merge.multiallelics.1.a.vcf.gz /tmp/4gcls0ICvB/merge.multiallelics.1.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --merge both /tmp/4gcls0ICvB/merge.multiallelics.1.a.vcf.gz /tmp/4gcls0ICvB/merge.multiallelics.1.b.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --merge both /tmp/4gcls0ICvB/merge.multiallelics.1.a.bcf /tmp/4gcls0ICvB/merge.multiallelics.1.b.bcf .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --merge both /tmp/4gcls0ICvB/merge.multiallelics.1.a.bcf /tmp/4gcls0ICvB/merge.multiallelics.1.b.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --merge none /tmp/4gcls0ICvB/merge.12.a.vcf.gz /tmp/4gcls0ICvB/merge.12.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --merge none /tmp/4gcls0ICvB/merge.12.a.vcf.gz /tmp/4gcls0ICvB/merge.12.b.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --merge none /tmp/4gcls0ICvB/merge.12.a.bcf /tmp/4gcls0ICvB/merge.12.b.bcf .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --merge none /tmp/4gcls0ICvB/merge.12.a.bcf /tmp/4gcls0ICvB/merge.12.b.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --merge both /tmp/4gcls0ICvB/merge.12.a.vcf.gz /tmp/4gcls0ICvB/merge.12.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --merge both /tmp/4gcls0ICvB/merge.12.a.vcf.gz /tmp/4gcls0ICvB/merge.12.b.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --merge both /tmp/4gcls0ICvB/merge.12.a.bcf /tmp/4gcls0ICvB/merge.12.b.bcf .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --merge both /tmp/4gcls0ICvB/merge.12.a.bcf /tmp/4gcls0ICvB/merge.12.b.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version /tmp/4gcls0ICvB/merge.phased.1.a.vcf.gz /tmp/4gcls0ICvB/merge.phased.1.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob /tmp/4gcls0ICvB/merge.phased.1.a.vcf.gz /tmp/4gcls0ICvB/merge.phased.1.b.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version /tmp/4gcls0ICvB/merge.phased.1.a.bcf /tmp/4gcls0ICvB/merge.phased.1.b.bcf .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob /tmp/4gcls0ICvB/merge.phased.1.a.bcf /tmp/4gcls0ICvB/merge.phased.1.b.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version /tmp/4gcls0ICvB/merge.11.a.vcf.gz /tmp/4gcls0ICvB/merge.11.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob /tmp/4gcls0ICvB/merge.11.a.vcf.gz /tmp/4gcls0ICvB/merge.11.b.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version /tmp/4gcls0ICvB/merge.11.a.bcf /tmp/4gcls0ICvB/merge.11.b.bcf .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob /tmp/4gcls0ICvB/merge.11.a.bcf /tmp/4gcls0ICvB/merge.11.b.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -i AF:join /tmp/4gcls0ICvB/merge.join.a.vcf.gz /tmp/4gcls0ICvB/merge.join.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob -i AF:join /tmp/4gcls0ICvB/merge.join.a.vcf.gz /tmp/4gcls0ICvB/merge.join.b.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -i AF:join /tmp/4gcls0ICvB/merge.join.a.bcf /tmp/4gcls0ICvB/merge.join.b.bcf .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob -i AF:join /tmp/4gcls0ICvB/merge.join.a.bcf /tmp/4gcls0ICvB/merge.join.b.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --force-single /tmp/4gcls0ICvB/merge.LPL.a.vcf.gz .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --force-single /tmp/4gcls0ICvB/merge.LPL.a.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --force-single /tmp/4gcls0ICvB/merge.LPL.a.bcf .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --force-single /tmp/4gcls0ICvB/merge.LPL.a.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --force-samples /tmp/4gcls0ICvB/merge.LPL.a.vcf.gz /tmp/4gcls0ICvB/merge.LPL.b.vcf.gz /tmp/4gcls0ICvB/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --force-samples /tmp/4gcls0ICvB/merge.LPL.a.vcf.gz /tmp/4gcls0ICvB/merge.LPL.b.vcf.gz /tmp/4gcls0ICvB/merge.LPL.c.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --force-samples /tmp/4gcls0ICvB/merge.LPL.a.bcf /tmp/4gcls0ICvB/merge.LPL.b.bcf /tmp/4gcls0ICvB/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --force-samples /tmp/4gcls0ICvB/merge.LPL.a.bcf /tmp/4gcls0ICvB/merge.LPL.b.bcf /tmp/4gcls0ICvB/merge.LPL.c.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --force-samples -L 1 /tmp/4gcls0ICvB/merge.LPL.a.vcf.gz /tmp/4gcls0ICvB/merge.LPL.b.vcf.gz /tmp/4gcls0ICvB/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --force-samples -L 1 /tmp/4gcls0ICvB/merge.LPL.a.vcf.gz /tmp/4gcls0ICvB/merge.LPL.b.vcf.gz /tmp/4gcls0ICvB/merge.LPL.c.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --force-samples -L 1 /tmp/4gcls0ICvB/merge.LPL.a.bcf /tmp/4gcls0ICvB/merge.LPL.b.bcf /tmp/4gcls0ICvB/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --force-samples -L 1 /tmp/4gcls0ICvB/merge.LPL.a.bcf /tmp/4gcls0ICvB/merge.LPL.b.bcf /tmp/4gcls0ICvB/merge.LPL.c.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --force-samples -L 2 /tmp/4gcls0ICvB/merge.LPL.a.vcf.gz /tmp/4gcls0ICvB/merge.LPL.b.vcf.gz /tmp/4gcls0ICvB/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --force-samples -L 2 /tmp/4gcls0ICvB/merge.LPL.a.vcf.gz /tmp/4gcls0ICvB/merge.LPL.b.vcf.gz /tmp/4gcls0ICvB/merge.LPL.c.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --force-samples -L 2 /tmp/4gcls0ICvB/merge.LPL.a.bcf /tmp/4gcls0ICvB/merge.LPL.b.bcf /tmp/4gcls0ICvB/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --force-samples -L 2 /tmp/4gcls0ICvB/merge.LPL.a.bcf /tmp/4gcls0ICvB/merge.LPL.b.bcf /tmp/4gcls0ICvB/merge.LPL.c.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --force-samples -L 3 /tmp/4gcls0ICvB/merge.LPL.a.vcf.gz /tmp/4gcls0ICvB/merge.LPL.b.vcf.gz /tmp/4gcls0ICvB/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --force-samples -L 3 /tmp/4gcls0ICvB/merge.LPL.a.vcf.gz /tmp/4gcls0ICvB/merge.LPL.b.vcf.gz /tmp/4gcls0ICvB/merge.LPL.c.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --force-samples -L 3 /tmp/4gcls0ICvB/merge.LPL.a.bcf /tmp/4gcls0ICvB/merge.LPL.b.bcf /tmp/4gcls0ICvB/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --force-samples -L 3 /tmp/4gcls0ICvB/merge.LPL.a.bcf /tmp/4gcls0ICvB/merge.LPL.b.bcf /tmp/4gcls0ICvB/merge.LPL.c.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --force-samples -L 4 /tmp/4gcls0ICvB/merge.LPL.a.vcf.gz /tmp/4gcls0ICvB/merge.LPL.b.vcf.gz /tmp/4gcls0ICvB/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --force-samples -L 4 /tmp/4gcls0ICvB/merge.LPL.a.vcf.gz /tmp/4gcls0ICvB/merge.LPL.b.vcf.gz /tmp/4gcls0ICvB/merge.LPL.c.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --force-samples -L 4 /tmp/4gcls0ICvB/merge.LPL.a.bcf /tmp/4gcls0ICvB/merge.LPL.b.bcf /tmp/4gcls0ICvB/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --force-samples -L 4 /tmp/4gcls0ICvB/merge.LPL.a.bcf /tmp/4gcls0ICvB/merge.LPL.b.bcf /tmp/4gcls0ICvB/merge.LPL.c.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --force-samples -L 5 /tmp/4gcls0ICvB/merge.LPL.a.vcf.gz /tmp/4gcls0ICvB/merge.LPL.b.vcf.gz /tmp/4gcls0ICvB/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --force-samples -L 5 /tmp/4gcls0ICvB/merge.LPL.a.vcf.gz /tmp/4gcls0ICvB/merge.LPL.b.vcf.gz /tmp/4gcls0ICvB/merge.LPL.c.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --force-samples -L 5 /tmp/4gcls0ICvB/merge.LPL.a.bcf /tmp/4gcls0ICvB/merge.LPL.b.bcf /tmp/4gcls0ICvB/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --force-samples -L 5 /tmp/4gcls0ICvB/merge.LPL.a.bcf /tmp/4gcls0ICvB/merge.LPL.b.bcf /tmp/4gcls0ICvB/merge.LPL.c.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --force-samples /tmp/4gcls0ICvB/merge.a.vcf.gz /tmp/4gcls0ICvB/merge.b.vcf.gz /tmp/4gcls0ICvB/merge.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --force-samples /tmp/4gcls0ICvB/merge.a.vcf.gz /tmp/4gcls0ICvB/merge.b.vcf.gz /tmp/4gcls0ICvB/merge.c.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --force-samples /tmp/4gcls0ICvB/merge.a.bcf /tmp/4gcls0ICvB/merge.b.bcf /tmp/4gcls0ICvB/merge.c.bcf .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --force-samples /tmp/4gcls0ICvB/merge.a.bcf /tmp/4gcls0ICvB/merge.b.bcf /tmp/4gcls0ICvB/merge.c.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --force-samples -Fx /tmp/4gcls0ICvB/merge.a.vcf.gz /tmp/4gcls0ICvB/merge.b.vcf.gz /tmp/4gcls0ICvB/merge.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --force-samples -Fx /tmp/4gcls0ICvB/merge.a.vcf.gz /tmp/4gcls0ICvB/merge.b.vcf.gz /tmp/4gcls0ICvB/merge.c.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --force-samples -Fx /tmp/4gcls0ICvB/merge.a.bcf /tmp/4gcls0ICvB/merge.b.bcf /tmp/4gcls0ICvB/merge.c.bcf .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --force-samples -Fx /tmp/4gcls0ICvB/merge.a.bcf /tmp/4gcls0ICvB/merge.b.bcf /tmp/4gcls0ICvB/merge.c.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --force-samples -0 /tmp/4gcls0ICvB/merge.a.vcf.gz /tmp/4gcls0ICvB/merge.b.vcf.gz /tmp/4gcls0ICvB/merge.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --force-samples -0 /tmp/4gcls0ICvB/merge.a.vcf.gz /tmp/4gcls0ICvB/merge.b.vcf.gz /tmp/4gcls0ICvB/merge.c.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --force-samples -0 /tmp/4gcls0ICvB/merge.a.bcf /tmp/4gcls0ICvB/merge.b.bcf /tmp/4gcls0ICvB/merge.c.bcf .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --force-samples -0 /tmp/4gcls0ICvB/merge.a.bcf /tmp/4gcls0ICvB/merge.b.bcf /tmp/4gcls0ICvB/merge.c.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --force-samples -m none /tmp/4gcls0ICvB/merge.2.a.vcf.gz /tmp/4gcls0ICvB/merge.2.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --force-samples -m none /tmp/4gcls0ICvB/merge.2.a.vcf.gz /tmp/4gcls0ICvB/merge.2.b.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --force-samples -m none /tmp/4gcls0ICvB/merge.2.a.bcf /tmp/4gcls0ICvB/merge.2.b.bcf .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --force-samples -m none /tmp/4gcls0ICvB/merge.2.a.bcf /tmp/4gcls0ICvB/merge.2.b.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --force-samples -m both /tmp/4gcls0ICvB/merge.2.a.vcf.gz /tmp/4gcls0ICvB/merge.2.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --force-samples -m both /tmp/4gcls0ICvB/merge.2.a.vcf.gz /tmp/4gcls0ICvB/merge.2.b.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --force-samples -m both /tmp/4gcls0ICvB/merge.2.a.bcf /tmp/4gcls0ICvB/merge.2.b.bcf .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --force-samples -m both /tmp/4gcls0ICvB/merge.2.a.bcf /tmp/4gcls0ICvB/merge.2.b.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --force-samples -m all /tmp/4gcls0ICvB/merge.2.a.vcf.gz /tmp/4gcls0ICvB/merge.2.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --force-samples -m all /tmp/4gcls0ICvB/merge.2.a.vcf.gz /tmp/4gcls0ICvB/merge.2.b.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --force-samples -m all /tmp/4gcls0ICvB/merge.2.a.bcf /tmp/4gcls0ICvB/merge.2.b.bcf .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --force-samples -m all /tmp/4gcls0ICvB/merge.2.a.bcf /tmp/4gcls0ICvB/merge.2.b.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/4gcls0ICvB/merge.3.a.vcf.gz /tmp/4gcls0ICvB/merge.3.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/4gcls0ICvB/merge.3.a.vcf.gz /tmp/4gcls0ICvB/merge.3.b.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/4gcls0ICvB/merge.3.a.bcf /tmp/4gcls0ICvB/merge.3.b.bcf .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/4gcls0ICvB/merge.3.a.bcf /tmp/4gcls0ICvB/merge.3.b.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --force-samples -m id /tmp/4gcls0ICvB/merge.4.a.vcf.gz /tmp/4gcls0ICvB/merge.4.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --force-samples -m id /tmp/4gcls0ICvB/merge.4.a.vcf.gz /tmp/4gcls0ICvB/merge.4.b.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --force-samples -m id /tmp/4gcls0ICvB/merge.4.a.bcf /tmp/4gcls0ICvB/merge.4.b.bcf .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --force-samples -m id /tmp/4gcls0ICvB/merge.4.a.bcf /tmp/4gcls0ICvB/merge.4.b.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --gvcf - /tmp/4gcls0ICvB/gvcf.merge.1.vcf.gz /tmp/4gcls0ICvB/gvcf.merge.2.vcf.gz /tmp/4gcls0ICvB/gvcf.merge.3.vcf.gz .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --gvcf - /tmp/4gcls0ICvB/gvcf.merge.1.vcf.gz /tmp/4gcls0ICvB/gvcf.merge.2.vcf.gz /tmp/4gcls0ICvB/gvcf.merge.3.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --gvcf - /tmp/4gcls0ICvB/gvcf.merge.1.bcf /tmp/4gcls0ICvB/gvcf.merge.2.bcf /tmp/4gcls0ICvB/gvcf.merge.3.bcf .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --gvcf - /tmp/4gcls0ICvB/gvcf.merge.1.bcf /tmp/4gcls0ICvB/gvcf.merge.2.bcf /tmp/4gcls0ICvB/gvcf.merge.3.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --gvcf - /tmp/4gcls0ICvB/merge.gvcf.2.a.vcf.gz /tmp/4gcls0ICvB/merge.gvcf.2.b.vcf.gz /tmp/4gcls0ICvB/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --gvcf - /tmp/4gcls0ICvB/merge.gvcf.2.a.vcf.gz /tmp/4gcls0ICvB/merge.gvcf.2.b.vcf.gz /tmp/4gcls0ICvB/merge.gvcf.2.c.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --gvcf - -m both,* /tmp/4gcls0ICvB/merge.gvcf.2.a.vcf.gz /tmp/4gcls0ICvB/merge.gvcf.2.b.vcf.gz /tmp/4gcls0ICvB/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --gvcf - -m both,* /tmp/4gcls0ICvB/merge.gvcf.2.a.vcf.gz /tmp/4gcls0ICvB/merge.gvcf.2.b.vcf.gz /tmp/4gcls0ICvB/merge.gvcf.2.c.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --gvcf - -m both,** /tmp/4gcls0ICvB/merge.gvcf.2.a.vcf.gz /tmp/4gcls0ICvB/merge.gvcf.2.b.vcf.gz /tmp/4gcls0ICvB/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --gvcf - -m both,** /tmp/4gcls0ICvB/merge.gvcf.2.a.vcf.gz /tmp/4gcls0ICvB/merge.gvcf.2.b.vcf.gz /tmp/4gcls0ICvB/merge.gvcf.2.c.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --gvcf - -i SRC:join /tmp/4gcls0ICvB/merge.gvcf.3.a.vcf.gz /tmp/4gcls0ICvB/merge.gvcf.3.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --gvcf - -i SRC:join /tmp/4gcls0ICvB/merge.gvcf.3.a.vcf.gz /tmp/4gcls0ICvB/merge.gvcf.3.b.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --gvcf - /tmp/4gcls0ICvB/merge.gvcf.4.a.vcf.gz /tmp/4gcls0ICvB/merge.gvcf.4.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --gvcf - /tmp/4gcls0ICvB/merge.gvcf.4.a.vcf.gz /tmp/4gcls0ICvB/merge.gvcf.4.b.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --gvcf - /tmp/4gcls0ICvB/merge.gvcf.4.a.bcf /tmp/4gcls0ICvB/merge.gvcf.4.b.bcf .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --gvcf - /tmp/4gcls0ICvB/merge.gvcf.4.a.bcf /tmp/4gcls0ICvB/merge.gvcf.4.b.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version /tmp/4gcls0ICvB/merge.5.a.vcf.gz /tmp/4gcls0ICvB/merge.5.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob /tmp/4gcls0ICvB/merge.5.a.vcf.gz /tmp/4gcls0ICvB/merge.5.b.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version /tmp/4gcls0ICvB/merge.5.a.bcf /tmp/4gcls0ICvB/merge.5.b.bcf .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob /tmp/4gcls0ICvB/merge.5.a.bcf /tmp/4gcls0ICvB/merge.5.b.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version /tmp/4gcls0ICvB/merge.6.a.vcf.gz /tmp/4gcls0ICvB/merge.6.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob /tmp/4gcls0ICvB/merge.6.a.vcf.gz /tmp/4gcls0ICvB/merge.6.b.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version /tmp/4gcls0ICvB/merge.6.a.bcf /tmp/4gcls0ICvB/merge.6.b.bcf .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob /tmp/4gcls0ICvB/merge.6.a.bcf /tmp/4gcls0ICvB/merge.6.b.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --gvcf - /tmp/4gcls0ICvB/merge.gvcf.7.a.vcf.gz /tmp/4gcls0ICvB/merge.gvcf.7.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --gvcf - /tmp/4gcls0ICvB/merge.gvcf.7.a.vcf.gz /tmp/4gcls0ICvB/merge.gvcf.7.b.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --gvcf - /tmp/4gcls0ICvB/merge.gvcf.7.a.bcf /tmp/4gcls0ICvB/merge.gvcf.7.b.bcf .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --gvcf - /tmp/4gcls0ICvB/merge.gvcf.7.a.bcf /tmp/4gcls0ICvB/merge.gvcf.7.b.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --gvcf - /tmp/4gcls0ICvB/merge.gvcf.8.a.vcf.gz /tmp/4gcls0ICvB/merge.gvcf.8.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --gvcf - /tmp/4gcls0ICvB/merge.gvcf.8.a.vcf.gz /tmp/4gcls0ICvB/merge.gvcf.8.b.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --gvcf - /tmp/4gcls0ICvB/merge.gvcf.8.a.bcf /tmp/4gcls0ICvB/merge.gvcf.8.b.bcf .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --gvcf - /tmp/4gcls0ICvB/merge.gvcf.8.a.bcf /tmp/4gcls0ICvB/merge.gvcf.8.b.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --force-samples /tmp/4gcls0ICvB/merge.7.a.vcf.gz /tmp/4gcls0ICvB/merge.7.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --force-samples /tmp/4gcls0ICvB/merge.7.a.vcf.gz /tmp/4gcls0ICvB/merge.7.b.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --force-samples /tmp/4gcls0ICvB/merge.7.a.bcf /tmp/4gcls0ICvB/merge.7.b.bcf .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --force-samples /tmp/4gcls0ICvB/merge.7.a.bcf /tmp/4gcls0ICvB/merge.7.b.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --gvcf /build/bcftools-TfJ6sU/bcftools-1.22/test/gvcf.fa /tmp/4gcls0ICvB/merge.gvcf.9a.vcf.gz /tmp/4gcls0ICvB/merge.gvcf.9b.vcf.gz /tmp/4gcls0ICvB/merge.gvcf.9c.vcf.gz /tmp/4gcls0ICvB/merge.gvcf.9d.vcf.gz .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --gvcf /build/bcftools-TfJ6sU/bcftools-1.22/test/gvcf.fa /tmp/4gcls0ICvB/merge.gvcf.9a.vcf.gz /tmp/4gcls0ICvB/merge.gvcf.9b.vcf.gz /tmp/4gcls0ICvB/merge.gvcf.9c.vcf.gz /tmp/4gcls0ICvB/merge.gvcf.9d.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --gvcf /build/bcftools-TfJ6sU/bcftools-1.22/test/gvcf.fa /tmp/4gcls0ICvB/merge.gvcf.9a.bcf /tmp/4gcls0ICvB/merge.gvcf.9b.bcf /tmp/4gcls0ICvB/merge.gvcf.9c.bcf /tmp/4gcls0ICvB/merge.gvcf.9d.bcf .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --gvcf /build/bcftools-TfJ6sU/bcftools-1.22/test/gvcf.fa /tmp/4gcls0ICvB/merge.gvcf.9a.bcf /tmp/4gcls0ICvB/merge.gvcf.9b.bcf /tmp/4gcls0ICvB/merge.gvcf.9c.bcf /tmp/4gcls0ICvB/merge.gvcf.9d.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --gvcf /build/bcftools-TfJ6sU/bcftools-1.22/test/gvcf.fa -r 22:21-23 /tmp/4gcls0ICvB/merge.gvcf.9a.vcf.gz /tmp/4gcls0ICvB/merge.gvcf.9b.vcf.gz /tmp/4gcls0ICvB/merge.gvcf.9c.vcf.gz /tmp/4gcls0ICvB/merge.gvcf.9d.vcf.gz .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --gvcf /build/bcftools-TfJ6sU/bcftools-1.22/test/gvcf.fa -r 22:21-23 /tmp/4gcls0ICvB/merge.gvcf.9a.vcf.gz /tmp/4gcls0ICvB/merge.gvcf.9b.vcf.gz /tmp/4gcls0ICvB/merge.gvcf.9c.vcf.gz /tmp/4gcls0ICvB/merge.gvcf.9d.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --gvcf /build/bcftools-TfJ6sU/bcftools-1.22/test/gvcf.fa -r 22:21-23 /tmp/4gcls0ICvB/merge.gvcf.9a.bcf /tmp/4gcls0ICvB/merge.gvcf.9b.bcf /tmp/4gcls0ICvB/merge.gvcf.9c.bcf /tmp/4gcls0ICvB/merge.gvcf.9d.bcf .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --gvcf /build/bcftools-TfJ6sU/bcftools-1.22/test/gvcf.fa -r 22:21-23 /tmp/4gcls0ICvB/merge.gvcf.9a.bcf /tmp/4gcls0ICvB/merge.gvcf.9b.bcf /tmp/4gcls0ICvB/merge.gvcf.9c.bcf /tmp/4gcls0ICvB/merge.gvcf.9d.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --gvcf /build/bcftools-TfJ6sU/bcftools-1.22/test/gvcf.fa /tmp/4gcls0ICvB/merge.gvcf.9a.vcf.gz /tmp/4gcls0ICvB/merge.gvcf.9b.vcf.gz /tmp/4gcls0ICvB/merge.gvcf.9c.vcf.gz /tmp/4gcls0ICvB/merge.gvcf.9d.vcf.gz /tmp/4gcls0ICvB/merge.gvcf.9e.vcf.gz .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --gvcf /build/bcftools-TfJ6sU/bcftools-1.22/test/gvcf.fa /tmp/4gcls0ICvB/merge.gvcf.9a.vcf.gz /tmp/4gcls0ICvB/merge.gvcf.9b.vcf.gz /tmp/4gcls0ICvB/merge.gvcf.9c.vcf.gz /tmp/4gcls0ICvB/merge.gvcf.9d.vcf.gz /tmp/4gcls0ICvB/merge.gvcf.9e.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --gvcf /build/bcftools-TfJ6sU/bcftools-1.22/test/gvcf.fa /tmp/4gcls0ICvB/merge.gvcf.9a.bcf /tmp/4gcls0ICvB/merge.gvcf.9b.bcf /tmp/4gcls0ICvB/merge.gvcf.9c.bcf /tmp/4gcls0ICvB/merge.gvcf.9d.bcf /tmp/4gcls0ICvB/merge.gvcf.9e.bcf .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --gvcf /build/bcftools-TfJ6sU/bcftools-1.22/test/gvcf.fa /tmp/4gcls0ICvB/merge.gvcf.9a.bcf /tmp/4gcls0ICvB/merge.gvcf.9b.bcf /tmp/4gcls0ICvB/merge.gvcf.9c.bcf /tmp/4gcls0ICvB/merge.gvcf.9d.bcf /tmp/4gcls0ICvB/merge.gvcf.9e.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --gvcf /build/bcftools-TfJ6sU/bcftools-1.22/test/gvcf.fa -r 22:21-23 /tmp/4gcls0ICvB/merge.gvcf.9a.vcf.gz /tmp/4gcls0ICvB/merge.gvcf.9b.vcf.gz /tmp/4gcls0ICvB/merge.gvcf.9c.vcf.gz /tmp/4gcls0ICvB/merge.gvcf.9d.vcf.gz /tmp/4gcls0ICvB/merge.gvcf.9e.vcf.gz .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --gvcf /build/bcftools-TfJ6sU/bcftools-1.22/test/gvcf.fa -r 22:21-23 /tmp/4gcls0ICvB/merge.gvcf.9a.vcf.gz /tmp/4gcls0ICvB/merge.gvcf.9b.vcf.gz /tmp/4gcls0ICvB/merge.gvcf.9c.vcf.gz /tmp/4gcls0ICvB/merge.gvcf.9d.vcf.gz /tmp/4gcls0ICvB/merge.gvcf.9e.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --gvcf /build/bcftools-TfJ6sU/bcftools-1.22/test/gvcf.fa -r 22:21-23 /tmp/4gcls0ICvB/merge.gvcf.9a.bcf /tmp/4gcls0ICvB/merge.gvcf.9b.bcf /tmp/4gcls0ICvB/merge.gvcf.9c.bcf /tmp/4gcls0ICvB/merge.gvcf.9d.bcf /tmp/4gcls0ICvB/merge.gvcf.9e.bcf .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --gvcf /build/bcftools-TfJ6sU/bcftools-1.22/test/gvcf.fa -r 22:21-23 /tmp/4gcls0ICvB/merge.gvcf.9a.bcf /tmp/4gcls0ICvB/merge.gvcf.9b.bcf /tmp/4gcls0ICvB/merge.gvcf.9c.bcf /tmp/4gcls0ICvB/merge.gvcf.9d.bcf /tmp/4gcls0ICvB/merge.gvcf.9e.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version /tmp/4gcls0ICvB/merge.gvcf.10.a.vcf.gz /tmp/4gcls0ICvB/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob /tmp/4gcls0ICvB/merge.gvcf.10.a.vcf.gz /tmp/4gcls0ICvB/merge.gvcf.10.b.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version /tmp/4gcls0ICvB/merge.gvcf.10.a.bcf /tmp/4gcls0ICvB/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob /tmp/4gcls0ICvB/merge.gvcf.10.a.bcf /tmp/4gcls0ICvB/merge.gvcf.10.b.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -m none /tmp/4gcls0ICvB/merge.gvcf.10.a.vcf.gz /tmp/4gcls0ICvB/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob -m none /tmp/4gcls0ICvB/merge.gvcf.10.a.vcf.gz /tmp/4gcls0ICvB/merge.gvcf.10.b.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -m none /tmp/4gcls0ICvB/merge.gvcf.10.a.bcf /tmp/4gcls0ICvB/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob -m none /tmp/4gcls0ICvB/merge.gvcf.10.a.bcf /tmp/4gcls0ICvB/merge.gvcf.10.b.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -g /build/bcftools-TfJ6sU/bcftools-1.22/test/merge.gvcf.10.fa /tmp/4gcls0ICvB/merge.gvcf.10.a.vcf.gz /tmp/4gcls0ICvB/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob -g /build/bcftools-TfJ6sU/bcftools-1.22/test/merge.gvcf.10.fa /tmp/4gcls0ICvB/merge.gvcf.10.a.vcf.gz /tmp/4gcls0ICvB/merge.gvcf.10.b.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -g /build/bcftools-TfJ6sU/bcftools-1.22/test/merge.gvcf.10.fa /tmp/4gcls0ICvB/merge.gvcf.10.a.bcf /tmp/4gcls0ICvB/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob -g /build/bcftools-TfJ6sU/bcftools-1.22/test/merge.gvcf.10.fa /tmp/4gcls0ICvB/merge.gvcf.10.a.bcf /tmp/4gcls0ICvB/merge.gvcf.10.b.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -g /build/bcftools-TfJ6sU/bcftools-1.22/test/merge.gvcf.10.fa -m none /tmp/4gcls0ICvB/merge.gvcf.10.a.vcf.gz /tmp/4gcls0ICvB/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob -g /build/bcftools-TfJ6sU/bcftools-1.22/test/merge.gvcf.10.fa -m none /tmp/4gcls0ICvB/merge.gvcf.10.a.vcf.gz /tmp/4gcls0ICvB/merge.gvcf.10.b.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -g /build/bcftools-TfJ6sU/bcftools-1.22/test/merge.gvcf.10.fa -m none /tmp/4gcls0ICvB/merge.gvcf.10.a.bcf /tmp/4gcls0ICvB/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob -g /build/bcftools-TfJ6sU/bcftools-1.22/test/merge.gvcf.10.fa -m none /tmp/4gcls0ICvB/merge.gvcf.10.a.bcf /tmp/4gcls0ICvB/merge.gvcf.10.b.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version /tmp/4gcls0ICvB/merge.noidx.a.vcf.gz /tmp/4gcls0ICvB/merge.noidx.b.vcf.gz /tmp/4gcls0ICvB/merge.noidx.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob /tmp/4gcls0ICvB/merge.noidx.a.vcf.gz /tmp/4gcls0ICvB/merge.noidx.b.vcf.gz /tmp/4gcls0ICvB/merge.noidx.c.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version /tmp/4gcls0ICvB/merge.noidx.a.bcf /tmp/4gcls0ICvB/merge.noidx.b.bcf /tmp/4gcls0ICvB/merge.noidx.c.bcf .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob /tmp/4gcls0ICvB/merge.noidx.a.bcf /tmp/4gcls0ICvB/merge.noidx.b.bcf /tmp/4gcls0ICvB/merge.noidx.c.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --no-index /build/bcftools-TfJ6sU/bcftools-1.22/test/merge.noidx.a.vcf /build/bcftools-TfJ6sU/bcftools-1.22/test/merge.noidx.b.vcf /build/bcftools-TfJ6sU/bcftools-1.22/test/merge.noidx.c.vcf .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --no-index /build/bcftools-TfJ6sU/bcftools-1.22/test/merge.noidx.a.vcf /build/bcftools-TfJ6sU/bcftools-1.22/test/merge.noidx.b.vcf /build/bcftools-TfJ6sU/bcftools-1.22/test/merge.noidx.c.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --no-index /tmp/4gcls0ICvB/merge.noidx.a.bcf /tmp/4gcls0ICvB/merge.noidx.b.bcf /tmp/4gcls0ICvB/merge.noidx.c.bcf .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --no-index /tmp/4gcls0ICvB/merge.noidx.a.bcf /tmp/4gcls0ICvB/merge.noidx.b.bcf /tmp/4gcls0ICvB/merge.noidx.c.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version /tmp/4gcls0ICvB/merge.8.a.vcf.gz /tmp/4gcls0ICvB/merge.8.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob /tmp/4gcls0ICvB/merge.8.a.vcf.gz /tmp/4gcls0ICvB/merge.8.b.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version /tmp/4gcls0ICvB/merge.8.a.bcf /tmp/4gcls0ICvB/merge.8.b.bcf .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob /tmp/4gcls0ICvB/merge.8.a.bcf /tmp/4gcls0ICvB/merge.8.b.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -i AN:sum,AC:sum /tmp/4gcls0ICvB/merge.8.a.vcf.gz /tmp/4gcls0ICvB/merge.8.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/4gcls0ICvB/merge.8.a.vcf.gz /tmp/4gcls0ICvB/merge.8.b.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -i AN:sum,AC:sum /tmp/4gcls0ICvB/merge.8.a.bcf /tmp/4gcls0ICvB/merge.8.b.bcf .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/4gcls0ICvB/merge.8.a.bcf /tmp/4gcls0ICvB/merge.8.b.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version /tmp/4gcls0ICvB/merge.9.a.vcf.gz /tmp/4gcls0ICvB/merge.9.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob /tmp/4gcls0ICvB/merge.9.a.vcf.gz /tmp/4gcls0ICvB/merge.9.b.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version /tmp/4gcls0ICvB/merge.9.a.bcf /tmp/4gcls0ICvB/merge.9.b.bcf .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob /tmp/4gcls0ICvB/merge.9.a.bcf /tmp/4gcls0ICvB/merge.9.b.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -i AN:sum,AC:sum /tmp/4gcls0ICvB/merge.9.a.vcf.gz /tmp/4gcls0ICvB/merge.9.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/4gcls0ICvB/merge.9.a.vcf.gz /tmp/4gcls0ICvB/merge.9.b.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -i AN:sum,AC:sum /tmp/4gcls0ICvB/merge.9.a.bcf /tmp/4gcls0ICvB/merge.9.b.bcf .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/4gcls0ICvB/merge.9.a.bcf /tmp/4gcls0ICvB/merge.9.b.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -m none /tmp/4gcls0ICvB/merge.10.a.vcf.gz /tmp/4gcls0ICvB/merge.10.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob -m none /tmp/4gcls0ICvB/merge.10.a.vcf.gz /tmp/4gcls0ICvB/merge.10.b.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -m none /tmp/4gcls0ICvB/merge.10.a.bcf /tmp/4gcls0ICvB/merge.10.b.bcf .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob -m none /tmp/4gcls0ICvB/merge.10.a.bcf /tmp/4gcls0ICvB/merge.10.b.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -m both /tmp/4gcls0ICvB/merge.10.a.vcf.gz /tmp/4gcls0ICvB/merge.10.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob -m both /tmp/4gcls0ICvB/merge.10.a.vcf.gz /tmp/4gcls0ICvB/merge.10.b.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -m both /tmp/4gcls0ICvB/merge.10.a.bcf /tmp/4gcls0ICvB/merge.10.b.bcf .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob -m both /tmp/4gcls0ICvB/merge.10.a.bcf /tmp/4gcls0ICvB/merge.10.b.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -m snp-ins-del /tmp/4gcls0ICvB/merge.10.a.vcf.gz /tmp/4gcls0ICvB/merge.10.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob -m snp-ins-del /tmp/4gcls0ICvB/merge.10.a.vcf.gz /tmp/4gcls0ICvB/merge.10.b.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -m snp-ins-del /tmp/4gcls0ICvB/merge.10.a.bcf /tmp/4gcls0ICvB/merge.10.b.bcf .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob -m snp-ins-del /tmp/4gcls0ICvB/merge.10.a.bcf /tmp/4gcls0ICvB/merge.10.b.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --gvcf - /tmp/4gcls0ICvB/merge.mrules.1.a.vcf.gz /tmp/4gcls0ICvB/merge.mrules.1.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --gvcf - /tmp/4gcls0ICvB/merge.mrules.1.a.vcf.gz /tmp/4gcls0ICvB/merge.mrules.1.b.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --gvcf - /tmp/4gcls0ICvB/merge.mrules.1.a.bcf /tmp/4gcls0ICvB/merge.mrules.1.b.bcf .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --gvcf - /tmp/4gcls0ICvB/merge.mrules.1.a.bcf /tmp/4gcls0ICvB/merge.mrules.1.b.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --gvcf - -M AD:.,PL:. /tmp/4gcls0ICvB/merge.mrules.1.a.vcf.gz /tmp/4gcls0ICvB/merge.mrules.1.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --gvcf - -M AD:.,PL:. /tmp/4gcls0ICvB/merge.mrules.1.a.vcf.gz /tmp/4gcls0ICvB/merge.mrules.1.b.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --gvcf - -M AD:.,PL:. /tmp/4gcls0ICvB/merge.mrules.1.a.bcf /tmp/4gcls0ICvB/merge.mrules.1.b.bcf .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --gvcf - -M AD:.,PL:. /tmp/4gcls0ICvB/merge.mrules.1.a.bcf /tmp/4gcls0ICvB/merge.mrules.1.b.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --gvcf - /tmp/4gcls0ICvB/merge.gvcf.5.a.vcf.gz /tmp/4gcls0ICvB/merge.gvcf.5.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --gvcf - /tmp/4gcls0ICvB/merge.gvcf.5.a.vcf.gz /tmp/4gcls0ICvB/merge.gvcf.5.b.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --gvcf - /tmp/4gcls0ICvB/merge.gvcf.5.a.bcf /tmp/4gcls0ICvB/merge.gvcf.5.b.bcf .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --gvcf - /tmp/4gcls0ICvB/merge.gvcf.5.a.bcf /tmp/4gcls0ICvB/merge.gvcf.5.b.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --gvcf - --merge none /tmp/4gcls0ICvB/merge.gvcf.5.a.vcf.gz /tmp/4gcls0ICvB/merge.gvcf.5.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --gvcf - --merge none /tmp/4gcls0ICvB/merge.gvcf.5.a.vcf.gz /tmp/4gcls0ICvB/merge.gvcf.5.b.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --gvcf - --merge none /tmp/4gcls0ICvB/merge.gvcf.5.a.bcf /tmp/4gcls0ICvB/merge.gvcf.5.b.bcf .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --gvcf - --merge none /tmp/4gcls0ICvB/merge.gvcf.5.a.bcf /tmp/4gcls0ICvB/merge.gvcf.5.b.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --gvcf - /tmp/4gcls0ICvB/merge.gvcf.11.a.vcf.gz /tmp/4gcls0ICvB/merge.gvcf.11.b.vcf.gz /tmp/4gcls0ICvB/merge.gvcf.11.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --gvcf - /tmp/4gcls0ICvB/merge.gvcf.11.a.vcf.gz /tmp/4gcls0ICvB/merge.gvcf.11.b.vcf.gz /tmp/4gcls0ICvB/merge.gvcf.11.c.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version --gvcf - /tmp/4gcls0ICvB/merge.gvcf.11.a.bcf /tmp/4gcls0ICvB/merge.gvcf.11.b.bcf /tmp/4gcls0ICvB/merge.gvcf.11.c.bcf .. ok test_vcf_merge: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools merge --no-version -Ob --gvcf - /tmp/4gcls0ICvB/merge.gvcf.11.a.bcf /tmp/4gcls0ICvB/merge.gvcf.11.b.bcf /tmp/4gcls0ICvB/merge.gvcf.11.c.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%TAG' -i 'TAG[*]="."' /tmp/4gcls0ICvB/query.filter.15.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.filter.15.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%TAG' -i 'TAG[*]="."' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%TAG' -i 'TAG[*]~"\."' /tmp/4gcls0ICvB/query.filter.15.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.filter.15.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%TAG' -i 'TAG[*]~"\."' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%TAG' -i 'TAG[*]!="."' /tmp/4gcls0ICvB/query.filter.15.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.filter.15.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%TAG' -i 'TAG[*]!="."' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%TAG' -i 'TAG[*]!~"\."' /tmp/4gcls0ICvB/query.filter.15.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.filter.15.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%TAG' -i 'TAG[*]!~"\."' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%CHROM %POS %ID %REF %ALT %QUAL %FILTER \t %INFO/CHROM %INFO/POS %INFO/ID %INFO/REF %INFO/ALT %INFO/QUAL %INFO/FILTER' /tmp/4gcls0ICvB/query.3.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.3.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%CHROM %POS %ID %REF %ALT %QUAL %FILTER \t %INFO/CHROM %INFO/POS %INFO/ID %INFO/REF %INFO/ALT %INFO/QUAL %INFO/FILTER' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '[ %CHROM] \t [ %POS] \t [ %ID] \t [ %REF] \t [ %ALT] \t [ %QUAL] \t [ %FILTER]' /tmp/4gcls0ICvB/query.3.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.3.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '[ %CHROM] \t [ %POS] \t [ %ID] \t [ %REF] \t [ %ALT] \t [ %QUAL] \t [ %FILTER]' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '[ %/CHROM] \t [ %/POS] \t [ %/ID] \t [ %/REF] \t [ %/ALT] \t [ %/QUAL] \t [ %/FILTER]' /tmp/4gcls0ICvB/query.3.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.3.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '[ %/CHROM] \t [ %/POS] \t [ %/ID] \t [ %/REF] \t [ %/ALT] \t [ %/QUAL] \t [ %/FILTER]' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%CHROM:%POS [ %SAMPLE %GT]' /tmp/4gcls0ICvB/query.filter.14.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.filter.14.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%CHROM:%POS [ %SAMPLE %GT]' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%CHROM:%POS [ %SAMPLE %GT]' -i'GT="."' /tmp/4gcls0ICvB/query.filter.14.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.filter.14.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%CHROM:%POS [ %SAMPLE %GT]' -i'GT="."' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%CHROM:%POS [ %SAMPLE %GT]' -i'GT="0|1"' /tmp/4gcls0ICvB/query.filter.14.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.filter.14.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%CHROM:%POS [ %SAMPLE %GT]' -i'GT="0|1"' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%CHROM:%POS\t%INFO/AD\t%SUM(INFO/AD)' /tmp/4gcls0ICvB/query.func.1.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.func.1.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%CHROM:%POS\t%INFO/AD\t%SUM(INFO/AD)' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%CHROM:%POS\t[%AD ]\t%SUM(FORMAT/AD)' /tmp/4gcls0ICvB/query.func.1.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.func.1.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%CHROM:%POS\t[%AD ]\t%SUM(FORMAT/AD)' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%CHROM:%POS\t[%AD ]\t[ %SUM(FORMAT/AD)]' /tmp/4gcls0ICvB/query.func.1.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.func.1.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%CHROM:%POS\t[%AD ]\t[ %SUM(FORMAT/AD)]' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%CHROM:%POS\t[%AD ]\t[ %sSUM(FORMAT/AD)]' /tmp/4gcls0ICvB/query.func.1.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.func.1.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%CHROM:%POS\t[%AD ]\t[ %sSUM(FORMAT/AD)]' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided,_conflicting_interpretations"' /tmp/4gcls0ICvB/query.string.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.string.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided,_conflicting_interpretations"' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" || CLNREVSTAT="_conflicting_interpretations"' /tmp/4gcls0ICvB/query.string.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.string.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" || CLNREVSTAT="_conflicting_interpretations"' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" && CLNREVSTAT="_conflicting_interpretations"' /tmp/4gcls0ICvB/query.string.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.string.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" && CLNREVSTAT="_conflicting_interpretations"' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%CHROM\t%POS\t%INFO/STR\n' -i'INFO/STR=@/build/bcftools-TfJ6sU/bcftools-1.22/test/query.string.2.1.txt' /tmp/4gcls0ICvB/query.string.2.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.string.2.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%CHROM\t%POS\t%INFO/STR\n' -i'INFO/STR=@/build/bcftools-TfJ6sU/bcftools-1.22/test/query.string.2.1.txt' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%CHROM\t%POS[\t%STR]\n' -i'FMT/STR=@/build/bcftools-TfJ6sU/bcftools-1.22/test/query.string.2.2.txt' /tmp/4gcls0ICvB/query.string.2.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.string.2.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%CHROM\t%POS[\t%STR]\n' -i'FMT/STR=@/build/bcftools-TfJ6sU/bcftools-1.22/test/query.string.2.2.txt' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' /tmp/4gcls0ICvB/query.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/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-TfJ6sU/bcftools-1.22/bcftools query -f '%RSX\t%VKX\n' /tmp/4gcls0ICvB/query.variantkey.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.variantkey.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%RSX\t%VKX\n' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%XRI\n' -i'XRI[*]>1111' /tmp/4gcls0ICvB/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/view.filter.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%XRI\n' -i'XRI[*]>1111' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' /tmp/4gcls0ICvB/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/view.filter.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' /tmp/4gcls0ICvB/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/view.filter.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' /tmp/4gcls0ICvB/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/view.filter.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' /tmp/4gcls0ICvB/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/view.filter.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' /tmp/4gcls0ICvB/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/view.filter.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' /tmp/4gcls0ICvB/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/view.filter.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' /tmp/4gcls0ICvB/query.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' /tmp/4gcls0ICvB/query.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' /tmp/4gcls0ICvB/query.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' /tmp/4gcls0ICvB/query.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' /tmp/4gcls0ICvB/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/view.filter.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' /tmp/4gcls0ICvB/query.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' /tmp/4gcls0ICvB/query.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' /tmp/4gcls0ICvB/query.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' /tmp/4gcls0ICvB/query.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/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/4gcls0ICvB/view.vectors.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/view.vectors.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/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-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' /tmp/4gcls0ICvB/query.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.filter.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' /tmp/4gcls0ICvB/query.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.filter.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' /tmp/4gcls0ICvB/query.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.filter.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' /tmp/4gcls0ICvB/query.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.filter.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' /tmp/4gcls0ICvB/query.2.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.2.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -i'IINT="."' -f'%POS %IINT\n' /tmp/4gcls0ICvB/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/missing.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -i'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -i'IINT!="."' -f'%POS %IINT\n' /tmp/4gcls0ICvB/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/missing.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -i'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -e'IINT!="."' -f'%POS %IINT\n' /tmp/4gcls0ICvB/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/missing.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -e'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -e'IINT="."' -f'%POS %IINT\n' /tmp/4gcls0ICvB/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/missing.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -e'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' /tmp/4gcls0ICvB/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/missing.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' /tmp/4gcls0ICvB/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/missing.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' /tmp/4gcls0ICvB/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/missing.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' /tmp/4gcls0ICvB/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/missing.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' /tmp/4gcls0ICvB/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/missing.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' /tmp/4gcls0ICvB/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/missing.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' /tmp/4gcls0ICvB/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/missing.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' /tmp/4gcls0ICvB/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/missing.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' /tmp/4gcls0ICvB/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/missing.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -i'FILTER="A"' -f'%POS %FILTER\n' /tmp/4gcls0ICvB/filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/filter.11.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -i'FILTER="A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -i'FILTER!="A"' -f'%POS %FILTER\n' /tmp/4gcls0ICvB/filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/filter.11.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -i'FILTER!="A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -i'FILTER~"A"' -f'%POS %FILTER\n' /tmp/4gcls0ICvB/filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/filter.11.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -i'FILTER~"A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n' /tmp/4gcls0ICvB/filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/filter.11.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%LINE' /tmp/4gcls0ICvB/query.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%LINE' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' /tmp/4gcls0ICvB/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.filter-type.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' /tmp/4gcls0ICvB/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.filter-type.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' /tmp/4gcls0ICvB/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.filter-type.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' /tmp/4gcls0ICvB/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.filter-type.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\n' -i'INFO/TYPE="xxx"' /tmp/4gcls0ICvB/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.filter-type.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\n' -i'INFO/TYPE="xxx"' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/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/4gcls0ICvB/filter-missing-floats.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/filter-missing-floats.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/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-TfJ6sU/bcftools-1.22/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/4gcls0ICvB/filter-missing-floats.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/filter-missing-floats.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/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-TfJ6sU/bcftools-1.22/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' /tmp/4gcls0ICvB/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/missing.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' /tmp/4gcls0ICvB/query.filter.2.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.filter.2.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' /tmp/4gcls0ICvB/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/view.filter.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' /tmp/4gcls0ICvB/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/view.filter.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' /tmp/4gcls0ICvB/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/view.filter.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' /tmp/4gcls0ICvB/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/view.filter.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' /tmp/4gcls0ICvB/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/view.filter.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' /tmp/4gcls0ICvB/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/view.filter.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' /tmp/4gcls0ICvB/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/view.filter.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' /tmp/4gcls0ICvB/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/view.filter.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' /tmp/4gcls0ICvB/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/view.filter.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' /tmp/4gcls0ICvB/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/view.filter.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' /tmp/4gcls0ICvB/filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/filter.5.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' /tmp/4gcls0ICvB/filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/filter.5.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' /tmp/4gcls0ICvB/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/view.filter.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' /tmp/4gcls0ICvB/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/view.filter.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' /tmp/4gcls0ICvB/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/view.filter.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' /tmp/4gcls0ICvB/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/view.filter.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' /tmp/4gcls0ICvB/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/view.filter.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 & FMT/GQ=589' /tmp/4gcls0ICvB/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/view.filter.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 & FMT/GQ=589' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' /tmp/4gcls0ICvB/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/view.filter.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' /tmp/4gcls0ICvB/query.filter.3.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.filter.3.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"' /tmp/4gcls0ICvB/query.filter.3.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.filter.3.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' /tmp/4gcls0ICvB/query.filter.3.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.filter.3.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS %SAMPLE %AD\n]\n' -i'AD[:0]+AD[:1] > 12' /tmp/4gcls0ICvB/filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/filter.5.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS %SAMPLE %AD\n]\n' -i'AD[:0]+AD[:1] > 12' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' /tmp/4gcls0ICvB/query.filter.4.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.filter.4.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%ID\n' -i 'ID=@/build/bcftools-TfJ6sU/bcftools-1.22/test/query.56.out' /tmp/4gcls0ICvB/view.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/view.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%ID\n' -i 'ID=@/build/bcftools-TfJ6sU/bcftools-1.22/test/query.56.out' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD)>0.01' /tmp/4gcls0ICvB/query.filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.filter.5.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/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-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD[:0],FMT/AD[:1])>0.01' /tmp/4gcls0ICvB/query.filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.filter.5.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/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-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%AD\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01' /tmp/4gcls0ICvB/query.filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.filter.5.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%AD\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[GT]==10' /tmp/4gcls0ICvB/query.filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.filter.5.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[GT]==10' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'sSUM(FMT/AD[GT])==210' /tmp/4gcls0ICvB/query.filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.filter.5.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'sSUM(FMT/AD[GT])==210' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[0:GT]==30' /tmp/4gcls0ICvB/query.filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.filter.5.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[0:GT]==30' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TF[:GT]==1 && FMT/TF[:GT]==2' /tmp/4gcls0ICvB/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.gtidx.1.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TF[:GT]==1 && FMT/TF[:GT]==2' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TI[:GT]==1 && FMT/TF[:GT]==2' /tmp/4gcls0ICvB/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.gtidx.1.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TI[:GT]==1 && FMT/TF[:GT]==2' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TS[:GT]=="BB" && FMT/TS[:GT]=="CC"' /tmp/4gcls0ICvB/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.gtidx.1.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TS[:GT]=="BB" && FMT/TS[:GT]=="CC"' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TC[:GT]=="B" && FMT/TC[:GT]=="C"' /tmp/4gcls0ICvB/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.gtidx.1.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TC[:GT]=="B" && FMT/TC[:GT]=="C"' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%GT %TI\n]' -i'FMT/TI[:GT]=="."' /tmp/4gcls0ICvB/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.gtidx.1.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%GT %TI\n]' -i'FMT/TI[:GT]=="."' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%CHROM %POS\n' -i'CHROM="4"' /tmp/4gcls0ICvB/query.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%CHROM %POS\n' -i'CHROM="4"' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%TAG1\n' -i'(TAG1>=-129 && TAG1<=-120) || (TAG1>=-32769 && TAG1<=-32760)' /tmp/4gcls0ICvB/query.negative.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.negative.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%TAG1\n' -i'(TAG1>=-129 && TAG1<=-120) || (TAG1>=-32769 && TAG1<=-32760)' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%TAGV1\n' -i'(TAGV1>=-129 && TAGV1<=-120) || (TAGV1>=-32769 && TAGV1<=-32760)' /tmp/4gcls0ICvB/query.negative.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.negative.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%TAGV1\n' -i'(TAGV1>=-129 && TAGV1<=-120) || (TAGV1>=-32769 && TAGV1<=-32760)' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%TAG2\n' -i'(TAG2>=-129 && TAG2<=-120) || (TAG2>=-32769 && TAG2<=-32760)' /tmp/4gcls0ICvB/query.negative.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.negative.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%TAG2\n' -i'(TAG2>=-129 && TAG2<=-120) || (TAG2>=-32769 && TAG2<=-32760)' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%TAGV2\n' -i'(TAGV2>=-129 && TAGV2<=-120) || (TAGV2>=-32769 && TAGV2<=-32760)' /tmp/4gcls0ICvB/query.negative.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.negative.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%TAGV2\n' -i'(TAGV2>=-129 && TAGV2<=-120) || (TAGV2>=-32769 && TAGV2<=-32760)' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS\t%SAMPLE\t%GQ\n]' -i'N_PASS(GQ<20)==1' /tmp/4gcls0ICvB/query.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS\t%SAMPLE\t%GQ\n]' -i'N_PASS(GQ<20)==1' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")==1' /tmp/4gcls0ICvB/query.filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.filter.11.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")==1' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")!=1' /tmp/4gcls0ICvB/query.filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.filter.11.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")!=1' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")==1' /tmp/4gcls0ICvB/query.filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.filter.11.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")==1' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")!=1' /tmp/4gcls0ICvB/query.filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.filter.11.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")!=1' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%CHROM\t%POS\t%INFO\t%FORMAT\n' -s D,C /tmp/4gcls0ICvB/query.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%CHROM\t%POS\t%INFO\t%FORMAT\n' -s D,C .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\n' -i'POS==16777217 || POS==33554432 || POS=118673904' /tmp/4gcls0ICvB/query.filter.6.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.filter.6.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\n' -i'POS==16777217 || POS==33554432 || POS=118673904' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(II)==6' /tmp/4gcls0ICvB/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.filter.7.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(II)==6' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(FORMAT/FI)==7' /tmp/4gcls0ICvB/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.filter.7.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(FORMAT/FI)==7' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(II)==2' /tmp/4gcls0ICvB/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.filter.7.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(II)==2' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(FORMAT/FI)==1.75' /tmp/4gcls0ICvB/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.filter.7.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(FORMAT/FI)==1.75' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(II)==2' /tmp/4gcls0ICvB/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.filter.7.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(II)==2' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(FORMAT/FI)==1.75' /tmp/4gcls0ICvB/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.filter.7.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(FORMAT/FI)==1.75' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(II)==2' /tmp/4gcls0ICvB/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.filter.7.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(II)==2' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(FORMAT/FI)==1.5' /tmp/4gcls0ICvB/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.filter.7.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(FORMAT/FI)==1.5' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'%ILEN==1' /tmp/4gcls0ICvB/query.filter.8.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.filter.8.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'%ILEN==1' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'ILEN==1' /tmp/4gcls0ICvB/query.filter.8.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.filter.8.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'ILEN==1' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] < FMT/AD[:1]' /tmp/4gcls0ICvB/query.filter.9.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.filter.9.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] < FMT/AD[:1]' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] > FMT/AD[:1]' /tmp/4gcls0ICvB/query.filter.9.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.filter.9.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] > FMT/AD[:1]' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[ %AD\n]' -i'AD[:1] / sum(AD[*]) > 0.5' /tmp/4gcls0ICvB/query.filter.13.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.filter.13.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[ %AD\n]' -i'AD[:1] / sum(AD[*]) > 0.5' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS %NUM_TAG\n' -i'COUNT(INFO/NUM_TAG)=2' /tmp/4gcls0ICvB/query.filter.10.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.filter.10.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS %NUM_TAG\n' -i'COUNT(INFO/NUM_TAG)=2' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2' /tmp/4gcls0ICvB/query.filter.10.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.filter.10.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%CHROM:%POS\t%N_PASS(GT="alt" & GQ>110)\t[\t%GT]\t[\t%GQ]\n' /tmp/4gcls0ICvB/query.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/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-TfJ6sU/bcftools-1.22/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 1,3,0 /tmp/4gcls0ICvB/query.filter.12.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.filter.12.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 1,3,0 .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 0,1,3 /tmp/4gcls0ICvB/query.filter.12.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.filter.12.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 0,1,3 .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f "[%SAMPLE %GT\n]" -S /build/bcftools-TfJ6sU/bcftools-1.22/test/query.smpl.11.txt /tmp/4gcls0ICvB/query.smpl.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.smpl.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f "[%SAMPLE %GT\n]" -S /build/bcftools-TfJ6sU/bcftools-1.22/test/query.smpl.11.txt .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -l -S /build/bcftools-TfJ6sU/bcftools-1.22/test/query.smpl.11.txt /tmp/4gcls0ICvB/query.smpl.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.smpl.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -l -S /build/bcftools-TfJ6sU/bcftools-1.22/test/query.smpl.11.txt .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f "[%SAMPLE %GT\n]" -S ^/build/bcftools-TfJ6sU/bcftools-1.22/test/query.smpl.11.txt /tmp/4gcls0ICvB/query.smpl.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.smpl.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f "[%SAMPLE %GT\n]" -S ^/build/bcftools-TfJ6sU/bcftools-1.22/test/query.smpl.11.txt .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -l -S ^/build/bcftools-TfJ6sU/bcftools-1.22/test/query.smpl.11.txt /tmp/4gcls0ICvB/query.smpl.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.smpl.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -l -S ^/build/bcftools-TfJ6sU/bcftools-1.22/test/query.smpl.11.txt .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f "[%SAMPLE %GT\n]" -S /build/bcftools-TfJ6sU/bcftools-1.22/test/query.smpl.txt /tmp/4gcls0ICvB/query.smpl.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.smpl.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f "[%SAMPLE %GT\n]" -S /build/bcftools-TfJ6sU/bcftools-1.22/test/query.smpl.txt .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -l -S /build/bcftools-TfJ6sU/bcftools-1.22/test/query.smpl.txt /tmp/4gcls0ICvB/query.smpl.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.smpl.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -l -S /build/bcftools-TfJ6sU/bcftools-1.22/test/query.smpl.txt .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%ID\n' -i'ID~"s12"' /tmp/4gcls0ICvB/query.filter.id.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.filter.id.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%ID\n' -i'ID~"s12"' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%ID\n' -i'ID="rs123"' /tmp/4gcls0ICvB/query.filter.id.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.filter.id.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%ID\n' -i'ID="rs123"' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%ID\n' -i'ID="abc"' /tmp/4gcls0ICvB/query.filter.id.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.filter.id.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%ID\n' -i'ID="abc"' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%ID\n' -i'ID=@/build/bcftools-TfJ6sU/bcftools-1.22/test/query.filter.id.3.txt' /tmp/4gcls0ICvB/query.filter.id.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.filter.id.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%ID\n' -i'ID=@/build/bcftools-TfJ6sU/bcftools-1.22/test/query.filter.id.3.txt' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%ID\n' -i'ID!="abc"' /tmp/4gcls0ICvB/query.filter.id.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.filter.id.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%ID\n' -i'ID!="abc"' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%ID\n' -i'ID!=@/build/bcftools-TfJ6sU/bcftools-1.22/test/query.filter.id.3.txt' /tmp/4gcls0ICvB/query.filter.id.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.filter.id.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%ID\n' -i'ID!=@/build/bcftools-TfJ6sU/bcftools-1.22/test/query.filter.id.3.txt' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -i'FILTER="A"' -f'%FILTER\n' /tmp/4gcls0ICvB/filter.12.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/filter.12.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -i'FILTER="A"' -f'%FILTER\n' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -i'FILTER~"A"' -f'%FILTER\n' /tmp/4gcls0ICvB/filter.12.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/filter.12.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -i'FILTER~"A"' -f'%FILTER\n' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -i'FILTER="A;B"' -f'%FILTER\n' /tmp/4gcls0ICvB/filter.12.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/filter.12.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -i'FILTER="A;B"' -f'%FILTER\n' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -i'FILTER!="A;B"' -f'%FILTER\n' /tmp/4gcls0ICvB/filter.12.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/filter.12.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -i'FILTER!="A;B"' -f'%FILTER\n' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -i'FILTER~"A;B"' -f'%FILTER\n' /tmp/4gcls0ICvB/filter.12.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/filter.12.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -i'FILTER~"A;B"' -f'%FILTER\n' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -i'FILTER!~"A;B"' -f'%FILTER\n' /tmp/4gcls0ICvB/filter.12.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/filter.12.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -i'FILTER!~"A;B"' -f'%FILTER\n' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -i'DP%10==2' -f'[ %DP]\n' /tmp/4gcls0ICvB/filter.10.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/filter.10.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -i'DP%10==2' -f'[ %DP]\n' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -i'REF="N"' -f'%CHROM %POS %REF %ALT %QUAL\n' /tmp/4gcls0ICvB/filter.13.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/filter.13.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -i'REF="N"' -f'%CHROM %POS %REF %ALT %QUAL\n' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -H -f'[%CHROM %POS %SAMPLE %DP %GT\n]' /tmp/4gcls0ICvB/query.header.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.header.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -H -f'[%CHROM %POS %SAMPLE %DP %GT\n]' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -H -f'[%CHROM %POS %SAMPLE %DP %GT\t]\n' /tmp/4gcls0ICvB/query.header.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.header.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -H -f'[%CHROM %POS %SAMPLE %DP %GT\t]\n' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]\n' /tmp/4gcls0ICvB/query.header.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.header.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]\n' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]' /tmp/4gcls0ICvB/query.header.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.header.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]\n' /tmp/4gcls0ICvB/query.header.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.header.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]\n' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]' /tmp/4gcls0ICvB/query.header.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.header.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -HH -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]' /tmp/4gcls0ICvB/query.header.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.header.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -HH -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%SAMPLE %DP\n]' -i'DP=1 || DP=2' /tmp/4gcls0ICvB/query.filter-or.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.filter-or.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%SAMPLE %DP\n]' -i'DP=1 || DP=2' .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%SAMPLE %DP\n]' -i'DP=1 | DP=2' /tmp/4gcls0ICvB/query.filter-or.vcf.gz .. ok test_vcf_query: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/query.filter-or.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%SAMPLE %DP\n]' -i'DP=1 | DP=2' .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -c e /tmp/4gcls0ICvB/norm.6.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/norm.2.fa .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -c e /tmp/4gcls0ICvB/norm.6.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/norm.2.fa -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m - /tmp/4gcls0ICvB/norm.breakend.1.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/norm.breakend.1.fa .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m - /tmp/4gcls0ICvB/norm.breakend.1.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/norm.breakend.1.fa -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m - /tmp/4gcls0ICvB/norm.sort.vcf.gz .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m - /tmp/4gcls0ICvB/norm.sort.vcf.gz -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m - -S lex /tmp/4gcls0ICvB/norm.sort.vcf.gz .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m - -S lex /tmp/4gcls0ICvB/norm.sort.vcf.gz -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m +both /tmp/4gcls0ICvB/norm.join-missing-ploidy.vcf.gz .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m +both /tmp/4gcls0ICvB/norm.join-missing-ploidy.vcf.gz -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m - --multi-overlaps . /tmp/4gcls0ICvB/norm.split.5.vcf.gz .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m - --multi-overlaps . /tmp/4gcls0ICvB/norm.split.5.vcf.gz -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version /tmp/4gcls0ICvB/norm.symbolic.3.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/norm.symbolic.3.fa .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version /tmp/4gcls0ICvB/norm.symbolic.3.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/norm.symbolic.3.fa -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -cx /tmp/4gcls0ICvB/norm.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/norm.fa .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -cx /tmp/4gcls0ICvB/norm.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/norm.fa -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m- /tmp/4gcls0ICvB/norm.split.vcf.gz .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m- /tmp/4gcls0ICvB/norm.split.vcf.gz -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m- /tmp/4gcls0ICvB/norm.split.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m- /tmp/4gcls0ICvB/norm.split.2.vcf.gz -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m- --force /tmp/4gcls0ICvB/norm.split.3.vcf.gz .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m- --force /tmp/4gcls0ICvB/norm.split.3.vcf.gz -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m- /tmp/4gcls0ICvB/norm.split.4.vcf.gz .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m- /tmp/4gcls0ICvB/norm.split.4.vcf.gz -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m- --keep-sum AD /tmp/4gcls0ICvB/norm.split.4.vcf.gz .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m- --keep-sum AD /tmp/4gcls0ICvB/norm.split.4.vcf.gz -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m- /tmp/4gcls0ICvB/norm.split.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/norm.fa .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m- /tmp/4gcls0ICvB/norm.split.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/norm.fa -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m+ /tmp/4gcls0ICvB/norm.merge.vcf.gz .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m+ /tmp/4gcls0ICvB/norm.merge.vcf.gz -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m+ /tmp/4gcls0ICvB/norm.merge.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m+ /tmp/4gcls0ICvB/norm.merge.2.vcf.gz -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m+ /tmp/4gcls0ICvB/norm.merge.3.vcf.gz .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m+ /tmp/4gcls0ICvB/norm.merge.3.vcf.gz -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m+ -s /tmp/4gcls0ICvB/norm.merge.vcf.gz .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m+ -s /tmp/4gcls0ICvB/norm.merge.vcf.gz -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -Nc s /tmp/4gcls0ICvB/norm.setref.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/norm.fa .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -Nc s /tmp/4gcls0ICvB/norm.setref.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/norm.fa -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version /tmp/4gcls0ICvB/norm.telomere.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/norm.fa .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version /tmp/4gcls0ICvB/norm.telomere.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/norm.fa -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -d snps /tmp/4gcls0ICvB/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -d snps /tmp/4gcls0ICvB/norm.rmdup.vcf.gz -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -d indels /tmp/4gcls0ICvB/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -d indels /tmp/4gcls0ICvB/norm.rmdup.vcf.gz -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -d both /tmp/4gcls0ICvB/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -d both /tmp/4gcls0ICvB/norm.rmdup.vcf.gz -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -d all /tmp/4gcls0ICvB/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -d all /tmp/4gcls0ICvB/norm.rmdup.vcf.gz -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -d none /tmp/4gcls0ICvB/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -d none /tmp/4gcls0ICvB/norm.rmdup.vcf.gz -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -d exact /tmp/4gcls0ICvB/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -d exact /tmp/4gcls0ICvB/norm.rmdup.vcf.gz -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -d none /tmp/4gcls0ICvB/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -d none /tmp/4gcls0ICvB/norm.rmdup.2.vcf.gz -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -d exact /tmp/4gcls0ICvB/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -d exact /tmp/4gcls0ICvB/norm.rmdup.2.vcf.gz -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -d indels /tmp/4gcls0ICvB/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -d indels /tmp/4gcls0ICvB/norm.rmdup.2.vcf.gz -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -d any /tmp/4gcls0ICvB/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -d any /tmp/4gcls0ICvB/norm.rmdup.2.vcf.gz -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -d both /tmp/4gcls0ICvB/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -d both /tmp/4gcls0ICvB/norm.rmdup.2.vcf.gz -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -d snps /tmp/4gcls0ICvB/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -d snps /tmp/4gcls0ICvB/norm.rmdup.2.vcf.gz -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -d exact /tmp/4gcls0ICvB/norm.rmdup.3.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/norm.rmdup.3.fa .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -d exact /tmp/4gcls0ICvB/norm.rmdup.3.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/norm.rmdup.3.fa -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -d all /tmp/4gcls0ICvB/norm.rmdup.3.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/norm.rmdup.3.fa .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -d all /tmp/4gcls0ICvB/norm.rmdup.3.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/norm.rmdup.3.fa -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -c s -a --old-rec-tag XX /tmp/4gcls0ICvB/norm.2.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/norm.2.fa .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -c s -a --old-rec-tag XX /tmp/4gcls0ICvB/norm.2.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/norm.2.fa -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -c s --old-rec-tag XX /tmp/4gcls0ICvB/norm.iupac.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/norm.iupac.fa .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -c s --old-rec-tag XX /tmp/4gcls0ICvB/norm.iupac.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/norm.iupac.fa -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -c s --old-rec-tag XX /tmp/4gcls0ICvB/norm.3.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/norm.3.fa .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -c s --old-rec-tag XX /tmp/4gcls0ICvB/norm.3.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/norm.3.fa -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -c s -i'alt="N"' --old-rec-tag XX /tmp/4gcls0ICvB/norm.3.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/norm.3.fa .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -c s -i'alt="N"' --old-rec-tag XX /tmp/4gcls0ICvB/norm.3.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/norm.3.fa -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -a --old-rec-tag OLD_REC /tmp/4gcls0ICvB/atomize.split.1.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m -any --force .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -a --old-rec-tag OLD_REC /tmp/4gcls0ICvB/atomize.split.1.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m -any --force -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m -any --old-rec-tag OLD_REC --force /tmp/4gcls0ICvB/atomize.split.1.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -a .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m -any --old-rec-tag OLD_REC --force /tmp/4gcls0ICvB/atomize.split.1.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -a -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m -any --old-rec-tag OLD_REC --force -a /tmp/4gcls0ICvB/atomize.split.1.vcf.gz .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m -any --old-rec-tag OLD_REC --force -a /tmp/4gcls0ICvB/atomize.split.1.vcf.gz -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/4gcls0ICvB/atomize.split.1.vcf.gz .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/4gcls0ICvB/atomize.split.1.vcf.gz -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/4gcls0ICvB/atomize.split.1.vcf.gz .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/4gcls0ICvB/atomize.split.1.vcf.gz -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/4gcls0ICvB/atomize.split.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/4gcls0ICvB/atomize.split.2.vcf.gz -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/4gcls0ICvB/atomize.split.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/4gcls0ICvB/atomize.split.2.vcf.gz -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version --atomize --atom-overlaps . /tmp/4gcls0ICvB/atomize.split.3.vcf.gz .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version --atomize --atom-overlaps . /tmp/4gcls0ICvB/atomize.split.3.vcf.gz -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/4gcls0ICvB/atomize.split.4.vcf.gz .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/4gcls0ICvB/atomize.split.4.vcf.gz -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC -i 'ILEN=0' /tmp/4gcls0ICvB/atomize.split.4.vcf.gz .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC -i 'ILEN=0' /tmp/4gcls0ICvB/atomize.split.4.vcf.gz -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version --atomize --old-rec-tag OLD_REC --atom-overlaps . /tmp/4gcls0ICvB/atomize.split.5.vcf.gz .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version --atomize --old-rec-tag OLD_REC --atom-overlaps . /tmp/4gcls0ICvB/atomize.split.5.vcf.gz -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/4gcls0ICvB/atomize.split.5.vcf.gz .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/4gcls0ICvB/atomize.split.5.vcf.gz -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m +both /tmp/4gcls0ICvB/norm.4.vcf.gz .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m +both /tmp/4gcls0ICvB/norm.4.vcf.gz -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m +any /tmp/4gcls0ICvB/norm.4.vcf.gz .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m +any /tmp/4gcls0ICvB/norm.4.vcf.gz -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m - --multi-overlaps 0 /tmp/4gcls0ICvB/norm.5.vcf.gz .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m - --multi-overlaps 0 /tmp/4gcls0ICvB/norm.5.vcf.gz -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m - --multi-overlaps . /tmp/4gcls0ICvB/norm.5.vcf.gz .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m - --multi-overlaps . /tmp/4gcls0ICvB/norm.5.vcf.gz -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m -any /tmp/4gcls0ICvB/norm.m-any.vcf.gz .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m -any /tmp/4gcls0ICvB/norm.m-any.vcf.gz -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m -any /tmp/4gcls0ICvB/norm.phased-split.vcf.gz .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m -any /tmp/4gcls0ICvB/norm.phased-split.vcf.gz -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m +any /tmp/4gcls0ICvB/norm.phased-join.vcf.gz .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m +any /tmp/4gcls0ICvB/norm.phased-join.vcf.gz -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version --old-rec-tag ORI /tmp/4gcls0ICvB/norm.symbolic.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/norm.symbolic.fa .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version --old-rec-tag ORI /tmp/4gcls0ICvB/norm.symbolic.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/norm.symbolic.fa -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version --old-rec-tag ORI /tmp/4gcls0ICvB/norm.symbolic.2.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/norm.symbolic.fa .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version --old-rec-tag ORI /tmp/4gcls0ICvB/norm.symbolic.2.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/norm.symbolic.fa -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version --old-rec-tag ORI /tmp/4gcls0ICvB/norm.right-align.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/norm.right-align.fa .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version --old-rec-tag ORI /tmp/4gcls0ICvB/norm.right-align.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/norm.right-align.fa -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version --old-rec-tag ORI -g /build/bcftools-TfJ6sU/bcftools-1.22/test/norm.right-align.gff /tmp/4gcls0ICvB/norm.right-align.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/norm.right-align.fa .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version --old-rec-tag ORI -g /build/bcftools-TfJ6sU/bcftools-1.22/test/norm.right-align.gff /tmp/4gcls0ICvB/norm.right-align.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/norm.right-align.fa -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version --old-rec-tag ORI -a -m -any /tmp/4gcls0ICvB/norm.atom-split-norm.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/norm.atom-split-norm.fa .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version --old-rec-tag ORI -a -m -any /tmp/4gcls0ICvB/norm.atom-split-norm.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/norm.atom-split-norm.fa -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m -any /tmp/4gcls0ICvB/norm.string-tags.vcf.gz .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m -any /tmp/4gcls0ICvB/norm.string-tags.vcf.gz -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m - /tmp/4gcls0ICvB/norm.split.merge.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m +both .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m - /tmp/4gcls0ICvB/norm.split.merge.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m +both -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m - /tmp/4gcls0ICvB/norm.split.merge.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m +indels .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m - /tmp/4gcls0ICvB/norm.split.merge.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m +indels -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m - /tmp/4gcls0ICvB/norm.split.merge.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m +snps .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m - /tmp/4gcls0ICvB/norm.split.merge.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m +snps -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m - /tmp/4gcls0ICvB/norm.split.merge.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m +snps .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m - /tmp/4gcls0ICvB/norm.split.merge.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m +snps -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m - /tmp/4gcls0ICvB/norm.split.merge.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m +any .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m - /tmp/4gcls0ICvB/norm.split.merge.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m +any -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m - -i 'type="snp"' /tmp/4gcls0ICvB/norm.split.merge.vcf.gz .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m - -i 'type="snp"' /tmp/4gcls0ICvB/norm.split.merge.vcf.gz -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m +any /tmp/4gcls0ICvB/norm.merge.4.vcf.gz .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m +any /tmp/4gcls0ICvB/norm.merge.4.vcf.gz -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m +both /tmp/4gcls0ICvB/norm.merge.4.vcf.gz .. ok test_vcf_norm: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools norm --no-version -m +both /tmp/4gcls0ICvB/norm.merge.4.vcf.gz -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version -i 'INFO/TAG=@/build/bcftools-TfJ6sU/bcftools-1.22/test/filter.string.1.txt' /tmp/4gcls0ICvB/filter.string.1.vcf.gz .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob -i 'INFO/TAG=@/build/bcftools-TfJ6sU/bcftools-1.22/test/filter.string.1.txt' /tmp/4gcls0ICvB/filter.string.1.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version -i 'FMT/TAG=@/build/bcftools-TfJ6sU/bcftools-1.22/test/filter.string.1.txt' /tmp/4gcls0ICvB/filter.string.1.vcf.gz .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob -i 'FMT/TAG=@/build/bcftools-TfJ6sU/bcftools-1.22/test/filter.string.1.txt' /tmp/4gcls0ICvB/filter.string.1.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version -HA /tmp/4gcls0ICvB/merge.gvcf.2.a.vcf.gz .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version -HAA /tmp/4gcls0ICvB/merge.gvcf.2.a.vcf.gz .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version /tmp/4gcls0ICvB/weird-chr-names.vcf.gz -r 1 .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/weird-chr-names.vcf.gz -r 1 | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version /tmp/4gcls0ICvB/weird-chr-names.vcf.gz -r 1:1-2 .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/weird-chr-names.vcf.gz -r 1:1-2 | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version /tmp/4gcls0ICvB/weird-chr-names.vcf.gz -r 1:1,1:2 .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/weird-chr-names.vcf.gz -r 1:1,1:2 | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version /tmp/4gcls0ICvB/weird-chr-names.vcf.gz -r 1:1-1 .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/weird-chr-names.vcf.gz -r 1:1-1 | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version /tmp/4gcls0ICvB/weird-chr-names.vcf.gz -r {1:1} .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/weird-chr-names.vcf.gz -r {1:1} | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version /tmp/4gcls0ICvB/weird-chr-names.vcf.gz -r {1:1}:1-2 .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/weird-chr-names.vcf.gz -r {1:1}:1-2 | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version /tmp/4gcls0ICvB/weird-chr-names.vcf.gz -r {1:1}:1,{1:1}:2 .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/weird-chr-names.vcf.gz -r {1:1}:1,{1:1}:2 | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version /tmp/4gcls0ICvB/weird-chr-names.vcf.gz -r {1:1}:1-1 .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/weird-chr-names.vcf.gz -r {1:1}:1-1 | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version /tmp/4gcls0ICvB/weird-chr-names.vcf.gz -r {1:1-1} .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/weird-chr-names.vcf.gz -r {1:1-1} | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version /tmp/4gcls0ICvB/weird-chr-names.vcf.gz -r {1:1-1}:1-2 .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/weird-chr-names.vcf.gz -r {1:1-1}:1-2 | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version /tmp/4gcls0ICvB/weird-chr-names.vcf.gz -r {1:1-1}:1,{1:1-1}:2 .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/weird-chr-names.vcf.gz -r {1:1-1}:1,{1:1-1}:2 | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version /tmp/4gcls0ICvB/weird-chr-names.vcf.gz -r {1:1-1}:1-1 .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/weird-chr-names.vcf.gz -r {1:1-1}:1-1 | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version /tmp/4gcls0ICvB/weird-chr-names.vcf.gz -r {1:1-1}-2 .. ok, expected non-zero status test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/weird-chr-names.vcf.gz -r {1:1-1}-2 | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok, expected non-zero status test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version -aUc1 -C1 -s NA00002 -v snps /tmp/4gcls0ICvB/view.vcf.gz .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/4gcls0ICvB/view.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version -f PASS -Xks NA00003 /tmp/4gcls0ICvB/view.vcf.gz -r20,Y .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob -f PASS -Xks NA00003 /tmp/4gcls0ICvB/view.vcf.gz -r20,Y | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version -xs NA00003 /tmp/4gcls0ICvB/view.vcf.gz .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob -xs NA00003 /tmp/4gcls0ICvB/view.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/4gcls0ICvB/view.vcf.gz .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/4gcls0ICvB/view.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version -p /tmp/4gcls0ICvB/view.vcf.gz .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob -p /tmp/4gcls0ICvB/view.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version -P /tmp/4gcls0ICvB/view.vcf.gz .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob -P /tmp/4gcls0ICvB/view.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version -hm2 -M2 -q0.3 -Q0.7 /tmp/4gcls0ICvB/view.vcf.gz .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/4gcls0ICvB/view.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version -Hu /tmp/4gcls0ICvB/view.vcf.gz .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version -GVsnps /tmp/4gcls0ICvB/view.vcf.gz .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob -GVsnps /tmp/4gcls0ICvB/view.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version -ne 'INDEL=1 || PV4[0]<0.006' /tmp/4gcls0ICvB/view.vcf.gz .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/4gcls0ICvB/view.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version -s ^NA00003 /tmp/4gcls0ICvB/view.vcf.gz .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob -s ^NA00003 /tmp/4gcls0ICvB/view.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version /tmp/4gcls0ICvB/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/view.omitgenotypes.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version -G /tmp/4gcls0ICvB/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob -G /tmp/4gcls0ICvB/view.omitgenotypes.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version -HG /tmp/4gcls0ICvB/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version -a /tmp/4gcls0ICvB/many.alleles.vcf.gz .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob -a /tmp/4gcls0ICvB/many.alleles.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version -asA /tmp/4gcls0ICvB/view.vectors.vcf.gz .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob -asA /tmp/4gcls0ICvB/view.vectors.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version -asB /tmp/4gcls0ICvB/view.vectors.vcf.gz .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob -asB /tmp/4gcls0ICvB/view.vectors.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version -asA /tmp/4gcls0ICvB/view.vectors.2.vcf.gz .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob -asA /tmp/4gcls0ICvB/view.vectors.2.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version -H -i'FMT/FGS[*:0]="AAAAAA"' /tmp/4gcls0ICvB/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version -H -i'FMT/FGS[*:2]="C"' /tmp/4gcls0ICvB/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version -H -i'FMT/FGS[*:4]="EE"' /tmp/4gcls0ICvB/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version -H -i'FMT/FRS[*:1]="BB"' /tmp/4gcls0ICvB/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version -H -i'TXT0="text"' /tmp/4gcls0ICvB/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version -T /build/bcftools-TfJ6sU/bcftools-1.22/test/view.chrs.tab /tmp/4gcls0ICvB/view.chrs.vcf.gz .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob -T /build/bcftools-TfJ6sU/bcftools-1.22/test/view.chrs.tab /tmp/4gcls0ICvB/view.chrs.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version -i 'POS>=3062917' /tmp/4gcls0ICvB/filter.2.vcf.gz 1:3062917-3157410 .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob -i 'POS>=3062917' /tmp/4gcls0ICvB/filter.2.vcf.gz 1:3062917-3157410 | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version -H -r 1:10,1:12,1:10 /tmp/4gcls0ICvB/idx.1.vcf.gz .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version -H -r 1:1172777-1172804,1:1172806-1172808 /tmp/4gcls0ICvB/idx.2.vcf.gz .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version -H -R /build/bcftools-TfJ6sU/bcftools-1.22/test/idx.2.bed /tmp/4gcls0ICvB/idx.2.vcf.gz .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version -H -R /build/bcftools-TfJ6sU/bcftools-1.22/test/idx.3.bed /tmp/4gcls0ICvB/idx.3.vcf.gz .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version -H -R /build/bcftools-TfJ6sU/bcftools-1.22/test/idx.4.bed /tmp/4gcls0ICvB/idx.4.vcf.gz .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version -Ht 2 /tmp/4gcls0ICvB/view-t.vcf.gz .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version -Ht 3 /tmp/4gcls0ICvB/view-t.vcf.gz .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 0 /tmp/4gcls0ICvB/overlap.vcf.gz .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 1 /tmp/4gcls0ICvB/overlap.vcf.gz .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 2 /tmp/4gcls0ICvB/overlap.vcf.gz .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 0 /tmp/4gcls0ICvB/overlap.vcf.gz .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 1 /tmp/4gcls0ICvB/overlap.vcf.gz .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 2 /tmp/4gcls0ICvB/overlap.vcf.gz .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 0 /tmp/4gcls0ICvB/overlap.vcf.gz .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 1 /tmp/4gcls0ICvB/overlap.vcf.gz .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 2 /tmp/4gcls0ICvB/overlap.vcf.gz .. ok test_vcf_64bit: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view /build/bcftools-TfJ6sU/bcftools-1.22/test/view64bit.1.vcf -H .. ok test_vcf_64bit: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view /build/bcftools-TfJ6sU/bcftools-1.22/test/view64bit.1.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view /build/bcftools-TfJ6sU/bcftools-1.22/test/view64bit.1.vcf -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view /build/bcftools-TfJ6sU/bcftools-1.22/test/view64bit.2.vcf -H .. ok test_vcf_64bit: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view /build/bcftools-TfJ6sU/bcftools-1.22/test/view64bit.2.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view /build/bcftools-TfJ6sU/bcftools-1.22/test/view64bit.2.vcf -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view /build/bcftools-TfJ6sU/bcftools-1.22/test/view64bit.3.vcf -H .. ok test_vcf_64bit: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view /build/bcftools-TfJ6sU/bcftools-1.22/test/view64bit.3.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view /build/bcftools-TfJ6sU/bcftools-1.22/test/view64bit.4.vcf -H .. ok test_vcf_64bit: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view /build/bcftools-TfJ6sU/bcftools-1.22/test/view64bit.4.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view /build/bcftools-TfJ6sU/bcftools-1.22/test/view64bit.4.vcf -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view /build/bcftools-TfJ6sU/bcftools-1.22/test/view64bit.5.vcf -H .. ok test_vcf_64bit: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view /build/bcftools-TfJ6sU/bcftools-1.22/test/view64bit.5.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view /build/bcftools-TfJ6sU/bcftools-1.22/test/view64bit.5.vcf -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -H .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version -H -C5:nonmajor /tmp/4gcls0ICvB/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version -H -c6:nonmajor /tmp/4gcls0ICvB/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version -H -q0.3:major /tmp/4gcls0ICvB/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/4gcls0ICvB/view.filter.annovar.vcf.gz .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version -H -i 'Gene.refGene~"NOD"' /tmp/4gcls0ICvB/view.filter.annovar.vcf.gz .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version -H -i 'LJB2_MutationTaster=="0.291000"' /tmp/4gcls0ICvB/view.filter.annovar.vcf.gz .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version -H -a /tmp/4gcls0ICvB/view-a.vcf.gz .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version -T /build/bcftools-TfJ6sU/bcftools-1.22/test/view.sites.txt /tmp/4gcls0ICvB/view.sites.vcf.gz .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob -T /build/bcftools-TfJ6sU/bcftools-1.22/test/view.sites.txt /tmp/4gcls0ICvB/view.sites.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version -T /build/bcftools-TfJ6sU/bcftools-1.22/test/view.sites.txt.gz /tmp/4gcls0ICvB/view.sites.vcf.gz .. ok test_vcf_view: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob -T /build/bcftools-TfJ6sU/bcftools-1.22/test/view.sites.txt.gz /tmp/4gcls0ICvB/view.sites.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_head: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools head /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.2.vcf .. ok test_vcf_head: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools head -h 0 /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.2.vcf .. ok test_vcf_head: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools head -h 1 /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.2.vcf .. ok test_vcf_head: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools head -h 5 /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.2.vcf .. ok test_vcf_head: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools head -h 22 /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.2.vcf .. ok test_vcf_head: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools head -h 23 /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.2.vcf .. ok test_vcf_head: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools head -n 0 /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.2.vcf .. ok test_vcf_head: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools head -n 1 /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.2.vcf .. ok test_vcf_head: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools head -n 5 /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.2.vcf .. ok test_vcf_head: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools head -h 5 -n 5 < /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.2.vcf .. ok test_vcf_head2: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools head -s0 /tmp/4gcls0ICvB/mpileup.2.vcf.gz .. ok test_vcf_head2: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version -Ob /tmp/4gcls0ICvB/mpileup.2.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools head -s0 .. ok test_vcf_head2: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools head -s1 /tmp/4gcls0ICvB/mpileup.2.vcf.gz .. ok test_vcf_head2: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version -Ob /tmp/4gcls0ICvB/mpileup.2.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools head -s1 .. ok test_vcf_head2: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools head -s2 -h2 /tmp/4gcls0ICvB/mpileup.2.vcf.gz .. ok test_vcf_head2: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version -Ob /tmp/4gcls0ICvB/mpileup.2.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools head -s2 -h2 .. ok test_vcf_call: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call --no-version -m -s sample1 /build/bcftools-TfJ6sU/bcftools-1.22/test/samples.vcf .. ok test_vcf_call: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call -Ob -m -s sample1 /build/bcftools-TfJ6sU/bcftools-1.22/test/samples.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call --no-version -m -s ^sample2,sample3 /build/bcftools-TfJ6sU/bcftools-1.22/test/samples.vcf .. ok test_vcf_call: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call -Ob -m -s ^sample2,sample3 /build/bcftools-TfJ6sU/bcftools-1.22/test/samples.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call --no-version -m -s sample3 /build/bcftools-TfJ6sU/bcftools-1.22/test/samples.vcf .. ok test_vcf_call: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call -Ob -m -s sample3 /build/bcftools-TfJ6sU/bcftools-1.22/test/samples.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call --no-version -m -s ^sample1,sample2 /build/bcftools-TfJ6sU/bcftools-1.22/test/samples.vcf .. ok test_vcf_call: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call -Ob -m -s ^sample1,sample2 /build/bcftools-TfJ6sU/bcftools-1.22/test/samples.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call --no-version -m --ploidy-file /build/bcftools-TfJ6sU/bcftools-1.22/test/call-ploidy.1.txt -S /build/bcftools-TfJ6sU/bcftools-1.22/test/call-ploidy.1.ped /build/bcftools-TfJ6sU/bcftools-1.22/test/call-ploidy.1.vcf .. ok test_vcf_call: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call -Ob -m --ploidy-file /build/bcftools-TfJ6sU/bcftools-1.22/test/call-ploidy.1.txt -S /build/bcftools-TfJ6sU/bcftools-1.22/test/call-ploidy.1.ped /build/bcftools-TfJ6sU/bcftools-1.22/test/call-ploidy.1.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call --no-version -mv /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.vcf .. ok test_vcf_call: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call -Ob -mv /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call --no-version -mg0 /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.vcf .. ok test_vcf_call: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call -Ob -mg0 /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call --no-version -mv -S /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.3.samples /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.vcf .. ok test_vcf_call: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call -Ob -mv -S /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.3.samples /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call --no-version -mv -S /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.4.samples /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.vcf .. ok test_vcf_call: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call -Ob -mv -S /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.4.samples /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call --no-version -mv -S /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.5.samples /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.vcf .. ok test_vcf_call: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call -Ob -mv -S /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.5.samples /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call --no-version -mv --ploidy-file /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.ploidy -S /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.samples /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.X.vcf .. ok test_vcf_call: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call -Ob -mv --ploidy-file /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.ploidy -S /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.samples /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.X.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call --no-version -mv --ploidy-file /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.ploidy -S /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.ped /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.X.vcf .. ok test_vcf_call: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call -Ob -mv --ploidy-file /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.ploidy -S /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.ped /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.X.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call --no-version -mv --ploidy-file /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.ploidy -S /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.2.samples /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.X.vcf .. ok test_vcf_call: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call -Ob -mv --ploidy-file /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.ploidy -S /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.2.samples /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.X.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call --no-version -mv /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.NA19213.NA19129.vcf .. ok test_vcf_call: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call -Ob -mv /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.NA19213.NA19129.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call --no-version -mv -G - --group-samples-tag AD /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.NA19213.NA19129.vcf .. ok test_vcf_call: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call -Ob -mv -G - --group-samples-tag AD /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.NA19213.NA19129.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call --no-version -mv /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.hwe.vcf .. ok test_vcf_call: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call -Ob -mv /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.hwe.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call --no-version -mv -G - --group-samples-tag AD /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.hwe.vcf .. ok test_vcf_call: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call -Ob -mv -G - --group-samples-tag AD /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.hwe.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call --no-version -mv -G /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.hwe.samples --group-samples-tag AD /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.hwe.vcf .. ok test_vcf_call: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call -Ob -mv -G /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.hwe.samples --group-samples-tag AD /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.hwe.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call --no-version -mA -C alleles -T /tmp/4gcls0ICvB/mpileup.tab.gz /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.vcf .. ok test_vcf_call_cAls: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call -Ob -mA -C alleles -T /tmp/4gcls0ICvB/mpileup.tab.gz /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call --no-version -mA -C alleles -T /tmp/4gcls0ICvB/mpileup.2.tab.gz /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.2.vcf .. ok test_vcf_call_cAls: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call -Ob -mA -C alleles -T /tmp/4gcls0ICvB/mpileup.2.tab.gz /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.2.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call --no-version -mA -C alleles -T /tmp/4gcls0ICvB/mpileup.3.tab.gz -i /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call -Ob -mA -C alleles -T /tmp/4gcls0ICvB/mpileup.3.tab.gz -i /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.3.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call --no-version -mA -C alleles -T /tmp/4gcls0ICvB/mpileup.4.tab.gz -i /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call -Ob -mA -C alleles -T /tmp/4gcls0ICvB/mpileup.4.tab.gz -i /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.3.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call --no-version -mA -C alleles -T /tmp/4gcls0ICvB/mpileup.5.tab.gz -i /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call -Ob -mA -C alleles -T /tmp/4gcls0ICvB/mpileup.5.tab.gz -i /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.3.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call --no-version -mA -C alleles -T /tmp/4gcls0ICvB/mpileup.6.tab.gz -i /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.4.vcf .. ok test_vcf_call_cAls: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call -Ob -mA -C alleles -T /tmp/4gcls0ICvB/mpileup.6.tab.gz -i /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.4.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call --no-version -mA -C alleles -T /tmp/4gcls0ICvB/mpileup.7.tab.gz -i /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.5.vcf .. ok test_vcf_call_cAls: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call -Ob -mA -C alleles -T /tmp/4gcls0ICvB/mpileup.7.tab.gz -i /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.5.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call --no-version -mA -C alleles -T /tmp/4gcls0ICvB/mpileup.cals.1.tab.gz /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.cals.1.vcf .. ok test_vcf_call_cAls: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call -Ob -mA -C alleles -T /tmp/4gcls0ICvB/mpileup.cals.1.tab.gz /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.cals.1.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call --no-version -mA -C alleles -T /tmp/4gcls0ICvB/mpileup.cals.2.tab.gz /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.cals.2.vcf .. ok test_vcf_call_cAls: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call -Ob -mA -C alleles -T /tmp/4gcls0ICvB/mpileup.cals.2.tab.gz /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.cals.2.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call --no-version -cv /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.c.vcf .. ok test_vcf_call: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call -Ob -cv /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.c.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call --no-version -cv --ploidy-file /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.ploidy -S /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.samples /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.c.X.vcf .. ok test_vcf_call: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call -Ob -cv --ploidy-file /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.ploidy -S /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.samples /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.c.X.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call --no-version -cv --ploidy-file /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.ploidy -S /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.ped /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.c.X.vcf .. ok test_vcf_call: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call -Ob -cv --ploidy-file /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.ploidy -S /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.ped /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.c.X.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call --no-version -cv --ploidy-file /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.ploidy -S /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.2.samples /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.c.X.vcf .. ok test_vcf_call: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call -Ob -cv --ploidy-file /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.ploidy -S /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.2.samples /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup.c.X.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call --no-version -mv /build/bcftools-TfJ6sU/bcftools-1.22/test/call-G.vcf .. ok test_vcf_call: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call -Ob -mv /build/bcftools-TfJ6sU/bcftools-1.22/test/call-G.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call --no-version -mv -G - --group-samples-tag AD /build/bcftools-TfJ6sU/bcftools-1.22/test/call-G.vcf .. ok test_vcf_call: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call -Ob -mv -G - --group-samples-tag AD /build/bcftools-TfJ6sU/bcftools-1.22/test/call-G.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call --no-version -mv -F AN_POP,AC_POP /build/bcftools-TfJ6sU/bcftools-1.22/test/call-G.2.vcf .. ok test_vcf_call: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call -Ob -mv -F AN_POP,AC_POP /build/bcftools-TfJ6sU/bcftools-1.22/test/call-G.2.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call --no-version -m /build/bcftools-TfJ6sU/bcftools-1.22/test/call.af-fixation.vcf .. ok test_vcf_call: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call -Ob -m /build/bcftools-TfJ6sU/bcftools-1.22/test/call.af-fixation.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call --no-version -m -G /build/bcftools-TfJ6sU/bcftools-1.22/test/call.af-fixation.txt /build/bcftools-TfJ6sU/bcftools-1.22/test/call.af-fixation.vcf .. ok test_vcf_call: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call -Ob -m -G /build/bcftools-TfJ6sU/bcftools-1.22/test/call.af-fixation.txt /build/bcftools-TfJ6sU/bcftools-1.22/test/call.af-fixation.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call --no-version -m -G /build/bcftools-TfJ6sU/bcftools-1.22/test/call.af-fixation.txt -a GP,GQ /build/bcftools-TfJ6sU/bcftools-1.22/test/call.af-fixation.vcf .. ok test_vcf_call: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools call -Ob -m -G /build/bcftools-TfJ6sU/bcftools-1.22/test/call.af-fixation.txt -a GP,GQ /build/bcftools-TfJ6sU/bcftools-1.22/test/call.af-fixation.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -S. -e'TXT0="text"' /build/bcftools-TfJ6sU/bcftools-1.22/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -S. -e'TXT0="text"' /build/bcftools-TfJ6sU/bcftools-1.22/test/view.filter.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -S. -e'FMT/FRS[*:1]="BB"' /build/bcftools-TfJ6sU/bcftools-1.22/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -S. -e'FMT/FRS[*:1]="BB"' /build/bcftools-TfJ6sU/bcftools-1.22/test/view.filter.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -S. -e'FMT/FGS[*:0]="AAAAAA"' /build/bcftools-TfJ6sU/bcftools-1.22/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -S. -e'FMT/FGS[*:0]="AAAAAA"' /build/bcftools-TfJ6sU/bcftools-1.22/test/view.filter.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -S. -e'FMT/FGS[*:1]="BBB"' /build/bcftools-TfJ6sU/bcftools-1.22/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -S. -e'FMT/FGS[*:1]="BBB"' /build/bcftools-TfJ6sU/bcftools-1.22/test/view.filter.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -S. -e'FMT/FGS[*:4]="EE"' /build/bcftools-TfJ6sU/bcftools-1.22/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -S. -e'FMT/FGS[*:4]="EE"' /build/bcftools-TfJ6sU/bcftools-1.22/test/view.filter.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -S. -e'FMT/STR="XX"' /build/bcftools-TfJ6sU/bcftools-1.22/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -S. -e'FMT/STR="XX"' /build/bcftools-TfJ6sU/bcftools-1.22/test/view.filter.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -S. -e'FMT/FILTER="aaa"' /build/bcftools-TfJ6sU/bcftools-1.22/test/view.filter.2.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -S. -e'FMT/FILTER="aaa"' /build/bcftools-TfJ6sU/bcftools-1.22/test/view.filter.2.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -mx -g2 -G2 /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -mx -g2 -G2 /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.1.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.2.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.2.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -e'INFO/DP=19' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.3.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -e'INFO/DP=19' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.3.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -e'INFO/DP=19' -s XX /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.3.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -e'INFO/DP=19' -s XX /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.3.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -e'INFO/DP=19' -s XX -m+ /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.3.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+ /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.3.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -e'INFO/DP=19' -s XX -mx /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.3.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -e'INFO/DP=19' -s XX -mx /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.3.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -e'INFO/DP=19' -s XX -m+x /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.3.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+x /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.3.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -e'FMT/GT="0/2"' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.3.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -e'FMT/GT="0/2"' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.3.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -e'FMT/GT="0/2"' -s XX /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.3.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.3.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -e'FMT/GT="0/2"' -s XX -m+ /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.3.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+ /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.3.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -e'FMT/GT="0/2"' -s XX -mx /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.3.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -mx /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.3.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -e'FMT/GT="0/2"' -s XX -m+x /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.3.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+x /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.3.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -i'FMT/GT="0/0" && AC[*]=2' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.2.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -i'FMT/GT="0/0" && AC[*]=2' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.2.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -i'AC[*]=2 && FMT/GT="0/0"' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.2.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -i'AC[*]=2 && FMT/GT="0/0"' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.2.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -i'ALT="."' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.2.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -i'ALT="."' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.2.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -S . -i 'FORMAT/TEST3<25' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.4.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -S . -i 'FORMAT/TEST3<25' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.4.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -S . -i 'FORMAT/TEST4<25' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.4.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -S . -i 'FORMAT/TEST4<25' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.4.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -i'GT="A"' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.2.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -i'GT="A"' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.2.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -i'GT="RR"' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.2.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -i'GT="RR"' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.2.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -i'GT="RA"' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.2.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -i'GT="RA"' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.2.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -i'GT="AR"' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.2.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -i'GT="AR"' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.2.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -i'GT="AA"' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.2.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -i'GT="AA"' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.2.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -i'GT="aA"' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.2.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -i'GT="aA"' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.2.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -i'GT="Aa"' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.2.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -i'GT="Aa"' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.2.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -i'GT="HOM"' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.2.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -i'GT="HOM"' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.2.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -i'GT="HET"' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.2.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -i'GT="HET"' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.2.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -i'GT="HAP"' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.2.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -i'GT="HAP"' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.2.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -i'AD[:1]=11' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.5.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -i'AD[:1]=11' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.5.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -i'AD[1:]=11' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.5.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -i'AD[1:]=11' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.5.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -i'FR[0:1]=11' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.5.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS[\t%FR]\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -i'FR[0:1]=11' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.5.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS[\t%FR]\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -i'AD[*]="."' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.5.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -i'AD[*]="."' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.5.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -i'AD[0:0]=="."' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.5.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -i'AD[0:0]=="."' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.5.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -i'AD[0:0]!="."' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.5.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -i'AD[0:0]!="."' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.5.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -i'QUAL=="."' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.5.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS\t%QUAL\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -i'QUAL=="."' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.5.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS\t%QUAL\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -i'N_PASS(DP>32)=1' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.2.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -i'N_PASS(DP>32)=1' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.2.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -i'F_PASS(DP>32)=0.5' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.2.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -i'F_PASS(DP>32)=0.5' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.2.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -i'F_MISSING>=1/5' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.6.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -i'F_MISSING>=1/5' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.6.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -i'F_MISSING>=0.2' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.6.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -i'F_MISSING>=0.2' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.6.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -i'F_PASS(GT=="mis")>=1/5' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.6.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -i'F_PASS(GT=="mis")>=1/5' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.6.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -i'F_PASS(GT=="mis")>=0.2' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.6.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -i'F_PASS(GT=="mis")>=0.2' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.6.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -mx -s + -g2:mnp,indel,other /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.7.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -mx -s + -g2:mnp,indel,other /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.7.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -S . -e 'FORMAT/AO==4' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -S . -e 'FORMAT/AO==4' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.8.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -S . -e 'MAX(FORMAT/AO[0:])==4' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -S . -e 'MAX(FORMAT/AO[0:])==4' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.8.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -S . -e 'MAX(FORMAT/AO)==4' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -S . -e 'MAX(FORMAT/AO)==4' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.8.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -S . -e 'MIN(FORMAT/AO[0:])==3' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO[0:])==3' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.8.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -S . -e 'MIN(FORMAT/AO)==2' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO)==2' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.8.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -S . -e 'MIN(FORMAT/AO[0:])==3' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO[0:])==3' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.8.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -S . -e 'AVG(FORMAT/AO[2:])==4' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -S . -e 'AVG(FORMAT/AO[2:])==4' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.8.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -S . -e 'MEDIAN(FORMAT/AO[2:])==4' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -S . -e 'MEDIAN(FORMAT/AO[2:])==4' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.8.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -S . -e 'STDEV(FORMAT/AO[0:])=0.5' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -S . -e 'STDEV(FORMAT/AO[0:])=0.5' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.8.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -S . -e 'SUM(FORMAT/AO[0:])=7' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -S . -e 'SUM(FORMAT/AO[0:])=7' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.8.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -S . -e 'SMPL_MAX(FORMAT/AO)==4' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -S . -e 'SMPL_MAX(FORMAT/AO)==4' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.8.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -S . -e 'sMIN(FORMAT/AO)==2' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -S . -e 'sMIN(FORMAT/AO)==2' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.8.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -S . -e 'ABS(sAVG(FORMAT/AO)-3.66666)<1e-5' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -S . -e 'ABS(sAVG(FORMAT/AO)-3.66666)<1e-5' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.8.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -S . -e 'sMEDIAN(FORMAT/AO)==4' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -S . -e 'sMEDIAN(FORMAT/AO)==4' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.8.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -S . -e 'ABS(sSTDEV(FORMAT/AO)-1.2472191)<1e-5' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -S . -e 'ABS(sSTDEV(FORMAT/AO)-1.2472191)<1e-5' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.8.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -S . -e 'sSUM(FORMAT/AO)==11' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -S . -e 'sSUM(FORMAT/AO)==11' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.8.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -i 'QUAL/FMT/AD==55' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.9.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -i 'QUAL/FMT/AD==55' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.9.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -i 'QUAL/INFO/AD==10' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.9.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -i 'QUAL/INFO/AD==10' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.9.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -S . -e 'ABS(SMPL_MAX(FORMAT/AO))=5' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -S . -e 'ABS(SMPL_MAX(FORMAT/AO))=5' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.8.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -S . -e 'PHRED(AO[1:])>-4' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -S . -e 'PHRED(AO[1:])>-4' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.8.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -S . -e 'ABS(AO[1:])==2' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -S . -e 'ABS(AO[1:])==2' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.8.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -i 'sum(AD[*]) > FORMAT/DP' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -i 'sum(AD[*]) > FORMAT/DP' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.10.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -i 'FORMAT/DP < sum(AD[*])' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -i 'FORMAT/DP < sum(AD[*])' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.10.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -i 'sum(AD[*]) < FORMAT/DP' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -i 'sum(AD[*]) < FORMAT/DP' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.10.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -i 'FORMAT/DP > sum(AD[*])' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob -i 'FORMAT/DP > sum(AD[*])' /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.10.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 0 /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 0 /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.1.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 1 /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 1 /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.1.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 2 /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 2 /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.1.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter --soft-filter xxx --mask ^2:1005-1008 /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools filter -Ob --soft-filter xxx --mask ^2:1005-1008 /build/bcftools-TfJ6sU/bcftools-1.22/test/filter.1.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_sort: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools sort -m 0 /build/bcftools-TfJ6sU/bcftools-1.22/test/sort.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools sort -Ob -m 0 /build/bcftools-TfJ6sU/bcftools-1.22/test/sort.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools sort -m 1000 /build/bcftools-TfJ6sU/bcftools-1.22/test/sort.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools sort -Ob -m 1000 /build/bcftools-TfJ6sU/bcftools-1.22/test/sort.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_regions: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /build/bcftools-TfJ6sU/bcftools-1.22/test/regions.tab /tmp/4gcls0ICvB/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/regions.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /build/bcftools-TfJ6sU/bcftools-1.22/test/regions.tab .. ok test_vcf_regions: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /build/bcftools-TfJ6sU/bcftools-1.22/test/regions.tab /tmp/4gcls0ICvB/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/4gcls0ICvB/regions.tab.gz /tmp/4gcls0ICvB/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/regions.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/4gcls0ICvB/regions.tab.gz .. ok test_vcf_regions: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/4gcls0ICvB/regions.tab.gz /tmp/4gcls0ICvB/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/4gcls0ICvB/regions.bed /tmp/4gcls0ICvB/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/regions.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/4gcls0ICvB/regions.bed .. ok test_vcf_regions: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/4gcls0ICvB/regions.bed /tmp/4gcls0ICvB/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/4gcls0ICvB/regions.bed.gz /tmp/4gcls0ICvB/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/regions.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/4gcls0ICvB/regions.bed.gz .. ok test_vcf_regions: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/4gcls0ICvB/regions.bed.gz /tmp/4gcls0ICvB/regions.vcf.gz .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annots35.vcf.gz -c CHROM,POS,~ID,REF,ALT,INFO/src /tmp/4gcls0ICvB/annotate35.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annots35.vcf.gz -c CHROM,POS,~ID,REF,ALT,INFO/src /tmp/4gcls0ICvB/annotate35.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annots35.tab.gz -c CHROM,POS,~ID,REF,ALT,dst:=src /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate35.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annots35.tab.gz -c CHROM,POS,~ID,REF,ALT,dst:=src /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate35.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annotate.escape.1.tab.gz -c CHROM,POS,ISTR,FMT/FSTR /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate.escape.1.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annotate.escape.1.tab.gz -c CHROM,POS,ISTR,FMT/FSTR /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate.escape.1.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annotate.match.1.tab.gz -c CHROM,POS,-,-,SCORE,~X,-,- -i'STR={X}' /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate.match.1.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annotate.match.1.tab.gz -c CHROM,POS,-,-,SCORE,~X,-,- -i'STR={X}' /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate.match.1.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annotate.match.1.tab.gz -c CHROM,POS,REF,ALT,SCORE,-,~X,- -i'INT={X}' /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate.match.1.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annotate.match.1.tab.gz -c CHROM,POS,REF,ALT,SCORE,-,~X,- -i'INT={X}' /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate.match.1.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annotate.match.1.tab.gz -c CHROM,POS,REF,ALT,SCORE,-,-,~X -i'FLT={X}' /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate.match.1.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annotate.match.1.tab.gz -c CHROM,POS,REF,ALT,SCORE,-,-,~X -i'FLT={X}' /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate.match.1.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annotate.tab.gz -h /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annotate.tab.gz -h /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annotate2.tab.gz -h /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate.hdr -c CHROM,POS,-,T_STR /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annotate2.tab.gz -h /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate.hdr -c CHROM,POS,-,T_STR /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annotate2.tab.gz -h /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate.hdr -c CHROM,FROM,TO,T_STR /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annotate2.tab.gz -h /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate.hdr -c CHROM,FROM,TO,T_STR /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/4gcls0ICvB/annotate.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/4gcls0ICvB/annotate.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/4gcls0ICvB/annotate2.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/4gcls0ICvB/annotate2.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/4gcls0ICvB/annotate2.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/4gcls0ICvB/annotate2.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/4gcls0ICvB/annotate2.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/4gcls0ICvB/annotate2.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/4gcls0ICvB/annotate2.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/4gcls0ICvB/annotate2.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/4gcls0ICvB/annotate2.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/4gcls0ICvB/annotate2.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate3.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate3.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -x FORMAT /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate3.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -x FORMAT /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate3.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annots4.vcf.gz -c +INFO /tmp/4gcls0ICvB/annotate4.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annots4.vcf.gz -c +INFO /tmp/4gcls0ICvB/annotate4.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annots4.tab.gz -h /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate4.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annots4.tab.gz -h /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate4.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annots10.tab.gz -h /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate10.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annots10.tab.gz -h /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate10.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/4gcls0ICvB/annotate2.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/4gcls0ICvB/annotate2.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate2.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate2.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/4gcls0ICvB/annotate2.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/4gcls0ICvB/annotate2.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/4gcls0ICvB/annotate2.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/4gcls0ICvB/annotate2.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/4gcls0ICvB/annotate2.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/4gcls0ICvB/annotate2.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annots11.vcf.gz -c FMT /tmp/4gcls0ICvB/annotate11.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annots11.vcf.gz -c FMT /tmp/4gcls0ICvB/annotate11.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annots2.vcf.gz -c FMT/newGT:=GT /tmp/4gcls0ICvB/annotate2.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annots2.vcf.gz -c FMT/newGT:=GT /tmp/4gcls0ICvB/annotate2.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annots12.vcf.gz -c FMT/GT:=newGT /tmp/4gcls0ICvB/annotate2.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annots12.vcf.gz -c FMT/GT:=newGT /tmp/4gcls0ICvB/annotate2.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annots13.tab.gz -h /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate13.hdr -c CHROM,BEG,END,ABC /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate13.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annots13.tab.gz -h /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate13.hdr -c CHROM,BEG,END,ABC /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate13.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annots13.tab.gz -h /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:append /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate13.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annots13.tab.gz -h /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:append /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate13.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annots13.tab.gz -h /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:unique /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate13.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annots13.tab.gz -h /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:unique /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate13.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -x FILTER/XX,INFO/XX --force /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate14.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -x FILTER/XX,INFO/XX --force /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate14.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annotate15.tab.gz -h /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate15.hdr -s SAMPLE1 -c CHROM,FROM,TO,FMT/FOO,BAR /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate15.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annotate15.tab.gz -h /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate15.hdr -s SAMPLE1 -c CHROM,FROM,TO,FMT/FOO,BAR /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate15.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annotate15.tab.gz -h /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate15.hdr -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate15.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annotate15.tab.gz -h /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate15.hdr -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate15.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annotate15.tab.gz -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR -H '##FORMAT=' -H '##INFO=' /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate15.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annotate15.tab.gz -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR -H '##FORMAT=' -H '##INFO=' /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate15.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -x FILTER /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate16.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -x FILTER /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate16.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate17.1.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate17.1.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate17.2.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate17.2.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annotate17.3.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate17.3.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annotate17.3.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate17.3.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/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-TfJ6sU/bcftools-1.22/test/annotate18.1.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/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-TfJ6sU/bcftools-1.22/test/annotate18.1.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/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-TfJ6sU/bcftools-1.22/test/annotate18.2.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/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-TfJ6sU/bcftools-1.22/test/annotate18.2.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/4gcls0ICvB/annotate19.dst.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/4gcls0ICvB/annotate19.dst.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/4gcls0ICvB/annotate19.dst.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/4gcls0ICvB/annotate19.dst.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/4gcls0ICvB/annotate19.dst.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/4gcls0ICvB/annotate19.dst.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -c INFO/FILTER:=FILTER /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate19.dst.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -c INFO/FILTER:=FILTER /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate19.dst.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER /tmp/4gcls0ICvB/annotate19.dst.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER /tmp/4gcls0ICvB/annotate19.dst.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER /tmp/4gcls0ICvB/annotate19.dst.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER /tmp/4gcls0ICvB/annotate19.dst.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER,FILTER /tmp/4gcls0ICvB/annotate19.dst.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER,FILTER /tmp/4gcls0ICvB/annotate19.dst.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=./FILTER /tmp/4gcls0ICvB/annotate19.dst.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=./FILTER /tmp/4gcls0ICvB/annotate19.dst.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annotate20.src.vcf.gz -c FMT/GT /tmp/4gcls0ICvB/annotate20.dst.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annotate20.src.vcf.gz -c FMT/GT /tmp/4gcls0ICvB/annotate20.dst.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annotate20.src.vcf.gz -c +FMT/GT /tmp/4gcls0ICvB/annotate20.dst.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annotate20.src.vcf.gz -c +FMT/GT /tmp/4gcls0ICvB/annotate20.dst.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annotate20.src.vcf.gz -c -FMT/GT /tmp/4gcls0ICvB/annotate20.dst.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annotate20.src.vcf.gz -c -FMT/GT /tmp/4gcls0ICvB/annotate20.dst.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annotate.multi.tab.gz -c CHROM,POS,REF,ALT,ANN -l ANN:append /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate.multi.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annotate.multi.tab.gz -c CHROM,POS,REF,ALT,ANN -l ANN:append /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate.multi.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/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-TfJ6sU/bcftools-1.22/test/annotate.missing-append.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/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-TfJ6sU/bcftools-1.22/test/annotate.missing-append.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate9.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate9.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate --rename-annots /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate21.txt /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate21.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob --rename-annots /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate21.txt /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate21.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/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-TfJ6sU/bcftools-1.22/test/annotate21.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/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-TfJ6sU/bcftools-1.22/test/annotate21.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/4gcls0ICvB/annotate22.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/4gcls0ICvB/annotate22.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annotate23.tab.gz -c CHROM,POS,~ID,REF,ALT,INFO/END /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate23.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annotate23.tab.gz -c CHROM,POS,~ID,REF,ALT,INFO/END /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate23.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annotate24.src.vcf.gz -c XX /tmp/4gcls0ICvB/annotate24.dst.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annotate24.src.vcf.gz -c XX /tmp/4gcls0ICvB/annotate24.dst.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annotate25.tab.gz -c CHROM,POS,ID,REF,ALT,~INFO/END /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate25.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annotate25.tab.gz -c CHROM,POS,ID,REF,ALT,~INFO/END /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate25.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annotate26.tab.gz -c CHROM,POS,-POS /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate26.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annotate26.tab.gz -c CHROM,POS,-POS /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate26.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,TSTR,TFLT,TINT /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate.missing.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,TSTR,TFLT,TINT /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate.missing.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.TSTR,.TFLT,.TINT /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate.missing.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.TSTR,.TFLT,.TINT /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate.missing.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.+TSTR,.+TFLT,.+TINT /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate.missing.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.+TSTR,.+TFLT,.+TINT /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate.missing.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,+TSTR,+TFLT,+TINT /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate.missing.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,+TSTR,+TFLT,+TINT /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate.missing.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.=TSTR,.=TFLT,.=TINT /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate.missing.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.=TSTR,.=TFLT,.=TINT /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate.missing.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,=TSTR,=TFLT,=TINT /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate.missing.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,=TSTR,=TFLT,=TINT /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate.missing.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate.olap.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate.olap.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique --min-overlap 0.4:0.5 -m XXX /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate.olap.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique --min-overlap 0.4:0.5 -m XXX /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate.olap.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annots.id.vcf.gz -c ALT /tmp/4gcls0ICvB/annotate.id.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annots.id.vcf.gz -c ALT /tmp/4gcls0ICvB/annotate.id.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annots.id.vcf.gz -c +ALT /tmp/4gcls0ICvB/annotate.id.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annots.id.vcf.gz -c +ALT /tmp/4gcls0ICvB/annotate.id.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annots.id.2.vcf.gz --pair-logic some -c +ID /tmp/4gcls0ICvB/annotate.id.2.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annots.id.2.vcf.gz --pair-logic some -c +ID /tmp/4gcls0ICvB/annotate.id.2.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annots.id.2.vcf.gz --pair-logic any -c +ID /tmp/4gcls0ICvB/annotate.id.2.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annots.id.2.vcf.gz --pair-logic any -c +ID /tmp/4gcls0ICvB/annotate.id.2.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annotate27.tab.gz -c CHROM,POS,REF,ALT,EVIDENCE /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate27.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annotate27.tab.gz -c CHROM,POS,REF,ALT,EVIDENCE /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate27.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1,smpl2 /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate28.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1,smpl2 /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate28.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2,smpl1 /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate28.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2,smpl1 /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate28.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1 /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate28.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1 /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate28.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2 /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate28.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2 /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate28.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -m XXX /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -m XXX /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annots34.tab.gz -c CHROM,FROM,TO,INFO/END -H '##INFO=' /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate34.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annots34.tab.gz -c CHROM,FROM,TO,INFO/END -H '##INFO=' /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate34.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -a /tmp/4gcls0ICvB/annots-mark.bed.gz -c CHROM,FROM,TO -m TAG /build/bcftools-TfJ6sU/bcftools-1.22/test/annots-mark.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate -Ob -a /tmp/4gcls0ICvB/annots-mark.bed.gz -c CHROM,FROM,TO -m TAG /build/bcftools-TfJ6sU/bcftools-1.22/test/annots-mark.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools concat --no-version -G /tmp/4gcls0ICvB/concat.1.a.vcf.gz /tmp/4gcls0ICvB/concat.1.b.vcf.gz .. ok test_vcf_concat: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools concat -Ob -G /tmp/4gcls0ICvB/concat.1.a.vcf.gz /tmp/4gcls0ICvB/concat.1.b.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools concat --no-version -G /build/bcftools-TfJ6sU/bcftools-1.22/test/concat.1.a.vcf /build/bcftools-TfJ6sU/bcftools-1.22/test/concat.1.b.vcf .. ok test_vcf_concat: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools concat --no-version /tmp/4gcls0ICvB/concat.1.a.vcf.gz /tmp/4gcls0ICvB/concat.1.b.vcf.gz .. ok test_vcf_concat: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools concat -Ob /tmp/4gcls0ICvB/concat.1.a.vcf.gz /tmp/4gcls0ICvB/concat.1.b.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools concat --no-version /build/bcftools-TfJ6sU/bcftools-1.22/test/concat.1.a.vcf /build/bcftools-TfJ6sU/bcftools-1.22/test/concat.1.b.vcf .. ok test_vcf_concat: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools concat --no-version /tmp/4gcls0ICvB/concat.1.a.bcf /tmp/4gcls0ICvB/concat.1.b.bcf .. ok test_vcf_concat: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools concat -Ob /tmp/4gcls0ICvB/concat.1.a.bcf /tmp/4gcls0ICvB/concat.1.b.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools concat --no-version -a /tmp/4gcls0ICvB/concat.2.a.vcf.gz /tmp/4gcls0ICvB/concat.2.b.vcf.gz .. ok test_vcf_concat: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools concat -Ob -a /tmp/4gcls0ICvB/concat.2.a.vcf.gz /tmp/4gcls0ICvB/concat.2.b.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools concat --no-version -a /tmp/4gcls0ICvB/concat.2.a.bcf /tmp/4gcls0ICvB/concat.2.b.bcf .. ok test_vcf_concat: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools concat -Ob -a /tmp/4gcls0ICvB/concat.2.a.bcf /tmp/4gcls0ICvB/concat.2.b.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools concat --no-version -aD /tmp/4gcls0ICvB/concat.2.a.vcf.gz /tmp/4gcls0ICvB/concat.2.b.vcf.gz .. ok test_vcf_concat: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools concat -Ob -aD /tmp/4gcls0ICvB/concat.2.a.vcf.gz /tmp/4gcls0ICvB/concat.2.b.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools concat --no-version -aD /tmp/4gcls0ICvB/concat.2.a.bcf /tmp/4gcls0ICvB/concat.2.b.bcf .. ok test_vcf_concat: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools concat -Ob -aD /tmp/4gcls0ICvB/concat.2.a.bcf /tmp/4gcls0ICvB/concat.2.b.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools concat --no-version -l --ligate-warn /tmp/4gcls0ICvB/concat.3.a.vcf.gz /tmp/4gcls0ICvB/concat.3.b.vcf.gz /tmp/4gcls0ICvB/concat.3.0.vcf.gz /tmp/4gcls0ICvB/concat.3.c.vcf.gz /tmp/4gcls0ICvB/concat.3.d.vcf.gz /tmp/4gcls0ICvB/concat.3.e.vcf.gz /tmp/4gcls0ICvB/concat.3.f.vcf.gz .. ok test_vcf_concat: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools concat -Ob -l --ligate-warn /tmp/4gcls0ICvB/concat.3.a.vcf.gz /tmp/4gcls0ICvB/concat.3.b.vcf.gz /tmp/4gcls0ICvB/concat.3.0.vcf.gz /tmp/4gcls0ICvB/concat.3.c.vcf.gz /tmp/4gcls0ICvB/concat.3.d.vcf.gz /tmp/4gcls0ICvB/concat.3.e.vcf.gz /tmp/4gcls0ICvB/concat.3.f.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools concat --no-version -l --ligate-warn /tmp/4gcls0ICvB/concat.3.a.bcf /tmp/4gcls0ICvB/concat.3.b.bcf /tmp/4gcls0ICvB/concat.3.0.bcf /tmp/4gcls0ICvB/concat.3.c.bcf /tmp/4gcls0ICvB/concat.3.d.bcf /tmp/4gcls0ICvB/concat.3.e.bcf /tmp/4gcls0ICvB/concat.3.f.bcf .. ok test_vcf_concat: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools concat -Ob -l --ligate-warn /tmp/4gcls0ICvB/concat.3.a.bcf /tmp/4gcls0ICvB/concat.3.b.bcf /tmp/4gcls0ICvB/concat.3.0.bcf /tmp/4gcls0ICvB/concat.3.c.bcf /tmp/4gcls0ICvB/concat.3.d.bcf /tmp/4gcls0ICvB/concat.3.e.bcf /tmp/4gcls0ICvB/concat.3.f.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ Random seed for test_naive_concat: 16163745327930597982 .. ok test_naive_concat: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools concat --naive-force /tmp/4gcls0ICvB/naive_concat.0.bcf /tmp/4gcls0ICvB/naive_concat.1.bcf /tmp/4gcls0ICvB/naive_concat.2.bcf /tmp/4gcls0ICvB/naive_concat.3.bcf /tmp/4gcls0ICvB/naive_concat.4.bcf /tmp/4gcls0ICvB/naive_concat.5.bcf /tmp/4gcls0ICvB/naive_concat.6.bcf /tmp/4gcls0ICvB/naive_concat.7.bcf /tmp/4gcls0ICvB/naive_concat.8.bcf /tmp/4gcls0ICvB/naive_concat.9.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -H .. ok test_naive_concat: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools concat --naive /tmp/4gcls0ICvB/naive_concat.0.vcf.gz /tmp/4gcls0ICvB/naive_concat.1.vcf.gz /tmp/4gcls0ICvB/naive_concat.2.vcf.gz /tmp/4gcls0ICvB/naive_concat.3.vcf.gz /tmp/4gcls0ICvB/naive_concat.4.vcf.gz /tmp/4gcls0ICvB/naive_concat.5.vcf.gz /tmp/4gcls0ICvB/naive_concat.6.vcf.gz /tmp/4gcls0ICvB/naive_concat.7.vcf.gz /tmp/4gcls0ICvB/naive_concat.8.vcf.gz /tmp/4gcls0ICvB/naive_concat.9.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -H .. ok test_vcf_concat: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools concat --no-version -l /tmp/4gcls0ICvB/concat.4.a.vcf.gz /tmp/4gcls0ICvB/concat.4.b.vcf.gz .. ok test_vcf_concat: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools concat -Ob -l /tmp/4gcls0ICvB/concat.4.a.vcf.gz /tmp/4gcls0ICvB/concat.4.b.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools concat --no-version -l /tmp/4gcls0ICvB/concat.4.a.bcf /tmp/4gcls0ICvB/concat.4.b.bcf .. ok test_vcf_concat: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools concat -Ob -l /tmp/4gcls0ICvB/concat.4.a.bcf /tmp/4gcls0ICvB/concat.4.b.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools concat --no-version -l --ligate-warn /tmp/4gcls0ICvB/concat.5.a.vcf.gz /tmp/4gcls0ICvB/concat.5.b.vcf.gz /tmp/4gcls0ICvB/concat.5.c.vcf.gz .. ok test_vcf_concat: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools concat -Ob -l --ligate-warn /tmp/4gcls0ICvB/concat.5.a.vcf.gz /tmp/4gcls0ICvB/concat.5.b.vcf.gz /tmp/4gcls0ICvB/concat.5.c.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools concat --no-version -l --ligate-warn /tmp/4gcls0ICvB/concat.5.a.bcf /tmp/4gcls0ICvB/concat.5.b.bcf /tmp/4gcls0ICvB/concat.5.c.bcf .. ok test_vcf_concat: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools concat -Ob -l --ligate-warn /tmp/4gcls0ICvB/concat.5.a.bcf /tmp/4gcls0ICvB/concat.5.b.bcf /tmp/4gcls0ICvB/concat.5.c.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools concat --no-version -l --ligate-force /tmp/4gcls0ICvB/concat.5.a.bcf /tmp/4gcls0ICvB/concat.5.b.bcf /tmp/4gcls0ICvB/concat.5.c.bcf .. ok test_vcf_concat: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools concat -Ob -l --ligate-force /tmp/4gcls0ICvB/concat.5.a.bcf /tmp/4gcls0ICvB/concat.5.b.bcf /tmp/4gcls0ICvB/concat.5.c.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools concat --no-version -G -a -D /tmp/4gcls0ICvB/concat.5.a.vcf.gz /tmp/4gcls0ICvB/concat.5.b.vcf.gz /tmp/4gcls0ICvB/concat.5.c.vcf.gz .. ok test_vcf_concat: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools concat -Ob -G -a -D /tmp/4gcls0ICvB/concat.5.a.vcf.gz /tmp/4gcls0ICvB/concat.5.b.vcf.gz /tmp/4gcls0ICvB/concat.5.c.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools concat --no-version -G -a -D /tmp/4gcls0ICvB/concat.5.a.bcf /tmp/4gcls0ICvB/concat.5.b.bcf /tmp/4gcls0ICvB/concat.5.c.bcf .. ok test_vcf_concat: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools concat -Ob -G -a -D /tmp/4gcls0ICvB/concat.5.a.bcf /tmp/4gcls0ICvB/concat.5.b.bcf /tmp/4gcls0ICvB/concat.5.c.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_reheader: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools reheader -h /build/bcftools-TfJ6sU/bcftools-1.22/test/reheader.hdr /build/bcftools-TfJ6sU/bcftools-1.22/test/reheader.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-TfJ6sU/bcftools-1.22/test/reheader.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools reheader -h /build/bcftools-TfJ6sU/bcftools-1.22/test/reheader.hdr | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools reheader -h /build/bcftools-TfJ6sU/bcftools-1.22/test/reheader.hdr /tmp/4gcls0ICvB/reheader.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/4gcls0ICvB/reheader.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools reheader -h /build/bcftools-TfJ6sU/bcftools-1.22/test/reheader.hdr | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools reheader -h /build/bcftools-TfJ6sU/bcftools-1.22/test/reheader.hdr /tmp/4gcls0ICvB/reheader.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/4gcls0ICvB/reheader.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools reheader -h /build/bcftools-TfJ6sU/bcftools-1.22/test/reheader.hdr | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools reheader -s /build/bcftools-TfJ6sU/bcftools-1.22/test/reheader.samples /build/bcftools-TfJ6sU/bcftools-1.22/test/reheader.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-TfJ6sU/bcftools-1.22/test/reheader.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools reheader -s /build/bcftools-TfJ6sU/bcftools-1.22/test/reheader.samples | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools reheader -s /build/bcftools-TfJ6sU/bcftools-1.22/test/reheader.samples /tmp/4gcls0ICvB/reheader.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/4gcls0ICvB/reheader.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools reheader -s /build/bcftools-TfJ6sU/bcftools-1.22/test/reheader.samples | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools reheader -s /build/bcftools-TfJ6sU/bcftools-1.22/test/reheader.samples /tmp/4gcls0ICvB/reheader.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/4gcls0ICvB/reheader.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools reheader -s /build/bcftools-TfJ6sU/bcftools-1.22/test/reheader.samples | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools reheader -s /build/bcftools-TfJ6sU/bcftools-1.22/test/reheader.samples2 /build/bcftools-TfJ6sU/bcftools-1.22/test/reheader.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-TfJ6sU/bcftools-1.22/test/reheader.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools reheader -s /build/bcftools-TfJ6sU/bcftools-1.22/test/reheader.samples2 | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools reheader -s /build/bcftools-TfJ6sU/bcftools-1.22/test/reheader.samples2 /tmp/4gcls0ICvB/reheader.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/4gcls0ICvB/reheader.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools reheader -s /build/bcftools-TfJ6sU/bcftools-1.22/test/reheader.samples2 | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools reheader -s /build/bcftools-TfJ6sU/bcftools-1.22/test/reheader.samples2 /tmp/4gcls0ICvB/reheader.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/4gcls0ICvB/reheader.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools reheader -s /build/bcftools-TfJ6sU/bcftools-1.22/test/reheader.samples2 | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools reheader -s /build/bcftools-TfJ6sU/bcftools-1.22/test/reheader.samples3 /build/bcftools-TfJ6sU/bcftools-1.22/test/reheader.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-TfJ6sU/bcftools-1.22/test/reheader.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools reheader -s /build/bcftools-TfJ6sU/bcftools-1.22/test/reheader.samples3 | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools reheader -s /build/bcftools-TfJ6sU/bcftools-1.22/test/reheader.samples3 /tmp/4gcls0ICvB/reheader.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/4gcls0ICvB/reheader.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools reheader -s /build/bcftools-TfJ6sU/bcftools-1.22/test/reheader.samples3 | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools reheader -s /build/bcftools-TfJ6sU/bcftools-1.22/test/reheader.samples3 /tmp/4gcls0ICvB/reheader.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/4gcls0ICvB/reheader.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools reheader -s /build/bcftools-TfJ6sU/bcftools-1.22/test/reheader.samples3 | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools reheader -s /build/bcftools-TfJ6sU/bcftools-1.22/test/reheader.samples4 /build/bcftools-TfJ6sU/bcftools-1.22/test/reheader.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-TfJ6sU/bcftools-1.22/test/reheader.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools reheader -s /build/bcftools-TfJ6sU/bcftools-1.22/test/reheader.samples4 | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools reheader -s /build/bcftools-TfJ6sU/bcftools-1.22/test/reheader.samples4 /tmp/4gcls0ICvB/reheader.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/4gcls0ICvB/reheader.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools reheader -s /build/bcftools-TfJ6sU/bcftools-1.22/test/reheader.samples4 | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools reheader -s /build/bcftools-TfJ6sU/bcftools-1.22/test/reheader.samples4 /tmp/4gcls0ICvB/reheader.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/4gcls0ICvB/reheader.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools reheader -s /build/bcftools-TfJ6sU/bcftools-1.22/test/reheader.samples4 | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools reheader -h /build/bcftools-TfJ6sU/bcftools-1.22/test/reheader.empty.hdr /build/bcftools-TfJ6sU/bcftools-1.22/test/empty.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-TfJ6sU/bcftools-1.22/test/empty.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools reheader -h /build/bcftools-TfJ6sU/bcftools-1.22/test/reheader.empty.hdr | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools reheader -h /build/bcftools-TfJ6sU/bcftools-1.22/test/reheader.empty.hdr /tmp/4gcls0ICvB/empty.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/4gcls0ICvB/empty.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools reheader -h /build/bcftools-TfJ6sU/bcftools-1.22/test/reheader.empty.hdr | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools reheader -h /build/bcftools-TfJ6sU/bcftools-1.22/test/reheader.empty.hdr /tmp/4gcls0ICvB/empty.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/4gcls0ICvB/empty.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools reheader -h /build/bcftools-TfJ6sU/bcftools-1.22/test/reheader.empty.hdr | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools reheader -f /build/bcftools-TfJ6sU/bcftools-1.22/test/reheader.fai /build/bcftools-TfJ6sU/bcftools-1.22/test/reheader.2.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools reheader -f /build/bcftools-TfJ6sU/bcftools-1.22/test/reheader.fai /tmp/4gcls0ICvB/reheader.2.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools reheader -f /build/bcftools-TfJ6sU/bcftools-1.22/test/reheader.fai /tmp/4gcls0ICvB/reheader.2.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools reheader -h /build/bcftools-TfJ6sU/bcftools-1.22/test/reheader.2.hdr -f /build/bcftools-TfJ6sU/bcftools-1.22/test/reheader.fai /build/bcftools-TfJ6sU/bcftools-1.22/test/reheader.2.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools reheader -h /build/bcftools-TfJ6sU/bcftools-1.22/test/reheader.2.hdr -f /build/bcftools-TfJ6sU/bcftools-1.22/test/reheader.fai /tmp/4gcls0ICvB/reheader.2.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools reheader -h /build/bcftools-TfJ6sU/bcftools-1.22/test/reheader.2.hdr -f /build/bcftools-TfJ6sU/bcftools-1.22/test/reheader.fai /tmp/4gcls0ICvB/reheader.2.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools reheader -f /build/bcftools-TfJ6sU/bcftools-1.22/test/reheader.3.fai /build/bcftools-TfJ6sU/bcftools-1.22/test/reheader.3.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools reheader -f /build/bcftools-TfJ6sU/bcftools-1.22/test/reheader.3.fai /tmp/4gcls0ICvB/reheader.3.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools reheader -f /build/bcftools-TfJ6sU/bcftools-1.22/test/reheader.3.fai /tmp/4gcls0ICvB/reheader.3.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version .. ok test_rename_chrs: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate --rename-chrs /tmp/4gcls0ICvB/rename.map -Ov /tmp/4gcls0ICvB/annotate.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate --rename-chrs /tmp/4gcls0ICvB/rename.map -Ob /tmp/4gcls0ICvB/annotate.bcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate --rename-chrs /tmp/4gcls0ICvB/rename.map -Ov /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools annotate --rename-chrs /tmp/4gcls0ICvB/rename.map -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/annotate.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%CHROM\t%POS\n' .. ok test_vcf_convert: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools convert -g -,. /tmp/4gcls0ICvB/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/convert.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools convert -g -,. .. ok test_vcf_convert: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools convert -g -,. --vcf-ids /tmp/4gcls0ICvB/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/convert.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools convert -g -,. --vcf-ids .. ok test_vcf_convert: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools convert -g -,. --vcf-ids --3N6 /tmp/4gcls0ICvB/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/convert.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools convert -g -,. --vcf-ids --3N6 .. ok test_vcf_convert: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools convert -g .,- /tmp/4gcls0ICvB/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/convert.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools convert -g .,- .. ok test_vcf_convert_hs2vcf: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools convert --vcf-ids -G /build/bcftools-TfJ6sU/bcftools-1.22/test/convert.gs.gt.ids.gen,/build/bcftools-TfJ6sU/bcftools-1.22/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools convert --vcf-ids -G /build/bcftools-TfJ6sU/bcftools-1.22/test/convert.gs.gt.ids.gen,/build/bcftools-TfJ6sU/bcftools-1.22/test/convert.gs.gt.samples -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools convert -G /build/bcftools-TfJ6sU/bcftools-1.22/test/convert.gs.gt.ids.gen,/build/bcftools-TfJ6sU/bcftools-1.22/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools convert -G /build/bcftools-TfJ6sU/bcftools-1.22/test/convert.gs.gt.ids.gen,/build/bcftools-TfJ6sU/bcftools-1.22/test/convert.gs.gt.samples -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools convert --3N6 -G /build/bcftools-TfJ6sU/bcftools-1.22/test/convert.gs.gt.ids.3N6.gen,/build/bcftools-TfJ6sU/bcftools-1.22/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools convert --3N6 -G /build/bcftools-TfJ6sU/bcftools-1.22/test/convert.gs.gt.ids.3N6.gen,/build/bcftools-TfJ6sU/bcftools-1.22/test/convert.gs.gt.samples -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools convert --vcf-ids -G /build/bcftools-TfJ6sU/bcftools-1.22/test/convert.gs.gt.ids.gen.rev,/build/bcftools-TfJ6sU/bcftools-1.22/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools convert --vcf-ids -G /build/bcftools-TfJ6sU/bcftools-1.22/test/convert.gs.gt.ids.gen.rev,/build/bcftools-TfJ6sU/bcftools-1.22/test/convert.gs.gt.samples -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools convert -G /build/bcftools-TfJ6sU/bcftools-1.22/test/convert.gs.gt.ids.gen.rev,/build/bcftools-TfJ6sU/bcftools-1.22/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools convert -G /build/bcftools-TfJ6sU/bcftools-1.22/test/convert.gs.gt.ids.gen.rev,/build/bcftools-TfJ6sU/bcftools-1.22/test/convert.gs.gt.samples -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^## .. ok test_vcf_convert: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools convert -g -,. --tag PL /tmp/4gcls0ICvB/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/convert.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools convert -g -,. --tag PL .. ok test_vcf_convert: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools convert -g .,- --tag PL /tmp/4gcls0ICvB/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/convert.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools convert -g .,- --tag PL .. ok test_vcf_convert: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools convert -g -,. --vcf-ids /tmp/4gcls0ICvB/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/check.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools convert -g -,. --vcf-ids .. ok test_vcf_convert: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools convert -g .,- --vcf-ids /tmp/4gcls0ICvB/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/check.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools convert -g .,- --vcf-ids .. ok test_vcf_convert: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools convert -g -,. --3N6 /tmp/4gcls0ICvB/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/check.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools convert -g -,. --3N6 .. ok test_vcf_convert: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools convert -g .,- --3N6 /tmp/4gcls0ICvB/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/check.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools convert -g .,- --3N6 .. ok test_vcf_convert: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools convert -g -,. --3N6 --vcf-ids /tmp/4gcls0ICvB/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/check.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools convert -g -,. --3N6 --vcf-ids .. ok test_vcf_convert: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools convert -g .,- --3N6 --vcf-ids /tmp/4gcls0ICvB/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/check.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools convert -g .,- --3N6 --vcf-ids .. ok test_vcf_convert: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools convert -h -,.,. /tmp/4gcls0ICvB/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/convert.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools convert -h -,.,. .. ok test_vcf_convert: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools convert -h .,-,. /tmp/4gcls0ICvB/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/convert.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools convert -h .,-,. .. ok test_vcf_convert: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools convert -h .,-,. --vcf-ids /tmp/4gcls0ICvB/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/convert.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools convert -h .,-,. --vcf-ids .. ok test_vcf_convert: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools convert -h .,.,- /tmp/4gcls0ICvB/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/convert.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools convert -h .,.,- .. ok test_vcf_convert_hls2vcf: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools convert -H /build/bcftools-TfJ6sU/bcftools-1.22/test/convert.hls.gt.hap,/build/bcftools-TfJ6sU/bcftools-1.22/test/convert.hls.gt.legend,/build/bcftools-TfJ6sU/bcftools-1.22/test/convert.hls.gt.samples | grep -v ^## .. ok test_vcf_convert_hls2vcf: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools convert -H /build/bcftools-TfJ6sU/bcftools-1.22/test/convert.hls.gt.hap,/build/bcftools-TfJ6sU/bcftools-1.22/test/convert.hls.gt.legend,/build/bcftools-TfJ6sU/bcftools-1.22/test/convert.hls.gt.samples -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^## .. ok test_vcf_convert: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools convert --haplegendsample -,.,. /tmp/4gcls0ICvB/convert.hap-missing.vcf.gz .. ok test_vcf_convert: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/convert.hap-missing.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools convert --haplegendsample -,.,. .. ok test_vcf_convert: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools convert --hapsample -,. /tmp/4gcls0ICvB/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/convert.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools convert --hapsample -,. .. ok test_vcf_convert: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools convert --hapsample -,. --vcf-ids /tmp/4gcls0ICvB/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/convert.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools convert --hapsample -,. --vcf-ids .. ok test_vcf_convert: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools convert --hapsample .,- /tmp/4gcls0ICvB/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/convert.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools convert --hapsample .,- .. ok test_vcf_convert_hs2vcf: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools convert --hapsample2vcf /build/bcftools-TfJ6sU/bcftools-1.22/test/convert.hs.gt.hap,/build/bcftools-TfJ6sU/bcftools-1.22/test/convert.hs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools convert --hapsample2vcf /build/bcftools-TfJ6sU/bcftools-1.22/test/convert.hs.gt.hap,/build/bcftools-TfJ6sU/bcftools-1.22/test/convert.hs.gt.samples -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools convert --vcf-ids --hapsample2vcf /build/bcftools-TfJ6sU/bcftools-1.22/test/convert.hs.gt.ids.hap,/build/bcftools-TfJ6sU/bcftools-1.22/test/convert.hs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools convert --vcf-ids --hapsample2vcf /build/bcftools-TfJ6sU/bcftools-1.22/test/convert.hs.gt.ids.hap,/build/bcftools-TfJ6sU/bcftools-1.22/test/convert.hs.gt.samples -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^## .. ok test_vcf_convert_gvcf: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools convert --no-version --gvcf2vcf -i'FILTER="PASS"' -f /build/bcftools-TfJ6sU/bcftools-1.22/test/gvcf.fa /tmp/4gcls0ICvB/convert.gvcf.vcf.gz .. ok test_vcf_convert_gvcf: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools convert --no-version --gvcf2vcf -i'FILTER="PASS"' -f /build/bcftools-TfJ6sU/bcftools-1.22/test/gvcf.fa /tmp/4gcls0ICvB/convert.gvcf.vcf.gz -Ou | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view --no-version .. ok test_vcf_convert_gvcf: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view -Ob /tmp/4gcls0ICvB/convert.gvcf.vcf.gz | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools convert --gvcf2vcf -i'FILTER="PASS"' -f /build/bcftools-TfJ6sU/bcftools-1.22/test/gvcf.fa | grep -v ^##bcftools .. ok test_vcf_convert_tsv2vcf: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools convert --no-version -c ID,CHROM,POS,AA -s SAMPLE1 -f /build/bcftools-TfJ6sU/bcftools-1.22/test/23andme.fa --tsv2vcf /build/bcftools-TfJ6sU/bcftools-1.22/test/convert.23andme .. ok test_vcf_convert_tsv2vcf: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools convert -Ou -c ID,CHROM,POS,AA -s SAMPLE1 -f /build/bcftools-TfJ6sU/bcftools-1.22/test/23andme.fa --tsv2vcf /build/bcftools-TfJ6sU/bcftools-1.22/test/convert.23andme | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_convert_tsv2vcf: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools convert --no-version -c -,CHROM,POS,REF,ALT -f /build/bcftools-TfJ6sU/bcftools-1.22/test/23andme.fa --tsv2vcf /build/bcftools-TfJ6sU/bcftools-1.22/test/convert.tsv .. ok test_vcf_convert_tsv2vcf: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools convert -Ou -c -,CHROM,POS,REF,ALT -f /build/bcftools-TfJ6sU/bcftools-1.22/test/23andme.fa --tsv2vcf /build/bcftools-TfJ6sU/bcftools-1.22/test/convert.tsv | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.gvcf-missing.1.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.gvcf-missing.fa --missing N .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.gvcf-missing.1.bcf -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.gvcf-missing.fa --missing N .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.overlaps.1.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.overlaps.1.fa -s A .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.overlaps.1.bcf -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.overlaps.1.fa -s A .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.overlaps.1.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.overlaps.1.fa -s B .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.overlaps.1.bcf -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.overlaps.1.fa -s B .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.overlaps.1.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.overlaps.1.fa -s A -a N .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.overlaps.1.bcf -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.overlaps.1.fa -s A -a N .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.overlaps.1.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.overlaps.1.fa -s B -a N .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.overlaps.1.bcf -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.overlaps.1.fa -s B -a N .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.beyond.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.beyond.fa .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.beyond.bcf -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.beyond.fa .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.fa -s - -m /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.tab .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.bcf -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.fa -s - -m /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.tab .. ok test_vcf_consensus_chain: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.fa -s - -m /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.tab -c /tmp/4gcls0ICvB/consensus.1.chain.new >/dev/null; cat /tmp/4gcls0ICvB/consensus.1.chain.new .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.fa -H 1 -m /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.tab .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.bcf -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.fa -H 1 -m /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.tab .. ok test_vcf_consensus_chain: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.fa -H 1 -m /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.tab -c /tmp/4gcls0ICvB/consensus.2.chain.new >/dev/null; cat /tmp/4gcls0ICvB/consensus.2.chain.new .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.fa -I -s - -m /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.tab .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.bcf -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.fa -I -s - -m /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.tab .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.fa -s - -I -m /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.tab --mask-with X -m /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.tab --mask-with lc .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.bcf -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.fa -s - -I -m /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.tab --mask-with X -m /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.tab --mask-with lc .. ok test_vcf_consensus_chain: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.fa -I -m /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.tab -c /tmp/4gcls0ICvB/consensus.3.chain.new >/dev/null; cat /tmp/4gcls0ICvB/consensus.3.chain.new .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.fa -H 1 .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.bcf -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.fa -H 1 .. ok test_vcf_consensus_chain: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.fa -H 1 -c /tmp/4gcls0ICvB/consensus.4.chain.new >/dev/null; cat /tmp/4gcls0ICvB/consensus.4.chain.new .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus2.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus2.fa -H 1 .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus2.bcf -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus2.fa -H 1 .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus2.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus2.fa -H 2 .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus2.bcf -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus2.fa -H 2 .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/empty.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.fa -s - .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/empty.bcf -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.fa -s - .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus3.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus2.fa -H 2 -M "?" .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus3.bcf -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus2.fa -H 2 -M "?" .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus3.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus2.fa -H 2 -M "?" -p xx_ .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus3.bcf -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus2.fa -H 2 -M "?" -p xx_ .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus4.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus2.fa -s - .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus4.bcf -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus2.fa -s - .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus5.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus5.fa --haplotype LA .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus5.bcf -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus5.fa --haplotype LA .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus6.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus6.fa -s - .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus6.bcf -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus6.fa -s - .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus7.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus7.fa -H 2 .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus7.bcf -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus7.fa -H 2 .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus7.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus7.fa -H 4 .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus7.bcf -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus7.fa -H 4 .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus7.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus7.fa -H 2pIu .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus7.bcf -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus7.fa -H 2pIu .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus7.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus7.fa -H 4pIu .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus7.bcf -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus7.fa -H 4pIu .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus7.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus7.fa -H 1 .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus7.bcf -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus7.fa -H 1 .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus7.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus7.fa -H 3 .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus7.bcf -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus7.fa -H 3 .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus7.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus7.fa -H 1pIu .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus7.bcf -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus7.fa -H 1pIu .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus7.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus7.fa -H 3pIu .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus7.bcf -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus7.fa -H 3pIu .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus8.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.fa -s - .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus8.bcf -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.fa -s - .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus8.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.fa -s - -a . .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus8.bcf -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.fa -s - -a . .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus8.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.fa -s - -a . -i 'type="snp" || type="ref"' .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus8.bcf -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.fa -s - -a . -i 'type="snp" || type="ref"' .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus8.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.fa -s - -a . -i 'ALT!=""' .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus8.bcf -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.fa -s - -a . -i 'ALT!=""' .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus8.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.fa -s - -a . -e 'MinDP>15' .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus8.bcf -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.fa -s - -a . -e 'MinDP>15' .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus8.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.fa -s - -a . -e 'MinDP<15' .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus8.bcf -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.fa -s - -a . -e 'MinDP<15' .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.9.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.9.bcf -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.9.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.9.bcf -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.10.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.10.bcf -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.10.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.10.bcf -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.11.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.11.fa -s smpl .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.11.bcf -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.11.fa -s smpl .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.11.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.11.fa -s smpl -a N .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.11.bcf -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.11.fa -s smpl -a N .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.12.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.12.fa -s - .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.12.bcf -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.12.fa -s - .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.13.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.13.fa -s - .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.13.bcf -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.13.fa -s - .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.14.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.14.fa -s - .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.14.bcf -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.14.fa -s - .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.12.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.12.fa -s - --mark-del - --mark-ins uc --mark-snv uc .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.12.bcf -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.12.fa -s - --mark-del - --mark-ins uc --mark-snv uc .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.12.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.12.fa -s - --mark-del - --mark-ins + --mark-snv : .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.12.bcf -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.12.fa -s - --mark-del - --mark-ins + --mark-snv : .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.15.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.15.fa -H I --mark-ins lc --mark-snv lc .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.15.bcf -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.15.fa -H I --mark-ins lc --mark-snv lc .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.16.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.fa -s - -I .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.16.bcf -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.fa -s - -I .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.16.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.fa -H I .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.16.bcf -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.fa -H I .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.17.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus2.fa -s - -M N -m /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.17.bed .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.17.bcf -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus2.fa -s - -M N -m /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.17.bed .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.18.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.18.fa -s - .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.18.bcf -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.18.fa -s - .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.19.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.19.fa -s - .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.19.bcf -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.19.fa -s - .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.20.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.20.fa -s - .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.20.bcf -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.20.fa -s - .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.20.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.20.fa .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.20.bcf -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.20.fa .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.20.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.20.fa -M . -s b .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.20.bcf -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.20.fa -M . -s b .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.20.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.20.fa -M . -s a .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.20.bcf -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.20.fa -M . -s a .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.20.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.20.fa -M . -S /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.20.b.txt .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.20.bcf -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.20.fa -M . -S /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.20.b.txt .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.20.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.20.fa -M . -S /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.20.a.txt .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.20.bcf -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.20.fa -M . -S /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.20.a.txt .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.21.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.21.fa .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.21.bcf -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.21.fa .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.22.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.22.fa --regions-overlap 0 --mark-del . .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.22.bcf -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.22.fa --regions-overlap 0 --mark-del . .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.22.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.22.fa --regions-overlap 1 --mark-del . .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.22.bcf -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.22.fa --regions-overlap 1 --mark-del . .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.22.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.22.fa --regions-overlap 2 --mark-del . .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.22.bcf -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.22.fa --regions-overlap 2 --mark-del . .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.22.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.22.fa --regions-overlap 0 .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.22.bcf -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.22.fa --regions-overlap 0 .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.22.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.22.fa --regions-overlap 1 .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.22.bcf -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.22.fa --regions-overlap 1 .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.22.vcf.gz -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.22.fa --regions-overlap 2 .. ok test_vcf_consensus: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools consensus /tmp/4gcls0ICvB/consensus.22.bcf -f /build/bcftools-TfJ6sU/bcftools-1.22/test/consensus.22.fa --regions-overlap 2 .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -r 11:10-20 -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/iupac.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/iupac.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -r 11:10-20 -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/iupac.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/iupac.bam | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -r17:100-102,17:102-103,17:103-104,17:104-105,17:100-105 -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.1.bam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.2.bam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -r17:100-102,17:102-103,17:103-104,17:104-105,17:100-105 -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.1.bam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.2.bam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.bam | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -r17:100-102,17:102-103,17:103-104,17:104-105,17:100-105 -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa -b /tmp/4gcls0ICvB/mpileup.bam.list --no-version | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -r17:100-102,17:102-103,17:103-104,17:104-105,17:100-105 -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa -Ob -b /tmp/4gcls0ICvB/mpileup.bam.urllist | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -r17:100-102,17:102-103,17:103-104,17:104-105,17:100-105 -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.1.cram /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.2.cram /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -r17:100-102,17:102-103,17:103-104,17:104-105,17:100-105 -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.1.cram /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.2.cram /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.cram | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -r17:100-102,17:102-103,17:103-104,17:104-105,17:100-105 -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa -b /tmp/4gcls0ICvB/mpileup.cram.list --no-version | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -r17:100-102,17:102-103,17:103-104,17:104-105,17:100-105 -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa -Ob -b /tmp/4gcls0ICvB/mpileup.cram.urllist | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -r17:100-150 -a -AD -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.1.bam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.2.bam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -r17:100-150 -a -AD -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.1.bam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.2.bam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.bam | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -r17:100-150 -a -AD -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa -b /tmp/4gcls0ICvB/mpileup.bam.list --no-version | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -r17:100-150 -a -AD -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa -Ob -b /tmp/4gcls0ICvB/mpileup.bam.urllist | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -r17:100-150 -a -AD -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.1.cram /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.2.cram /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -r17:100-150 -a -AD -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.1.cram /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.2.cram /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.cram | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -r17:100-150 -a -AD -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa -b /tmp/4gcls0ICvB/mpileup.cram.list --no-version | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -r17:100-150 -a -AD -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa -Ob -b /tmp/4gcls0ICvB/mpileup.cram.urllist | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a DP,DV -r17:100-600 -a -AD -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.1.bam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.2.bam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a DP,DV -r17:100-600 -a -AD -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.1.bam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.2.bam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.bam | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a DP,DV -r17:100-600 -a -AD -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.1.cram /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.2.cram /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a DP,DV -r17:100-600 -a -AD -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.1.cram /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.2.cram /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.cram | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -a -AD -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -a -AD -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.1.bam | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -a -AD -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.1.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -a -AD -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.1.cram | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP,-AD -r17:100-600 -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.1.bam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.2.bam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP,-AD -r17:100-600 -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.1.bam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.2.bam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.bam | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP,-AD -r17:100-600 -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.1.cram /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.2.cram /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP,-AD -r17:100-600 -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.1.cram /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.2.cram /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.cram | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.1.bam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.2.bam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.1.bam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.2.bam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.bam | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.1.cram /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.2.cram /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.1.cram /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.2.cram /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.cram | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a DP,DV,-AD -r17:100-600 --gvcf 0,2,5 -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.1.bam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.2.bam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a DP,DV,-AD -r17:100-600 --gvcf 0,2,5 -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.1.bam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.2.bam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.bam | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a DP,DV,-AD -r17:100-600 --gvcf 0,2,5 -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.1.cram /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.2.cram /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a DP,DV,-AD -r17:100-600 --gvcf 0,2,5 -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.1.cram /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.2.cram /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.cram | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/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-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.1.bam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.2.bam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/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-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.1.bam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.2.bam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.bam | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/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-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.1.cram /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.2.cram /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/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-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.1.cram /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.2.cram /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.cram | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -r17:100-150 -s HG00101,HG00102 -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.1.bam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.2.bam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -r17:100-150 -s HG00101,HG00102 -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.1.bam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.2.bam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.bam | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -r17:100-150 -s HG00101,HG00102 -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.1.cram /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.2.cram /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -r17:100-150 -s HG00101,HG00102 -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.1.cram /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.2.cram /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.cram | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -r17:100-150 -S /build/bcftools-TfJ6sU/bcftools-1.22/test/mplp.samples -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.1.bam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.2.bam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -r17:100-150 -S /build/bcftools-TfJ6sU/bcftools-1.22/test/mplp.samples -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.1.bam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.2.bam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.bam | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -r17:100-150 -S /build/bcftools-TfJ6sU/bcftools-1.22/test/mplp.samples -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.1.cram /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.2.cram /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -r17:100-150 -S /build/bcftools-TfJ6sU/bcftools-1.22/test/mplp.samples -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.1.cram /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.2.cram /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.cram | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -r17:100-150 -s ^HG00101,HG00102 -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.1.bam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.2.bam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -r17:100-150 -s ^HG00101,HG00102 -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.1.bam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.2.bam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.bam | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -r17:100-150 -s ^HG00101,HG00102 -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.1.cram /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.2.cram /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -r17:100-150 -s ^HG00101,HG00102 -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.1.cram /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.2.cram /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.cram | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -r17:100-150 -S ^/build/bcftools-TfJ6sU/bcftools-1.22/test/mplp.samples -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.1.bam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.2.bam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -r17:100-150 -S ^/build/bcftools-TfJ6sU/bcftools-1.22/test/mplp.samples -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.1.bam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.2.bam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.bam | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -r17:100-150 -S ^/build/bcftools-TfJ6sU/bcftools-1.22/test/mplp.samples -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.1.cram /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.2.cram /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -r17:100-150 -S ^/build/bcftools-TfJ6sU/bcftools-1.22/test/mplp.samples -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.1.cram /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.2.cram /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.cram | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -t17:100-150 -S /build/bcftools-TfJ6sU/bcftools-1.22/test/mplp.9.samples -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.1.sam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.2.sam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -t17:100-150 -S /build/bcftools-TfJ6sU/bcftools-1.22/test/mplp.9.samples -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.1.sam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.2.sam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.sam | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -t17:100-150 -S /build/bcftools-TfJ6sU/bcftools-1.22/test/mplp.9.samples -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.1.bam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.2.bam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -t17:100-150 -S /build/bcftools-TfJ6sU/bcftools-1.22/test/mplp.9.samples -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.1.bam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.2.bam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.bam | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -t17:100-150 -S /build/bcftools-TfJ6sU/bcftools-1.22/test/mplp.9.samples -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.1.cram /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.2.cram /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -t17:100-150 -S /build/bcftools-TfJ6sU/bcftools-1.22/test/mplp.9.samples -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.1.cram /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.2.cram /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.cram | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -t17:100-150 -G /build/bcftools-TfJ6sU/bcftools-1.22/test/mplp.10.samples -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.1.sam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.2.sam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -t17:100-150 -G /build/bcftools-TfJ6sU/bcftools-1.22/test/mplp.10.samples -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.1.sam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.2.sam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.sam | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -t17:100-150 -G /build/bcftools-TfJ6sU/bcftools-1.22/test/mplp.10.samples -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.1.bam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.2.bam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -t17:100-150 -G /build/bcftools-TfJ6sU/bcftools-1.22/test/mplp.10.samples -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.1.bam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.2.bam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.bam | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -t17:100-150 -G /build/bcftools-TfJ6sU/bcftools-1.22/test/mplp.10.samples -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.1.cram /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.2.cram /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -t17:100-150 -G /build/bcftools-TfJ6sU/bcftools-1.22/test/mplp.10.samples -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.1.cram /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.2.cram /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.cram | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.sam | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.bam | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.cram | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -s HG00102 -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.sam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -s HG00102 -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.sam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.4.sam | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -s HG00102 -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.bam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -s HG00102 -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.bam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.4.bam | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -s HG00102 -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.cram /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -s HG00102 -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.cram /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.4.cram | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -s ^HG99999 -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.sam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -s ^HG99999 -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.sam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.4.sam | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -s ^HG99999 -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.bam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -s ^HG99999 -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.bam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.4.bam | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -s ^HG99999 -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.cram /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -s ^HG99999 -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.cram /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.4.cram | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -G /build/bcftools-TfJ6sU/bcftools-1.22/test/mplp.11.rgs -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.sam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -G /build/bcftools-TfJ6sU/bcftools-1.22/test/mplp.11.rgs -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.sam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.4.sam | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -G /build/bcftools-TfJ6sU/bcftools-1.22/test/mplp.11.rgs -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.bam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -G /build/bcftools-TfJ6sU/bcftools-1.22/test/mplp.11.rgs -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.bam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.4.bam | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -G /build/bcftools-TfJ6sU/bcftools-1.22/test/mplp.11.rgs -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.cram /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -G /build/bcftools-TfJ6sU/bcftools-1.22/test/mplp.11.rgs -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.cram /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.4.cram | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -G /build/bcftools-TfJ6sU/bcftools-1.22/test/mplp.11.rgs -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.sam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -G /build/bcftools-TfJ6sU/bcftools-1.22/test/mplp.11.rgs -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.sam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.4.sam | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -G /build/bcftools-TfJ6sU/bcftools-1.22/test/mplp.11.rgs -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.bam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -G /build/bcftools-TfJ6sU/bcftools-1.22/test/mplp.11.rgs -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.bam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.4.bam | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -G /build/bcftools-TfJ6sU/bcftools-1.22/test/mplp.11.rgs -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.cram /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -G /build/bcftools-TfJ6sU/bcftools-1.22/test/mplp.11.rgs -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.3.cram /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup.4.cram | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a AD -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/indel-AD.1.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/indel-AD.1.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a AD -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/indel-AD.1.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/indel-AD.1.sam | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a AD -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/indel-AD.1.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/indel-AD.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a AD -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/indel-AD.1.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/indel-AD.1.bam | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a AD -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/indel-AD.1.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/indel-AD.1.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a AD -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/indel-AD.1.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/indel-AD.1.cram | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a AD --indels-cns -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/indel-AD.1.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/indel-AD.1.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a AD --indels-cns -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/indel-AD.1.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/indel-AD.1.sam | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a AD --indels-cns -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/indel-AD.1.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/indel-AD.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a AD --indels-cns -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/indel-AD.1.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/indel-AD.1.bam | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a AD --indels-cns -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/indel-AD.1.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/indel-AD.1.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a AD --indels-cns -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/indel-AD.1.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/indel-AD.1.cram | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a AD -r 11:75 -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/indel-AD.2.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a AD -r 11:75 -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/indel-AD.2.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/indel-AD.2.bam | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a AD -r 11:75 -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/indel-AD.2.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a AD -r 11:75 -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/indel-AD.2.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/indel-AD.2.cram | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/indel-AD.2.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/indel-AD.2.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/indel-AD.2.bam | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/indel-AD.2.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/indel-AD.2.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/indel-AD.2.cram | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/indel-AD.2.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/indel-AD.2.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/indel-AD.2.bam | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/indel-AD.2.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/indel-AD.2.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/indel-AD.2.cram | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD,INFO/SCR,FMT/SCR -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup-SCR.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup-SCR.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD,INFO/SCR,FMT/SCR -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup-SCR.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup-SCR.bam | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD,INFO/SCR,FMT/SCR -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup-SCR.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup-SCR.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD,INFO/SCR,FMT/SCR -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup-SCR.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup-SCR.cram | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -t 1:100 --skip-all-set PAIRED,PROPER_PAIR,MREVERSE -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup-SCR.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -t 1:100 --skip-all-set PAIRED,PROPER_PAIR,MREVERSE -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup-SCR.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup-filter.sam | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -t 1:100 --skip-any-set READ1 -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup-SCR.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -t 1:100 --skip-any-set READ1 -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup-SCR.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup-filter.sam | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -t 1:100 --skip-all-unset READ1 -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup-SCR.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -t 1:100 --skip-all-unset READ1 -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup-SCR.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup-filter.sam | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -t 1:100 --skip-any-unset READ1 -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup-SCR.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD -t 1:100 --skip-any-unset READ1 -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup-SCR.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/mpileup-filter.sam | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD,INFO/NMBZ -r chr19:69-99 -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/annot-NMBZ.1.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/annot-NMBZ.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD,INFO/NMBZ -r chr19:69-99 -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/annot-NMBZ.1.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/annot-NMBZ.1.bam | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD,INFO/NMBZ -r chr6:75 -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/annot-NMBZ.2.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/annot-NMBZ.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD,INFO/NMBZ -r chr6:75 -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/annot-NMBZ.2.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/annot-NMBZ.2.bam | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD,INFO/NMBZ -r chr16:75 -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/annot-NMBZ.3.fa /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/annot-NMBZ.3.1.bam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/annot-NMBZ.3.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools mpileup -a -AD,INFO/NMBZ -r chr16:75 -f /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/annot-NMBZ.3.fa -Ob /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/annot-NMBZ.3.1.bam /build/bcftools-TfJ6sU/bcftools-1.22/test/mpileup/annot-NMBZ.3.2.bam | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_csq: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq.gff3 /build/bcftools-TfJ6sU/bcftools-1.22/test/csq.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/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-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq.chr.gff3 --unify-chr-names -,chr,- /build/bcftools-TfJ6sU/bcftools-1.22/test/csq.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/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-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq.2.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq.2.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq.2.gff --ncsq 64 /build/bcftools-TfJ6sU/bcftools-1.22/test/csq.2.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq.nchr.gff -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq.nchr.fa --unify-chr-names -,-,- /build/bcftools-TfJ6sU/bcftools-1.22/test/csq.nchr.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq.nchr.gff -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq.ychr.fa --unify-chr-names -,-,chr /build/bcftools-TfJ6sU/bcftools-1.22/test/csq.nchr.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq.ychr.gff -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq.nchr.fa --unify-chr-names -,chr,- /build/bcftools-TfJ6sU/bcftools-1.22/test/csq.nchr.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq.ychr.gff -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq.ychr.fa --unify-chr-names -,chr,chr /build/bcftools-TfJ6sU/bcftools-1.22/test/csq.nchr.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq.ychr.gff -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq.ychr.fa --unify-chr-names chr,chr,chr /build/bcftools-TfJ6sU/bcftools-1.22/test/csq.ychr.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq.nchr.gff -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq.ychr.fa --unify-chr-names chr,-,chr /build/bcftools-TfJ6sU/bcftools-1.22/test/csq.ychr.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq.ychr.gff -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq.nchr.fa --unify-chr-names chr,chr,- /build/bcftools-TfJ6sU/bcftools-1.22/test/csq.ychr.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq.nchr.gff -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq.nchr.fa --unify-chr-names chr,-,- /build/bcftools-TfJ6sU/bcftools-1.22/test/csq.ychr.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq.nchr.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq.ychr.gff --unify-chr-names Chromosome,chr,- /build/bcftools-TfJ6sU/bcftools-1.22/test/csq.yychr.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000373833/ENST00000373833.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000373833/ENST00000373833.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000373833/boundary-insertion.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -l -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000373833/ENST00000373833.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000373833/ENST00000373833.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000373833/boundary-insertion.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/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-TfJ6sU/bcftools-1.22/test/csq/ENST00000422159 && /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f ENST00000422159.fa -g ENST00000422159.gff multiallelic.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS\t%REF\t%ALT\t%GT\t%TBCSQ\n]' | ../sort-csq -q ; echo ; /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f ENST00000422159.fa -g short.gff multiallelic.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS\t%REF\t%ALT\t%GT\t%TBCSQ\n]' | ../sort-csq -q .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000378322/ENST00000378322.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000378322/ENST00000378322.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000378322/end-overlap-tscript.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -l -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000378322/ENST00000378322.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000378322/ENST00000378322.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000378322/end-overlap-tscript.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000263103-INS/ENST00000263103-INS.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000263103-INS/ENST00000263103-INS.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000263103-INS/insertions.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000269081/ENST00000269081.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000269081/ENST00000269081.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000269081/stop-gained-not-inframe-insertion.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000420190/ENST00000420190.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000420190/ENST00000420190.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000420190/abort-in-csq-push.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000329454/ENST00000329454.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000329454/ENST00000329454.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000329454/boundary-deletion.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -l -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000329454/ENST00000329454.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000329454/ENST00000329454.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000329454/boundary-deletion.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000294661/ENST00000294661.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000294661/ENST00000294661.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000294661/non-coding-boundary.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -l -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000294661/ENST00000294661.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000294661/ENST00000294661.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000294661/non-coding-boundary.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000285021/ENST00000285021.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000285021/ENST00000285021.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000285021/stop-gained-inframe-indel.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000381157/ENST00000381157.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000381157/ENST00000381157.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000381157/haploid-diploid.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n' .. ok test_csq_real: cd /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000410009 && /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -lb -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000410009 && /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -B 5 -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000410009 && /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -b -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000410009/ENST00000410009.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000410009/ENST00000410009.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000410009/frameshift.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/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-TfJ6sU/bcftools-1.22/test/csq/ENSMUST00000133836 && /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f ENSMUST00000133836.fa -g ENSMUST00000133836.gff filter-problem.vcf -i 'FILTER="PASS"' --phase m | ../sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/EMN908947 && /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f EMN908947.fa -g ribosomal-slippage.gff ribosomal-slippage.vcf --force | ../sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/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-TfJ6sU/bcftools-1.22/test/csq/EMN908947 && /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f EMN908947.fa -g simple.gff simple.vcf | ../sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000519442/ENST00000519442.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000519442/ENST00000519442.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000519442/synon-splice-region-del.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000557788/ENST00000557788.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000557788/ENST00000557788.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000557788/long-overlap-del.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/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-TfJ6sU/bcftools-1.22/test/csq/ENSMUST00000121418 && /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25105' --phase m | ../sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENSMUST00000121418 && /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25500' --phase m | ../sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENSMUST00000121418 && /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25496' --phase m | ../sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000420670/ENST00000420670.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000420670/ENST00000420670.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000420670/start-stop-lost.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000420670/ENST00000420670.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000420670/ENST00000420670.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000420670/segfault.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000409523/ENST00000409523.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000409523/ENST00000409523.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000409523/long-overlapping-del.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000520795/ENST00000520795.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000520795/ENST00000520795.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000520795/long-inside-del.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -l -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000520795/ENST00000520795.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000520795/ENST00000520795.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000520795/long-inside-del.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000382647/ENST00000382647.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000382647/ENST00000382647.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000382647/synon-splice-region-insert.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000545279/ENST00000545279.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000545279/ENST00000545279.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000545279/splice-region-insert.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000528237/ENST00000528237.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000528237/ENST00000528237.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000528237/retained-stop-incomplete-cds.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/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-TfJ6sU/bcftools-1.22/test/csq/ENST00000379416 && /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.del-snp.vcf | ../sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-del.vcf | ../sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-ins.vcf | ../sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-snp.vcf | ../sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff single.vcf | ../sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000400151/ENST00000400151.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000400151/ENST00000400151.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000400151/long-del.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000624631/ENST00000624631.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000624631/ENST00000624631.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000624631/ambiguous.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000218032/ENST00000218032.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000218032/ENST00000218032.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000218032/start-lost-del.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000218032/ENST00000218032.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000218032/ENST00000218032.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000218032/start-lost.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -l -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000218032/ENST00000218032.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000218032/ENST00000218032.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000218032/start-lost.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000542803/ENST00000542803.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000542803/ENST00000542803.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000542803/splice-region.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -l -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000542803/ENST00000542803.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000542803/ENST00000542803.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000542803/splice-region.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000543077/ENST00000543077.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000543077/ENST00000543077.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000543077/not-a-start-lost.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -l -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000543077/ENST00000543077.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000543077/ENST00000543077.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000543077/not-a-start-lost.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -l -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -l -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -l -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/frame3.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -l -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/frame3.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -l -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -l -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -l -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/frame2.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -l -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/frame2.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/not-a-start-lost.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -l -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/not-a-start-lost.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/frame1.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -l -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/frame1.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -l -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -l -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -l -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000536784/ENST00000536784.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000536784/ENST00000536784.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000536784/not-a-start-lost.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -l -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000536784/ENST00000536784.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000536784/ENST00000536784.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000536784/not-a-start-lost.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/EDUMMY0003/EDUMMY0003.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/EDUMMY0003/EDUMMY0003.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/EDUMMY0003/long-del.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/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-TfJ6sU/bcftools-1.22/test/csq/ENST00000000000 && /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -p a -f ENST00000000000.fa -g ENST00000000000.gff upstream-stop.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'[%POS\t%REF\t%ALT\t%SAMPLE\t%GT\t%TBCSQ\n]' | ../sort-csq -q .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000448695/ENST00000448695.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000448695/ENST00000448695.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000448695/syn-and-splice-reg.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENSCAFT00000047742/ENSCAFT00000047742.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENSCAFT00000047742/ENSCAFT00000047742.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENSCAFT00000047742/test.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/EDUMMY0002/EDUMMY0002.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/EDUMMY0002/EDUMMY0002.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/EDUMMY0002/boundaries.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000318249/ENST00000318249.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000318249/ENST00000318249.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000318249/start-lost.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -l -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000318249/ENST00000318249.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000318249/ENST00000318249.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000318249/start-lost.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/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-TfJ6sU/bcftools-1.22/test/csq/ENST00000580206 && /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.ins-snv.vcf | ../sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f ENST00000580206.fa -g short.gff compound.ins-snv.vcf | ../sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff single.ins-snv.vcf | ../sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f ENST00000580206.fa -g short.gff single.ins-snv.vcf | ../sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.del-snv.vcf | ../sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f ENST00000580206.fa -g short.gff compound.del-snv.vcf | ../sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f ENST00000580206.fa -g short.gff single.del-snv.vcf | ../sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.del-ins.vcf | ../sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f ENST00000580206.fa -g short.gff compound.del-ins.vcf | ../sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f ENST00000580206.fa -g short.gff single.del-ins.vcf | ../sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000520868/ENST00000520868.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000520868/ENST00000520868.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000520868/long-deletion.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000413103/ENST00000413103.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000413103/ENST00000413103.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000413103/long-deletion.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENSG00000173376/ENSG00000173376.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENSG00000173376/ENSG00000173376.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENSG00000173376/synon.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000571540/ENST00000571540.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000571540/ENST00000571540.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000571540/nmd.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000227471/ENST00000227471.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000227471/ENST00000227471.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000227471/insert-splice-vs-frameshift.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000271583/ENST00000271583.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000271583/ENST00000271583.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000271583/splice-acceptor.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000368801/ENST00000368801.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000368801/ENST00000368801.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000368801/compound-lost.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000301246/ENST00000301246.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000301246/ENST00000301246.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000301246/15bp-insert.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000318249.2/ENST00000318249.2.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000318249.2/ENST00000318249.2.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000318249.2/synonymous-start-lost.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/EDUMMY0001/EDUMMY0001.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/EDUMMY0001/EDUMMY0001.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/EDUMMY0001/starts-with-1.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -l -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/EDUMMY0001/EDUMMY0001.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/EDUMMY0001/EDUMMY0001.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/EDUMMY0001/starts-with-1.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000295641/ENST00000295641.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000295641/ENST00000295641.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000295641/not-a-start-lost.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -l -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000295641/ENST00000295641.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000295641/ENST00000295641.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000295641/not-a-start-lost.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000479739/ENST00000479739.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000479739/ENST00000479739.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000479739/short-cds-start-lost.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -l -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000479739/ENST00000479739.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000479739/ENST00000479739.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000479739/short-cds-start-lost.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000436063/ENST00000436063.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000436063/ENST00000436063.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000436063/insert-before-utr.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000573035-bt2212/ENST00000573035-bt2212.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000573035-bt2212/ENST00000573035-bt2212.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000573035-bt2212/complex-event.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000518414/ENST00000518414.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000518414/ENST00000518414.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000518414/incorrect-inframe-del.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/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-TfJ6sU/bcftools-1.22/test/csq/ENST00000368801.2 && /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f ENST00000368801.2.fa -g ENST00000368801.2.gff alt-gencode.vcf -v 0 -C 1 | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%BCSQ\n' | ../sort-csq -q .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000368801.2/ENST00000368801.2.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000368801.2/ENST00000368801.2.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000368801.2/start-lost.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/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-TfJ6sU/bcftools-1.22/test/csq/ENST00000368801.2 && /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f ENST00000368801.2.fa -g ENST00000368801.2.gff alt-gencode.vcf -v 0 -C 0 | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%BCSQ\n' | ../sort-csq -q .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000518414-ENST00000521270/valgrind.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000423372/ENST00000423372.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000423372/ENST00000423372.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000423372/snps.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -l -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000423372/ENST00000423372.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000423372/ENST00000423372.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000423372/snps.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000423372/ENST00000423372.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000423372/ENST00000423372.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000423372/insert3.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -l -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000423372/ENST00000423372.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000423372/ENST00000423372.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000423372/insert3.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000303039/ENST00000303039.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000303039/ENST00000303039.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000303039/not-a-stop.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -l -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000303039/ENST00000303039.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000303039/ENST00000303039.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000303039/not-a-stop.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000256452/ENST00000256452.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000256452/ENST00000256452.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000256452/intron.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000357367/ENST00000357367.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000357367/ENST00000357367.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000357367/stop-retained.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000375992/ENST00000375992.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000375992/ENST00000375992.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000375992/incorrect-synon-del-not-start-lost.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000593942/ENST00000593942.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000593942/ENST00000593942.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000593942/last-codon-deletion.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000360372/ENST00000360372.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000360372/ENST00000360372.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000360372/mnp.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000230048/ENST00000230048.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000230048/ENST00000230048.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000230048/start-del.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000573314/ENST00000573314.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000573314/ENST00000573314.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -l -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000573314/ENST00000573314.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000573314/ENST00000573314.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools csq -f /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000390520/ENST00000390520.fa -g /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000390520/ENST00000390520.gff /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/ENST00000390520/deletion-overlap.vcf | /build/bcftools-TfJ6sU/bcftools-1.22/test/csq/sort-csq | /build/bcftools-TfJ6sU/bcftools-1.22/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-TfJ6sU/bcftools-1.22/bcftools roh /build/bcftools-TfJ6sU/bcftools-1.22/test/roh.1.vcf.gz -Or -G30 --AF-dflt 0.4| grep -v ^# .. ok test_roh: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools roh /build/bcftools-TfJ6sU/bcftools-1.22/test/roh.1.vcf.gz -Or -G30 --AF-file /build/bcftools-TfJ6sU/bcftools-1.22/test/roh.1.tab.gz| grep -v ^# .. ok test_roh: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools roh /build/bcftools-TfJ6sU/bcftools-1.22/test/roh.1.vcf.gz -Or -G30 --AF-file /build/bcftools-TfJ6sU/bcftools-1.22/test/roh.1.tab.gz --ignore-homref| grep -v ^# .. ok test_roh: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools roh /build/bcftools-TfJ6sU/bcftools-1.22/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245| grep -v ^# .. ok test_roh: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools roh /build/bcftools-TfJ6sU/bcftools-1.22/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --ignore-homref| grep -v ^# .. ok test_roh: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools roh /build/bcftools-TfJ6sU/bcftools-1.22/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-TfJ6sU/bcftools-1.22/bcftools roh /build/bcftools-TfJ6sU/bcftools-1.22/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --include-noalt| grep -v ^# .. ok test_gtcheck: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools gtcheck -e 0 --no-HWE-prob /tmp/4gcls0ICvB/gtcheck.1.vcf.gz -g /tmp/4gcls0ICvB/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools gtcheck -e 0 /tmp/4gcls0ICvB/gtcheck.1.vcf.gz -g /tmp/4gcls0ICvB/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools gtcheck -e 0 -u GT,GT /tmp/4gcls0ICvB/gtcheck.1.vcf.gz -g /tmp/4gcls0ICvB/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools gtcheck -e 0 -u GT,PL /tmp/4gcls0ICvB/gtcheck.1.vcf.gz -g /tmp/4gcls0ICvB/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools gtcheck -e 0 -u PL,GT /tmp/4gcls0ICvB/gtcheck.1.vcf.gz -g /tmp/4gcls0ICvB/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools gtcheck -e 0 -u PL,PL /tmp/4gcls0ICvB/gtcheck.1.vcf.gz -g /tmp/4gcls0ICvB/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools gtcheck -e 0 -p s1,s1 /tmp/4gcls0ICvB/gtcheck.1.vcf.gz -g /tmp/4gcls0ICvB/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools gtcheck -e 0 /tmp/4gcls0ICvB/gtcheck.2.vcf.gz -g /tmp/4gcls0ICvB/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools gtcheck -e 0 /tmp/4gcls0ICvB/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-TfJ6sU/bcftools-1.22/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/4gcls0ICvB/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools gtcheck -e 0 -P /build/bcftools-TfJ6sU/bcftools-1.22/test/gtcheck.3.pairs /tmp/4gcls0ICvB/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools gtcheck -e 0 -u PL /tmp/4gcls0ICvB/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools gtcheck -e 0 --n-matches 4 /tmp/4gcls0ICvB/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO | sort .. ok test_gtcheck: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools gtcheck -e 0 -s qry:E,D,C /tmp/4gcls0ICvB/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools gtcheck -e 0 -s qry:E,D,C -u PL /tmp/4gcls0ICvB/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools gtcheck -e 0 -s qry:B -s gt:D /tmp/4gcls0ICvB/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools gtcheck -e 0 -s qry:B -s gt:D -u PL /tmp/4gcls0ICvB/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools gtcheck -e 0 -s qry:B -s gt:D,C /tmp/4gcls0ICvB/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools gtcheck -e 0 -p B,C,B,D /tmp/4gcls0ICvB/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools gtcheck -e 0 -u GT,GT -H /tmp/4gcls0ICvB/gtcheck.1.vcf.gz -g /tmp/4gcls0ICvB/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools gtcheck -e 0 -u GT,PL -H /tmp/4gcls0ICvB/gtcheck.1.vcf.gz -g /tmp/4gcls0ICvB/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools gtcheck -e 0 -u PL,GT -H /tmp/4gcls0ICvB/gtcheck.1.vcf.gz -g /tmp/4gcls0ICvB/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools gtcheck -e 0 -u PL,PL -H /tmp/4gcls0ICvB/gtcheck.1.vcf.gz -g /tmp/4gcls0ICvB/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools gtcheck -e 0 -P /build/bcftools-TfJ6sU/bcftools-1.22/test/gtcheck.4.pairs --distinctive-sites 3 /tmp/4gcls0ICvB/gtcheck.4.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools gtcheck -e 0 -P /build/bcftools-TfJ6sU/bcftools-1.22/test/gtcheck.4.pairs --distinctive-sites 3,1 /tmp/4gcls0ICvB/gtcheck.4.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools gtcheck -u GT -e 30 /tmp/4gcls0ICvB/gtcheck.1.vcf.gz -g /tmp/4gcls0ICvB/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools gtcheck -u GT -e 30 -p s1,s1 /tmp/4gcls0ICvB/gtcheck.1.vcf.gz -g /tmp/4gcls0ICvB/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools gtcheck -u GT -e 300 /tmp/4gcls0ICvB/gtcheck.1.vcf.gz -g /tmp/4gcls0ICvB/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools gtcheck -u PL -e 30 /tmp/4gcls0ICvB/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools gtcheck /tmp/4gcls0ICvB/gtcheck.ntop.vcf.gz -g /tmp/4gcls0ICvB/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools gtcheck --n-matches 2 /tmp/4gcls0ICvB/gtcheck.ntop.vcf.gz -g /tmp/4gcls0ICvB/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools gtcheck /tmp/4gcls0ICvB/gtcheck.5.vcf.gz -g /tmp/4gcls0ICvB/gtcheck.5.gts.vcf.gz | grep -v ^# | grep -v Time .. ok test_gtcheck: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools gtcheck -p A,B,B,C /tmp/4gcls0ICvB/gtcheck.6.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-TfJ6sU/bcftools-1.22/bcftools gtcheck -t 11:33 -p A,D,A,E,D,E -u GT -e 10 /tmp/4gcls0ICvB/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok Number of tests: total .. 1897 passed .. 1897 failed .. 0 make[2]: Leaving directory '/build/bcftools-TfJ6sU/bcftools-1.22' make[1]: Leaving directory '/build/bcftools-TfJ6sU/bcftools-1.22' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/bcftools/ make -j2 install DESTDIR=/build/bcftools-TfJ6sU/bcftools-1.22/debian/bcftools AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/bcftools-TfJ6sU/bcftools-1.22' mkdir -p -m 755 /build/bcftools-TfJ6sU/bcftools-1.22/debian/bcftools/usr/bin /build/bcftools-TfJ6sU/bcftools-1.22/debian/bcftools/usr/share/man/man1 /build/bcftools-TfJ6sU/bcftools-1.22/debian/bcftools/usr/lib/x86_64-linux-gnu/bcftools install -p bcftools /build/bcftools-TfJ6sU/bcftools-1.22/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-TfJ6sU/bcftools-1.22/debian/bcftools/usr/bin install -p -m 644 doc/bcftools.1 /build/bcftools-TfJ6sU/bcftools-1.22/debian/bcftools/usr/share/man/man1 install -p plugins/*.so /build/bcftools-TfJ6sU/bcftools-1.22/debian/bcftools/usr/lib/x86_64-linux-gnu/bcftools make[1]: Leaving directory '/build/bcftools-TfJ6sU/bcftools-1.22' debian/rules override_dh_install make[1]: Entering directory '/build/bcftools-TfJ6sU/bcftools-1.22' 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-TfJ6sU/bcftools-1.22' dh_installdocs dh_installchangelogs debian/rules override_dh_installman make[1]: Entering directory '/build/bcftools-TfJ6sU/bcftools-1.22' dh_installman --language=C make[1]: Leaving directory '/build/bcftools-TfJ6sU/bcftools-1.22' dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dpkg-gencontrol: warning: package bcftools: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package bcftools: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'bcftools' in '../bcftools_1.22-1_amd64.deb'. dpkg-deb: building package 'bcftools-dbgsym' in '../bcftools-dbgsym_1.22-1_amd64.deb'. dpkg-genbuildinfo -O../bcftools_1.22-1_amd64.buildinfo dpkg-genchanges -O../bcftools_1.22-1_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 2026-07-09T03:57:48Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Thu, 09 Jul 2026 03:57:49 +0000 | +------------------------------------------------------------------------------+ bcftools_1.22-1_amd64.changes: ------------------------------ Format: 1.8 Date: Sun, 17 Aug 2025 20:55:49 +0200 Source: bcftools Binary: bcftools bcftools-dbgsym Architecture: source amd64 Version: 1.22-1 Distribution: perl-5.44-throwaway Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Steffen Möller Description: bcftools - genomic variant calling and manipulation of VCF/BCF files Changes: bcftools (1.22-1) unstable; urgency=medium . * Team upload. * New upstream version * Standards-Version: 4.7.2 (routine-update) Checksums-Sha1: 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c6839a219b624261eb0e5c62de9b8de9 2394804 bcftools-dbgsym_1.22-1_amd64.deb 83f786a03247d3b00d96746b9e2a0602 832436 bcftools_1.22-1_amd64.deb Checksums-Sha1: 91a11cdd15547c146e8ab52e5158059cfb6caddf 1242 bcftools_1.22-1.dsc 20766713a8a88810db613d1879957c4ac24039b3 2394804 bcftools-dbgsym_1.22-1_amd64.deb 4628128b80b079fe3713976f95ba2021c6f6be4c 832436 bcftools_1.22-1_amd64.deb Checksums-Sha256: 0813173f07dc0930b1658ee7344b75a60b510a54128d3d5ecd723f0c7fd45a1f 1242 bcftools_1.22-1.dsc 2f2ab4edfef4b72dc9df3e7bc2d0fb58c0c7c55380b65c6972544f9db60d6c2b 2394804 bcftools-dbgsym_1.22-1_amd64.deb 67ad462de7a11d6a073a84daa0a992baf0efe5e986d010e26f0486c0e28ba592 832436 bcftools_1.22-1_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Thu, 09 Jul 2026 03:57:48 +0000 Build-Path: /build/bcftools-TfJ6sU/bcftools-1.22 Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: autoconf (= 2.73-2), automake (= 1:1.18.1-4), autopoint (= 1.0-3), autotools-dev (= 20240727.1+nmu1), base-files (= 14.2), base-passwd (= 3.6.8), bash (= 5.3-3), binutils (= 2.46.50.20260617-1), binutils-common (= 2.46.50.20260617-1), binutils-x86-64-linux-gnu (= 2.46.50.20260617-1), bsdextrautils (= 2.42.2-1), build-essential (= 12.12), bzip2 (= 1.0.8-6+b2), comerr-dev (= 2.1-1.47.4-1), coreutils (= 9.10-1), cpp (= 4:15.2.0-5+b1), cpp-15 (= 15.3.0-1), cpp-15-x86-64-linux-gnu (= 15.3.0-1), cpp-x86-64-linux-gnu (= 4:15.2.0-5+b1), dash (= 0.5.12-12), debconf (= 1.5.92), debhelper (= 14.3), debianutils (= 5.23.2), dh-autoreconf (= 22), dh-strip-nondeterminism (= 1.15.1-1), diffutils (= 1:3.12-1), dpkg (= 1.23.7), dpkg-dev (= 1.23.7), dwz (= 0.16-4), file (= 1:5.47-4), findutils (= 4.10.0-4), g++ (= 4:15.2.0-5+b1), g++-15 (= 15.3.0-1), g++-15-x86-64-linux-gnu (= 15.3.0-1), g++-x86-64-linux-gnu (= 4:15.2.0-5+b1), gcc (= 4:15.2.0-5+b1), gcc-15 (= 15.3.0-1), gcc-15-base (= 15.3.0-1), gcc-15-x86-64-linux-gnu (= 15.3.0-1), gcc-16-base (= 16.1.0-2), gcc-x86-64-linux-gnu (= 4:15.2.0-5+b1), gettext (= 1.0-3), gettext-base (= 1.0-3), grep (= 3.12-1), groff-base (= 1.24.1-1), gzip (= 1.13-1), hostname (= 3.25), init-system-helpers (= 1.69), intltool-debian (= 0.35.0+20060710.6), krb5-multidev (= 1.22.1-3), libacl1 (= 2.4.0-1), libarchive-zip-perl (= 1.68-1), libasan8 (= 16.1.0-2), libatomic1 (= 16.1.0-2), libattr1 (= 1:2.6.0-1), libaudit-common (= 1:4.1.2-1), libaudit1 (= 1:4.1.2-1+b1), libbinutils (= 2.46.50.20260617-1), libblkid1 (= 2.42.2-1), libbrotli-dev (= 1.2.0-3), libbrotli1 (= 1.2.0-3), libbz2-1.0 (= 1.0.8-6+b2), libbz2-dev (= 1.0.8-6+b2), libc-bin (= 2.42-17), libc-dev-bin (= 2.42-17), libc-gconv-modules-extra (= 2.42-17), libc6 (= 2.42-17), libc6-dev (= 2.42-17), libcap-ng0 (= 0.9.3-1+b1), libcc1-0 (= 16.1.0-2), libcom-err2 (= 1.47.4-1), libcrypt1 (= 1:4.5.1-1+b1), libctf-nobfd0 (= 2.46.50.20260617-1), libctf0 (= 2.46.50.20260617-1), libcurl3t64-gnutls (= 8.21.0-2), libcurl4-gnutls (= 8.21.0-2), libcurl4-gnutls-dev (= 8.21.0-2), libdb5.3t64 (= 5.3.28+dfsg2-11+b1), libdebconfclient0 (= 0.283), libdebhelper-perl (= 14.3), libdeflate-dev (= 1.25-1), libdeflate0 (= 1.25-1), libdpkg-perl (= 1.23.7), libelf1t64 (= 0.195-1), libevent-2.1-7t64 (= 2.1.13-stable-1), libffi8 (= 3.5.2-4), libfile-stripnondeterminism-perl (= 1.15.1-1), libgcc-15-dev (= 15.3.0-1), libgcc-s1 (= 16.1.0-2), libgdbm-compat4t64 (= 1.26-1+b2), libgdbm6t64 (= 1.26-1+b2), libgmp-dev (= 2:6.3.0+dfsg-5+b2), libgmp10 (= 2:6.3.0+dfsg-5+b2), libgmpxx4ldbl (= 2:6.3.0+dfsg-5+b2), libgnutls-dane0t64 (= 3.8.13-1), libgnutls28-dev (= 3.8.13-1), libgnutls30t64 (= 3.8.13-1), libgomp1 (= 16.1.0-2), libgprofng0 (= 2.46.50.20260617-1), libgsl-dev (= 2.8+dfsg-6+b1), libgsl28 (= 2.8+dfsg-6+b1), libgslcblas0 (= 2.8+dfsg-6+b1), libgssapi-krb5-2 (= 1.22.1-3), libgssrpc4t64 (= 1.22.1-3), libhogweed6t64 (= 3.10.2-1+b1), libhts-dev (= 1.22.1+ds2-1+b2), libhts3t64 (= 1.22.1+ds2-1+b2), libhtscodecs2 (= 1.6.6-1), libhwasan0 (= 16.1.0-2), libidn2-0 (= 2.3.8-5), libidn2-dev (= 2.3.8-5), libio-pty-perl (= 1:1.31-1+b1), libisl23 (= 0.27-2), libitm1 (= 16.1.0-2), libjansson4 (= 2.15.1-1), libk5crypto3 (= 1.22.1-3), libkadm5clnt-mit12 (= 1.22.1-3), libkadm5srv-mit12 (= 1.22.1-3), libkdb5-10t64 (= 1.22.1-3), libkeyutils1 (= 1.6.3-6+b2), libkrb5-3 (= 1.22.1-3), libkrb5-dev (= 1.22.1-3), libkrb5support0 (= 1.22.1-3), libldap-dev (= 2.6.13+dfsg-1+b1), libldap2 (= 2.6.13+dfsg-1+b1), liblsan0 (= 16.1.0-2), liblzma-dev (= 5.8.3-1), liblzma5 (= 5.8.3-1), libmagic-mgc (= 1:5.47-4), libmagic1t64 (= 1:5.47-4), libmd0 (= 1.2.0-2), libmount1 (= 2.42.2-1), libmpc3 (= 1.3.1-3), libmpfr6 (= 4.2.2-3), libnettle8t64 (= 3.10.2-1+b1), libnghttp2-14 (= 1.69.0-1), libnghttp2-dev (= 1.69.0-1), libnghttp3-9 (= 1.15.0-1), libnghttp3-dev (= 1.15.0-1), libngtcp2-16 (= 1.22.1-1), libngtcp2-crypto-gnutls-dev (= 1.22.1-1), libngtcp2-crypto-gnutls8 (= 1.22.1-1), libngtcp2-dev (= 1.22.1-1), libp11-kit-dev (= 0.26.2-3), libp11-kit0 (= 0.26.2-3), libpam-modules (= 1.7.0-8), libpam-modules-bin (= 1.7.0-8), libpam-runtime (= 1.7.0-8), libpam0g (= 1.7.0-8), libpcre2-8-0 (= 10.46-1+b2), libperl5.44 (= 5.44.0~rc2-1), libpipeline1 (= 1.5.8-3), libpkgconf7 (= 2.5.1-4), libpsl-dev (= 0.22.0-1), libpsl5t64 (= 0.22.0-1), libquadmath0 (= 16.1.0-2), librtmp-dev (= 2.6-1), librtmp1 (= 2.6-1), libsasl2-2 (= 2.1.28+dfsg1-11), libsasl2-modules-db (= 2.1.28+dfsg1-11), libseccomp2 (= 2.6.0-2+b1), libselinux1 (= 3.10-1), libsframe3 (= 2.46.50.20260617-1), libsmartcols1 (= 2.42.2-1), libssh2-1-dev (= 1.11.1-4), libssh2-1t64 (= 1.11.1-4), libssl-dev (= 3.6.3-1), libssl3t64 (= 3.6.3-1), libstdc++-15-dev (= 15.3.0-1), libstdc++6 (= 16.1.0-2), libsystemd0 (= 261.1-2), libtasn1-6 (= 4.21.0-2+b1), libtasn1-6-dev (= 4.21.0-2+b1), libtinfo6 (= 6.6+20260608-2), libtool (= 2.5.4-11), libtsan2 (= 16.1.0-2), libubsan1 (= 16.1.0-2), libuchardet0 (= 0.0.8-2+b2), libudev1 (= 261.1-2), libunbound8 (= 1.25.1-1+b1), libunistring-dev (= 1.4.2-1), libunistring5 (= 1.4.2-1), libuuid1 (= 2.42.2-1), libxml2-16 (= 2.15.3+dfsg-1), libzstd-dev (= 1.5.7+dfsg-3+b2), libzstd1 (= 1.5.7+dfsg-3+b2), linux-libc-dev (= 7.1.3-1), m4 (= 1.4.21-1), make (= 4.4.1-3), man-db (= 2.13.1-1), mawk (= 1.3.4.20260302-1), ncurses-base (= 6.6+20260608-2), ncurses-bin (= 6.6+20260608-2), nettle-dev (= 3.10.2-1+b1), openssl-provider-legacy (= 3.6.3-1), patch (= 2.8-2), perl (= 5.44.0~rc2-1), perl-base (= 5.44.0~rc2-1), perl-modules-5.44 (= 5.44.0~rc2-1), pkgconf (= 2.5.1-4), pkgconf-bin (= 2.5.1-4), po-debconf (= 1.0.22), rpcsvc-proto (= 1.4.4-1), sed (= 4.9-3), sensible-utils (= 0.0.26), sysvinit-utils (= 3.18-1), tabix (= 1.22.1+ds2-1+b2), tar (= 1.35+dfsg-4), util-linux (= 2.42.2-1), xz-utils (= 5.8.3-1), zlib1g (= 1:1.3.dfsg+really1.3.2-3), zlib1g-dev (= 1:1.3.dfsg+really1.3.2-3) Environment: DEB_BUILD_OPTIONS="parallel=2" LANG="C.UTF-8" LANGUAGE="en_GB:en" LC_COLLATE="C.UTF-8" LC_CTYPE="C.UTF-8" LD_LIBRARY_PATH="/usr/lib/libeatmydata" LD_PRELOAD="libeatmydata.so" SOURCE_DATE_EPOCH="1755456949" 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root/root 0 2025-08-17 18:55 ./usr/share/doc/bcftools-dbgsym -> bcftools bcftools_1.22-1_amd64.deb ------------------------- new Debian package, version 2.0. size 832436 bytes: control archive=2320 bytes. 703 bytes, 15 lines control 4340 bytes, 57 lines md5sums Package: bcftools Version: 1.22-1 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 2876 Depends: libc6 (>= 2.38), libhts3t64 (>= 1.22.1) Recommends: perl, python3-gffutils, python3-matplotlib Suggests: python3, python3-numpy, texlive-latex-recommended Section: science Priority: optional Homepage: https://samtools.github.io/bcftools/ Description: genomic variant calling and manipulation of VCF/BCF files BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. 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+------------------------------------------------------------------------------+ | Post Build Thu, 09 Jul 2026 03:57:50 +0000 | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup Thu, 09 Jul 2026 03:57:50 +0000 | +------------------------------------------------------------------------------+ Purging /build/bcftools-TfJ6sU Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Thu, 09 Jul 2026 03:57:51 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 55080 Build-Time: 163 Distribution: perl-5.44-throwaway Host Architecture: amd64 Install-Time: 12 Job: /srv/debomatic/incoming/bcftools_1.22-1.dsc Machine Architecture: amd64 Package: bcftools Package-Time: 182 Source-Version: 1.22-1 Space: 55080 Status: successful Version: 1.22-1 -------------------------------------------------------------------------------- Finished at 2026-07-09T03:57:48Z Build needed 00:03:02, 55080k disk space