sbuild (Debian sbuild) 0.89.1 (28 April 2025) on carme.larted.org.uk +==============================================================================+ | bcftools 1.21-1 (amd64) Mon, 30 Jun 2025 04:15:50 +0000 | +==============================================================================+ Package: bcftools Version: 1.21-1 Source Version: 1.21-1 Distribution: perl-5.40-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 Mon, 30 Jun 2025 04:15:51 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup bcftools_1.21-1 perl-5.40-throwaway amd64 ---------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup bcftools_1.21-1 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: Setting up apt archive... +------------------------------------------------------------------------------+ | Update chroot Mon, 30 Jun 2025 04:15:51 +0000 | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.40 InRelease [3042 B] Hit:2 http://deb.debian.org/debian unstable InRelease Get:1 file:/srv/reprepro perl-5.40 InRelease [3042 B] Get:3 http://localhost:3142/debian sid InRelease [208 kB] Get:4 http://localhost:3142/debian sid/main Sources.diff/Index [63.6 kB] Get:5 http://localhost:3142/debian sid/main Sources T-2025-06-30-0204.28-F-2025-06-30-0204.28.pdiff [2990 B] Get:5 http://localhost:3142/debian sid/main Sources T-2025-06-30-0204.28-F-2025-06-30-0204.28.pdiff [2990 B] Fetched 275 kB in 6s (44.8 kB/s) 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 Mon, 30 Jun 2025 04:16:00 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/bcftools_1.21-1.dsc exists in /srv/debomatic/incoming; copying to chroot +------------------------------------------------------------------------------+ | Install package build dependencies Mon, 30 Jun 2025 04:16:01 +0000 | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), zlib1g-dev, libbz2-dev, liblzma-dev, libhts-dev (>= 1.14), libgsl-dev, tabix, libio-pty-perl, build-essential Filtered Build-Depends: debhelper-compat (= 13), zlib1g-dev, libbz2-dev, liblzma-dev, libhts-dev (>= 1.14), libgsl-dev, tabix, libio-pty-perl, build-essential dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/build/bcftools-Mlf9dV/resolver-cpNy9c/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/build/bcftools-Mlf9dV/resolver-cpNy9c/apt_archive ./ InRelease Get:2 copy:/build/bcftools-Mlf9dV/resolver-cpNy9c/apt_archive ./ Release [609 B] Ign:3 copy:/build/bcftools-Mlf9dV/resolver-cpNy9c/apt_archive ./ Release.gpg Get:4 copy:/build/bcftools-Mlf9dV/resolver-cpNy9c/apt_archive ./ Sources [716 B] Get:5 copy:/build/bcftools-Mlf9dV/resolver-cpNy9c/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... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils comerr-dev debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian krb5-multidev libarchive-zip-perl libbrotli-dev libbrotli1 libbz2-dev libcom-err2 libcurl3t64-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libelf1t64 libevent-2.1-7t64 libfile-stripnondeterminism-perl libgmp-dev libgmpxx4ldbl libgnutls-dane0t64 libgnutls-openssl27t64 libgnutls28-dev libgsl-dev libgsl28 libgslcblas0 libgssapi-krb5-2 libgssrpc4t64 libhts-dev libhts3t64 libhtscodecs2 libidn2-dev libio-pty-perl libk5crypto3 libkadm5clnt-mit12 libkadm5srv-mit12 libkdb5-10t64 libkeyutils1 libkrb5-3 libkrb5-dev libkrb5support0 libldap-dev liblzma-dev libmagic-mgc libmagic1t64 libnghttp2-14 libnghttp2-dev libnghttp3-9 libnghttp3-dev libngtcp2-16 libngtcp2-crypto-gnutls-dev libngtcp2-crypto-gnutls8 libngtcp2-dev libp11-kit-dev libpipeline1 libpkgconf3 libpsl-dev libpsl5t64 librtmp-dev librtmp1 libssh2-1-dev libssh2-1t64 libssl-dev libtasn1-6-dev libtool libuchardet0 libunbound8 libxml2 libzstd-dev m4 man-db nettle-dev pkgconf pkgconf-bin po-debconf sensible-utils tabix zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc doc-base dh-make gettext-doc libasprintf-dev libgettextpo-dev gnulib-l10n groff krb5-doc libcurl4-doc libidn-dev gmp-doc libgmp10-doc libmpfr-dev dns-root-data gnutls-bin gnutls-doc gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html krb5-user liblzma-doc libnghttp2-doc p11-kit-doc libssl-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx bzip2-doc ca-certificates libarchive-cpio-perl krb5-locales publicsuffix libtasn1-doc libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils comerr-dev debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian krb5-multidev libarchive-zip-perl libbrotli-dev libbrotli1 libbz2-dev libcom-err2 libcurl3t64-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libelf1t64 libevent-2.1-7t64 libfile-stripnondeterminism-perl libgmp-dev libgmpxx4ldbl libgnutls-dane0t64 libgnutls-openssl27t64 libgnutls28-dev libgsl-dev libgsl28 libgslcblas0 libgssapi-krb5-2 libgssrpc4t64 libhts-dev libhts3t64 libhtscodecs2 libidn2-dev libio-pty-perl libk5crypto3 libkadm5clnt-mit12 libkadm5srv-mit12 libkdb5-10t64 libkeyutils1 libkrb5-3 libkrb5-dev libkrb5support0 libldap-dev liblzma-dev libmagic-mgc libmagic1t64 libnghttp2-14 libnghttp2-dev libnghttp3-9 libnghttp3-dev libngtcp2-16 libngtcp2-crypto-gnutls-dev libngtcp2-crypto-gnutls8 libngtcp2-dev libp11-kit-dev libpipeline1 libpkgconf3 libpsl-dev libpsl5t64 librtmp-dev librtmp1 libssh2-1-dev libssh2-1t64 libssl-dev libtasn1-6-dev libtool libuchardet0 libunbound8 libxml2 libzstd-dev m4 man-db nettle-dev pkgconf pkgconf-bin po-debconf sbuild-build-depends-main-dummy sensible-utils tabix zlib1g-dev 0 upgraded, 90 newly installed, 0 to remove and 0 not upgraded. Need to get 30.6 MB/31.0 MB of archives. After this operation, 115 MB of additional disk space will be used. Get:1 copy:/build/bcftools-Mlf9dV/resolver-cpNy9c/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [904 B] Get:2 file:/srv/reprepro perl-5.40/main amd64 libldap-dev amd64 2.6.10+dfsg-1+b1 [312 kB] Get:3 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.25 [25.0 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get:7 file:/srv/reprepro perl-5.40/main amd64 libio-pty-perl amd64 1:1.20-1+b4 [34.3 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2 [243 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41-5 [94.6 kB] Get:12 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get:13 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get:14 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-8 [294 kB] Get:15 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get:16 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get:17 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-3+b1 [25.0 kB] Get:20 http://deb.debian.org/debian unstable/main amd64 comerr-dev amd64 2.1-1.47.2-3+b1 [56.7 kB] Get:21 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.2 [90.9 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-4 [539 kB] Get:23 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get:24 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:25 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get:26 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get:27 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get:29 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-1 [698 kB] Get:30 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2 [1680 kB] Get:31 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:32 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:33 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.2 [919 kB] Get:34 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get:35 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get:36 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get:37 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get:38 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get:39 http://deb.debian.org/debian unstable/main amd64 libgssrpc4t64 amd64 1.21.3-5 [60.0 kB] Get:40 http://deb.debian.org/debian unstable/main amd64 libkadm5clnt-mit12 amd64 1.21.3-5 [42.5 kB] Get:41 http://deb.debian.org/debian unstable/main amd64 libkdb5-10t64 amd64 1.21.3-5 [42.6 kB] Get:42 http://deb.debian.org/debian unstable/main amd64 libkadm5srv-mit12 amd64 1.21.3-5 [54.2 kB] Get:43 http://deb.debian.org/debian unstable/main amd64 krb5-multidev amd64 1.21.3-5 [126 kB] Get:44 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get:45 http://deb.debian.org/debian unstable/main amd64 libbrotli-dev amd64 1.1.0-2+b7 [316 kB] Get:46 http://deb.debian.org/debian unstable/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Get:47 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1.1 [76.0 kB] Get:48 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.8.0-1 [67.7 kB] Get:49 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.11.0-1 [131 kB] Get:50 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.11.0-1 [29.3 kB] Get:51 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get:52 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get:53 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get:54 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.14.1-2 [384 kB] Get:55 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get:56 http://deb.debian.org/debian unstable/main amd64 libunbound8 amd64 1.22.0-1+b1 [598 kB] Get:57 http://deb.debian.org/debian unstable/main amd64 libgnutls-dane0t64 amd64 3.8.9-2 [455 kB] Get:58 http://deb.debian.org/debian unstable/main amd64 libgnutls-openssl27t64 amd64 3.8.9-2 [455 kB] Get:59 http://deb.debian.org/debian unstable/main amd64 libidn2-dev amd64 2.3.8-2 [103 kB] Get:60 http://deb.debian.org/debian unstable/main amd64 libp11-kit-dev amd64 0.25.5-3 [208 kB] Get:61 http://deb.debian.org/debian unstable/main amd64 libtasn1-6-dev amd64 4.20.0-2 [99.2 kB] Get:62 http://deb.debian.org/debian unstable/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-3 [329 kB] Get:63 http://deb.debian.org/debian unstable/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-3 [642 kB] Get:64 http://deb.debian.org/debian unstable/main amd64 nettle-dev amd64 3.10.1-1 [1318 kB] Get:65 http://deb.debian.org/debian unstable/main amd64 libgnutls28-dev amd64 3.8.9-2 [1401 kB] Get:66 http://deb.debian.org/debian unstable/main amd64 libkrb5-dev amd64 1.21.3-5 [16.1 kB] Get:67 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get:68 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get:69 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get:70 http://deb.debian.org/debian unstable/main amd64 libnghttp2-dev amd64 1.64.0-1.1 [116 kB] Get:71 http://deb.debian.org/debian unstable/main amd64 libnghttp3-dev amd64 1.8.0-1 [91.3 kB] Get:72 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.11.0-1 [34.0 kB] Get:73 http://deb.debian.org/debian unstable/main amd64 libngtcp2-dev amd64 1.11.0-1 [179 kB] Get:74 http://deb.debian.org/debian unstable/main amd64 libpsl-dev amd64 0.21.2-1.1+b1 [77.6 kB] Get:75 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get:76 http://deb.debian.org/debian unstable/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-2+b5 [68.0 kB] Get:77 http://deb.debian.org/debian unstable/main amd64 libssl-dev amd64 3.5.0-2 [2950 kB] Get:78 http://deb.debian.org/debian unstable/main amd64 libssh2-1-dev amd64 1.11.1-1 [393 kB] Get:79 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.7+dfsg-1 [371 kB] Get:80 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls-dev amd64 8.14.1-2 [503 kB] Get:81 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.23-2 [47.3 kB] Get:82 http://deb.debian.org/debian unstable/main amd64 libdeflate-dev amd64 1.23-2 [55.9 kB] Get:83 http://deb.debian.org/debian unstable/main amd64 libgslcblas0 amd64 2.8+dfsg-5 [116 kB] Get:84 http://deb.debian.org/debian unstable/main amd64 libgsl28 amd64 2.8+dfsg-5 [994 kB] Get:85 http://deb.debian.org/debian unstable/main amd64 libgsl-dev amd64 2.8+dfsg-5 [1222 kB] Get:86 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.1-2 [95.8 kB] Get:87 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.21+ds-1 [463 kB] Get:88 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.8.1-1 [348 kB] Get:89 http://deb.debian.org/debian unstable/main amd64 libhts-dev amd64 1.21+ds-1 [1733 kB] Get:90 http://deb.debian.org/debian unstable/main amd64 tabix amd64 1.21+ds-1 [496 kB] Preconfiguring packages ... Fetched 30.6 MB in 0s (77.5 MB/s) Selecting previously unselected package sensible-utils. (Reading database ... 23092 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.25_all.deb ... Unpacking sensible-utils (0.0.25) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.46-5_amd64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-2_amd64.deb ... Unpacking gettext-base (0.23.1-2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-9_amd64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.41-5_amd64.deb ... Unpacking bsdextrautils (2.41-5) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... 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_1.4.19-8_amd64.deb ... Unpacking m4 (1.4.19-8) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. 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Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.24.2) ... Setting up libbrotli1:amd64 (1.1.0-2+b7) ... Setting up libmagic1t64:amd64 (1:5.46-5) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up libnghttp2-14:amd64 (1.64.0-1.1) ... Setting up libdeflate0:amd64 (1.23-2) ... Setting up gettext-base (0.23.1-2) ... Setting up m4 (1.4.19-8) ... Setting up libevent-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up libcom-err2:amd64 (1.47.2-3+b1) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up libpsl-dev:amd64 (0.21.2-1.1+b1) ... Setting up libkrb5support0:amd64 (1.21.3-5) ... Setting up autotools-dev (20240727.1) ... Setting up libunbound8:amd64 (1.22.0-1+b1) ... Setting up libpkgconf3:amd64 (1.8.1-4) ... Setting up libgmpxx4ldbl:amd64 (2:6.3.0+dfsg-3) ... Setting up libgnutls-dane0t64:amd64 (3.8.9-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libldap-dev:amd64 (2.6.10+dfsg-1+b1) ... Setting up comerr-dev:amd64 (2.1-1.47.2-3+b1) ... Setting up libssl-dev:amd64 (3.5.0-2) ... Setting up autopoint (0.23.1-2) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libk5crypto3:amd64 (1.21.3-5) ... Setting up libidn2-dev:amd64 (2.3.8-2) ... Setting up autoconf (2.72-3.1) ... Setting up libnghttp3-9:amd64 (1.8.0-1) ... Setting up libnghttp3-dev:amd64 (1.8.0-1) ... Setting up liblzma-dev:amd64 (5.8.1-1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.25) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up libngtcp2-16:amd64 (1.11.0-1) ... Setting up libkrb5-3:amd64 (1.21.3-5) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up libgsl28:amd64 (2.8+dfsg-5) ... Setting up libtasn1-6-dev:amd64 (4.20.0-2) ... Setting up libdeflate-dev:amd64 (1.23-2) ... Setting up tabix (1.21+ds-1) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-1) ... Setting up libbrotli-dev:amd64 (1.1.0-2+b7) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.11.0-1) ... Setting up libp11-kit-dev:amd64 (0.25.5-3) ... Setting up libbz2-dev:amd64 (1.0.8-6) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up gettext (0.23.1-2) ... Setting up libgsl-dev (2.8+dfsg-5) ... Setting up libgmp-dev:amd64 (2:6.3.0+dfsg-3) ... Setting up nettle-dev:amd64 (3.10.1-1) ... Setting up libtool (2.5.4-4) ... Setting up libngtcp2-crypto-gnutls-dev:amd64 (1.11.0-1) ... Setting up libngtcp2-dev:amd64 (1.11.0-1) ... Setting up pkgconf:amd64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-5) ... Setting up libssh2-1-dev:amd64 (1.11.1-1) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-9) ... Setting up libgnutls28-dev:amd64 (3.8.9-2) ... Setting up libnghttp2-dev:amd64 (1.64.0-1.1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3t64-gnutls:amd64 (8.14.1-2) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libgssrpc4t64:amd64 (1.21.3-5) ... Setting up librtmp-dev:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libhts3t64:amd64 (1.21+ds-1) ... Setting up libkadm5clnt-mit12:amd64 (1.21.3-5) ... Setting up libkdb5-10t64:amd64 (1.21.3-5) ... Setting up debhelper (13.24.2) ... Setting up libkadm5srv-mit12:amd64 (1.21.3-5) ... Setting up krb5-multidev:amd64 (1.21.3-5) ... Setting up libkrb5-dev:amd64 (1.21.3-5) ... Setting up libcurl4-gnutls-dev:amd64 (8.14.1-2) ... Setting up libhts-dev:amd64 (1.21+ds-1) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.41-9) ... +------------------------------------------------------------------------------+ | Check architectures Mon, 30 Jun 2025 04:16:12 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Build environment Mon, 30 Jun 2025 04:16:12 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 6.12.25-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.25-1 (2025-04-25) amd64 (x86_64) Toolchain package versions: binutils_2.44-3 dpkg-dev_1.22.20 g++-13_13.4.0-1 g++-14_14.2.0-19 gcc-13_13.4.0-1 gcc-14_14.2.0-19 libc6-dev_2.41-9 libstdc++-13-dev_13.4.0-1 libstdc++-14-dev_14.2.0-19 libstdc++6_14.2.0-19 linux-libc-dev_6.12.33-1 Package versions: adduser_3.152 apt_3.0.3 autoconf_2.72-3.1 automake_1:1.17-4 autopoint_0.23.1-2 autotools-dev_20240727.1 base-files_13.8 base-passwd_3.6.7 bash_5.2.37-2+b3 binutils_2.44-3 binutils-common_2.44-3 binutils-x86-64-linux-gnu_2.44-3 bsdextrautils_2.41-5 bsdutils_1:2.41-5 build-essential_12.12 bzip2_1.0.8-6 comerr-dev_2.1-1.47.2-3+b1 coreutils_9.7-3 cpp_4:14.2.0-1 cpp-13_13.4.0-1 cpp-13-x86-64-linux-gnu_13.4.0-1 cpp-14_14.2.0-19 cpp-14-x86-64-linux-gnu_14.2.0-19 cpp-x86-64-linux-gnu_4:14.2.0-1 dash_0.5.12-12 debconf_1.5.91 debhelper_13.24.2 debian-archive-keyring_2025.1 debianutils_5.23.1 dh-autoreconf_20 dh-strip-nondeterminism_1.14.1-2 diffutils_1:3.10-4 dirmngr_2.4.7-21+b1 dpkg_1.22.20 dpkg-dev_1.22.20 dwz_0.15-1+b1 eatmydata_131-2 file_1:5.46-5 findutils_4.10.0-3 g++_4:14.2.0-1 g++-13_13.4.0-1 g++-13-x86-64-linux-gnu_13.4.0-1 g++-14_14.2.0-19 g++-14-x86-64-linux-gnu_14.2.0-19 g++-x86-64-linux-gnu_4:14.2.0-1 gcc_4:14.2.0-1 gcc-13_13.4.0-1 gcc-13-base_13.4.0-1 gcc-13-x86-64-linux-gnu_13.4.0-1 gcc-14_14.2.0-19 gcc-14-base_14.2.0-19 gcc-14-x86-64-linux-gnu_14.2.0-19 gcc-x86-64-linux-gnu_4:14.2.0-1 gettext_0.23.1-2 gettext-base_0.23.1-2 gnupg_2.4.7-21 gnupg-l10n_2.4.7-21 gnupg-utils_2.4.7-21+b1 gpg_2.4.7-21+b1 gpg-agent_2.4.7-21+b1 gpg-wks-client_2.4.7-21+b1 gpgconf_2.4.7-21+b1 gpgsm_2.4.7-21+b1 gpgv_2.4.7-21+b1 grep_3.11-4 groff-base_1.23.0-9 gzip_1.13-1 hostname_3.25 init-system-helpers_1.68 intltool-debian_0.35.0+20060710.6 krb5-multidev_1.21.3-5 libacl1_2.3.2-2+b1 libapt-pkg6.0t64_2.9.25 libapt-pkg7.0_3.0.3 libarchive-zip-perl_1.68-1 libasan8_14.2.0-19 libassuan0_2.5.6-1+b1 libassuan9_3.0.2-2 libatomic1_14.2.0-19 libattr1_1:2.5.2-3 libaudit-common_1:4.0.2-2 libaudit1_1:4.0.2-2+b2 libbinutils_2.44-3 libblkid1_2.41-5 libbrotli-dev_1.1.0-2+b7 libbrotli1_1.1.0-2+b7 libbsd0_0.12.2-2 libbz2-1.0_1.0.8-6 libbz2-dev_1.0.8-6 libc-bin_2.41-9 libc-dev-bin_2.41-9 libc-l10n_2.41-9 libc6_2.41-9 libc6-dev_2.41-9 libcap-ng0_0.8.5-4+b1 libcap2_1:2.75-9 libcc1-0_14.2.0-19 libcom-err2_1.47.2-3+b1 libcrypt-dev_1:4.4.38-1 libcrypt1_1:4.4.38-1 libctf-nobfd0_2.44-3 libctf0_2.44-3 libcurl3t64-gnutls_8.14.1-2 libcurl4-gnutls-dev_8.14.1-2 libdb5.3t64_5.3.28+dfsg2-9 libdebconfclient0_0.279 libdebhelper-perl_13.24.2 libdeflate-dev_1.23-2 libdeflate0_1.23-2 libdpkg-perl_1.22.20 libeatmydata1_131-2+b1 libelf1t64_0.192-4 libevent-2.1-7t64_2.1.12-stable-10+b1 libffi8_3.4.8-2 libfile-stripnondeterminism-perl_1.14.1-2 libgcc-13-dev_13.4.0-1 libgcc-14-dev_14.2.0-19 libgcc-s1_14.2.0-19 libgcrypt20_1.11.0-7 libgdbm-compat4t64_1.24-2 libgdbm6t64_1.24-2 libgmp-dev_2:6.3.0+dfsg-3 libgmp10_2:6.3.0+dfsg-3 libgmpxx4ldbl_2:6.3.0+dfsg-3 libgnutls-dane0t64_3.8.9-2 libgnutls-openssl27t64_3.8.9-2 libgnutls28-dev_3.8.9-2 libgnutls30t64_3.8.9-2 libgomp1_14.2.0-19 libgpg-error0_1.51-4 libgprofng0_2.44-3 libgsl-dev_2.8+dfsg-5 libgsl28_2.8+dfsg-5 libgslcblas0_2.8+dfsg-5 libgssapi-krb5-2_1.21.3-5 libgssrpc4t64_1.21.3-5 libhogweed6t64_3.10.1-1 libhts-dev_1.21+ds-1 libhts3t64_1.21+ds-1 libhtscodecs2_1.6.1-2 libhwasan0_14.2.0-19 libidn2-0_2.3.8-2 libidn2-dev_2.3.8-2 libio-pty-perl_1:1.20-1+b4 libisl23_0.27-1 libitm1_14.2.0-19 libjansson4_2.14-2+b3 libk5crypto3_1.21.3-5 libkadm5clnt-mit12_1.21.3-5 libkadm5srv-mit12_1.21.3-5 libkdb5-10t64_1.21.3-5 libkeyutils1_1.6.3-6 libkrb5-3_1.21.3-5 libkrb5-dev_1.21.3-5 libkrb5support0_1.21.3-5 libksba8_1.6.7-2+b1 liblastlog2-2_2.41-5 libldap-2.5-0_2.5.19+dfsg-1 libldap-dev_2.6.10+dfsg-1+b1 libldap2_2.6.10+dfsg-1+b1 liblsan0_14.2.0-19 liblz4-1_1.10.0-4 liblzma-dev_5.8.1-1 liblzma5_5.8.1-1 libmagic-mgc_1:5.46-5 libmagic1t64_1:5.46-5 libmd0_1.1.0-2+b1 libmount1_2.41-5 libmpc3_1.3.1-1+b3 libmpfr6_4.2.2-1 libncursesw6_6.5+20250216-2 libnettle8t64_3.10.1-1 libnghttp2-14_1.64.0-1.1 libnghttp2-dev_1.64.0-1.1 libnghttp3-9_1.8.0-1 libnghttp3-dev_1.8.0-1 libngtcp2-16_1.11.0-1 libngtcp2-crypto-gnutls-dev_1.11.0-1 libngtcp2-crypto-gnutls8_1.11.0-1 libngtcp2-dev_1.11.0-1 libnpth0t64_1.8-3 libp11-kit-dev_0.25.5-3 libp11-kit0_0.25.5-3 libpam-modules_1.7.0-5 libpam-modules-bin_1.7.0-5 libpam-runtime_1.7.0-5 libpam0g_1.7.0-5 libpcre2-8-0_10.45-1 libperl5.38t64_5.38.2-5 libperl5.40_5.40.1-4 libpipeline1_1.5.8-1 libpkgconf3_1.8.1-4 libpsl-dev_0.21.2-1.1+b1 libpsl5t64_0.21.2-1.1+b1 libquadmath0_14.2.0-19 libreadline8t64_8.2-6 librtmp-dev_2.4+20151223.gitfa8646d.1-2+b5 librtmp1_2.4+20151223.gitfa8646d.1-2+b5 libsasl2-2_2.1.28+dfsg1-9 libsasl2-modules-db_2.1.28+dfsg1-9 libseccomp2_2.6.0-2 libselinux1_3.8.1-1 libsemanage-common_3.8.1-1 libsemanage2_3.8.1-1 libsepol2_3.8.1-1 libsframe1_2.44-3 libsmartcols1_2.41-5 libsqlite3-0_3.46.1-6 libssh2-1-dev_1.11.1-1 libssh2-1t64_1.11.1-1 libssl-dev_3.5.0-2 libssl3t64_3.5.0-2 libstdc++-13-dev_13.4.0-1 libstdc++-14-dev_14.2.0-19 libstdc++6_14.2.0-19 libsystemd0_257.7-1 libtasn1-6_4.20.0-2 libtasn1-6-dev_4.20.0-2 libtinfo6_6.5+20250216-2 libtool_2.5.4-4 libtsan2_14.2.0-19 libubsan1_14.2.0-19 libuchardet0_0.0.8-1+b2 libudev1_257.7-1 libunbound8_1.22.0-1+b1 libunistring5_1.3-2 libuuid1_2.41-5 libxml2_2.12.7+dfsg+really2.9.14-1 libxxhash0_0.8.3-2 libzstd-dev_1.5.7+dfsg-1 libzstd1_1.5.7+dfsg-1 linux-libc-dev_6.12.33-1 locales-all_2.41-9 login_1:4.16.0-2+really2.41-5 login.defs_1:4.17.4-2 m4_1.4.19-8 make_4.4.1-2 man-db_2.13.1-1 mawk_1.3.4.20250131-1 ncurses-base_6.5+20250216-2 ncurses-bin_6.5+20250216-2 nettle-dev_3.10.1-1 openssl-provider-legacy_3.5.0-2 passwd_1:4.17.4-2 patch_2.8-2 perl_5.40.1-4 perl-base_5.40.1-4 perl-modules-5.38_5.38.2-5 perl-modules-5.40_5.40.1-4 pinentry-curses_1.3.1-2 pkgconf_1.8.1-4 pkgconf-bin_1.8.1-4 po-debconf_1.0.21+nmu1 readline-common_8.2-6 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.25 sqv_1.3.0-3 sysvinit-utils_3.14-4 tabix_1.21+ds-1 tar_1.35+dfsg-3.1 usr-is-merged_39+nmu2 util-linux_2.41-5 xz-utils_5.8.1-1 zlib1g_1:1.3.dfsg+really1.3.1-1+b1 zlib1g-dev_1:1.3.dfsg+really1.3.1-1+b1 +------------------------------------------------------------------------------+ | Build Mon, 30 Jun 2025 04:16:12 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: bcftools Binary: bcftools Architecture: any Version: 1.21-1 Maintainer: Debian Med Packaging Team Uploaders: Michael R. Crusoe , Étienne Mollier Homepage: https://samtools.github.io/bcftools/ Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/bcftools Vcs-Git: https://salsa.debian.org/med-team/bcftools.git Testsuite: autopkgtest Testsuite-Triggers: perl, tabix Build-Depends: debhelper-compat (= 13), zlib1g-dev, libbz2-dev, liblzma-dev, libhts-dev (>= 1.14), libgsl-dev, tabix , libio-pty-perl Package-List: bcftools deb science optional arch=any Checksums-Sha1: 7f367e0f03d4f56ca88d5f3a79435f196591fbce 3665160 bcftools_1.21.orig.tar.gz 5b3b3f9251d64665efa2c5ed61c6e2aef032cde1 7504 bcftools_1.21-1.debian.tar.xz Checksums-Sha256: 7484695c5d833fb1a89c2b886ec302db0514ba3c8e5ef7397b9302fa8bd37f8d 3665160 bcftools_1.21.orig.tar.gz d1332716453f270248afa7476a5a824b0289150a7829442f691559209dcc38cf 7504 bcftools_1.21-1.debian.tar.xz Files: e144a5777c606c69eb643ae8ff613dbb 3665160 bcftools_1.21.orig.tar.gz 756abc1b4df76e455bd705ddf6ef5c9e 7504 bcftools_1.21-1.debian.tar.xz Dgit: 1cbbbd21cccc5d95d73df54271b167d9e450842a debian archive/debian/1.21-1 https://git.dgit.debian.org/bcftools -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmeuYIEUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdpyzRAAlczvukE0/A+j5esHHalBAeaq8nnO SC4BULLNsaVcn31OlRTGS1RXt1zU6u3ise+jLfRMAbhM4Qx57Ek9S+2+uvX2M5lh 6Wlz3M6DvyTEXN0MZTztIinmdxODYf/IiD8d4qDf8KYZNBeKE+spfINNeRiWyl6e /QXwVTUB0jRc5ZBqsOONR4uOliMKk3LWUy3xwM3YzUKhVlFQpf2OJXk5bQSew6NM PIwjBLcHdDE42tplpMuRjT0FdWk4i8EeZlR8oIdBwoVc1ffNqRpWbz77OJouDhe8 dz7kPHok/2DEBod4k3yeIZH0deK+G47sycXhhSOA7IS+43opAYIHFscpHZMdnoaA lQjIMES546gBHagarHdb5dbHKcvWuq2aQdsuyc0Z2kOnS4Kaop/YugT14ba0pu73 50x5eyPJL2LgnFDb+36HygKNL0CCA6v6EOC7qEU5zzqkmXYXBWEKGxht4KvXbdtc NAvxqxbw2AtQF1kRH6dur00lo9ZCjVq+wa5NnQHZh+BILAIrdo8lpM5Gm6yCifwE 9HU+bY2IaF3LMMgTxvRVyT8yeu65YtA6FbZjnYW6Y0ZeVlQLFvn+830b4L4fWlt3 waTPrdRQcvexseaLFmxuZY2igfMRPtzyf3UXQaomDkitd4jC0WhH+Tg6OoTD88Fa IFTp1pvu+xmgjw4= =1qOu -----END PGP SIGNATURE----- dpkg-source: warning: cannot verify inline signature for ./bcftools_1.21-1.dsc: no acceptable signature found dpkg-source: info: extracting bcftools in /build/bcftools-Mlf9dV/bcftools-1.21 dpkg-source: info: unpacking bcftools_1.21.orig.tar.gz dpkg-source: info: unpacking bcftools_1.21-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying skip_new_test_failing_on_32bit.patch dpkg-source: info: applying 2to3.patch Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Timed Build Commands Mon, 30 Jun 2025 04:16:13 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network bcftools_1.21-1 perl-5.40-throwaway amd64 ---------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network bcftools_1.21-1 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANG=en_GB.UTF-8 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-Mlf9dV/bcftools-1.21 SCHROOT_ALIAS_NAME=perl-5.40-throwaway-amd64-debomatic SCHROOT_CHROOT_NAME=perl-5.40-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=110 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=perl-5.40-amd64-debomatic-cad9bd0f-aa56-4f06-bf05-ae128723318f SCHROOT_UID=1002 SCHROOT_USER=debomatic SHELL=/bin/sh USER=debomatic dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -Zxz dpkg-buildpackage: info: source package bcftools dpkg-buildpackage: info: source version 1.21-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source -Zxz --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean rm -f config.mk && touch config.mk dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/bcftools-Mlf9dV/bcftools-1.21' dh_auto_clean make -j2 distclean make[2]: Entering directory '/build/bcftools-Mlf9dV/bcftools-1.21' rm -f test/*.o test/*.fa.fai test/*~ test/test-rbuf test/test-regidx rm -f plugins/*.so plugins/*.P rm -f test/*.unsorted.hex test/*.unsorted.tsv rm -rf plugins/*.dSYM rm -f gmon.out *.o *.a *~ bcftools version.h rm -rf *.dSYM test/*.dSYM rm -f config.cache config.h config.log config.mk config.status rm -rf autom4te.cache rm -f TAGS make[2]: Leaving directory '/build/bcftools-Mlf9dV/bcftools-1.21' rm -f test/mpileup/indel-AD.1.out.new test/view-t.1.out.new test/view-t.2.out.new make[1]: Leaving directory '/build/bcftools-Mlf9dV/bcftools-1.21' dh_clean dpkg-source -Zxz -b . dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building bcftools using existing ./bcftools_1.21.orig.tar.gz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: building bcftools in bcftools_1.21-1.debian.tar.xz dpkg-source: info: building bcftools in bcftools_1.21-1.dsc debian/rules binary dh binary dh_update_autotools_config debian/rules override_dh_autoreconf make[1]: Entering directory '/build/bcftools-Mlf9dV/bcftools-1.21' rm -f config.mk && touch config.mk export MAKEFLAGS="-s"; dh_autoreconf configure.ac:94: warning: _AC_CONFIG_SUBDIRS: you should use literals ./lib/autoconf/status.m4:1096: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:94: the top level make[1]: Leaving directory '/build/bcftools-Mlf9dV/bcftools-1.21' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/bcftools-Mlf9dV/bcftools-1.21' dh_auto_configure -- \ --with-htslib=system \ --enable-gsl \ --with-cblas=gslcblas \ --with-bcf-plugin-dir=/usr/lib/x86_64-linux-gnu/bcftools ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system --enable-gsl --with-cblas=gslcblas --with-bcf-plugin-dir=/usr/lib/x86_64-linux-gnu/bcftools checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking for -Wdate-time -D_FORTIFY_SOURCE=2 option for large files... none needed checking for htslib/sam.h... yes checking for hts_version in -lhts... yes checking shared library type... plain .so checking for library containing dlopen... none required checking if the compiler accepts -rdynamic... yes checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing regcomp... none required configure: creating ./config.status config.status: creating config.mk config.status: creating config.h make[1]: Leaving directory '/build/bcftools-Mlf9dV/bcftools-1.21' dh_auto_build make -j2 make[1]: Entering directory '/build/bcftools-Mlf9dV/bcftools-1.21' echo '#define BCFTOOLS_VERSION "1.21"' > version.h gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-Mlf9dV/bcftools-1.21=. -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 gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-Mlf9dV/bcftools-1.21=. -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 gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-Mlf9dV/bcftools-1.21=. -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 gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-Mlf9dV/bcftools-1.21=. -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 gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-Mlf9dV/bcftools-1.21=. -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 gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-Mlf9dV/bcftools-1.21=. -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 gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-Mlf9dV/bcftools-1.21=. -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 gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-Mlf9dV/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time 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-D_FORTIFY_SOURCE=2 -DPLUGINPATH='"/usr/lib/x86_64-linux-gnu/bcftools"' -c -o vcfplugin.o vcfplugin.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-Mlf9dV/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-rbuf.o test/test-rbuf.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-Mlf9dV/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-regidx.o test/test-regidx.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-Mlf9dV/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/GTisec.so version.c plugins/GTisec.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-Mlf9dV/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/GTsubset.so version.c plugins/GTsubset.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-Mlf9dV/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/ad-bias.so convert.c version.c plugins/ad-bias.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-Mlf9dV/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/add-variantkey.so version.c plugins/add-variantkey.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-Mlf9dV/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/af-dist.so bin.c version.c plugins/af-dist.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-Mlf9dV/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/allele-length.so version.c plugins/allele-length.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-Mlf9dV/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/check-ploidy.so version.c plugins/check-ploidy.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-Mlf9dV/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/check-sparsity.so version.c plugins/check-sparsity.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-Mlf9dV/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/color-chrs.so HMM.c version.c plugins/color-chrs.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-Mlf9dV/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/contrast.so version.c plugins/contrast.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-Mlf9dV/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/counts.so version.c plugins/counts.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-Mlf9dV/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/dosage.so version.c plugins/dosage.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-Mlf9dV/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/fill-AN-AC.so version.c plugins/fill-AN-AC.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-Mlf9dV/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/fill-from-fasta.so filter.c version.c plugins/fill-from-fasta.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-Mlf9dV/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/fill-tags.so version.c plugins/fill-tags.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-Mlf9dV/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/fixploidy.so ploidy.c regidx.c version.c plugins/fixploidy.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-Mlf9dV/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/fixref.so version.c plugins/fixref.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-Mlf9dV/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/frameshifts.so version.c plugins/frameshifts.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-Mlf9dV/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/guess-ploidy.so version.c plugins/guess-ploidy.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-Mlf9dV/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/gvcfz.so version.c plugins/gvcfz.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-Mlf9dV/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/impute-info.so version.c plugins/impute-info.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-Mlf9dV/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/indel-stats.so version.c plugins/indel-stats.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-Mlf9dV/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/isecGT.so smpl_ilist.c version.c plugins/isecGT.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-Mlf9dV/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/mendelian2.so version.c plugins/mendelian2.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-Mlf9dV/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/missing2ref.so version.c plugins/missing2ref.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-Mlf9dV/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/parental-origin.so version.c plugins/parental-origin.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-Mlf9dV/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/prune.so version.c plugins/prune.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-Mlf9dV/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/remove-overlaps.so version.c plugins/remove-overlaps.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-Mlf9dV/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/scatter.so version.c plugins/scatter.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-Mlf9dV/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/setGT.so version.c plugins/setGT.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-Mlf9dV/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/smpl-stats.so version.c plugins/smpl-stats.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-Mlf9dV/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/split-vep.so version.c plugins/split-vep.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-Mlf9dV/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/split.so version.c plugins/split.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-Mlf9dV/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/tag2tag.so version.c plugins/tag2tag.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-Mlf9dV/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/trio-dnm2.so version.c plugins/trio-dnm2.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-Mlf9dV/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/trio-stats.so version.c plugins/trio-stats.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-Mlf9dV/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/trio-switch-rate.so version.c plugins/trio-switch-rate.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-Mlf9dV/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/variant-distance.so version.c plugins/variant-distance.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-Mlf9dV/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/variantkey-hex.so version.c plugins/variantkey-hex.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-Mlf9dV/bcftools-1.21=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o main.o main.c gcc -Wl,-z,relro -Wl,-z,now -o test/test-rbuf test/test-rbuf.o -lz gcc -Wl,-z,relro -Wl,-z,now -o test/test-regidx test/test-regidx.o regidx.o -lhts -lpthread -lz gcc -rdynamic -Wl,-z,relro -Wl,-z,now -o bcftools main.o vcfindex.o tabix.o vcfstats.o vcfisec.o vcfmerge.o vcfquery.o vcffilter.o filter.o vcfsom.o vcfnorm.o vcfgtcheck.o vcfview.o vcfannotate.o vcfroh.o vcfconcat.o vcfcall.o mcall.o vcmp.o gvcf.o reheader.o convert.o vcfconvert.o tsv2vcf.o vcfcnv.o vcfhead.o HMM.o consensus.o ploidy.o bin.o hclust.o version.o regidx.o smpl_ilist.o csq.o vcfbuf.o mpileup.o bam2bcf.o bam2bcf_indel.o bam2bcf_iaux.o bam2bcf_edlib.o read_consensus.o bam_sample.o vcfsort.o cols.o extsort.o dist.o abuf.o ccall.o em.o prob1.o kmin.o str_finder.o gff.o edlib.o vcfplugin.o -lhts -lm -lz -lpthread make[1]: Leaving directory '/build/bcftools-Mlf9dV/bcftools-1.21' debian/rules override_dh_auto_test make[1]: Entering directory '/build/bcftools-Mlf9dV/bcftools-1.21' make test-no-plugins VERBOSE=1 make[2]: Entering directory '/build/bcftools-Mlf9dV/bcftools-1.21' ./test/test-rbuf Inserted 1-9 starting at offset 5: 5 6 7 8 9 0 1 2 3 1 2 3 4 5 6 7 8 9 4th is 4 Deleting 1-2: 7 8 9 0 1 2 3 3 4 5 6 7 8 9 Prepending 0-8: 8 9 0 1 2 3 4 5 6 7 8 7 6 5 4 3 2 1 0 3 Expanding: 8 9 10 11 12 13 14 15 16 17 8 7 6 5 4 3 2 1 0 3 ./test/test-regidx REF_PATH=: ./test/test.pl --exec bgzip= --exec tabix= --htsdir= ${TEST_OPTS:-} test_usage: bcftools .. ok test_usage_subcommand: bcftools index .. ok test_usage_subcommand: bcftools annotate .. ok test_usage_subcommand: bcftools concat .. ok test_usage_subcommand: bcftools convert .. ok test_usage_subcommand: bcftools head .. ok test_usage_subcommand: bcftools isec .. ok test_usage_subcommand: bcftools merge .. ok test_usage_subcommand: bcftools norm .. ok test_usage_subcommand: bcftools plugin .. ok test_usage_subcommand: bcftools query .. ok test_usage_subcommand: bcftools reheader .. ok test_usage_subcommand: bcftools sort .. ok test_usage_subcommand: bcftools view .. ok test_usage_subcommand: bcftools call .. ok test_usage_subcommand: bcftools consensus .. ok test_usage_subcommand: bcftools cnv .. ok test_usage_subcommand: bcftools csq .. ok test_usage_subcommand: bcftools filter .. ok test_usage_subcommand: bcftools gtcheck .. ok test_usage_subcommand: bcftools mpileup .. ok test_usage_subcommand: bcftools roh .. ok test_usage_subcommand: bcftools stats .. ok test_tabix: tabix /tmp/MadjcxLl4P/merge.a.vcf.gz 2:3199812-3199812 .. ok test_tabix: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -H /tmp/MadjcxLl4P/merge.a.bcf 2:3199812-3199812 .. ok test_tabix: tabix /tmp/MadjcxLl4P/merge.a.vcf.gz 1:3000151-3000151 .. ok test_tabix: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -H /tmp/MadjcxLl4P/merge.a.bcf 1:3000151-3000151 .. ok test_index: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -H /tmp/MadjcxLl4P/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -H /tmp/MadjcxLl4P/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -H /tmp/MadjcxLl4P/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -H /tmp/MadjcxLl4P/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -H /tmp/MadjcxLl4P/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -H /tmp/MadjcxLl4P/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -H /tmp/MadjcxLl4P/large_chrom_csi_limit.bcf chr20 .. ok test_index: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -H /tmp/MadjcxLl4P/large_chrom_csi_limit.bcf chr20 .. ok test_index: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -H /tmp/MadjcxLl4P/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -H /tmp/MadjcxLl4P/large_chrom_csi_limit.bcf chr20 .. ok test_vcf_idxstats: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools index -s /tmp/MadjcxLl4P/idx.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools index -s /tmp/MadjcxLl4P/idx.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools index -s /tmp/MadjcxLl4P/idx.bcf .. ok test_vcf_idxstats: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools index -n /tmp/MadjcxLl4P/idx.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools index -n /tmp/MadjcxLl4P/idx.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools index -n /tmp/MadjcxLl4P/idx.vcf.gz.csi .. ok test_vcf_idxstats: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools index -n /tmp/MadjcxLl4P/idx.bcf .. ok test_vcf_idxstats: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools index -n /tmp/MadjcxLl4P/idx.bcf.csi .. ok test_vcf_idxstats: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools index -s /tmp/MadjcxLl4P/empty.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools index -s /tmp/MadjcxLl4P/empty.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools index -s /tmp/MadjcxLl4P/empty.bcf .. ok test_vcf_idxstats: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools index -n /tmp/MadjcxLl4P/empty.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools index -n /tmp/MadjcxLl4P/empty.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools index -n /tmp/MadjcxLl4P/empty.vcf.gz.csi .. ok test_vcf_idxstats: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools index -n /tmp/MadjcxLl4P/empty.bcf .. ok test_vcf_idxstats: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools index -n /tmp/MadjcxLl4P/empty.bcf.csi .. ok test_vcf_check: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools stats -s - /tmp/MadjcxLl4P/check.vcf.gz | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/check.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools stats -s - | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check_merge: /build/bcftools-Mlf9dV/bcftools-1.21/misc/plot-vcfstats -m /tmp/MadjcxLl4P/check.1.chk /tmp/MadjcxLl4P/check.2.chk /tmp/MadjcxLl4P/check.3.chk /tmp/MadjcxLl4P/check.4.chk | grep -v 'plot-vcfstats' | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_stats: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools stats -s - /tmp/MadjcxLl4P/stats.a.vcf.gz /tmp/MadjcxLl4P/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools stats -s B /tmp/MadjcxLl4P/stats.a.vcf.gz /tmp/MadjcxLl4P/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools stats -s - /tmp/MadjcxLl4P/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools stats -s - -i 'type="snp"' /tmp/MadjcxLl4P/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools stats -s - /tmp/MadjcxLl4P/stats.vaf.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_isec: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools isec -n =2 /tmp/MadjcxLl4P/isec.a.vcf.gz /tmp/MadjcxLl4P/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools isec -Ob -n =2 /tmp/MadjcxLl4P/isec.a.vcf.gz /tmp/MadjcxLl4P/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/MadjcxLl4P/isec.a.vcf.gz /tmp/MadjcxLl4P/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools isec -Ob -n =2 -i"STRLEN(REF)==2" /tmp/MadjcxLl4P/isec.a.vcf.gz /tmp/MadjcxLl4P/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools isec -n =2 -c both /tmp/MadjcxLl4P/isec.a.vcf.gz /tmp/MadjcxLl4P/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools isec -Ob -n =2 -c both /tmp/MadjcxLl4P/isec.a.vcf.gz /tmp/MadjcxLl4P/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools isec -n =2 -c any /tmp/MadjcxLl4P/isec.a.vcf.gz /tmp/MadjcxLl4P/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools isec -Ob -n =2 -c any /tmp/MadjcxLl4P/isec.a.vcf.gz /tmp/MadjcxLl4P/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools isec -C -c any /tmp/MadjcxLl4P/isec.a.vcf.gz /tmp/MadjcxLl4P/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools isec -Ob -C -c any /tmp/MadjcxLl4P/isec.a.vcf.gz /tmp/MadjcxLl4P/isec.b.vcf.gz .. ok test_vcf_isec2: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools isec --no-version -T /tmp/MadjcxLl4P/isec.tab.gz /tmp/MadjcxLl4P/isec.a.vcf.gz .. ok test_vcf_isec2: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools isec -Ob -T /tmp/MadjcxLl4P/isec.tab.gz /tmp/MadjcxLl4P/isec.a.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_isec: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools isec -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/MadjcxLl4P/isec-miss.1.1.vcf.gz /tmp/MadjcxLl4P/isec-miss.1.2.vcf.gz /tmp/MadjcxLl4P/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools isec -Ob -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/MadjcxLl4P/isec-miss.1.1.vcf.gz /tmp/MadjcxLl4P/isec-miss.1.2.vcf.gz /tmp/MadjcxLl4P/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools isec -R /build/bcftools-Mlf9dV/bcftools-1.21/test/isec-miss.1.regs.txt -n +1 /tmp/MadjcxLl4P/isec-miss.1.1.vcf.gz /tmp/MadjcxLl4P/isec-miss.1.2.vcf.gz /tmp/MadjcxLl4P/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools isec -Ob -R /build/bcftools-Mlf9dV/bcftools-1.21/test/isec-miss.1.regs.txt -n +1 /tmp/MadjcxLl4P/isec-miss.1.1.vcf.gz /tmp/MadjcxLl4P/isec-miss.1.2.vcf.gz /tmp/MadjcxLl4P/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools isec -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/MadjcxLl4P/isec-miss.2.1.vcf.gz /tmp/MadjcxLl4P/isec-miss.2.2.vcf.gz /tmp/MadjcxLl4P/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools isec -Ob -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/MadjcxLl4P/isec-miss.2.1.vcf.gz /tmp/MadjcxLl4P/isec-miss.2.2.vcf.gz /tmp/MadjcxLl4P/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools isec -R /build/bcftools-Mlf9dV/bcftools-1.21/test/isec-miss.1.regs.txt -n +1 /tmp/MadjcxLl4P/isec-miss.2.1.vcf.gz /tmp/MadjcxLl4P/isec-miss.2.2.vcf.gz /tmp/MadjcxLl4P/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools isec -Ob -R /build/bcftools-Mlf9dV/bcftools-1.21/test/isec-miss.1.regs.txt -n +1 /tmp/MadjcxLl4P/isec-miss.2.1.vcf.gz /tmp/MadjcxLl4P/isec-miss.2.2.vcf.gz /tmp/MadjcxLl4P/isec-miss.2.3.vcf.gz .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version /tmp/MadjcxLl4P/merge.11.a.vcf.gz /tmp/MadjcxLl4P/merge.11.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob /tmp/MadjcxLl4P/merge.11.a.vcf.gz /tmp/MadjcxLl4P/merge.11.b.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version /tmp/MadjcxLl4P/merge.11.a.bcf /tmp/MadjcxLl4P/merge.11.b.bcf .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob /tmp/MadjcxLl4P/merge.11.a.bcf /tmp/MadjcxLl4P/merge.11.b.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -i AF:join /tmp/MadjcxLl4P/merge.join.a.vcf.gz /tmp/MadjcxLl4P/merge.join.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob -i AF:join /tmp/MadjcxLl4P/merge.join.a.vcf.gz /tmp/MadjcxLl4P/merge.join.b.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -i AF:join /tmp/MadjcxLl4P/merge.join.a.bcf /tmp/MadjcxLl4P/merge.join.b.bcf .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob -i AF:join /tmp/MadjcxLl4P/merge.join.a.bcf /tmp/MadjcxLl4P/merge.join.b.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version --force-single /tmp/MadjcxLl4P/merge.LPL.a.vcf.gz .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob --force-single /tmp/MadjcxLl4P/merge.LPL.a.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version --force-single /tmp/MadjcxLl4P/merge.LPL.a.bcf .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob --force-single /tmp/MadjcxLl4P/merge.LPL.a.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version --force-samples /tmp/MadjcxLl4P/merge.LPL.a.vcf.gz /tmp/MadjcxLl4P/merge.LPL.b.vcf.gz /tmp/MadjcxLl4P/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/MadjcxLl4P/merge.LPL.a.vcf.gz /tmp/MadjcxLl4P/merge.LPL.b.vcf.gz /tmp/MadjcxLl4P/merge.LPL.c.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version --force-samples /tmp/MadjcxLl4P/merge.LPL.a.bcf /tmp/MadjcxLl4P/merge.LPL.b.bcf /tmp/MadjcxLl4P/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/MadjcxLl4P/merge.LPL.a.bcf /tmp/MadjcxLl4P/merge.LPL.b.bcf /tmp/MadjcxLl4P/merge.LPL.c.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version --force-samples -L 1 /tmp/MadjcxLl4P/merge.LPL.a.vcf.gz /tmp/MadjcxLl4P/merge.LPL.b.vcf.gz /tmp/MadjcxLl4P/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 1 /tmp/MadjcxLl4P/merge.LPL.a.vcf.gz /tmp/MadjcxLl4P/merge.LPL.b.vcf.gz /tmp/MadjcxLl4P/merge.LPL.c.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version --force-samples -L 1 /tmp/MadjcxLl4P/merge.LPL.a.bcf /tmp/MadjcxLl4P/merge.LPL.b.bcf /tmp/MadjcxLl4P/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 1 /tmp/MadjcxLl4P/merge.LPL.a.bcf /tmp/MadjcxLl4P/merge.LPL.b.bcf /tmp/MadjcxLl4P/merge.LPL.c.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version --force-samples -L 2 /tmp/MadjcxLl4P/merge.LPL.a.vcf.gz /tmp/MadjcxLl4P/merge.LPL.b.vcf.gz /tmp/MadjcxLl4P/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 2 /tmp/MadjcxLl4P/merge.LPL.a.vcf.gz /tmp/MadjcxLl4P/merge.LPL.b.vcf.gz /tmp/MadjcxLl4P/merge.LPL.c.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version --force-samples -L 2 /tmp/MadjcxLl4P/merge.LPL.a.bcf /tmp/MadjcxLl4P/merge.LPL.b.bcf /tmp/MadjcxLl4P/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 2 /tmp/MadjcxLl4P/merge.LPL.a.bcf /tmp/MadjcxLl4P/merge.LPL.b.bcf /tmp/MadjcxLl4P/merge.LPL.c.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version --force-samples -L 3 /tmp/MadjcxLl4P/merge.LPL.a.vcf.gz /tmp/MadjcxLl4P/merge.LPL.b.vcf.gz /tmp/MadjcxLl4P/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 3 /tmp/MadjcxLl4P/merge.LPL.a.vcf.gz /tmp/MadjcxLl4P/merge.LPL.b.vcf.gz /tmp/MadjcxLl4P/merge.LPL.c.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version --force-samples -L 3 /tmp/MadjcxLl4P/merge.LPL.a.bcf /tmp/MadjcxLl4P/merge.LPL.b.bcf /tmp/MadjcxLl4P/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 3 /tmp/MadjcxLl4P/merge.LPL.a.bcf /tmp/MadjcxLl4P/merge.LPL.b.bcf /tmp/MadjcxLl4P/merge.LPL.c.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version --force-samples -L 4 /tmp/MadjcxLl4P/merge.LPL.a.vcf.gz /tmp/MadjcxLl4P/merge.LPL.b.vcf.gz /tmp/MadjcxLl4P/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 4 /tmp/MadjcxLl4P/merge.LPL.a.vcf.gz /tmp/MadjcxLl4P/merge.LPL.b.vcf.gz /tmp/MadjcxLl4P/merge.LPL.c.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version --force-samples -L 4 /tmp/MadjcxLl4P/merge.LPL.a.bcf /tmp/MadjcxLl4P/merge.LPL.b.bcf /tmp/MadjcxLl4P/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 4 /tmp/MadjcxLl4P/merge.LPL.a.bcf /tmp/MadjcxLl4P/merge.LPL.b.bcf /tmp/MadjcxLl4P/merge.LPL.c.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version --force-samples -L 5 /tmp/MadjcxLl4P/merge.LPL.a.vcf.gz /tmp/MadjcxLl4P/merge.LPL.b.vcf.gz /tmp/MadjcxLl4P/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 5 /tmp/MadjcxLl4P/merge.LPL.a.vcf.gz /tmp/MadjcxLl4P/merge.LPL.b.vcf.gz /tmp/MadjcxLl4P/merge.LPL.c.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version --force-samples -L 5 /tmp/MadjcxLl4P/merge.LPL.a.bcf /tmp/MadjcxLl4P/merge.LPL.b.bcf /tmp/MadjcxLl4P/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -L 5 /tmp/MadjcxLl4P/merge.LPL.a.bcf /tmp/MadjcxLl4P/merge.LPL.b.bcf /tmp/MadjcxLl4P/merge.LPL.c.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version --force-samples /tmp/MadjcxLl4P/merge.a.vcf.gz /tmp/MadjcxLl4P/merge.b.vcf.gz /tmp/MadjcxLl4P/merge.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/MadjcxLl4P/merge.a.vcf.gz /tmp/MadjcxLl4P/merge.b.vcf.gz /tmp/MadjcxLl4P/merge.c.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version --force-samples /tmp/MadjcxLl4P/merge.a.bcf /tmp/MadjcxLl4P/merge.b.bcf /tmp/MadjcxLl4P/merge.c.bcf .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/MadjcxLl4P/merge.a.bcf /tmp/MadjcxLl4P/merge.b.bcf /tmp/MadjcxLl4P/merge.c.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version --force-samples -Fx /tmp/MadjcxLl4P/merge.a.vcf.gz /tmp/MadjcxLl4P/merge.b.vcf.gz /tmp/MadjcxLl4P/merge.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -Fx /tmp/MadjcxLl4P/merge.a.vcf.gz /tmp/MadjcxLl4P/merge.b.vcf.gz /tmp/MadjcxLl4P/merge.c.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version --force-samples -Fx /tmp/MadjcxLl4P/merge.a.bcf /tmp/MadjcxLl4P/merge.b.bcf /tmp/MadjcxLl4P/merge.c.bcf .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -Fx /tmp/MadjcxLl4P/merge.a.bcf /tmp/MadjcxLl4P/merge.b.bcf /tmp/MadjcxLl4P/merge.c.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version --force-samples -0 /tmp/MadjcxLl4P/merge.a.vcf.gz /tmp/MadjcxLl4P/merge.b.vcf.gz /tmp/MadjcxLl4P/merge.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -0 /tmp/MadjcxLl4P/merge.a.vcf.gz /tmp/MadjcxLl4P/merge.b.vcf.gz /tmp/MadjcxLl4P/merge.c.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version --force-samples -0 /tmp/MadjcxLl4P/merge.a.bcf /tmp/MadjcxLl4P/merge.b.bcf /tmp/MadjcxLl4P/merge.c.bcf .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -0 /tmp/MadjcxLl4P/merge.a.bcf /tmp/MadjcxLl4P/merge.b.bcf /tmp/MadjcxLl4P/merge.c.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version --force-samples -m none /tmp/MadjcxLl4P/merge.2.a.vcf.gz /tmp/MadjcxLl4P/merge.2.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m none /tmp/MadjcxLl4P/merge.2.a.vcf.gz /tmp/MadjcxLl4P/merge.2.b.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version --force-samples -m none /tmp/MadjcxLl4P/merge.2.a.bcf /tmp/MadjcxLl4P/merge.2.b.bcf .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m none /tmp/MadjcxLl4P/merge.2.a.bcf /tmp/MadjcxLl4P/merge.2.b.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version --force-samples -m both /tmp/MadjcxLl4P/merge.2.a.vcf.gz /tmp/MadjcxLl4P/merge.2.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m both /tmp/MadjcxLl4P/merge.2.a.vcf.gz /tmp/MadjcxLl4P/merge.2.b.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version --force-samples -m both /tmp/MadjcxLl4P/merge.2.a.bcf /tmp/MadjcxLl4P/merge.2.b.bcf .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m both /tmp/MadjcxLl4P/merge.2.a.bcf /tmp/MadjcxLl4P/merge.2.b.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version --force-samples -m all /tmp/MadjcxLl4P/merge.2.a.vcf.gz /tmp/MadjcxLl4P/merge.2.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m all /tmp/MadjcxLl4P/merge.2.a.vcf.gz /tmp/MadjcxLl4P/merge.2.b.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version --force-samples -m all /tmp/MadjcxLl4P/merge.2.a.bcf /tmp/MadjcxLl4P/merge.2.b.bcf .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m all /tmp/MadjcxLl4P/merge.2.a.bcf /tmp/MadjcxLl4P/merge.2.b.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/MadjcxLl4P/merge.3.a.vcf.gz /tmp/MadjcxLl4P/merge.3.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/MadjcxLl4P/merge.3.a.vcf.gz /tmp/MadjcxLl4P/merge.3.b.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/MadjcxLl4P/merge.3.a.bcf /tmp/MadjcxLl4P/merge.3.b.bcf .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/MadjcxLl4P/merge.3.a.bcf /tmp/MadjcxLl4P/merge.3.b.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version --force-samples -m id /tmp/MadjcxLl4P/merge.4.a.vcf.gz /tmp/MadjcxLl4P/merge.4.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m id /tmp/MadjcxLl4P/merge.4.a.vcf.gz /tmp/MadjcxLl4P/merge.4.b.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version --force-samples -m id /tmp/MadjcxLl4P/merge.4.a.bcf /tmp/MadjcxLl4P/merge.4.b.bcf .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob --force-samples -m id /tmp/MadjcxLl4P/merge.4.a.bcf /tmp/MadjcxLl4P/merge.4.b.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/MadjcxLl4P/gvcf.merge.1.vcf.gz /tmp/MadjcxLl4P/gvcf.merge.2.vcf.gz /tmp/MadjcxLl4P/gvcf.merge.3.vcf.gz .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/MadjcxLl4P/gvcf.merge.1.vcf.gz /tmp/MadjcxLl4P/gvcf.merge.2.vcf.gz /tmp/MadjcxLl4P/gvcf.merge.3.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/MadjcxLl4P/gvcf.merge.1.bcf /tmp/MadjcxLl4P/gvcf.merge.2.bcf /tmp/MadjcxLl4P/gvcf.merge.3.bcf .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/MadjcxLl4P/gvcf.merge.1.bcf /tmp/MadjcxLl4P/gvcf.merge.2.bcf /tmp/MadjcxLl4P/gvcf.merge.3.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/MadjcxLl4P/merge.gvcf.2.a.vcf.gz /tmp/MadjcxLl4P/merge.gvcf.2.b.vcf.gz /tmp/MadjcxLl4P/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/MadjcxLl4P/merge.gvcf.2.a.vcf.gz /tmp/MadjcxLl4P/merge.gvcf.2.b.vcf.gz /tmp/MadjcxLl4P/merge.gvcf.2.c.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version --gvcf - -m both,* /tmp/MadjcxLl4P/merge.gvcf.2.a.vcf.gz /tmp/MadjcxLl4P/merge.gvcf.2.b.vcf.gz /tmp/MadjcxLl4P/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - -m both,* /tmp/MadjcxLl4P/merge.gvcf.2.a.vcf.gz /tmp/MadjcxLl4P/merge.gvcf.2.b.vcf.gz /tmp/MadjcxLl4P/merge.gvcf.2.c.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version --gvcf - -m both,** /tmp/MadjcxLl4P/merge.gvcf.2.a.vcf.gz /tmp/MadjcxLl4P/merge.gvcf.2.b.vcf.gz /tmp/MadjcxLl4P/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - -m both,** /tmp/MadjcxLl4P/merge.gvcf.2.a.vcf.gz /tmp/MadjcxLl4P/merge.gvcf.2.b.vcf.gz /tmp/MadjcxLl4P/merge.gvcf.2.c.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version --gvcf - -i SRC:join /tmp/MadjcxLl4P/merge.gvcf.3.a.vcf.gz /tmp/MadjcxLl4P/merge.gvcf.3.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - -i SRC:join /tmp/MadjcxLl4P/merge.gvcf.3.a.vcf.gz /tmp/MadjcxLl4P/merge.gvcf.3.b.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/MadjcxLl4P/merge.gvcf.4.a.vcf.gz /tmp/MadjcxLl4P/merge.gvcf.4.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/MadjcxLl4P/merge.gvcf.4.a.vcf.gz /tmp/MadjcxLl4P/merge.gvcf.4.b.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/MadjcxLl4P/merge.gvcf.4.a.bcf /tmp/MadjcxLl4P/merge.gvcf.4.b.bcf .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/MadjcxLl4P/merge.gvcf.4.a.bcf /tmp/MadjcxLl4P/merge.gvcf.4.b.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version /tmp/MadjcxLl4P/merge.5.a.vcf.gz /tmp/MadjcxLl4P/merge.5.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob /tmp/MadjcxLl4P/merge.5.a.vcf.gz /tmp/MadjcxLl4P/merge.5.b.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version /tmp/MadjcxLl4P/merge.5.a.bcf /tmp/MadjcxLl4P/merge.5.b.bcf .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob /tmp/MadjcxLl4P/merge.5.a.bcf /tmp/MadjcxLl4P/merge.5.b.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version /tmp/MadjcxLl4P/merge.6.a.vcf.gz /tmp/MadjcxLl4P/merge.6.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob /tmp/MadjcxLl4P/merge.6.a.vcf.gz /tmp/MadjcxLl4P/merge.6.b.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version /tmp/MadjcxLl4P/merge.6.a.bcf /tmp/MadjcxLl4P/merge.6.b.bcf .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob /tmp/MadjcxLl4P/merge.6.a.bcf /tmp/MadjcxLl4P/merge.6.b.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/MadjcxLl4P/merge.gvcf.7.a.vcf.gz /tmp/MadjcxLl4P/merge.gvcf.7.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/MadjcxLl4P/merge.gvcf.7.a.vcf.gz /tmp/MadjcxLl4P/merge.gvcf.7.b.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/MadjcxLl4P/merge.gvcf.7.a.bcf /tmp/MadjcxLl4P/merge.gvcf.7.b.bcf .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/MadjcxLl4P/merge.gvcf.7.a.bcf /tmp/MadjcxLl4P/merge.gvcf.7.b.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/MadjcxLl4P/merge.gvcf.8.a.vcf.gz /tmp/MadjcxLl4P/merge.gvcf.8.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/MadjcxLl4P/merge.gvcf.8.a.vcf.gz /tmp/MadjcxLl4P/merge.gvcf.8.b.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/MadjcxLl4P/merge.gvcf.8.a.bcf /tmp/MadjcxLl4P/merge.gvcf.8.b.bcf .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/MadjcxLl4P/merge.gvcf.8.a.bcf /tmp/MadjcxLl4P/merge.gvcf.8.b.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version --force-samples /tmp/MadjcxLl4P/merge.7.a.vcf.gz /tmp/MadjcxLl4P/merge.7.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/MadjcxLl4P/merge.7.a.vcf.gz /tmp/MadjcxLl4P/merge.7.b.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version --force-samples /tmp/MadjcxLl4P/merge.7.a.bcf /tmp/MadjcxLl4P/merge.7.b.bcf .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob --force-samples /tmp/MadjcxLl4P/merge.7.a.bcf /tmp/MadjcxLl4P/merge.7.b.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version --gvcf /build/bcftools-Mlf9dV/bcftools-1.21/test/gvcf.fa /tmp/MadjcxLl4P/merge.gvcf.9a.vcf.gz /tmp/MadjcxLl4P/merge.gvcf.9b.vcf.gz /tmp/MadjcxLl4P/merge.gvcf.9c.vcf.gz /tmp/MadjcxLl4P/merge.gvcf.9d.vcf.gz .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob --gvcf /build/bcftools-Mlf9dV/bcftools-1.21/test/gvcf.fa /tmp/MadjcxLl4P/merge.gvcf.9a.vcf.gz /tmp/MadjcxLl4P/merge.gvcf.9b.vcf.gz /tmp/MadjcxLl4P/merge.gvcf.9c.vcf.gz /tmp/MadjcxLl4P/merge.gvcf.9d.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version --gvcf /build/bcftools-Mlf9dV/bcftools-1.21/test/gvcf.fa /tmp/MadjcxLl4P/merge.gvcf.9a.bcf /tmp/MadjcxLl4P/merge.gvcf.9b.bcf /tmp/MadjcxLl4P/merge.gvcf.9c.bcf /tmp/MadjcxLl4P/merge.gvcf.9d.bcf .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob --gvcf /build/bcftools-Mlf9dV/bcftools-1.21/test/gvcf.fa /tmp/MadjcxLl4P/merge.gvcf.9a.bcf /tmp/MadjcxLl4P/merge.gvcf.9b.bcf /tmp/MadjcxLl4P/merge.gvcf.9c.bcf /tmp/MadjcxLl4P/merge.gvcf.9d.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version --gvcf /build/bcftools-Mlf9dV/bcftools-1.21/test/gvcf.fa -r 22:21-23 /tmp/MadjcxLl4P/merge.gvcf.9a.vcf.gz /tmp/MadjcxLl4P/merge.gvcf.9b.vcf.gz /tmp/MadjcxLl4P/merge.gvcf.9c.vcf.gz /tmp/MadjcxLl4P/merge.gvcf.9d.vcf.gz .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob --gvcf /build/bcftools-Mlf9dV/bcftools-1.21/test/gvcf.fa -r 22:21-23 /tmp/MadjcxLl4P/merge.gvcf.9a.vcf.gz /tmp/MadjcxLl4P/merge.gvcf.9b.vcf.gz /tmp/MadjcxLl4P/merge.gvcf.9c.vcf.gz /tmp/MadjcxLl4P/merge.gvcf.9d.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version --gvcf /build/bcftools-Mlf9dV/bcftools-1.21/test/gvcf.fa -r 22:21-23 /tmp/MadjcxLl4P/merge.gvcf.9a.bcf /tmp/MadjcxLl4P/merge.gvcf.9b.bcf /tmp/MadjcxLl4P/merge.gvcf.9c.bcf /tmp/MadjcxLl4P/merge.gvcf.9d.bcf .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob --gvcf /build/bcftools-Mlf9dV/bcftools-1.21/test/gvcf.fa -r 22:21-23 /tmp/MadjcxLl4P/merge.gvcf.9a.bcf /tmp/MadjcxLl4P/merge.gvcf.9b.bcf /tmp/MadjcxLl4P/merge.gvcf.9c.bcf /tmp/MadjcxLl4P/merge.gvcf.9d.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version --gvcf /build/bcftools-Mlf9dV/bcftools-1.21/test/gvcf.fa /tmp/MadjcxLl4P/merge.gvcf.9a.vcf.gz /tmp/MadjcxLl4P/merge.gvcf.9b.vcf.gz /tmp/MadjcxLl4P/merge.gvcf.9c.vcf.gz /tmp/MadjcxLl4P/merge.gvcf.9d.vcf.gz /tmp/MadjcxLl4P/merge.gvcf.9e.vcf.gz .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob --gvcf /build/bcftools-Mlf9dV/bcftools-1.21/test/gvcf.fa /tmp/MadjcxLl4P/merge.gvcf.9a.vcf.gz /tmp/MadjcxLl4P/merge.gvcf.9b.vcf.gz /tmp/MadjcxLl4P/merge.gvcf.9c.vcf.gz /tmp/MadjcxLl4P/merge.gvcf.9d.vcf.gz /tmp/MadjcxLl4P/merge.gvcf.9e.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version --gvcf /build/bcftools-Mlf9dV/bcftools-1.21/test/gvcf.fa /tmp/MadjcxLl4P/merge.gvcf.9a.bcf /tmp/MadjcxLl4P/merge.gvcf.9b.bcf /tmp/MadjcxLl4P/merge.gvcf.9c.bcf /tmp/MadjcxLl4P/merge.gvcf.9d.bcf /tmp/MadjcxLl4P/merge.gvcf.9e.bcf .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob --gvcf /build/bcftools-Mlf9dV/bcftools-1.21/test/gvcf.fa /tmp/MadjcxLl4P/merge.gvcf.9a.bcf /tmp/MadjcxLl4P/merge.gvcf.9b.bcf /tmp/MadjcxLl4P/merge.gvcf.9c.bcf /tmp/MadjcxLl4P/merge.gvcf.9d.bcf /tmp/MadjcxLl4P/merge.gvcf.9e.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version --gvcf /build/bcftools-Mlf9dV/bcftools-1.21/test/gvcf.fa -r 22:21-23 /tmp/MadjcxLl4P/merge.gvcf.9a.vcf.gz /tmp/MadjcxLl4P/merge.gvcf.9b.vcf.gz /tmp/MadjcxLl4P/merge.gvcf.9c.vcf.gz /tmp/MadjcxLl4P/merge.gvcf.9d.vcf.gz /tmp/MadjcxLl4P/merge.gvcf.9e.vcf.gz .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob --gvcf /build/bcftools-Mlf9dV/bcftools-1.21/test/gvcf.fa -r 22:21-23 /tmp/MadjcxLl4P/merge.gvcf.9a.vcf.gz /tmp/MadjcxLl4P/merge.gvcf.9b.vcf.gz /tmp/MadjcxLl4P/merge.gvcf.9c.vcf.gz /tmp/MadjcxLl4P/merge.gvcf.9d.vcf.gz /tmp/MadjcxLl4P/merge.gvcf.9e.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version --gvcf /build/bcftools-Mlf9dV/bcftools-1.21/test/gvcf.fa -r 22:21-23 /tmp/MadjcxLl4P/merge.gvcf.9a.bcf /tmp/MadjcxLl4P/merge.gvcf.9b.bcf /tmp/MadjcxLl4P/merge.gvcf.9c.bcf /tmp/MadjcxLl4P/merge.gvcf.9d.bcf /tmp/MadjcxLl4P/merge.gvcf.9e.bcf .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob --gvcf /build/bcftools-Mlf9dV/bcftools-1.21/test/gvcf.fa -r 22:21-23 /tmp/MadjcxLl4P/merge.gvcf.9a.bcf /tmp/MadjcxLl4P/merge.gvcf.9b.bcf /tmp/MadjcxLl4P/merge.gvcf.9c.bcf /tmp/MadjcxLl4P/merge.gvcf.9d.bcf /tmp/MadjcxLl4P/merge.gvcf.9e.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version /tmp/MadjcxLl4P/merge.gvcf.10.a.vcf.gz /tmp/MadjcxLl4P/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob /tmp/MadjcxLl4P/merge.gvcf.10.a.vcf.gz /tmp/MadjcxLl4P/merge.gvcf.10.b.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version /tmp/MadjcxLl4P/merge.gvcf.10.a.bcf /tmp/MadjcxLl4P/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob /tmp/MadjcxLl4P/merge.gvcf.10.a.bcf /tmp/MadjcxLl4P/merge.gvcf.10.b.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -m none /tmp/MadjcxLl4P/merge.gvcf.10.a.vcf.gz /tmp/MadjcxLl4P/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob -m none /tmp/MadjcxLl4P/merge.gvcf.10.a.vcf.gz /tmp/MadjcxLl4P/merge.gvcf.10.b.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -m none /tmp/MadjcxLl4P/merge.gvcf.10.a.bcf /tmp/MadjcxLl4P/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob -m none /tmp/MadjcxLl4P/merge.gvcf.10.a.bcf /tmp/MadjcxLl4P/merge.gvcf.10.b.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -g /build/bcftools-Mlf9dV/bcftools-1.21/test/merge.gvcf.10.fa /tmp/MadjcxLl4P/merge.gvcf.10.a.vcf.gz /tmp/MadjcxLl4P/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob -g /build/bcftools-Mlf9dV/bcftools-1.21/test/merge.gvcf.10.fa /tmp/MadjcxLl4P/merge.gvcf.10.a.vcf.gz /tmp/MadjcxLl4P/merge.gvcf.10.b.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -g /build/bcftools-Mlf9dV/bcftools-1.21/test/merge.gvcf.10.fa /tmp/MadjcxLl4P/merge.gvcf.10.a.bcf /tmp/MadjcxLl4P/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob -g /build/bcftools-Mlf9dV/bcftools-1.21/test/merge.gvcf.10.fa /tmp/MadjcxLl4P/merge.gvcf.10.a.bcf /tmp/MadjcxLl4P/merge.gvcf.10.b.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -g /build/bcftools-Mlf9dV/bcftools-1.21/test/merge.gvcf.10.fa -m none /tmp/MadjcxLl4P/merge.gvcf.10.a.vcf.gz /tmp/MadjcxLl4P/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob -g /build/bcftools-Mlf9dV/bcftools-1.21/test/merge.gvcf.10.fa -m none /tmp/MadjcxLl4P/merge.gvcf.10.a.vcf.gz /tmp/MadjcxLl4P/merge.gvcf.10.b.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -g /build/bcftools-Mlf9dV/bcftools-1.21/test/merge.gvcf.10.fa -m none /tmp/MadjcxLl4P/merge.gvcf.10.a.bcf /tmp/MadjcxLl4P/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob -g /build/bcftools-Mlf9dV/bcftools-1.21/test/merge.gvcf.10.fa -m none /tmp/MadjcxLl4P/merge.gvcf.10.a.bcf /tmp/MadjcxLl4P/merge.gvcf.10.b.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version /tmp/MadjcxLl4P/merge.noidx.a.vcf.gz /tmp/MadjcxLl4P/merge.noidx.b.vcf.gz /tmp/MadjcxLl4P/merge.noidx.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob /tmp/MadjcxLl4P/merge.noidx.a.vcf.gz /tmp/MadjcxLl4P/merge.noidx.b.vcf.gz /tmp/MadjcxLl4P/merge.noidx.c.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version /tmp/MadjcxLl4P/merge.noidx.a.bcf /tmp/MadjcxLl4P/merge.noidx.b.bcf /tmp/MadjcxLl4P/merge.noidx.c.bcf .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob /tmp/MadjcxLl4P/merge.noidx.a.bcf /tmp/MadjcxLl4P/merge.noidx.b.bcf /tmp/MadjcxLl4P/merge.noidx.c.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version --no-index /build/bcftools-Mlf9dV/bcftools-1.21/test/merge.noidx.a.vcf /build/bcftools-Mlf9dV/bcftools-1.21/test/merge.noidx.b.vcf /build/bcftools-Mlf9dV/bcftools-1.21/test/merge.noidx.c.vcf .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob --no-index /build/bcftools-Mlf9dV/bcftools-1.21/test/merge.noidx.a.vcf /build/bcftools-Mlf9dV/bcftools-1.21/test/merge.noidx.b.vcf /build/bcftools-Mlf9dV/bcftools-1.21/test/merge.noidx.c.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version --no-index /tmp/MadjcxLl4P/merge.noidx.a.bcf /tmp/MadjcxLl4P/merge.noidx.b.bcf /tmp/MadjcxLl4P/merge.noidx.c.bcf .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob --no-index /tmp/MadjcxLl4P/merge.noidx.a.bcf /tmp/MadjcxLl4P/merge.noidx.b.bcf /tmp/MadjcxLl4P/merge.noidx.c.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version /tmp/MadjcxLl4P/merge.8.a.vcf.gz /tmp/MadjcxLl4P/merge.8.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob /tmp/MadjcxLl4P/merge.8.a.vcf.gz /tmp/MadjcxLl4P/merge.8.b.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version /tmp/MadjcxLl4P/merge.8.a.bcf /tmp/MadjcxLl4P/merge.8.b.bcf .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob /tmp/MadjcxLl4P/merge.8.a.bcf /tmp/MadjcxLl4P/merge.8.b.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -i AN:sum,AC:sum /tmp/MadjcxLl4P/merge.8.a.vcf.gz /tmp/MadjcxLl4P/merge.8.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/MadjcxLl4P/merge.8.a.vcf.gz /tmp/MadjcxLl4P/merge.8.b.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -i AN:sum,AC:sum /tmp/MadjcxLl4P/merge.8.a.bcf /tmp/MadjcxLl4P/merge.8.b.bcf .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/MadjcxLl4P/merge.8.a.bcf /tmp/MadjcxLl4P/merge.8.b.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version /tmp/MadjcxLl4P/merge.9.a.vcf.gz /tmp/MadjcxLl4P/merge.9.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob /tmp/MadjcxLl4P/merge.9.a.vcf.gz /tmp/MadjcxLl4P/merge.9.b.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version /tmp/MadjcxLl4P/merge.9.a.bcf /tmp/MadjcxLl4P/merge.9.b.bcf .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob /tmp/MadjcxLl4P/merge.9.a.bcf /tmp/MadjcxLl4P/merge.9.b.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -i AN:sum,AC:sum /tmp/MadjcxLl4P/merge.9.a.vcf.gz /tmp/MadjcxLl4P/merge.9.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/MadjcxLl4P/merge.9.a.vcf.gz /tmp/MadjcxLl4P/merge.9.b.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -i AN:sum,AC:sum /tmp/MadjcxLl4P/merge.9.a.bcf /tmp/MadjcxLl4P/merge.9.b.bcf .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/MadjcxLl4P/merge.9.a.bcf /tmp/MadjcxLl4P/merge.9.b.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -m none /tmp/MadjcxLl4P/merge.10.a.vcf.gz /tmp/MadjcxLl4P/merge.10.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob -m none /tmp/MadjcxLl4P/merge.10.a.vcf.gz /tmp/MadjcxLl4P/merge.10.b.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -m none /tmp/MadjcxLl4P/merge.10.a.bcf /tmp/MadjcxLl4P/merge.10.b.bcf .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob -m none /tmp/MadjcxLl4P/merge.10.a.bcf /tmp/MadjcxLl4P/merge.10.b.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -m both /tmp/MadjcxLl4P/merge.10.a.vcf.gz /tmp/MadjcxLl4P/merge.10.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob -m both /tmp/MadjcxLl4P/merge.10.a.vcf.gz /tmp/MadjcxLl4P/merge.10.b.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -m both /tmp/MadjcxLl4P/merge.10.a.bcf /tmp/MadjcxLl4P/merge.10.b.bcf .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob -m both /tmp/MadjcxLl4P/merge.10.a.bcf /tmp/MadjcxLl4P/merge.10.b.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -m snp-ins-del /tmp/MadjcxLl4P/merge.10.a.vcf.gz /tmp/MadjcxLl4P/merge.10.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob -m snp-ins-del /tmp/MadjcxLl4P/merge.10.a.vcf.gz /tmp/MadjcxLl4P/merge.10.b.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -m snp-ins-del /tmp/MadjcxLl4P/merge.10.a.bcf /tmp/MadjcxLl4P/merge.10.b.bcf .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob -m snp-ins-del /tmp/MadjcxLl4P/merge.10.a.bcf /tmp/MadjcxLl4P/merge.10.b.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/MadjcxLl4P/merge.mrules.1.a.vcf.gz /tmp/MadjcxLl4P/merge.mrules.1.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/MadjcxLl4P/merge.mrules.1.a.vcf.gz /tmp/MadjcxLl4P/merge.mrules.1.b.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/MadjcxLl4P/merge.mrules.1.a.bcf /tmp/MadjcxLl4P/merge.mrules.1.b.bcf .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/MadjcxLl4P/merge.mrules.1.a.bcf /tmp/MadjcxLl4P/merge.mrules.1.b.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version --gvcf - -M AD:.,PL:. /tmp/MadjcxLl4P/merge.mrules.1.a.vcf.gz /tmp/MadjcxLl4P/merge.mrules.1.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - -M AD:.,PL:. /tmp/MadjcxLl4P/merge.mrules.1.a.vcf.gz /tmp/MadjcxLl4P/merge.mrules.1.b.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version --gvcf - -M AD:.,PL:. /tmp/MadjcxLl4P/merge.mrules.1.a.bcf /tmp/MadjcxLl4P/merge.mrules.1.b.bcf .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - -M AD:.,PL:. /tmp/MadjcxLl4P/merge.mrules.1.a.bcf /tmp/MadjcxLl4P/merge.mrules.1.b.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/MadjcxLl4P/merge.gvcf.5.a.vcf.gz /tmp/MadjcxLl4P/merge.gvcf.5.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/MadjcxLl4P/merge.gvcf.5.a.vcf.gz /tmp/MadjcxLl4P/merge.gvcf.5.b.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/MadjcxLl4P/merge.gvcf.5.a.bcf /tmp/MadjcxLl4P/merge.gvcf.5.b.bcf .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/MadjcxLl4P/merge.gvcf.5.a.bcf /tmp/MadjcxLl4P/merge.gvcf.5.b.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version --gvcf - --merge none /tmp/MadjcxLl4P/merge.gvcf.5.a.vcf.gz /tmp/MadjcxLl4P/merge.gvcf.5.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - --merge none /tmp/MadjcxLl4P/merge.gvcf.5.a.vcf.gz /tmp/MadjcxLl4P/merge.gvcf.5.b.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version --gvcf - --merge none /tmp/MadjcxLl4P/merge.gvcf.5.a.bcf /tmp/MadjcxLl4P/merge.gvcf.5.b.bcf .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - --merge none /tmp/MadjcxLl4P/merge.gvcf.5.a.bcf /tmp/MadjcxLl4P/merge.gvcf.5.b.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/MadjcxLl4P/merge.gvcf.11.a.vcf.gz /tmp/MadjcxLl4P/merge.gvcf.11.b.vcf.gz /tmp/MadjcxLl4P/merge.gvcf.11.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/MadjcxLl4P/merge.gvcf.11.a.vcf.gz /tmp/MadjcxLl4P/merge.gvcf.11.b.vcf.gz /tmp/MadjcxLl4P/merge.gvcf.11.c.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version --gvcf - /tmp/MadjcxLl4P/merge.gvcf.11.a.bcf /tmp/MadjcxLl4P/merge.gvcf.11.b.bcf /tmp/MadjcxLl4P/merge.gvcf.11.c.bcf .. ok test_vcf_merge: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools merge --no-version -Ob --gvcf - /tmp/MadjcxLl4P/merge.gvcf.11.a.bcf /tmp/MadjcxLl4P/merge.gvcf.11.b.bcf /tmp/MadjcxLl4P/merge.gvcf.11.c.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided,_conflicting_interpretations"' /tmp/MadjcxLl4P/query.string.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.string.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided,_conflicting_interpretations"' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" || CLNREVSTAT="_conflicting_interpretations"' /tmp/MadjcxLl4P/query.string.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.string.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" || CLNREVSTAT="_conflicting_interpretations"' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" && CLNREVSTAT="_conflicting_interpretations"' /tmp/MadjcxLl4P/query.string.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.string.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" && CLNREVSTAT="_conflicting_interpretations"' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%INFO/STR\n' -i'INFO/STR=@/build/bcftools-Mlf9dV/bcftools-1.21/test/query.string.2.1.txt' /tmp/MadjcxLl4P/query.string.2.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.string.2.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%INFO/STR\n' -i'INFO/STR=@/build/bcftools-Mlf9dV/bcftools-1.21/test/query.string.2.1.txt' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%CHROM\t%POS[\t%STR]\n' -i'FMT/STR=@/build/bcftools-Mlf9dV/bcftools-1.21/test/query.string.2.2.txt' /tmp/MadjcxLl4P/query.string.2.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.string.2.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%CHROM\t%POS[\t%STR]\n' -i'FMT/STR=@/build/bcftools-Mlf9dV/bcftools-1.21/test/query.string.2.2.txt' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' /tmp/MadjcxLl4P/query.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%RSX\t%VKX\n' /tmp/MadjcxLl4P/query.variantkey.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.variantkey.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%RSX\t%VKX\n' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%XRI\n' -i'XRI[*]>1111' /tmp/MadjcxLl4P/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/view.filter.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%XRI\n' -i'XRI[*]>1111' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' /tmp/MadjcxLl4P/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/view.filter.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' /tmp/MadjcxLl4P/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/view.filter.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' /tmp/MadjcxLl4P/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/view.filter.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' /tmp/MadjcxLl4P/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/view.filter.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' /tmp/MadjcxLl4P/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/view.filter.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' /tmp/MadjcxLl4P/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/view.filter.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' /tmp/MadjcxLl4P/query.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' /tmp/MadjcxLl4P/query.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' /tmp/MadjcxLl4P/query.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' /tmp/MadjcxLl4P/query.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' /tmp/MadjcxLl4P/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/view.filter.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' /tmp/MadjcxLl4P/query.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' /tmp/MadjcxLl4P/query.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' /tmp/MadjcxLl4P/query.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' /tmp/MadjcxLl4P/query.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'I8=%I8 I16=%I16 I32=%I32 IF=%IF IA8=%IA8 IA16=%IA16 IA32=%IA32 IAF=%IAF IA8=%IA8{1} IA16=%IA16{1} IA32=%IA32{1} IAF=%IAF{1} [ %F8:%F16:%F32:%FF]\n' /tmp/MadjcxLl4P/view.vectors.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/view.vectors.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'I8=%I8 I16=%I16 I32=%I32 IF=%IF IA8=%IA8 IA16=%IA16 IA32=%IA32 IAF=%IAF IA8=%IA8{1} IA16=%IA16{1} IA32=%IA32{1} IAF=%IAF{1} [ %F8:%F16:%F32:%FF]\n' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' /tmp/MadjcxLl4P/query.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.filter.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' /tmp/MadjcxLl4P/query.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.filter.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' /tmp/MadjcxLl4P/query.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.filter.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' /tmp/MadjcxLl4P/query.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.filter.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' /tmp/MadjcxLl4P/query.2.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.2.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -i'IINT="."' -f'%POS %IINT\n' /tmp/MadjcxLl4P/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/missing.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -i'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -i'IINT!="."' -f'%POS %IINT\n' /tmp/MadjcxLl4P/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/missing.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -i'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -e'IINT!="."' -f'%POS %IINT\n' /tmp/MadjcxLl4P/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/missing.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -e'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -e'IINT="."' -f'%POS %IINT\n' /tmp/MadjcxLl4P/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/missing.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -e'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' /tmp/MadjcxLl4P/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/missing.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' /tmp/MadjcxLl4P/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/missing.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' /tmp/MadjcxLl4P/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/missing.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' /tmp/MadjcxLl4P/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/missing.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' /tmp/MadjcxLl4P/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/missing.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' /tmp/MadjcxLl4P/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/missing.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' /tmp/MadjcxLl4P/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/missing.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' /tmp/MadjcxLl4P/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/missing.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' /tmp/MadjcxLl4P/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/missing.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -i'FILTER="A"' -f'%POS %FILTER\n' /tmp/MadjcxLl4P/filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/filter.11.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -i'FILTER="A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -i'FILTER!="A"' -f'%POS %FILTER\n' /tmp/MadjcxLl4P/filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/filter.11.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -i'FILTER!="A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -i'FILTER~"A"' -f'%POS %FILTER\n' /tmp/MadjcxLl4P/filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/filter.11.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -i'FILTER~"A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n' /tmp/MadjcxLl4P/filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/filter.11.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%LINE' /tmp/MadjcxLl4P/query.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%LINE' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' /tmp/MadjcxLl4P/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.filter-type.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' /tmp/MadjcxLl4P/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.filter-type.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' /tmp/MadjcxLl4P/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.filter-type.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' /tmp/MadjcxLl4P/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.filter-type.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'INFO/TYPE="xxx"' /tmp/MadjcxLl4P/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.filter-type.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\n' -i'INFO/TYPE="xxx"' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -i'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001' /tmp/MadjcxLl4P/filter-missing-floats.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/filter-missing-floats.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -i'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -e'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001' /tmp/MadjcxLl4P/filter-missing-floats.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/filter-missing-floats.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%A_AF\t%B_AF\t%C_AF\n' -e'A_AF>=0.0001 || B_AF >= 0.0001 || C_AF >= 0.0001' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' /tmp/MadjcxLl4P/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/missing.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' /tmp/MadjcxLl4P/query.filter.2.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.filter.2.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' /tmp/MadjcxLl4P/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/view.filter.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' /tmp/MadjcxLl4P/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/view.filter.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' /tmp/MadjcxLl4P/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/view.filter.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' /tmp/MadjcxLl4P/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/view.filter.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' /tmp/MadjcxLl4P/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/view.filter.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' /tmp/MadjcxLl4P/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/view.filter.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' /tmp/MadjcxLl4P/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/view.filter.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' /tmp/MadjcxLl4P/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/view.filter.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' /tmp/MadjcxLl4P/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/view.filter.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' /tmp/MadjcxLl4P/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/view.filter.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' /tmp/MadjcxLl4P/filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/filter.5.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' /tmp/MadjcxLl4P/filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/filter.5.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' /tmp/MadjcxLl4P/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/view.filter.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' /tmp/MadjcxLl4P/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/view.filter.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' /tmp/MadjcxLl4P/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/view.filter.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' /tmp/MadjcxLl4P/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/view.filter.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' /tmp/MadjcxLl4P/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/view.filter.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 & FMT/GQ=589' /tmp/MadjcxLl4P/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/view.filter.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 & FMT/GQ=589' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' /tmp/MadjcxLl4P/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/view.filter.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' /tmp/MadjcxLl4P/query.filter.3.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.filter.3.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"' /tmp/MadjcxLl4P/query.filter.3.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.filter.3.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' /tmp/MadjcxLl4P/query.filter.3.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.filter.3.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %AD\n]\n' -i'AD[:0]+AD[:1] > 12' /tmp/MadjcxLl4P/filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/filter.5.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %AD\n]\n' -i'AD[:0]+AD[:1] > 12' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' /tmp/MadjcxLl4P/query.filter.4.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.filter.4.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%ID\n' -i 'ID=@/build/bcftools-Mlf9dV/bcftools-1.21/test/query.56.out' /tmp/MadjcxLl4P/view.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/view.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%ID\n' -i 'ID=@/build/bcftools-Mlf9dV/bcftools-1.21/test/query.56.out' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD)>0.01' /tmp/MadjcxLl4P/query.filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.filter.5.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD)>0.01' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD[:0],FMT/AD[:1])>0.01' /tmp/MadjcxLl4P/query.filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.filter.5.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD[:0],FMT/AD[:1])>0.01' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%AD\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01' /tmp/MadjcxLl4P/query.filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.filter.5.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%AD\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[GT]==10' /tmp/MadjcxLl4P/query.filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.filter.5.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[GT]==10' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'sSUM(FMT/AD[GT])==210' /tmp/MadjcxLl4P/query.filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.filter.5.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'sSUM(FMT/AD[GT])==210' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[0:GT]==30' /tmp/MadjcxLl4P/query.filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.filter.5.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[0:GT]==30' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TF[:GT]==1 && FMT/TF[:GT]==2' /tmp/MadjcxLl4P/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.gtidx.1.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TF[:GT]==1 && FMT/TF[:GT]==2' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TI[:GT]==1 && FMT/TF[:GT]==2' /tmp/MadjcxLl4P/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.gtidx.1.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TI[:GT]==1 && FMT/TF[:GT]==2' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TS[:GT]=="BB" && FMT/TS[:GT]=="CC"' /tmp/MadjcxLl4P/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.gtidx.1.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TS[:GT]=="BB" && FMT/TS[:GT]=="CC"' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TC[:GT]=="B" && FMT/TC[:GT]=="C"' /tmp/MadjcxLl4P/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.gtidx.1.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TC[:GT]=="B" && FMT/TC[:GT]=="C"' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%GT %TI\n]' -i'FMT/TI[:GT]=="."' /tmp/MadjcxLl4P/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.gtidx.1.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%GT %TI\n]' -i'FMT/TI[:GT]=="."' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%CHROM %POS\n' -i'CHROM="4"' /tmp/MadjcxLl4P/query.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%CHROM %POS\n' -i'CHROM="4"' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%TAG1\n' -i'(TAG1>=-129 && TAG1<=-120) || (TAG1>=-32769 && TAG1<=-32760)' /tmp/MadjcxLl4P/query.negative.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.negative.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%TAG1\n' -i'(TAG1>=-129 && TAG1<=-120) || (TAG1>=-32769 && TAG1<=-32760)' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%TAGV1\n' -i'(TAGV1>=-129 && TAGV1<=-120) || (TAGV1>=-32769 && TAGV1<=-32760)' /tmp/MadjcxLl4P/query.negative.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.negative.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%TAGV1\n' -i'(TAGV1>=-129 && TAGV1<=-120) || (TAGV1>=-32769 && TAGV1<=-32760)' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%TAG2\n' -i'(TAG2>=-129 && TAG2<=-120) || (TAG2>=-32769 && TAG2<=-32760)' /tmp/MadjcxLl4P/query.negative.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.negative.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%TAG2\n' -i'(TAG2>=-129 && TAG2<=-120) || (TAG2>=-32769 && TAG2<=-32760)' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%TAGV2\n' -i'(TAGV2>=-129 && TAGV2<=-120) || (TAGV2>=-32769 && TAGV2<=-32760)' /tmp/MadjcxLl4P/query.negative.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.negative.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%TAGV2\n' -i'(TAGV2>=-129 && TAGV2<=-120) || (TAGV2>=-32769 && TAGV2<=-32760)' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GQ\n]' -i'N_PASS(GQ<20)==1' /tmp/MadjcxLl4P/query.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GQ\n]' -i'N_PASS(GQ<20)==1' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")==1' /tmp/MadjcxLl4P/query.filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.filter.11.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")==1' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")!=1' /tmp/MadjcxLl4P/query.filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.filter.11.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")!=1' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")==1' /tmp/MadjcxLl4P/query.filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.filter.11.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")==1' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")!=1' /tmp/MadjcxLl4P/query.filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.filter.11.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")!=1' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%CHROM\t%POS\t%INFO\t%FORMAT\n' -s D,C /tmp/MadjcxLl4P/query.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%CHROM\t%POS\t%INFO\t%FORMAT\n' -s D,C .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\n' -i'POS==16777217 || POS==33554432 || POS=118673904' /tmp/MadjcxLl4P/query.filter.6.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.filter.6.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\n' -i'POS==16777217 || POS==33554432 || POS=118673904' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(II)==6' /tmp/MadjcxLl4P/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.filter.7.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(II)==6' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(FORMAT/FI)==7' /tmp/MadjcxLl4P/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.filter.7.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(FORMAT/FI)==7' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(II)==2' /tmp/MadjcxLl4P/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.filter.7.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(II)==2' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(FORMAT/FI)==1.75' /tmp/MadjcxLl4P/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.filter.7.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(FORMAT/FI)==1.75' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(II)==2' /tmp/MadjcxLl4P/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.filter.7.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(II)==2' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(FORMAT/FI)==1.75' /tmp/MadjcxLl4P/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.filter.7.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(FORMAT/FI)==1.75' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(II)==2' /tmp/MadjcxLl4P/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.filter.7.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(II)==2' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(FORMAT/FI)==1.5' /tmp/MadjcxLl4P/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.filter.7.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(FORMAT/FI)==1.5' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'%ILEN==1' /tmp/MadjcxLl4P/query.filter.8.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.filter.8.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'%ILEN==1' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'ILEN==1' /tmp/MadjcxLl4P/query.filter.8.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.filter.8.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'ILEN==1' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] < FMT/AD[:1]' /tmp/MadjcxLl4P/query.filter.9.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.filter.9.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] < FMT/AD[:1]' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] > FMT/AD[:1]' /tmp/MadjcxLl4P/query.filter.9.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.filter.9.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] > FMT/AD[:1]' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[ %AD\n]' -i'AD[:1] / sum(AD[*]) > 0.5' /tmp/MadjcxLl4P/query.filter.13.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.filter.13.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[ %AD\n]' -i'AD[:1] / sum(AD[*]) > 0.5' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS %NUM_TAG\n' -i'COUNT(INFO/NUM_TAG)=2' /tmp/MadjcxLl4P/query.filter.10.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.filter.10.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS %NUM_TAG\n' -i'COUNT(INFO/NUM_TAG)=2' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2' /tmp/MadjcxLl4P/query.filter.10.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.filter.10.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%CHROM:%POS\t%N_PASS(GT="alt" & GQ>110)\t[\t%GT]\t[\t%GQ]\n' /tmp/MadjcxLl4P/query.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%CHROM:%POS\t%N_PASS(GT="alt" & GQ>110)\t[\t%GT]\t[\t%GQ]\n' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 1,3,0 /tmp/MadjcxLl4P/query.filter.12.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.filter.12.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 1,3,0 .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 0,1,3 /tmp/MadjcxLl4P/query.filter.12.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.filter.12.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 0,1,3 .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f "[%SAMPLE %GT\n]" -S /build/bcftools-Mlf9dV/bcftools-1.21/test/query.smpl.11.txt /tmp/MadjcxLl4P/query.smpl.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.smpl.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f "[%SAMPLE %GT\n]" -S /build/bcftools-Mlf9dV/bcftools-1.21/test/query.smpl.11.txt .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -l -S /build/bcftools-Mlf9dV/bcftools-1.21/test/query.smpl.11.txt /tmp/MadjcxLl4P/query.smpl.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.smpl.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -l -S /build/bcftools-Mlf9dV/bcftools-1.21/test/query.smpl.11.txt .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f "[%SAMPLE %GT\n]" -S ^/build/bcftools-Mlf9dV/bcftools-1.21/test/query.smpl.11.txt /tmp/MadjcxLl4P/query.smpl.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.smpl.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f "[%SAMPLE %GT\n]" -S ^/build/bcftools-Mlf9dV/bcftools-1.21/test/query.smpl.11.txt .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -l -S ^/build/bcftools-Mlf9dV/bcftools-1.21/test/query.smpl.11.txt /tmp/MadjcxLl4P/query.smpl.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.smpl.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -l -S ^/build/bcftools-Mlf9dV/bcftools-1.21/test/query.smpl.11.txt .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f "[%SAMPLE %GT\n]" -S /build/bcftools-Mlf9dV/bcftools-1.21/test/query.smpl.txt /tmp/MadjcxLl4P/query.smpl.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.smpl.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f "[%SAMPLE %GT\n]" -S /build/bcftools-Mlf9dV/bcftools-1.21/test/query.smpl.txt .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -l -S /build/bcftools-Mlf9dV/bcftools-1.21/test/query.smpl.txt /tmp/MadjcxLl4P/query.smpl.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.smpl.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -l -S /build/bcftools-Mlf9dV/bcftools-1.21/test/query.smpl.txt .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%ID\n' -i'ID~"s12"' /tmp/MadjcxLl4P/query.filter.id.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.filter.id.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%ID\n' -i'ID~"s12"' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%ID\n' -i'ID="rs123"' /tmp/MadjcxLl4P/query.filter.id.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.filter.id.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%ID\n' -i'ID="rs123"' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%ID\n' -i'ID="abc"' /tmp/MadjcxLl4P/query.filter.id.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.filter.id.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%ID\n' -i'ID="abc"' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%ID\n' -i'ID=@/build/bcftools-Mlf9dV/bcftools-1.21/test/query.filter.id.3.txt' /tmp/MadjcxLl4P/query.filter.id.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.filter.id.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%ID\n' -i'ID=@/build/bcftools-Mlf9dV/bcftools-1.21/test/query.filter.id.3.txt' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%ID\n' -i'ID!="abc"' /tmp/MadjcxLl4P/query.filter.id.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.filter.id.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%ID\n' -i'ID!="abc"' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%ID\n' -i'ID!=@/build/bcftools-Mlf9dV/bcftools-1.21/test/query.filter.id.3.txt' /tmp/MadjcxLl4P/query.filter.id.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.filter.id.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%ID\n' -i'ID!=@/build/bcftools-Mlf9dV/bcftools-1.21/test/query.filter.id.3.txt' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -i'FILTER="A"' -f'%FILTER\n' /tmp/MadjcxLl4P/filter.12.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/filter.12.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -i'FILTER="A"' -f'%FILTER\n' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -i'FILTER~"A"' -f'%FILTER\n' /tmp/MadjcxLl4P/filter.12.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/filter.12.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -i'FILTER~"A"' -f'%FILTER\n' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -i'FILTER="A;B"' -f'%FILTER\n' /tmp/MadjcxLl4P/filter.12.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/filter.12.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -i'FILTER="A;B"' -f'%FILTER\n' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -i'FILTER!="A;B"' -f'%FILTER\n' /tmp/MadjcxLl4P/filter.12.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/filter.12.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -i'FILTER!="A;B"' -f'%FILTER\n' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -i'FILTER~"A;B"' -f'%FILTER\n' /tmp/MadjcxLl4P/filter.12.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/filter.12.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -i'FILTER~"A;B"' -f'%FILTER\n' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -i'FILTER!~"A;B"' -f'%FILTER\n' /tmp/MadjcxLl4P/filter.12.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/filter.12.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -i'FILTER!~"A;B"' -f'%FILTER\n' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -i'DP%10==2' -f'[ %DP]\n' /tmp/MadjcxLl4P/filter.10.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/filter.10.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -i'DP%10==2' -f'[ %DP]\n' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -i'REF="N"' -f'%CHROM %POS %REF %ALT %QUAL\n' /tmp/MadjcxLl4P/filter.13.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/filter.13.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -i'REF="N"' -f'%CHROM %POS %REF %ALT %QUAL\n' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -H -f'[%CHROM %POS %SAMPLE %DP %GT\n]' /tmp/MadjcxLl4P/query.header.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.header.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -H -f'[%CHROM %POS %SAMPLE %DP %GT\n]' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -H -f'[%CHROM %POS %SAMPLE %DP %GT\t]\n' /tmp/MadjcxLl4P/query.header.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.header.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -H -f'[%CHROM %POS %SAMPLE %DP %GT\t]\n' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]\n' /tmp/MadjcxLl4P/query.header.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.header.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]\n' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]' /tmp/MadjcxLl4P/query.header.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.header.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]\n' /tmp/MadjcxLl4P/query.header.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.header.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]\n' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]' /tmp/MadjcxLl4P/query.header.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.header.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -HH -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]' /tmp/MadjcxLl4P/query.header.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.header.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -HH -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%SAMPLE %DP\n]' -i'DP=1 || DP=2' /tmp/MadjcxLl4P/query.filter-or.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.filter-or.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%SAMPLE %DP\n]' -i'DP=1 || DP=2' .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%SAMPLE %DP\n]' -i'DP=1 | DP=2' /tmp/MadjcxLl4P/query.filter-or.vcf.gz .. ok test_vcf_query: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/query.filter-or.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%SAMPLE %DP\n]' -i'DP=1 | DP=2' .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m - /tmp/MadjcxLl4P/norm.sort.vcf.gz .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m - /tmp/MadjcxLl4P/norm.sort.vcf.gz -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m - -S lex /tmp/MadjcxLl4P/norm.sort.vcf.gz .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m - -S lex /tmp/MadjcxLl4P/norm.sort.vcf.gz -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m +both /tmp/MadjcxLl4P/norm.join-missing-ploidy.vcf.gz .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m +both /tmp/MadjcxLl4P/norm.join-missing-ploidy.vcf.gz -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m - --multi-overlaps . /tmp/MadjcxLl4P/norm.split.5.vcf.gz .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m - --multi-overlaps . /tmp/MadjcxLl4P/norm.split.5.vcf.gz -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version /tmp/MadjcxLl4P/norm.symbolic.3.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/norm.symbolic.3.fa .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version /tmp/MadjcxLl4P/norm.symbolic.3.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/norm.symbolic.3.fa -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -cx /tmp/MadjcxLl4P/norm.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/norm.fa .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -cx /tmp/MadjcxLl4P/norm.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/norm.fa -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m- /tmp/MadjcxLl4P/norm.split.vcf.gz .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m- /tmp/MadjcxLl4P/norm.split.vcf.gz -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m- /tmp/MadjcxLl4P/norm.split.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m- /tmp/MadjcxLl4P/norm.split.2.vcf.gz -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m- --force /tmp/MadjcxLl4P/norm.split.3.vcf.gz .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m- --force /tmp/MadjcxLl4P/norm.split.3.vcf.gz -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m- /tmp/MadjcxLl4P/norm.split.4.vcf.gz .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m- /tmp/MadjcxLl4P/norm.split.4.vcf.gz -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m- --keep-sum AD /tmp/MadjcxLl4P/norm.split.4.vcf.gz .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m- --keep-sum AD /tmp/MadjcxLl4P/norm.split.4.vcf.gz -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m- /tmp/MadjcxLl4P/norm.split.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/norm.fa .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m- /tmp/MadjcxLl4P/norm.split.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/norm.fa -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m+ /tmp/MadjcxLl4P/norm.merge.vcf.gz .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m+ /tmp/MadjcxLl4P/norm.merge.vcf.gz -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m+ /tmp/MadjcxLl4P/norm.merge.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m+ /tmp/MadjcxLl4P/norm.merge.2.vcf.gz -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m+ /tmp/MadjcxLl4P/norm.merge.3.vcf.gz .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m+ /tmp/MadjcxLl4P/norm.merge.3.vcf.gz -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m+ -s /tmp/MadjcxLl4P/norm.merge.vcf.gz .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m+ -s /tmp/MadjcxLl4P/norm.merge.vcf.gz -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -Nc s /tmp/MadjcxLl4P/norm.setref.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/norm.fa .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -Nc s /tmp/MadjcxLl4P/norm.setref.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/norm.fa -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version /tmp/MadjcxLl4P/norm.telomere.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/norm.fa .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version /tmp/MadjcxLl4P/norm.telomere.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/norm.fa -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -d snps /tmp/MadjcxLl4P/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -d snps /tmp/MadjcxLl4P/norm.rmdup.vcf.gz -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -d indels /tmp/MadjcxLl4P/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -d indels /tmp/MadjcxLl4P/norm.rmdup.vcf.gz -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -d both /tmp/MadjcxLl4P/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -d both /tmp/MadjcxLl4P/norm.rmdup.vcf.gz -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -d all /tmp/MadjcxLl4P/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -d all /tmp/MadjcxLl4P/norm.rmdup.vcf.gz -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -d none /tmp/MadjcxLl4P/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -d none /tmp/MadjcxLl4P/norm.rmdup.vcf.gz -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -d exact /tmp/MadjcxLl4P/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -d exact /tmp/MadjcxLl4P/norm.rmdup.vcf.gz -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -d none /tmp/MadjcxLl4P/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -d none /tmp/MadjcxLl4P/norm.rmdup.2.vcf.gz -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -d exact /tmp/MadjcxLl4P/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -d exact /tmp/MadjcxLl4P/norm.rmdup.2.vcf.gz -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -d indels /tmp/MadjcxLl4P/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -d indels /tmp/MadjcxLl4P/norm.rmdup.2.vcf.gz -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -d any /tmp/MadjcxLl4P/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -d any /tmp/MadjcxLl4P/norm.rmdup.2.vcf.gz -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -d both /tmp/MadjcxLl4P/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -d both /tmp/MadjcxLl4P/norm.rmdup.2.vcf.gz -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -d snps /tmp/MadjcxLl4P/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -d snps /tmp/MadjcxLl4P/norm.rmdup.2.vcf.gz -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -d exact /tmp/MadjcxLl4P/norm.rmdup.3.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/norm.rmdup.3.fa .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -d exact /tmp/MadjcxLl4P/norm.rmdup.3.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/norm.rmdup.3.fa -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -d all /tmp/MadjcxLl4P/norm.rmdup.3.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/norm.rmdup.3.fa .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -d all /tmp/MadjcxLl4P/norm.rmdup.3.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/norm.rmdup.3.fa -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -c s -a /tmp/MadjcxLl4P/norm.2.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/norm.2.fa .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -c s -a /tmp/MadjcxLl4P/norm.2.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/norm.2.fa -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -c s /tmp/MadjcxLl4P/norm.iupac.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/norm.iupac.fa .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -c s /tmp/MadjcxLl4P/norm.iupac.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/norm.iupac.fa -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -c s /tmp/MadjcxLl4P/norm.3.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/norm.3.fa .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -c s /tmp/MadjcxLl4P/norm.3.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/norm.3.fa -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -c s -i'alt="N"' /tmp/MadjcxLl4P/norm.3.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/norm.3.fa .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -c s -i'alt="N"' /tmp/MadjcxLl4P/norm.3.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/norm.3.fa -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -a --old-rec-tag OLD_REC /tmp/MadjcxLl4P/atomize.split.1.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m -any --force .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -a --old-rec-tag OLD_REC /tmp/MadjcxLl4P/atomize.split.1.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m -any --force -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m -any --old-rec-tag OLD_REC --force /tmp/MadjcxLl4P/atomize.split.1.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -a .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m -any --old-rec-tag OLD_REC --force /tmp/MadjcxLl4P/atomize.split.1.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -a -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m -any --old-rec-tag OLD_REC --force -a /tmp/MadjcxLl4P/atomize.split.1.vcf.gz .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m -any --old-rec-tag OLD_REC --force -a /tmp/MadjcxLl4P/atomize.split.1.vcf.gz -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/MadjcxLl4P/atomize.split.1.vcf.gz .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/MadjcxLl4P/atomize.split.1.vcf.gz -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/MadjcxLl4P/atomize.split.1.vcf.gz .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/MadjcxLl4P/atomize.split.1.vcf.gz -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/MadjcxLl4P/atomize.split.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/MadjcxLl4P/atomize.split.2.vcf.gz -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/MadjcxLl4P/atomize.split.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/MadjcxLl4P/atomize.split.2.vcf.gz -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . /tmp/MadjcxLl4P/atomize.split.3.vcf.gz .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . /tmp/MadjcxLl4P/atomize.split.3.vcf.gz -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/MadjcxLl4P/atomize.split.4.vcf.gz .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/MadjcxLl4P/atomize.split.4.vcf.gz -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC -i 'ILEN=0' /tmp/MadjcxLl4P/atomize.split.4.vcf.gz .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC -i 'ILEN=0' /tmp/MadjcxLl4P/atomize.split.4.vcf.gz -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version --atomize --old-rec-tag OLD_REC --atom-overlaps . /tmp/MadjcxLl4P/atomize.split.5.vcf.gz .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version --atomize --old-rec-tag OLD_REC --atom-overlaps . /tmp/MadjcxLl4P/atomize.split.5.vcf.gz -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/MadjcxLl4P/atomize.split.5.vcf.gz .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/MadjcxLl4P/atomize.split.5.vcf.gz -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m +both /tmp/MadjcxLl4P/norm.4.vcf.gz .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m +both /tmp/MadjcxLl4P/norm.4.vcf.gz -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m +any /tmp/MadjcxLl4P/norm.4.vcf.gz .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m +any /tmp/MadjcxLl4P/norm.4.vcf.gz -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m - --multi-overlaps 0 /tmp/MadjcxLl4P/norm.5.vcf.gz .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m - --multi-overlaps 0 /tmp/MadjcxLl4P/norm.5.vcf.gz -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m - --multi-overlaps . /tmp/MadjcxLl4P/norm.5.vcf.gz .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m - --multi-overlaps . /tmp/MadjcxLl4P/norm.5.vcf.gz -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m -any /tmp/MadjcxLl4P/norm.m-any.vcf.gz .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m -any /tmp/MadjcxLl4P/norm.m-any.vcf.gz -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m -any /tmp/MadjcxLl4P/norm.phased-split.vcf.gz .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m -any /tmp/MadjcxLl4P/norm.phased-split.vcf.gz -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m +any /tmp/MadjcxLl4P/norm.phased-join.vcf.gz .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m +any /tmp/MadjcxLl4P/norm.phased-join.vcf.gz -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI /tmp/MadjcxLl4P/norm.symbolic.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/norm.symbolic.fa .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI /tmp/MadjcxLl4P/norm.symbolic.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/norm.symbolic.fa -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI /tmp/MadjcxLl4P/norm.symbolic.2.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/norm.symbolic.fa .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI /tmp/MadjcxLl4P/norm.symbolic.2.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/norm.symbolic.fa -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI /tmp/MadjcxLl4P/norm.right-align.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/norm.right-align.fa .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI /tmp/MadjcxLl4P/norm.right-align.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/norm.right-align.fa -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI -g /build/bcftools-Mlf9dV/bcftools-1.21/test/norm.right-align.gff /tmp/MadjcxLl4P/norm.right-align.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/norm.right-align.fa .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI -g /build/bcftools-Mlf9dV/bcftools-1.21/test/norm.right-align.gff /tmp/MadjcxLl4P/norm.right-align.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/norm.right-align.fa -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI -a -m -any /tmp/MadjcxLl4P/norm.atom-split-norm.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/norm.atom-split-norm.fa .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version --old-rec-tag ORI -a -m -any /tmp/MadjcxLl4P/norm.atom-split-norm.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/norm.atom-split-norm.fa -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m -any /tmp/MadjcxLl4P/norm.string-tags.vcf.gz .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m -any /tmp/MadjcxLl4P/norm.string-tags.vcf.gz -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m - /tmp/MadjcxLl4P/norm.split.merge.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m +both .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m - /tmp/MadjcxLl4P/norm.split.merge.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m +both -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m - /tmp/MadjcxLl4P/norm.split.merge.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m +indels .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m - /tmp/MadjcxLl4P/norm.split.merge.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m +indels -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m - /tmp/MadjcxLl4P/norm.split.merge.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m +snps .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m - /tmp/MadjcxLl4P/norm.split.merge.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m +snps -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m - /tmp/MadjcxLl4P/norm.split.merge.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m +snps .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m - /tmp/MadjcxLl4P/norm.split.merge.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m +snps -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m - /tmp/MadjcxLl4P/norm.split.merge.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m +any .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m - /tmp/MadjcxLl4P/norm.split.merge.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m +any -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m - -i 'type="snp"' /tmp/MadjcxLl4P/norm.split.merge.vcf.gz .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m - -i 'type="snp"' /tmp/MadjcxLl4P/norm.split.merge.vcf.gz -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m +any /tmp/MadjcxLl4P/norm.merge.4.vcf.gz .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m +any /tmp/MadjcxLl4P/norm.merge.4.vcf.gz -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m +both /tmp/MadjcxLl4P/norm.merge.4.vcf.gz .. ok test_vcf_norm: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools norm --no-version -m +both /tmp/MadjcxLl4P/norm.merge.4.vcf.gz -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version -i 'INFO/TAG=@/build/bcftools-Mlf9dV/bcftools-1.21/test/filter.string.1.txt' /tmp/MadjcxLl4P/filter.string.1.vcf.gz .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob -i 'INFO/TAG=@/build/bcftools-Mlf9dV/bcftools-1.21/test/filter.string.1.txt' /tmp/MadjcxLl4P/filter.string.1.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version -i 'FMT/TAG=@/build/bcftools-Mlf9dV/bcftools-1.21/test/filter.string.1.txt' /tmp/MadjcxLl4P/filter.string.1.vcf.gz .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob -i 'FMT/TAG=@/build/bcftools-Mlf9dV/bcftools-1.21/test/filter.string.1.txt' /tmp/MadjcxLl4P/filter.string.1.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version -HA /tmp/MadjcxLl4P/merge.gvcf.2.a.vcf.gz .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version -HAA /tmp/MadjcxLl4P/merge.gvcf.2.a.vcf.gz .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version /tmp/MadjcxLl4P/weird-chr-names.vcf.gz -r 1 .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/weird-chr-names.vcf.gz -r 1 | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version /tmp/MadjcxLl4P/weird-chr-names.vcf.gz -r 1:1-2 .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/weird-chr-names.vcf.gz -r 1:1-2 | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version /tmp/MadjcxLl4P/weird-chr-names.vcf.gz -r 1:1,1:2 .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/weird-chr-names.vcf.gz -r 1:1,1:2 | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version /tmp/MadjcxLl4P/weird-chr-names.vcf.gz -r 1:1-1 .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/weird-chr-names.vcf.gz -r 1:1-1 | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version /tmp/MadjcxLl4P/weird-chr-names.vcf.gz -r {1:1} .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/weird-chr-names.vcf.gz -r {1:1} | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version /tmp/MadjcxLl4P/weird-chr-names.vcf.gz -r {1:1}:1-2 .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/weird-chr-names.vcf.gz -r {1:1}:1-2 | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version /tmp/MadjcxLl4P/weird-chr-names.vcf.gz -r {1:1}:1,{1:1}:2 .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/weird-chr-names.vcf.gz -r {1:1}:1,{1:1}:2 | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version /tmp/MadjcxLl4P/weird-chr-names.vcf.gz -r {1:1}:1-1 .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/weird-chr-names.vcf.gz -r {1:1}:1-1 | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version /tmp/MadjcxLl4P/weird-chr-names.vcf.gz -r {1:1-1} .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/weird-chr-names.vcf.gz -r {1:1-1} | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version /tmp/MadjcxLl4P/weird-chr-names.vcf.gz -r {1:1-1}:1-2 .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/weird-chr-names.vcf.gz -r {1:1-1}:1-2 | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version /tmp/MadjcxLl4P/weird-chr-names.vcf.gz -r {1:1-1}:1,{1:1-1}:2 .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/weird-chr-names.vcf.gz -r {1:1-1}:1,{1:1-1}:2 | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version /tmp/MadjcxLl4P/weird-chr-names.vcf.gz -r {1:1-1}:1-1 .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/weird-chr-names.vcf.gz -r {1:1-1}:1-1 | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version /tmp/MadjcxLl4P/weird-chr-names.vcf.gz -r {1:1-1}-2 .. ok, expected non-zero status test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/weird-chr-names.vcf.gz -r {1:1-1}-2 | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok, expected non-zero status test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version -aUc1 -C1 -s NA00002 -v snps /tmp/MadjcxLl4P/view.vcf.gz .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/MadjcxLl4P/view.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version -f PASS -Xks NA00003 /tmp/MadjcxLl4P/view.vcf.gz -r20,Y .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob -f PASS -Xks NA00003 /tmp/MadjcxLl4P/view.vcf.gz -r20,Y | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version -xs NA00003 /tmp/MadjcxLl4P/view.vcf.gz .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob -xs NA00003 /tmp/MadjcxLl4P/view.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/MadjcxLl4P/view.vcf.gz .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/MadjcxLl4P/view.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version -p /tmp/MadjcxLl4P/view.vcf.gz .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob -p /tmp/MadjcxLl4P/view.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version -P /tmp/MadjcxLl4P/view.vcf.gz .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob -P /tmp/MadjcxLl4P/view.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version -hm2 -M2 -q0.3 -Q0.7 /tmp/MadjcxLl4P/view.vcf.gz .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/MadjcxLl4P/view.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version -Hu /tmp/MadjcxLl4P/view.vcf.gz .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version -GVsnps /tmp/MadjcxLl4P/view.vcf.gz .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob -GVsnps /tmp/MadjcxLl4P/view.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version -ne 'INDEL=1 || PV4[0]<0.006' /tmp/MadjcxLl4P/view.vcf.gz .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/MadjcxLl4P/view.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version -s ^NA00003 /tmp/MadjcxLl4P/view.vcf.gz .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob -s ^NA00003 /tmp/MadjcxLl4P/view.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version /tmp/MadjcxLl4P/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/view.omitgenotypes.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version -G /tmp/MadjcxLl4P/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob -G /tmp/MadjcxLl4P/view.omitgenotypes.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version -HG /tmp/MadjcxLl4P/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version -a /tmp/MadjcxLl4P/many.alleles.vcf.gz .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob -a /tmp/MadjcxLl4P/many.alleles.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version -asA /tmp/MadjcxLl4P/view.vectors.vcf.gz .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob -asA /tmp/MadjcxLl4P/view.vectors.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version -asB /tmp/MadjcxLl4P/view.vectors.vcf.gz .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob -asB /tmp/MadjcxLl4P/view.vectors.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version -asA /tmp/MadjcxLl4P/view.vectors.2.vcf.gz .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob -asA /tmp/MadjcxLl4P/view.vectors.2.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version -H -i'FMT/FGS[*:0]="AAAAAA"' /tmp/MadjcxLl4P/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version -H -i'FMT/FGS[*:2]="C"' /tmp/MadjcxLl4P/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version -H -i'FMT/FGS[*:4]="EE"' /tmp/MadjcxLl4P/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version -H -i'FMT/FRS[*:1]="BB"' /tmp/MadjcxLl4P/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version -H -i'TXT0="text"' /tmp/MadjcxLl4P/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version -T /build/bcftools-Mlf9dV/bcftools-1.21/test/view.chrs.tab /tmp/MadjcxLl4P/view.chrs.vcf.gz .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob -T /build/bcftools-Mlf9dV/bcftools-1.21/test/view.chrs.tab /tmp/MadjcxLl4P/view.chrs.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version -i 'POS>=3062917' /tmp/MadjcxLl4P/filter.2.vcf.gz 1:3062917-3157410 .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob -i 'POS>=3062917' /tmp/MadjcxLl4P/filter.2.vcf.gz 1:3062917-3157410 | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version -H -r 1:10,1:12,1:10 /tmp/MadjcxLl4P/idx.1.vcf.gz .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version -H -r 1:1172777-1172804,1:1172806-1172808 /tmp/MadjcxLl4P/idx.2.vcf.gz .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version -H -R /build/bcftools-Mlf9dV/bcftools-1.21/test/idx.2.bed /tmp/MadjcxLl4P/idx.2.vcf.gz .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version -H -R /build/bcftools-Mlf9dV/bcftools-1.21/test/idx.3.bed /tmp/MadjcxLl4P/idx.3.vcf.gz .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version -H -R /build/bcftools-Mlf9dV/bcftools-1.21/test/idx.4.bed /tmp/MadjcxLl4P/idx.4.vcf.gz .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version -Ht 2 /tmp/MadjcxLl4P/view-t.vcf.gz .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version -Ht 3 /tmp/MadjcxLl4P/view-t.vcf.gz .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 0 /tmp/MadjcxLl4P/overlap.vcf.gz .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 1 /tmp/MadjcxLl4P/overlap.vcf.gz .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 2 /tmp/MadjcxLl4P/overlap.vcf.gz .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 0 /tmp/MadjcxLl4P/overlap.vcf.gz .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 1 /tmp/MadjcxLl4P/overlap.vcf.gz .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 2 /tmp/MadjcxLl4P/overlap.vcf.gz .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 0 /tmp/MadjcxLl4P/overlap.vcf.gz .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 1 /tmp/MadjcxLl4P/overlap.vcf.gz .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 2 /tmp/MadjcxLl4P/overlap.vcf.gz .. ok test_vcf_64bit: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view /build/bcftools-Mlf9dV/bcftools-1.21/test/view64bit.1.vcf -H .. ok test_vcf_64bit: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view /build/bcftools-Mlf9dV/bcftools-1.21/test/view64bit.1.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view /build/bcftools-Mlf9dV/bcftools-1.21/test/view64bit.1.vcf -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view /build/bcftools-Mlf9dV/bcftools-1.21/test/view64bit.2.vcf -H .. ok test_vcf_64bit: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view /build/bcftools-Mlf9dV/bcftools-1.21/test/view64bit.2.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view /build/bcftools-Mlf9dV/bcftools-1.21/test/view64bit.2.vcf -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view /build/bcftools-Mlf9dV/bcftools-1.21/test/view64bit.3.vcf -H .. ok test_vcf_64bit: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view /build/bcftools-Mlf9dV/bcftools-1.21/test/view64bit.3.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view /build/bcftools-Mlf9dV/bcftools-1.21/test/view64bit.4.vcf -H .. ok test_vcf_64bit: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view /build/bcftools-Mlf9dV/bcftools-1.21/test/view64bit.4.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view /build/bcftools-Mlf9dV/bcftools-1.21/test/view64bit.4.vcf -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view /build/bcftools-Mlf9dV/bcftools-1.21/test/view64bit.5.vcf -H .. ok test_vcf_64bit: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view /build/bcftools-Mlf9dV/bcftools-1.21/test/view64bit.5.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view /build/bcftools-Mlf9dV/bcftools-1.21/test/view64bit.5.vcf -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -H .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version -H -C5:nonmajor /tmp/MadjcxLl4P/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version -H -c6:nonmajor /tmp/MadjcxLl4P/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version -H -q0.3:major /tmp/MadjcxLl4P/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/MadjcxLl4P/view.filter.annovar.vcf.gz .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version -H -i 'Gene.refGene~"NOD"' /tmp/MadjcxLl4P/view.filter.annovar.vcf.gz .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version -H -i 'LJB2_MutationTaster=="0.291000"' /tmp/MadjcxLl4P/view.filter.annovar.vcf.gz .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version -H -a /tmp/MadjcxLl4P/view-a.vcf.gz .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version -T /build/bcftools-Mlf9dV/bcftools-1.21/test/view.sites.txt /tmp/MadjcxLl4P/view.sites.vcf.gz .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob -T /build/bcftools-Mlf9dV/bcftools-1.21/test/view.sites.txt /tmp/MadjcxLl4P/view.sites.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version -T /build/bcftools-Mlf9dV/bcftools-1.21/test/view.sites.txt.gz /tmp/MadjcxLl4P/view.sites.vcf.gz .. ok test_vcf_view: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob -T /build/bcftools-Mlf9dV/bcftools-1.21/test/view.sites.txt.gz /tmp/MadjcxLl4P/view.sites.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_head: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools head /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_head: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools head -h 0 /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_head: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools head -h 1 /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_head: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools head -h 5 /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_head: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools head -h 22 /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_head: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools head -h 23 /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_head: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools head -n 0 /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_head: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools head -n 1 /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_head: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools head -n 5 /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_head: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools head -h 5 -n 5 < /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_head2: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools head -s0 /tmp/MadjcxLl4P/mpileup.2.vcf.gz .. ok test_vcf_head2: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version -Ob /tmp/MadjcxLl4P/mpileup.2.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools head -s0 .. ok test_vcf_head2: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools head -s1 /tmp/MadjcxLl4P/mpileup.2.vcf.gz .. ok test_vcf_head2: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version -Ob /tmp/MadjcxLl4P/mpileup.2.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools head -s1 .. ok test_vcf_head2: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools head -s2 -h2 /tmp/MadjcxLl4P/mpileup.2.vcf.gz .. ok test_vcf_head2: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version -Ob /tmp/MadjcxLl4P/mpileup.2.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools head -s2 -h2 .. ok test_vcf_call: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools call --no-version -mv /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.vcf .. ok test_vcf_call: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools call -Ob -mv /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools call --no-version -mg0 /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.vcf .. ok test_vcf_call: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools call -Ob -mg0 /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools call --no-version -mv -S /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.3.samples /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.vcf .. ok test_vcf_call: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools call -Ob -mv -S /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.3.samples /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools call --no-version -mv -S /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.4.samples /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.vcf .. ok test_vcf_call: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools call -Ob -mv -S /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.4.samples /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools call --no-version -mv -S /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.5.samples /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.vcf .. ok test_vcf_call: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools call -Ob -mv -S /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.5.samples /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools call --no-version -mv --ploidy-file /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.ploidy -S /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.samples /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.X.vcf .. ok test_vcf_call: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools call -Ob -mv --ploidy-file /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.ploidy -S /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.samples /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.X.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools call --no-version -mv --ploidy-file /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.ploidy -S /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.ped /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.X.vcf .. ok test_vcf_call: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools call -Ob -mv --ploidy-file /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.ploidy -S /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.ped /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.X.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools call --no-version -mv --ploidy-file /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.ploidy -S /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.2.samples /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.X.vcf .. ok test_vcf_call: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools call -Ob -mv --ploidy-file /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.ploidy -S /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.2.samples /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.X.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools call --no-version -mv /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.NA19213.NA19129.vcf .. ok test_vcf_call: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools call -Ob -mv /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.NA19213.NA19129.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools call --no-version -mv -G - --group-samples-tag AD /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.NA19213.NA19129.vcf .. ok test_vcf_call: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools call -Ob -mv -G - --group-samples-tag AD /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.NA19213.NA19129.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools call --no-version -mv /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.hwe.vcf .. ok test_vcf_call: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools call -Ob -mv /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.hwe.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools call --no-version -mv -G - --group-samples-tag AD /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.hwe.vcf .. ok test_vcf_call: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools call -Ob -mv -G - --group-samples-tag AD /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.hwe.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools call --no-version -mv -G /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.hwe.samples --group-samples-tag AD /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.hwe.vcf .. ok test_vcf_call: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools call -Ob -mv -G /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.hwe.samples --group-samples-tag AD /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.hwe.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/MadjcxLl4P/mpileup.tab.gz /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.vcf .. ok test_vcf_call_cAls: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/MadjcxLl4P/mpileup.tab.gz /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/MadjcxLl4P/mpileup.2.tab.gz /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.2.vcf .. ok test_vcf_call_cAls: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/MadjcxLl4P/mpileup.2.tab.gz /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.2.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/MadjcxLl4P/mpileup.3.tab.gz -i /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/MadjcxLl4P/mpileup.3.tab.gz -i /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.3.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/MadjcxLl4P/mpileup.4.tab.gz -i /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/MadjcxLl4P/mpileup.4.tab.gz -i /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.3.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/MadjcxLl4P/mpileup.5.tab.gz -i /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/MadjcxLl4P/mpileup.5.tab.gz -i /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.3.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/MadjcxLl4P/mpileup.6.tab.gz -i /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.4.vcf .. ok test_vcf_call_cAls: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/MadjcxLl4P/mpileup.6.tab.gz -i /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.4.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/MadjcxLl4P/mpileup.7.tab.gz -i /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.5.vcf .. ok test_vcf_call_cAls: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/MadjcxLl4P/mpileup.7.tab.gz -i /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.5.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/MadjcxLl4P/mpileup.cals.1.tab.gz /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.cals.1.vcf .. ok test_vcf_call_cAls: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/MadjcxLl4P/mpileup.cals.1.tab.gz /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.cals.1.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools call --no-version -mA -C alleles -T /tmp/MadjcxLl4P/mpileup.cals.2.tab.gz /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.cals.2.vcf .. ok test_vcf_call_cAls: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools call -Ob -mA -C alleles -T /tmp/MadjcxLl4P/mpileup.cals.2.tab.gz /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.cals.2.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools call --no-version -cv /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.c.vcf .. ok test_vcf_call: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools call -Ob -cv /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.c.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools call --no-version -cv --ploidy-file /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.ploidy -S /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.samples /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.c.X.vcf .. ok test_vcf_call: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools call -Ob -cv --ploidy-file /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.ploidy -S /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.samples /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.c.X.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools call --no-version -cv --ploidy-file /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.ploidy -S /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.ped /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.c.X.vcf .. ok test_vcf_call: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools call -Ob -cv --ploidy-file /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.ploidy -S /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.ped /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.c.X.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools call --no-version -cv --ploidy-file /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.ploidy -S /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.2.samples /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.c.X.vcf .. ok test_vcf_call: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools call -Ob -cv --ploidy-file /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.ploidy -S /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.2.samples /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup.c.X.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools call --no-version -mv /build/bcftools-Mlf9dV/bcftools-1.21/test/call-G.vcf .. ok test_vcf_call: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools call -Ob -mv /build/bcftools-Mlf9dV/bcftools-1.21/test/call-G.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools call --no-version -mv -G - --group-samples-tag AD /build/bcftools-Mlf9dV/bcftools-1.21/test/call-G.vcf .. ok test_vcf_call: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools call -Ob -mv -G - --group-samples-tag AD /build/bcftools-Mlf9dV/bcftools-1.21/test/call-G.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools call --no-version -mv -F AN_POP,AC_POP /build/bcftools-Mlf9dV/bcftools-1.21/test/call-G.2.vcf .. ok test_vcf_call: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools call -Ob -mv -F AN_POP,AC_POP /build/bcftools-Mlf9dV/bcftools-1.21/test/call-G.2.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools call --no-version -m /build/bcftools-Mlf9dV/bcftools-1.21/test/call.af-fixation.vcf .. ok test_vcf_call: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools call -Ob -m /build/bcftools-Mlf9dV/bcftools-1.21/test/call.af-fixation.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools call --no-version -m -G /build/bcftools-Mlf9dV/bcftools-1.21/test/call.af-fixation.txt /build/bcftools-Mlf9dV/bcftools-1.21/test/call.af-fixation.vcf .. ok test_vcf_call: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools call -Ob -m -G /build/bcftools-Mlf9dV/bcftools-1.21/test/call.af-fixation.txt /build/bcftools-Mlf9dV/bcftools-1.21/test/call.af-fixation.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools call --no-version -m -G /build/bcftools-Mlf9dV/bcftools-1.21/test/call.af-fixation.txt -a GP,GQ /build/bcftools-Mlf9dV/bcftools-1.21/test/call.af-fixation.vcf .. ok test_vcf_call: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools call -Ob -m -G /build/bcftools-Mlf9dV/bcftools-1.21/test/call.af-fixation.txt -a GP,GQ /build/bcftools-Mlf9dV/bcftools-1.21/test/call.af-fixation.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -S. -e'TXT0="text"' /build/bcftools-Mlf9dV/bcftools-1.21/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -S. -e'TXT0="text"' /build/bcftools-Mlf9dV/bcftools-1.21/test/view.filter.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -S. -e'FMT/FRS[*:1]="BB"' /build/bcftools-Mlf9dV/bcftools-1.21/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -S. -e'FMT/FRS[*:1]="BB"' /build/bcftools-Mlf9dV/bcftools-1.21/test/view.filter.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -S. -e'FMT/FGS[*:0]="AAAAAA"' /build/bcftools-Mlf9dV/bcftools-1.21/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -S. -e'FMT/FGS[*:0]="AAAAAA"' /build/bcftools-Mlf9dV/bcftools-1.21/test/view.filter.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -S. -e'FMT/FGS[*:1]="BBB"' /build/bcftools-Mlf9dV/bcftools-1.21/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -S. -e'FMT/FGS[*:1]="BBB"' /build/bcftools-Mlf9dV/bcftools-1.21/test/view.filter.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -S. -e'FMT/FGS[*:4]="EE"' /build/bcftools-Mlf9dV/bcftools-1.21/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -S. -e'FMT/FGS[*:4]="EE"' /build/bcftools-Mlf9dV/bcftools-1.21/test/view.filter.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -S. -e'FMT/STR="XX"' /build/bcftools-Mlf9dV/bcftools-1.21/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -S. -e'FMT/STR="XX"' /build/bcftools-Mlf9dV/bcftools-1.21/test/view.filter.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -S. -e'FMT/FILTER="aaa"' /build/bcftools-Mlf9dV/bcftools-1.21/test/view.filter.2.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -S. -e'FMT/FILTER="aaa"' /build/bcftools-Mlf9dV/bcftools-1.21/test/view.filter.2.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -mx -g2 -G2 /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -mx -g2 -G2 /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.1.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.2.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.2.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -e'INFO/DP=19' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.3.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -e'INFO/DP=19' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.3.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -e'INFO/DP=19' -s XX /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.3.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -e'INFO/DP=19' -s XX /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.3.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -e'INFO/DP=19' -s XX -m+ /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.3.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+ /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.3.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -e'INFO/DP=19' -s XX -mx /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.3.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -e'INFO/DP=19' -s XX -mx /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.3.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -e'INFO/DP=19' -s XX -m+x /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.3.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+x /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.3.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -e'FMT/GT="0/2"' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.3.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -e'FMT/GT="0/2"' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.3.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -e'FMT/GT="0/2"' -s XX /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.3.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.3.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -e'FMT/GT="0/2"' -s XX -m+ /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.3.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+ /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.3.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -e'FMT/GT="0/2"' -s XX -mx /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.3.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -mx /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.3.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -e'FMT/GT="0/2"' -s XX -m+x /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.3.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+x /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.3.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -i'FMT/GT="0/0" && AC[*]=2' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.2.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -i'FMT/GT="0/0" && AC[*]=2' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.2.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -i'AC[*]=2 && FMT/GT="0/0"' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.2.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -i'AC[*]=2 && FMT/GT="0/0"' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.2.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -i'ALT="."' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.2.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -i'ALT="."' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.2.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -S . -i 'FORMAT/TEST3<25' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.4.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -S . -i 'FORMAT/TEST3<25' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.4.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -S . -i 'FORMAT/TEST4<25' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.4.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -S . -i 'FORMAT/TEST4<25' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.4.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -i'GT="A"' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.2.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -i'GT="A"' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.2.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -i'GT="RR"' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.2.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -i'GT="RR"' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.2.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -i'GT="RA"' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.2.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -i'GT="RA"' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.2.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -i'GT="AR"' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.2.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -i'GT="AR"' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.2.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -i'GT="AA"' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.2.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -i'GT="AA"' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.2.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -i'GT="aA"' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.2.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -i'GT="aA"' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.2.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -i'GT="Aa"' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.2.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -i'GT="Aa"' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.2.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -i'GT="HOM"' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.2.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -i'GT="HOM"' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.2.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -i'GT="HET"' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.2.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -i'GT="HET"' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.2.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -i'GT="HAP"' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.2.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -i'GT="HAP"' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.2.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -i'AD[:1]=11' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.5.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -i'AD[:1]=11' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.5.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -i'AD[1:]=11' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.5.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -i'AD[1:]=11' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.5.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -i'FR[0:1]=11' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.5.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS[\t%FR]\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -i'FR[0:1]=11' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.5.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS[\t%FR]\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -i'AD[*]="."' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.5.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -i'AD[*]="."' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.5.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -i'AD[0:0]=="."' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.5.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -i'AD[0:0]=="."' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.5.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -i'AD[0:0]!="."' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.5.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -i'AD[0:0]!="."' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.5.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -i'QUAL=="."' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.5.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS\t%QUAL\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -i'QUAL=="."' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.5.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS\t%QUAL\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -i'N_PASS(DP>32)=1' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.2.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -i'N_PASS(DP>32)=1' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.2.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -i'F_PASS(DP>32)=0.5' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.2.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -i'F_PASS(DP>32)=0.5' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.2.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -i'F_MISSING>=1/5' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.6.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -i'F_MISSING>=1/5' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.6.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -i'F_MISSING>=0.2' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.6.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -i'F_MISSING>=0.2' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.6.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -i'F_PASS(GT=="mis")>=1/5' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.6.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -i'F_PASS(GT=="mis")>=1/5' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.6.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -i'F_PASS(GT=="mis")>=0.2' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.6.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -i'F_PASS(GT=="mis")>=0.2' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.6.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -mx -s + -g2:mnp,indel,other /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.7.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -mx -s + -g2:mnp,indel,other /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.7.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -S . -e 'FORMAT/AO==4' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -S . -e 'FORMAT/AO==4' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.8.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -S . -e 'MAX(FORMAT/AO[0:])==4' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -S . -e 'MAX(FORMAT/AO[0:])==4' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.8.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -S . -e 'MAX(FORMAT/AO)==4' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -S . -e 'MAX(FORMAT/AO)==4' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.8.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -S . -e 'MIN(FORMAT/AO[0:])==3' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO[0:])==3' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.8.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -S . -e 'MIN(FORMAT/AO)==2' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO)==2' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.8.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -S . -e 'MIN(FORMAT/AO[0:])==3' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO[0:])==3' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.8.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -S . -e 'AVG(FORMAT/AO[2:])==4' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -S . -e 'AVG(FORMAT/AO[2:])==4' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.8.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -S . -e 'MEDIAN(FORMAT/AO[2:])==4' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -S . -e 'MEDIAN(FORMAT/AO[2:])==4' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.8.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -S . -e 'STDEV(FORMAT/AO[0:])=0.5' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -S . -e 'STDEV(FORMAT/AO[0:])=0.5' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.8.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -S . -e 'SUM(FORMAT/AO[0:])=7' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -S . -e 'SUM(FORMAT/AO[0:])=7' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.8.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -S . -e 'SMPL_MAX(FORMAT/AO)==4' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -S . -e 'SMPL_MAX(FORMAT/AO)==4' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.8.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -S . -e 'sMIN(FORMAT/AO)==2' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -S . -e 'sMIN(FORMAT/AO)==2' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.8.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -S . -e 'ABS(sAVG(FORMAT/AO)-3.66666)<1e-5' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -S . -e 'ABS(sAVG(FORMAT/AO)-3.66666)<1e-5' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.8.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -S . -e 'sMEDIAN(FORMAT/AO)==4' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -S . -e 'sMEDIAN(FORMAT/AO)==4' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.8.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -S . -e 'ABS(sSTDEV(FORMAT/AO)-1.2472191)<1e-5' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -S . -e 'ABS(sSTDEV(FORMAT/AO)-1.2472191)<1e-5' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.8.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -S . -e 'sSUM(FORMAT/AO)==11' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -S . -e 'sSUM(FORMAT/AO)==11' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.8.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -i 'QUAL/FMT/AD==55' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.9.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -i 'QUAL/FMT/AD==55' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.9.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -i 'QUAL/INFO/AD==10' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.9.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -i 'QUAL/INFO/AD==10' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.9.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -S . -e 'ABS(SMPL_MAX(FORMAT/AO))=5' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -S . -e 'ABS(SMPL_MAX(FORMAT/AO))=5' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.8.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -S . -e 'PHRED(AO[1:])>-4' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -S . -e 'PHRED(AO[1:])>-4' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.8.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -S . -e 'ABS(AO[1:])==2' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -S . -e 'ABS(AO[1:])==2' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.8.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -i 'sum(AD[*]) > FORMAT/DP' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -i 'sum(AD[*]) > FORMAT/DP' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.10.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -i 'FORMAT/DP < sum(AD[*])' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -i 'FORMAT/DP < sum(AD[*])' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.10.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -i 'sum(AD[*]) < FORMAT/DP' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -i 'sum(AD[*]) < FORMAT/DP' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.10.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -i 'FORMAT/DP > sum(AD[*])' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob -i 'FORMAT/DP > sum(AD[*])' /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.10.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 0 /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 0 /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.1.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 1 /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 1 /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.1.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 2 /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 2 /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.1.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter --soft-filter xxx --mask ^2:1005-1008 /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools filter -Ob --soft-filter xxx --mask ^2:1005-1008 /build/bcftools-Mlf9dV/bcftools-1.21/test/filter.1.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_sort: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools sort -m 0 /build/bcftools-Mlf9dV/bcftools-1.21/test/sort.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools sort -Ob -m 0 /build/bcftools-Mlf9dV/bcftools-1.21/test/sort.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools sort -m 1000 /build/bcftools-Mlf9dV/bcftools-1.21/test/sort.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools sort -Ob -m 1000 /build/bcftools-Mlf9dV/bcftools-1.21/test/sort.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_regions: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /build/bcftools-Mlf9dV/bcftools-1.21/test/regions.tab /tmp/MadjcxLl4P/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/regions.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /build/bcftools-Mlf9dV/bcftools-1.21/test/regions.tab .. ok test_vcf_regions: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /build/bcftools-Mlf9dV/bcftools-1.21/test/regions.tab /tmp/MadjcxLl4P/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/MadjcxLl4P/regions.tab.gz /tmp/MadjcxLl4P/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/regions.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/MadjcxLl4P/regions.tab.gz .. ok test_vcf_regions: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/MadjcxLl4P/regions.tab.gz /tmp/MadjcxLl4P/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/MadjcxLl4P/regions.bed /tmp/MadjcxLl4P/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/regions.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/MadjcxLl4P/regions.bed .. ok test_vcf_regions: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/MadjcxLl4P/regions.bed /tmp/MadjcxLl4P/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/MadjcxLl4P/regions.bed.gz /tmp/MadjcxLl4P/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/regions.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/MadjcxLl4P/regions.bed.gz .. ok test_vcf_regions: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/MadjcxLl4P/regions.bed.gz /tmp/MadjcxLl4P/regions.vcf.gz .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annotate.escape.1.tab.gz -c CHROM,POS,ISTR,FMT/FSTR /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate.escape.1.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annotate.escape.1.tab.gz -c CHROM,POS,ISTR,FMT/FSTR /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate.escape.1.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annotate.match.1.tab.gz -c CHROM,POS,-,-,SCORE,~X,-,- -i'STR={X}' /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate.match.1.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annotate.match.1.tab.gz -c CHROM,POS,-,-,SCORE,~X,-,- -i'STR={X}' /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate.match.1.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annotate.match.1.tab.gz -c CHROM,POS,REF,ALT,SCORE,-,~X,- -i'INT={X}' /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate.match.1.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annotate.match.1.tab.gz -c CHROM,POS,REF,ALT,SCORE,-,~X,- -i'INT={X}' /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate.match.1.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annotate.match.1.tab.gz -c CHROM,POS,REF,ALT,SCORE,-,-,~X -i'FLT={X}' /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate.match.1.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annotate.match.1.tab.gz -c CHROM,POS,REF,ALT,SCORE,-,-,~X -i'FLT={X}' /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate.match.1.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annotate.tab.gz -h /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annotate.tab.gz -h /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annotate2.tab.gz -h /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate.hdr -c CHROM,POS,-,T_STR /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annotate2.tab.gz -h /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate.hdr -c CHROM,POS,-,T_STR /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annotate2.tab.gz -h /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate.hdr -c CHROM,FROM,TO,T_STR /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annotate2.tab.gz -h /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate.hdr -c CHROM,FROM,TO,T_STR /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/MadjcxLl4P/annotate.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/MadjcxLl4P/annotate.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/MadjcxLl4P/annotate2.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/MadjcxLl4P/annotate2.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/MadjcxLl4P/annotate2.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/MadjcxLl4P/annotate2.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/MadjcxLl4P/annotate2.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/MadjcxLl4P/annotate2.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/MadjcxLl4P/annotate2.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/MadjcxLl4P/annotate2.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/MadjcxLl4P/annotate2.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/MadjcxLl4P/annotate2.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate3.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate3.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -x FORMAT /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate3.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -x FORMAT /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate3.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annots4.vcf.gz -c +INFO /tmp/MadjcxLl4P/annotate4.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annots4.vcf.gz -c +INFO /tmp/MadjcxLl4P/annotate4.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annots4.tab.gz -h /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate4.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annots4.tab.gz -h /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate4.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annots10.tab.gz -h /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate10.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annots10.tab.gz -h /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate10.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/MadjcxLl4P/annotate2.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/MadjcxLl4P/annotate2.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate2.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate2.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/MadjcxLl4P/annotate2.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/MadjcxLl4P/annotate2.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/MadjcxLl4P/annotate2.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/MadjcxLl4P/annotate2.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/MadjcxLl4P/annotate2.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/MadjcxLl4P/annotate2.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annots11.vcf.gz -c FMT /tmp/MadjcxLl4P/annotate11.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annots11.vcf.gz -c FMT /tmp/MadjcxLl4P/annotate11.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annots2.vcf.gz -c FMT/newGT:=GT /tmp/MadjcxLl4P/annotate2.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annots2.vcf.gz -c FMT/newGT:=GT /tmp/MadjcxLl4P/annotate2.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annots12.vcf.gz -c FMT/GT:=newGT /tmp/MadjcxLl4P/annotate2.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annots12.vcf.gz -c FMT/GT:=newGT /tmp/MadjcxLl4P/annotate2.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annots13.tab.gz -h /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate13.hdr -c CHROM,BEG,END,ABC /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate13.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annots13.tab.gz -h /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate13.hdr -c CHROM,BEG,END,ABC /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate13.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annots13.tab.gz -h /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:append /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate13.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annots13.tab.gz -h /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:append /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate13.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annots13.tab.gz -h /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:unique /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate13.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annots13.tab.gz -h /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:unique /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate13.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -x FILTER/XX,INFO/XX --force /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate14.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -x FILTER/XX,INFO/XX --force /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate14.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annotate15.tab.gz -h /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate15.hdr -s SAMPLE1 -c CHROM,FROM,TO,FMT/FOO,BAR /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate15.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annotate15.tab.gz -h /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate15.hdr -s SAMPLE1 -c CHROM,FROM,TO,FMT/FOO,BAR /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate15.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annotate15.tab.gz -h /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate15.hdr -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate15.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annotate15.tab.gz -h /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate15.hdr -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate15.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annotate15.tab.gz -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR -H '##FORMAT=' -H '##INFO=' /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate15.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annotate15.tab.gz -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR -H '##FORMAT=' -H '##INFO=' /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate15.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -x FILTER /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate16.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -x FILTER /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate16.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate17.1.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate17.1.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate17.2.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate17.2.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annotate17.3.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate17.3.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annotate17.3.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate17.3.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/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-Mlf9dV/bcftools-1.21/test/annotate18.1.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/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-Mlf9dV/bcftools-1.21/test/annotate18.1.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/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-Mlf9dV/bcftools-1.21/test/annotate18.2.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/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-Mlf9dV/bcftools-1.21/test/annotate18.2.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/MadjcxLl4P/annotate19.dst.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/MadjcxLl4P/annotate19.dst.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/MadjcxLl4P/annotate19.dst.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/MadjcxLl4P/annotate19.dst.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/MadjcxLl4P/annotate19.dst.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/MadjcxLl4P/annotate19.dst.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -c INFO/FILTER:=FILTER /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate19.dst.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -c INFO/FILTER:=FILTER /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate19.dst.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER /tmp/MadjcxLl4P/annotate19.dst.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER /tmp/MadjcxLl4P/annotate19.dst.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER /tmp/MadjcxLl4P/annotate19.dst.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER /tmp/MadjcxLl4P/annotate19.dst.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER,FILTER /tmp/MadjcxLl4P/annotate19.dst.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER,FILTER /tmp/MadjcxLl4P/annotate19.dst.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=./FILTER /tmp/MadjcxLl4P/annotate19.dst.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=./FILTER /tmp/MadjcxLl4P/annotate19.dst.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annotate20.src.vcf.gz -c FMT/GT /tmp/MadjcxLl4P/annotate20.dst.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annotate20.src.vcf.gz -c FMT/GT /tmp/MadjcxLl4P/annotate20.dst.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annotate20.src.vcf.gz -c +FMT/GT /tmp/MadjcxLl4P/annotate20.dst.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annotate20.src.vcf.gz -c +FMT/GT /tmp/MadjcxLl4P/annotate20.dst.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annotate20.src.vcf.gz -c -FMT/GT /tmp/MadjcxLl4P/annotate20.dst.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annotate20.src.vcf.gz -c -FMT/GT /tmp/MadjcxLl4P/annotate20.dst.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annotate.multi.tab.gz -c CHROM,POS,REF,ALT,ANN -l ANN:append /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate.multi.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annotate.multi.tab.gz -c CHROM,POS,REF,ALT,ANN -l ANN:append /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate.multi.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/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-Mlf9dV/bcftools-1.21/test/annotate.missing-append.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/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-Mlf9dV/bcftools-1.21/test/annotate.missing-append.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate9.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate9.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate --rename-annots /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate21.txt /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate21.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob --rename-annots /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate21.txt /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate21.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -c XX:=FORMAT/X-X,YY:=FORMAT/Y-Y,AA:=FORMAT/A-A,AA:=INFO/A-A,BB:=INFO/B-B,XX:=INFO/X-X,YY:=INFO/Y-Y,fltA:=FILTER/flt-A,fltB:=FILTER/flt-B,fltX:=FILTER/flt-X,fltY:=FILTER/flt-Y /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate21.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -c XX:=FORMAT/X-X,YY:=FORMAT/Y-Y,AA:=FORMAT/A-A,AA:=INFO/A-A,BB:=INFO/B-B,XX:=INFO/X-X,YY:=INFO/Y-Y,fltA:=FILTER/flt-A,fltB:=FILTER/flt-B,fltX:=FILTER/flt-X,fltY:=FILTER/flt-Y /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate21.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/MadjcxLl4P/annotate22.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/MadjcxLl4P/annotate22.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annotate23.tab.gz -c CHROM,POS,~ID,REF,ALT,INFO/END /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate23.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annotate23.tab.gz -c CHROM,POS,~ID,REF,ALT,INFO/END /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate23.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annotate24.src.vcf.gz -c XX /tmp/MadjcxLl4P/annotate24.dst.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annotate24.src.vcf.gz -c XX /tmp/MadjcxLl4P/annotate24.dst.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annotate25.tab.gz -c CHROM,POS,ID,REF,ALT,~INFO/END /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate25.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annotate25.tab.gz -c CHROM,POS,ID,REF,ALT,~INFO/END /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate25.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annotate26.tab.gz -c CHROM,POS,-POS /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate26.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annotate26.tab.gz -c CHROM,POS,-POS /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate26.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,TSTR,TFLT,TINT /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate.missing.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,TSTR,TFLT,TINT /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate.missing.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.TSTR,.TFLT,.TINT /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate.missing.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.TSTR,.TFLT,.TINT /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate.missing.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.+TSTR,.+TFLT,.+TINT /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate.missing.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.+TSTR,.+TFLT,.+TINT /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate.missing.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,+TSTR,+TFLT,+TINT /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate.missing.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,+TSTR,+TFLT,+TINT /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate.missing.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.=TSTR,.=TFLT,.=TINT /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate.missing.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.=TSTR,.=TFLT,.=TINT /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate.missing.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,=TSTR,=TFLT,=TINT /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate.missing.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,=TSTR,=TFLT,=TINT /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate.missing.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate.olap.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate.olap.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique --min-overlap 0.4:0.5 -m XXX /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate.olap.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique --min-overlap 0.4:0.5 -m XXX /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate.olap.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annots.id.vcf.gz -c ALT /tmp/MadjcxLl4P/annotate.id.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annots.id.vcf.gz -c ALT /tmp/MadjcxLl4P/annotate.id.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annots.id.vcf.gz -c +ALT /tmp/MadjcxLl4P/annotate.id.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annots.id.vcf.gz -c +ALT /tmp/MadjcxLl4P/annotate.id.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annots.id.2.vcf.gz --pair-logic some -c +ID /tmp/MadjcxLl4P/annotate.id.2.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annots.id.2.vcf.gz --pair-logic some -c +ID /tmp/MadjcxLl4P/annotate.id.2.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annots.id.2.vcf.gz --pair-logic any -c +ID /tmp/MadjcxLl4P/annotate.id.2.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annots.id.2.vcf.gz --pair-logic any -c +ID /tmp/MadjcxLl4P/annotate.id.2.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annotate27.tab.gz -c CHROM,POS,REF,ALT,EVIDENCE /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate27.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annotate27.tab.gz -c CHROM,POS,REF,ALT,EVIDENCE /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate27.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1,smpl2 /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate28.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1,smpl2 /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate28.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2,smpl1 /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate28.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2,smpl1 /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate28.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1 /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate28.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1 /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate28.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2 /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate28.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2 /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate28.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -m XXX /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -m XXX /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annots34.tab.gz -c CHROM,FROM,TO,INFO/END -H '##INFO=' /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate34.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annots34.tab.gz -c CHROM,FROM,TO,INFO/END -H '##INFO=' /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate34.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -a /tmp/MadjcxLl4P/annots-mark.bed.gz -c CHROM,FROM,TO -m TAG /build/bcftools-Mlf9dV/bcftools-1.21/test/annots-mark.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate -Ob -a /tmp/MadjcxLl4P/annots-mark.bed.gz -c CHROM,FROM,TO -m TAG /build/bcftools-Mlf9dV/bcftools-1.21/test/annots-mark.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools concat --no-version /tmp/MadjcxLl4P/concat.1.a.vcf.gz /tmp/MadjcxLl4P/concat.1.b.vcf.gz .. ok test_vcf_concat: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools concat -Ob /tmp/MadjcxLl4P/concat.1.a.vcf.gz /tmp/MadjcxLl4P/concat.1.b.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools concat --no-version /tmp/MadjcxLl4P/concat.1.a.bcf /tmp/MadjcxLl4P/concat.1.b.bcf .. ok test_vcf_concat: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools concat -Ob /tmp/MadjcxLl4P/concat.1.a.bcf /tmp/MadjcxLl4P/concat.1.b.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools concat --no-version -a /tmp/MadjcxLl4P/concat.2.a.vcf.gz /tmp/MadjcxLl4P/concat.2.b.vcf.gz .. ok test_vcf_concat: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools concat -Ob -a /tmp/MadjcxLl4P/concat.2.a.vcf.gz /tmp/MadjcxLl4P/concat.2.b.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools concat --no-version -a /tmp/MadjcxLl4P/concat.2.a.bcf /tmp/MadjcxLl4P/concat.2.b.bcf .. ok test_vcf_concat: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools concat -Ob -a /tmp/MadjcxLl4P/concat.2.a.bcf /tmp/MadjcxLl4P/concat.2.b.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools concat --no-version -aD /tmp/MadjcxLl4P/concat.2.a.vcf.gz /tmp/MadjcxLl4P/concat.2.b.vcf.gz .. ok test_vcf_concat: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools concat -Ob -aD /tmp/MadjcxLl4P/concat.2.a.vcf.gz /tmp/MadjcxLl4P/concat.2.b.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools concat --no-version -aD /tmp/MadjcxLl4P/concat.2.a.bcf /tmp/MadjcxLl4P/concat.2.b.bcf .. ok test_vcf_concat: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools concat -Ob -aD /tmp/MadjcxLl4P/concat.2.a.bcf /tmp/MadjcxLl4P/concat.2.b.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools concat --no-version -l --ligate-warn /tmp/MadjcxLl4P/concat.3.a.vcf.gz /tmp/MadjcxLl4P/concat.3.b.vcf.gz /tmp/MadjcxLl4P/concat.3.0.vcf.gz /tmp/MadjcxLl4P/concat.3.c.vcf.gz /tmp/MadjcxLl4P/concat.3.d.vcf.gz /tmp/MadjcxLl4P/concat.3.e.vcf.gz /tmp/MadjcxLl4P/concat.3.f.vcf.gz .. ok test_vcf_concat: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools concat -Ob -l --ligate-warn /tmp/MadjcxLl4P/concat.3.a.vcf.gz /tmp/MadjcxLl4P/concat.3.b.vcf.gz /tmp/MadjcxLl4P/concat.3.0.vcf.gz /tmp/MadjcxLl4P/concat.3.c.vcf.gz /tmp/MadjcxLl4P/concat.3.d.vcf.gz /tmp/MadjcxLl4P/concat.3.e.vcf.gz /tmp/MadjcxLl4P/concat.3.f.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools concat --no-version -l --ligate-warn /tmp/MadjcxLl4P/concat.3.a.bcf /tmp/MadjcxLl4P/concat.3.b.bcf /tmp/MadjcxLl4P/concat.3.0.bcf /tmp/MadjcxLl4P/concat.3.c.bcf /tmp/MadjcxLl4P/concat.3.d.bcf /tmp/MadjcxLl4P/concat.3.e.bcf /tmp/MadjcxLl4P/concat.3.f.bcf .. ok test_vcf_concat: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools concat -Ob -l --ligate-warn /tmp/MadjcxLl4P/concat.3.a.bcf /tmp/MadjcxLl4P/concat.3.b.bcf /tmp/MadjcxLl4P/concat.3.0.bcf /tmp/MadjcxLl4P/concat.3.c.bcf /tmp/MadjcxLl4P/concat.3.d.bcf /tmp/MadjcxLl4P/concat.3.e.bcf /tmp/MadjcxLl4P/concat.3.f.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ Random seed for test_naive_concat: 3852036536 .. ok test_naive_concat: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools concat --naive-force /tmp/MadjcxLl4P/naive_concat.0.bcf /tmp/MadjcxLl4P/naive_concat.1.bcf /tmp/MadjcxLl4P/naive_concat.2.bcf /tmp/MadjcxLl4P/naive_concat.3.bcf /tmp/MadjcxLl4P/naive_concat.4.bcf /tmp/MadjcxLl4P/naive_concat.5.bcf /tmp/MadjcxLl4P/naive_concat.6.bcf /tmp/MadjcxLl4P/naive_concat.7.bcf /tmp/MadjcxLl4P/naive_concat.8.bcf /tmp/MadjcxLl4P/naive_concat.9.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -H .. ok test_naive_concat: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools concat --naive /tmp/MadjcxLl4P/naive_concat.0.vcf.gz /tmp/MadjcxLl4P/naive_concat.1.vcf.gz /tmp/MadjcxLl4P/naive_concat.2.vcf.gz /tmp/MadjcxLl4P/naive_concat.3.vcf.gz /tmp/MadjcxLl4P/naive_concat.4.vcf.gz /tmp/MadjcxLl4P/naive_concat.5.vcf.gz /tmp/MadjcxLl4P/naive_concat.6.vcf.gz /tmp/MadjcxLl4P/naive_concat.7.vcf.gz /tmp/MadjcxLl4P/naive_concat.8.vcf.gz /tmp/MadjcxLl4P/naive_concat.9.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -H .. ok test_vcf_concat: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools concat --no-version -l /tmp/MadjcxLl4P/concat.4.a.vcf.gz /tmp/MadjcxLl4P/concat.4.b.vcf.gz .. ok test_vcf_concat: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools concat -Ob -l /tmp/MadjcxLl4P/concat.4.a.vcf.gz /tmp/MadjcxLl4P/concat.4.b.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools concat --no-version -l /tmp/MadjcxLl4P/concat.4.a.bcf /tmp/MadjcxLl4P/concat.4.b.bcf .. ok test_vcf_concat: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools concat -Ob -l /tmp/MadjcxLl4P/concat.4.a.bcf /tmp/MadjcxLl4P/concat.4.b.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools concat --no-version -l --ligate-warn /tmp/MadjcxLl4P/concat.5.a.vcf.gz /tmp/MadjcxLl4P/concat.5.b.vcf.gz /tmp/MadjcxLl4P/concat.5.c.vcf.gz .. ok test_vcf_concat: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools concat -Ob -l --ligate-warn /tmp/MadjcxLl4P/concat.5.a.vcf.gz /tmp/MadjcxLl4P/concat.5.b.vcf.gz /tmp/MadjcxLl4P/concat.5.c.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools concat --no-version -l --ligate-warn /tmp/MadjcxLl4P/concat.5.a.bcf /tmp/MadjcxLl4P/concat.5.b.bcf /tmp/MadjcxLl4P/concat.5.c.bcf .. ok test_vcf_concat: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools concat -Ob -l --ligate-warn /tmp/MadjcxLl4P/concat.5.a.bcf /tmp/MadjcxLl4P/concat.5.b.bcf /tmp/MadjcxLl4P/concat.5.c.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools concat --no-version -l --ligate-force /tmp/MadjcxLl4P/concat.5.a.bcf /tmp/MadjcxLl4P/concat.5.b.bcf /tmp/MadjcxLl4P/concat.5.c.bcf .. ok test_vcf_concat: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools concat -Ob -l --ligate-force /tmp/MadjcxLl4P/concat.5.a.bcf /tmp/MadjcxLl4P/concat.5.b.bcf /tmp/MadjcxLl4P/concat.5.c.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools concat --no-version -G -a -D /tmp/MadjcxLl4P/concat.5.a.vcf.gz /tmp/MadjcxLl4P/concat.5.b.vcf.gz /tmp/MadjcxLl4P/concat.5.c.vcf.gz .. ok test_vcf_concat: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools concat -Ob -G -a -D /tmp/MadjcxLl4P/concat.5.a.vcf.gz /tmp/MadjcxLl4P/concat.5.b.vcf.gz /tmp/MadjcxLl4P/concat.5.c.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools concat --no-version -G -a -D /tmp/MadjcxLl4P/concat.5.a.bcf /tmp/MadjcxLl4P/concat.5.b.bcf /tmp/MadjcxLl4P/concat.5.c.bcf .. ok test_vcf_concat: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools concat -Ob -G -a -D /tmp/MadjcxLl4P/concat.5.a.bcf /tmp/MadjcxLl4P/concat.5.b.bcf /tmp/MadjcxLl4P/concat.5.c.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_reheader: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools reheader -h /build/bcftools-Mlf9dV/bcftools-1.21/test/reheader.hdr /build/bcftools-Mlf9dV/bcftools-1.21/test/reheader.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-Mlf9dV/bcftools-1.21/test/reheader.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools reheader -h /build/bcftools-Mlf9dV/bcftools-1.21/test/reheader.hdr | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools reheader -h /build/bcftools-Mlf9dV/bcftools-1.21/test/reheader.hdr /tmp/MadjcxLl4P/reheader.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/MadjcxLl4P/reheader.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools reheader -h /build/bcftools-Mlf9dV/bcftools-1.21/test/reheader.hdr | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools reheader -h /build/bcftools-Mlf9dV/bcftools-1.21/test/reheader.hdr /tmp/MadjcxLl4P/reheader.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/MadjcxLl4P/reheader.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools reheader -h /build/bcftools-Mlf9dV/bcftools-1.21/test/reheader.hdr | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools reheader -s /build/bcftools-Mlf9dV/bcftools-1.21/test/reheader.samples /build/bcftools-Mlf9dV/bcftools-1.21/test/reheader.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-Mlf9dV/bcftools-1.21/test/reheader.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools reheader -s /build/bcftools-Mlf9dV/bcftools-1.21/test/reheader.samples | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools reheader -s /build/bcftools-Mlf9dV/bcftools-1.21/test/reheader.samples /tmp/MadjcxLl4P/reheader.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/MadjcxLl4P/reheader.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools reheader -s /build/bcftools-Mlf9dV/bcftools-1.21/test/reheader.samples | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools reheader -s /build/bcftools-Mlf9dV/bcftools-1.21/test/reheader.samples /tmp/MadjcxLl4P/reheader.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/MadjcxLl4P/reheader.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools reheader -s /build/bcftools-Mlf9dV/bcftools-1.21/test/reheader.samples | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools reheader -s /build/bcftools-Mlf9dV/bcftools-1.21/test/reheader.samples2 /build/bcftools-Mlf9dV/bcftools-1.21/test/reheader.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-Mlf9dV/bcftools-1.21/test/reheader.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools reheader -s /build/bcftools-Mlf9dV/bcftools-1.21/test/reheader.samples2 | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools reheader -s /build/bcftools-Mlf9dV/bcftools-1.21/test/reheader.samples2 /tmp/MadjcxLl4P/reheader.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/MadjcxLl4P/reheader.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools reheader -s /build/bcftools-Mlf9dV/bcftools-1.21/test/reheader.samples2 | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools reheader -s /build/bcftools-Mlf9dV/bcftools-1.21/test/reheader.samples2 /tmp/MadjcxLl4P/reheader.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/MadjcxLl4P/reheader.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools reheader -s /build/bcftools-Mlf9dV/bcftools-1.21/test/reheader.samples2 | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools reheader -s /build/bcftools-Mlf9dV/bcftools-1.21/test/reheader.samples3 /build/bcftools-Mlf9dV/bcftools-1.21/test/reheader.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-Mlf9dV/bcftools-1.21/test/reheader.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools reheader -s /build/bcftools-Mlf9dV/bcftools-1.21/test/reheader.samples3 | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools reheader -s /build/bcftools-Mlf9dV/bcftools-1.21/test/reheader.samples3 /tmp/MadjcxLl4P/reheader.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/MadjcxLl4P/reheader.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools reheader -s /build/bcftools-Mlf9dV/bcftools-1.21/test/reheader.samples3 | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools reheader -s /build/bcftools-Mlf9dV/bcftools-1.21/test/reheader.samples3 /tmp/MadjcxLl4P/reheader.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/MadjcxLl4P/reheader.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools reheader -s /build/bcftools-Mlf9dV/bcftools-1.21/test/reheader.samples3 | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools reheader -s /build/bcftools-Mlf9dV/bcftools-1.21/test/reheader.samples4 /build/bcftools-Mlf9dV/bcftools-1.21/test/reheader.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-Mlf9dV/bcftools-1.21/test/reheader.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools reheader -s /build/bcftools-Mlf9dV/bcftools-1.21/test/reheader.samples4 | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools reheader -s /build/bcftools-Mlf9dV/bcftools-1.21/test/reheader.samples4 /tmp/MadjcxLl4P/reheader.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/MadjcxLl4P/reheader.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools reheader -s /build/bcftools-Mlf9dV/bcftools-1.21/test/reheader.samples4 | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools reheader -s /build/bcftools-Mlf9dV/bcftools-1.21/test/reheader.samples4 /tmp/MadjcxLl4P/reheader.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/MadjcxLl4P/reheader.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools reheader -s /build/bcftools-Mlf9dV/bcftools-1.21/test/reheader.samples4 | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools reheader -h /build/bcftools-Mlf9dV/bcftools-1.21/test/reheader.empty.hdr /build/bcftools-Mlf9dV/bcftools-1.21/test/empty.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-Mlf9dV/bcftools-1.21/test/empty.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools reheader -h /build/bcftools-Mlf9dV/bcftools-1.21/test/reheader.empty.hdr | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools reheader -h /build/bcftools-Mlf9dV/bcftools-1.21/test/reheader.empty.hdr /tmp/MadjcxLl4P/empty.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/MadjcxLl4P/empty.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools reheader -h /build/bcftools-Mlf9dV/bcftools-1.21/test/reheader.empty.hdr | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools reheader -h /build/bcftools-Mlf9dV/bcftools-1.21/test/reheader.empty.hdr /tmp/MadjcxLl4P/empty.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/MadjcxLl4P/empty.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools reheader -h /build/bcftools-Mlf9dV/bcftools-1.21/test/reheader.empty.hdr | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools reheader -f /build/bcftools-Mlf9dV/bcftools-1.21/test/reheader.fai /build/bcftools-Mlf9dV/bcftools-1.21/test/reheader.2.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools reheader -f /build/bcftools-Mlf9dV/bcftools-1.21/test/reheader.fai /tmp/MadjcxLl4P/reheader.2.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools reheader -f /build/bcftools-Mlf9dV/bcftools-1.21/test/reheader.fai /tmp/MadjcxLl4P/reheader.2.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools reheader -h /build/bcftools-Mlf9dV/bcftools-1.21/test/reheader.2.hdr -f /build/bcftools-Mlf9dV/bcftools-1.21/test/reheader.fai /build/bcftools-Mlf9dV/bcftools-1.21/test/reheader.2.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools reheader -h /build/bcftools-Mlf9dV/bcftools-1.21/test/reheader.2.hdr -f /build/bcftools-Mlf9dV/bcftools-1.21/test/reheader.fai /tmp/MadjcxLl4P/reheader.2.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools reheader -h /build/bcftools-Mlf9dV/bcftools-1.21/test/reheader.2.hdr -f /build/bcftools-Mlf9dV/bcftools-1.21/test/reheader.fai /tmp/MadjcxLl4P/reheader.2.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools reheader -f /build/bcftools-Mlf9dV/bcftools-1.21/test/reheader.3.fai /build/bcftools-Mlf9dV/bcftools-1.21/test/reheader.3.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools reheader -f /build/bcftools-Mlf9dV/bcftools-1.21/test/reheader.3.fai /tmp/MadjcxLl4P/reheader.3.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools reheader -f /build/bcftools-Mlf9dV/bcftools-1.21/test/reheader.3.fai /tmp/MadjcxLl4P/reheader.3.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view --no-version .. ok test_rename_chrs: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate --rename-chrs /tmp/MadjcxLl4P/rename.map -Ov /tmp/MadjcxLl4P/annotate.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate --rename-chrs /tmp/MadjcxLl4P/rename.map -Ob /tmp/MadjcxLl4P/annotate.bcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate --rename-chrs /tmp/MadjcxLl4P/rename.map -Ov /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools annotate --rename-chrs /tmp/MadjcxLl4P/rename.map -Ob /build/bcftools-Mlf9dV/bcftools-1.21/test/annotate.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%CHROM\t%POS\n' .. ok test_vcf_convert: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools convert -g -,. /tmp/MadjcxLl4P/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/convert.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools convert -g -,. .. ok test_vcf_convert: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools convert -g -,. --vcf-ids /tmp/MadjcxLl4P/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/convert.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools convert -g -,. --vcf-ids .. ok test_vcf_convert: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools convert -g -,. --vcf-ids --3N6 /tmp/MadjcxLl4P/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/convert.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools convert -g -,. --vcf-ids --3N6 .. ok test_vcf_convert: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools convert -g .,- /tmp/MadjcxLl4P/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/convert.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools convert -g .,- .. ok test_vcf_convert_hs2vcf: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools convert --vcf-ids -G /build/bcftools-Mlf9dV/bcftools-1.21/test/convert.gs.gt.ids.gen,/build/bcftools-Mlf9dV/bcftools-1.21/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools convert --vcf-ids -G /build/bcftools-Mlf9dV/bcftools-1.21/test/convert.gs.gt.ids.gen,/build/bcftools-Mlf9dV/bcftools-1.21/test/convert.gs.gt.samples -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools convert -G /build/bcftools-Mlf9dV/bcftools-1.21/test/convert.gs.gt.ids.gen,/build/bcftools-Mlf9dV/bcftools-1.21/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools convert -G /build/bcftools-Mlf9dV/bcftools-1.21/test/convert.gs.gt.ids.gen,/build/bcftools-Mlf9dV/bcftools-1.21/test/convert.gs.gt.samples -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools convert --3N6 -G /build/bcftools-Mlf9dV/bcftools-1.21/test/convert.gs.gt.ids.3N6.gen,/build/bcftools-Mlf9dV/bcftools-1.21/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools convert --3N6 -G /build/bcftools-Mlf9dV/bcftools-1.21/test/convert.gs.gt.ids.3N6.gen,/build/bcftools-Mlf9dV/bcftools-1.21/test/convert.gs.gt.samples -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools convert --vcf-ids -G /build/bcftools-Mlf9dV/bcftools-1.21/test/convert.gs.gt.ids.gen.rev,/build/bcftools-Mlf9dV/bcftools-1.21/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools convert --vcf-ids -G /build/bcftools-Mlf9dV/bcftools-1.21/test/convert.gs.gt.ids.gen.rev,/build/bcftools-Mlf9dV/bcftools-1.21/test/convert.gs.gt.samples -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools convert -G /build/bcftools-Mlf9dV/bcftools-1.21/test/convert.gs.gt.ids.gen.rev,/build/bcftools-Mlf9dV/bcftools-1.21/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools convert -G /build/bcftools-Mlf9dV/bcftools-1.21/test/convert.gs.gt.ids.gen.rev,/build/bcftools-Mlf9dV/bcftools-1.21/test/convert.gs.gt.samples -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^## .. ok test_vcf_convert: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools convert -g -,. --tag PL /tmp/MadjcxLl4P/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/convert.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools convert -g -,. --tag PL .. ok test_vcf_convert: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools convert -g .,- --tag PL /tmp/MadjcxLl4P/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/convert.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools convert -g .,- --tag PL .. ok test_vcf_convert: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools convert -g -,. --vcf-ids /tmp/MadjcxLl4P/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/check.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools convert -g -,. --vcf-ids .. ok test_vcf_convert: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools convert -g .,- --vcf-ids /tmp/MadjcxLl4P/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/check.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools convert -g .,- --vcf-ids .. ok test_vcf_convert: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools convert -g -,. --3N6 /tmp/MadjcxLl4P/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/check.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools convert -g -,. --3N6 .. ok test_vcf_convert: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools convert -g .,- --3N6 /tmp/MadjcxLl4P/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/check.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools convert -g .,- --3N6 .. ok test_vcf_convert: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools convert -g -,. --3N6 --vcf-ids /tmp/MadjcxLl4P/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/check.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools convert -g -,. --3N6 --vcf-ids .. ok test_vcf_convert: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools convert -g .,- --3N6 --vcf-ids /tmp/MadjcxLl4P/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/check.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools convert -g .,- --3N6 --vcf-ids .. ok test_vcf_convert: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools convert -h -,.,. /tmp/MadjcxLl4P/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/convert.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools convert -h -,.,. .. ok test_vcf_convert: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools convert -h .,-,. /tmp/MadjcxLl4P/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/convert.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools convert -h .,-,. .. ok test_vcf_convert: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools convert -h .,-,. --vcf-ids /tmp/MadjcxLl4P/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/convert.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools convert -h .,-,. --vcf-ids .. ok test_vcf_convert: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools convert -h .,.,- /tmp/MadjcxLl4P/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/convert.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools convert -h .,.,- .. ok test_vcf_convert_hls2vcf: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools convert -H /build/bcftools-Mlf9dV/bcftools-1.21/test/convert.hls.gt.hap,/build/bcftools-Mlf9dV/bcftools-1.21/test/convert.hls.gt.legend,/build/bcftools-Mlf9dV/bcftools-1.21/test/convert.hls.gt.samples | grep -v ^## .. ok test_vcf_convert_hls2vcf: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools convert -H /build/bcftools-Mlf9dV/bcftools-1.21/test/convert.hls.gt.hap,/build/bcftools-Mlf9dV/bcftools-1.21/test/convert.hls.gt.legend,/build/bcftools-Mlf9dV/bcftools-1.21/test/convert.hls.gt.samples -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^## .. ok test_vcf_convert: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools convert --haplegendsample -,.,. /tmp/MadjcxLl4P/convert.hap-missing.vcf.gz .. ok test_vcf_convert: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/convert.hap-missing.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools convert --haplegendsample -,.,. .. ok test_vcf_convert: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools convert --hapsample -,. /tmp/MadjcxLl4P/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/convert.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools convert --hapsample -,. .. ok test_vcf_convert: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools convert --hapsample -,. --vcf-ids /tmp/MadjcxLl4P/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/convert.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools convert --hapsample -,. --vcf-ids .. ok test_vcf_convert: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools convert --hapsample .,- /tmp/MadjcxLl4P/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/convert.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools convert --hapsample .,- .. ok test_vcf_convert_hs2vcf: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools convert --hapsample2vcf /build/bcftools-Mlf9dV/bcftools-1.21/test/convert.hs.gt.hap,/build/bcftools-Mlf9dV/bcftools-1.21/test/convert.hs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools convert --hapsample2vcf /build/bcftools-Mlf9dV/bcftools-1.21/test/convert.hs.gt.hap,/build/bcftools-Mlf9dV/bcftools-1.21/test/convert.hs.gt.samples -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools convert --vcf-ids --hapsample2vcf /build/bcftools-Mlf9dV/bcftools-1.21/test/convert.hs.gt.ids.hap,/build/bcftools-Mlf9dV/bcftools-1.21/test/convert.hs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools convert --vcf-ids --hapsample2vcf /build/bcftools-Mlf9dV/bcftools-1.21/test/convert.hs.gt.ids.hap,/build/bcftools-Mlf9dV/bcftools-1.21/test/convert.hs.gt.samples -Ou | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^## .. ok test_vcf_convert_gvcf: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools convert --no-version --gvcf2vcf -i'FILTER="PASS"' -f /build/bcftools-Mlf9dV/bcftools-1.21/test/gvcf.fa /tmp/MadjcxLl4P/convert.gvcf.vcf.gz .. ok test_vcf_convert_gvcf: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view -Ob /tmp/MadjcxLl4P/convert.gvcf.vcf.gz | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools convert --gvcf2vcf -i'FILTER="PASS"' -f /build/bcftools-Mlf9dV/bcftools-1.21/test/gvcf.fa | grep -v ^##bcftools .. ok test_vcf_convert_tsv2vcf: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools convert --no-version -c ID,CHROM,POS,AA -s SAMPLE1 -f /build/bcftools-Mlf9dV/bcftools-1.21/test/23andme.fa --tsv2vcf /build/bcftools-Mlf9dV/bcftools-1.21/test/convert.23andme .. ok test_vcf_convert_tsv2vcf: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools convert -Ou -c ID,CHROM,POS,AA -s SAMPLE1 -f /build/bcftools-Mlf9dV/bcftools-1.21/test/23andme.fa --tsv2vcf /build/bcftools-Mlf9dV/bcftools-1.21/test/convert.23andme | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_convert_tsv2vcf: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools convert --no-version -c -,CHROM,POS,REF,ALT -f /build/bcftools-Mlf9dV/bcftools-1.21/test/23andme.fa --tsv2vcf /build/bcftools-Mlf9dV/bcftools-1.21/test/convert.tsv .. ok test_vcf_convert_tsv2vcf: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools convert -Ou -c -,CHROM,POS,REF,ALT -f /build/bcftools-Mlf9dV/bcftools-1.21/test/23andme.fa --tsv2vcf /build/bcftools-Mlf9dV/bcftools-1.21/test/convert.tsv | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.overlaps.1.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.overlaps.1.fa -s A .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.overlaps.1.bcf -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.overlaps.1.fa -s A .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.overlaps.1.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.overlaps.1.fa -s B .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.overlaps.1.bcf -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.overlaps.1.fa -s B .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.overlaps.1.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.overlaps.1.fa -s A -a N .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.overlaps.1.bcf -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.overlaps.1.fa -s A -a N .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.overlaps.1.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.overlaps.1.fa -s B -a N .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.overlaps.1.bcf -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.overlaps.1.fa -s B -a N .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.beyond.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.beyond.fa .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.beyond.bcf -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.beyond.fa .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.fa -s - -m /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.tab .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.bcf -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.fa -s - -m /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.tab .. ok test_vcf_consensus_chain: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.fa -s - -m /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.tab -c /tmp/MadjcxLl4P/consensus.1.chain.new >/dev/null; cat /tmp/MadjcxLl4P/consensus.1.chain.new .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.fa -H 1 -m /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.tab .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.bcf -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.fa -H 1 -m /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.tab .. ok test_vcf_consensus_chain: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.fa -H 1 -m /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.tab -c /tmp/MadjcxLl4P/consensus.2.chain.new >/dev/null; cat /tmp/MadjcxLl4P/consensus.2.chain.new .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.fa -I -s - -m /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.tab .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.bcf -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.fa -I -s - -m /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.tab .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.fa -s - -I -m /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.tab --mask-with X -m /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.tab --mask-with lc .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.bcf -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.fa -s - -I -m /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.tab --mask-with X -m /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.tab --mask-with lc .. ok test_vcf_consensus_chain: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.fa -I -m /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.tab -c /tmp/MadjcxLl4P/consensus.3.chain.new >/dev/null; cat /tmp/MadjcxLl4P/consensus.3.chain.new .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.fa -H 1 .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.bcf -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.fa -H 1 .. ok test_vcf_consensus_chain: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.fa -H 1 -c /tmp/MadjcxLl4P/consensus.4.chain.new >/dev/null; cat /tmp/MadjcxLl4P/consensus.4.chain.new .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus2.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus2.fa -H 1 .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus2.bcf -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus2.fa -H 1 .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus2.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus2.fa -H 2 .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus2.bcf -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus2.fa -H 2 .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/empty.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.fa -s - .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/empty.bcf -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.fa -s - .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus3.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus2.fa -H 2 -M "?" .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus3.bcf -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus2.fa -H 2 -M "?" .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus3.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus2.fa -H 2 -M "?" -p xx_ .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus3.bcf -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus2.fa -H 2 -M "?" -p xx_ .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus4.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus2.fa -s - .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus4.bcf -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus2.fa -s - .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus5.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus5.fa --haplotype LA .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus5.bcf -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus5.fa --haplotype LA .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus6.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus6.fa -s - .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus6.bcf -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus6.fa -s - .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus7.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus7.fa -H 2 .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus7.bcf -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus7.fa -H 2 .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus7.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus7.fa -H 4 .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus7.bcf -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus7.fa -H 4 .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus7.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus7.fa -H 2pIu .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus7.bcf -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus7.fa -H 2pIu .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus7.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus7.fa -H 4pIu .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus7.bcf -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus7.fa -H 4pIu .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus7.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus7.fa -H 1 .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus7.bcf -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus7.fa -H 1 .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus7.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus7.fa -H 3 .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus7.bcf -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus7.fa -H 3 .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus7.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus7.fa -H 1pIu .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus7.bcf -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus7.fa -H 1pIu .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus7.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus7.fa -H 3pIu .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus7.bcf -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus7.fa -H 3pIu .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus8.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.fa -s - .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus8.bcf -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.fa -s - .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus8.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.fa -s - -a . .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus8.bcf -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.fa -s - -a . .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus8.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.fa -s - -a . -i 'type="snp" || type="ref"' .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus8.bcf -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.fa -s - -a . -i 'type="snp" || type="ref"' .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus8.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.fa -s - -a . -i 'ALT!=""' .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus8.bcf -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.fa -s - -a . -i 'ALT!=""' .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus8.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.fa -s - -a . -e 'MinDP>15' .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus8.bcf -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.fa -s - -a . -e 'MinDP>15' .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus8.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.fa -s - -a . -e 'MinDP<15' .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus8.bcf -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.fa -s - -a . -e 'MinDP<15' .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.9.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.9.bcf -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.9.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.9.bcf -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.10.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.10.bcf -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.10.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.10.bcf -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.11.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.11.fa -s smpl .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.11.bcf -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.11.fa -s smpl .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.11.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.11.fa -s smpl -a N .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.11.bcf -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.11.fa -s smpl -a N .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.12.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.12.fa -s - .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.12.bcf -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.12.fa -s - .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.13.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.13.fa -s - .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.13.bcf -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.13.fa -s - .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.14.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.14.fa -s - .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.14.bcf -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.14.fa -s - .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.12.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.12.fa -s - --mark-del - --mark-ins uc --mark-snv uc .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.12.bcf -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.12.fa -s - --mark-del - --mark-ins uc --mark-snv uc .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.12.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.12.fa -s - --mark-del - --mark-ins + --mark-snv : .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.12.bcf -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.12.fa -s - --mark-del - --mark-ins + --mark-snv : .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.15.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.15.fa -H I --mark-ins lc --mark-snv lc .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.15.bcf -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.15.fa -H I --mark-ins lc --mark-snv lc .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.16.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.fa -s - -I .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.16.bcf -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.fa -s - -I .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.16.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.fa -H I .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.16.bcf -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.fa -H I .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.17.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus2.fa -s - -M N -m /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.17.bed .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.17.bcf -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus2.fa -s - -M N -m /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.17.bed .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.18.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.18.fa -s - .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.18.bcf -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.18.fa -s - .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.19.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.19.fa -s - .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.19.bcf -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.19.fa -s - .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.20.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.20.fa -s - .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.20.bcf -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.20.fa -s - .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.20.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.20.fa .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.20.bcf -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.20.fa .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.20.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.20.fa -M . -s b .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.20.bcf -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.20.fa -M . -s b .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.20.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.20.fa -M . -s a .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.20.bcf -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.20.fa -M . -s a .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.21.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.21.fa .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.21.bcf -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.21.fa .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.22.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.22.fa --regions-overlap 0 --mark-del . .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.22.bcf -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.22.fa --regions-overlap 0 --mark-del . .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.22.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.22.fa --regions-overlap 1 --mark-del . .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.22.bcf -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.22.fa --regions-overlap 1 --mark-del . .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.22.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.22.fa --regions-overlap 2 --mark-del . .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.22.bcf -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.22.fa --regions-overlap 2 --mark-del . .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.22.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.22.fa --regions-overlap 0 .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.22.bcf -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.22.fa --regions-overlap 0 .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.22.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.22.fa --regions-overlap 1 .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.22.bcf -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.22.fa --regions-overlap 1 .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.22.vcf.gz -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.22.fa --regions-overlap 2 .. ok test_vcf_consensus: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools consensus /tmp/MadjcxLl4P/consensus.22.bcf -f /build/bcftools-Mlf9dV/bcftools-1.21/test/consensus.22.fa --regions-overlap 2 .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -r17:100-150 -a -AD -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.1.bam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.2.bam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -r17:100-150 -a -AD -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.1.bam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.2.bam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -r17:100-150 -a -AD -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa -b /tmp/MadjcxLl4P/mpileup.bam.list --no-version | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -r17:100-150 -a -AD -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob -b /tmp/MadjcxLl4P/mpileup.bam.urllist | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -r17:100-150 -a -AD -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.1.cram /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.2.cram /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -r17:100-150 -a -AD -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.1.cram /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.2.cram /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -r17:100-150 -a -AD -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa -b /tmp/MadjcxLl4P/mpileup.cram.list --no-version | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -r17:100-150 -a -AD -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob -b /tmp/MadjcxLl4P/mpileup.cram.urllist | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a DP,DV -r17:100-600 -a -AD -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.1.bam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.2.bam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a DP,DV -r17:100-600 -a -AD -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.1.bam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.2.bam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a DP,DV -r17:100-600 -a -AD -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.1.cram /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.2.cram /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a DP,DV -r17:100-600 -a -AD -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.1.cram /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.2.cram /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -a -AD -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -a -AD -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.1.bam | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -a -AD -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.1.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -a -AD -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.1.cram | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP,-AD -r17:100-600 -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.1.bam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.2.bam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP,-AD -r17:100-600 -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.1.bam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.2.bam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP,-AD -r17:100-600 -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.1.cram /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.2.cram /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP,-AD -r17:100-600 -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.1.cram /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.2.cram /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.1.bam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.2.bam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.1.bam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.2.bam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.1.cram /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.2.cram /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.1.cram /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.2.cram /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a DP,DV,-AD -r17:100-600 --gvcf 0,2,5 -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.1.bam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.2.bam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a DP,DV,-AD -r17:100-600 --gvcf 0,2,5 -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.1.bam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.2.bam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a DP,DV,-AD -r17:100-600 --gvcf 0,2,5 -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.1.cram /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.2.cram /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a DP,DV,-AD -r17:100-600 --gvcf 0,2,5 -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.1.cram /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.2.cram /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a DP,DV,-AD -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.1.bam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.2.bam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a DP,DV,-AD -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.1.bam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.2.bam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a DP,DV,-AD -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.1.cram /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.2.cram /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a DP,DV,-AD -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.1.cram /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.2.cram /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -s HG00101,HG00102 -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.1.bam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.2.bam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -s HG00101,HG00102 -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.1.bam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.2.bam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -s HG00101,HG00102 -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.1.cram /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.2.cram /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -s HG00101,HG00102 -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.1.cram /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.2.cram /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -S /build/bcftools-Mlf9dV/bcftools-1.21/test/mplp.samples -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.1.bam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.2.bam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -S /build/bcftools-Mlf9dV/bcftools-1.21/test/mplp.samples -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.1.bam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.2.bam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -S /build/bcftools-Mlf9dV/bcftools-1.21/test/mplp.samples -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.1.cram /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.2.cram /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -S /build/bcftools-Mlf9dV/bcftools-1.21/test/mplp.samples -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.1.cram /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.2.cram /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -s ^HG00101,HG00102 -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.1.bam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.2.bam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -s ^HG00101,HG00102 -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.1.bam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.2.bam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -s ^HG00101,HG00102 -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.1.cram /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.2.cram /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -s ^HG00101,HG00102 -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.1.cram /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.2.cram /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -S ^/build/bcftools-Mlf9dV/bcftools-1.21/test/mplp.samples -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.1.bam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.2.bam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -S ^/build/bcftools-Mlf9dV/bcftools-1.21/test/mplp.samples -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.1.bam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.2.bam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -S ^/build/bcftools-Mlf9dV/bcftools-1.21/test/mplp.samples -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.1.cram /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.2.cram /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -r17:100-150 -S ^/build/bcftools-Mlf9dV/bcftools-1.21/test/mplp.samples -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.1.cram /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.2.cram /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -S /build/bcftools-Mlf9dV/bcftools-1.21/test/mplp.9.samples -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.1.sam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.2.sam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -S /build/bcftools-Mlf9dV/bcftools-1.21/test/mplp.9.samples -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.1.sam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.2.sam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.sam | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -S /build/bcftools-Mlf9dV/bcftools-1.21/test/mplp.9.samples -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.1.bam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.2.bam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -S /build/bcftools-Mlf9dV/bcftools-1.21/test/mplp.9.samples -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.1.bam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.2.bam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -S /build/bcftools-Mlf9dV/bcftools-1.21/test/mplp.9.samples -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.1.cram /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.2.cram /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -S /build/bcftools-Mlf9dV/bcftools-1.21/test/mplp.9.samples -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.1.cram /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.2.cram /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -G /build/bcftools-Mlf9dV/bcftools-1.21/test/mplp.10.samples -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.1.sam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.2.sam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -G /build/bcftools-Mlf9dV/bcftools-1.21/test/mplp.10.samples -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.1.sam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.2.sam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.sam | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -G /build/bcftools-Mlf9dV/bcftools-1.21/test/mplp.10.samples -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.1.bam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.2.bam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -G /build/bcftools-Mlf9dV/bcftools-1.21/test/mplp.10.samples -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.1.bam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.2.bam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -G /build/bcftools-Mlf9dV/bcftools-1.21/test/mplp.10.samples -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.1.cram /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.2.cram /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -t17:100-150 -G /build/bcftools-Mlf9dV/bcftools-1.21/test/mplp.10.samples -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.1.cram /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.2.cram /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.sam | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.bam | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.cram | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -s HG00102 -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.sam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -s HG00102 -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.sam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.4.sam | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -s HG00102 -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.bam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -s HG00102 -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.bam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.4.bam | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -s HG00102 -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.cram /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -s HG00102 -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.cram /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.4.cram | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -s ^HG99999 -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.sam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -s ^HG99999 -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.sam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.4.sam | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -s ^HG99999 -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.bam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -s ^HG99999 -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.bam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.4.bam | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -s ^HG99999 -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.cram /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -s ^HG99999 -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.cram /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.4.cram | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -G /build/bcftools-Mlf9dV/bcftools-1.21/test/mplp.11.rgs -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.sam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -G /build/bcftools-Mlf9dV/bcftools-1.21/test/mplp.11.rgs -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.sam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.4.sam | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -G /build/bcftools-Mlf9dV/bcftools-1.21/test/mplp.11.rgs -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.bam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -G /build/bcftools-Mlf9dV/bcftools-1.21/test/mplp.11.rgs -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.bam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.4.bam | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -G /build/bcftools-Mlf9dV/bcftools-1.21/test/mplp.11.rgs -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.cram /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -G /build/bcftools-Mlf9dV/bcftools-1.21/test/mplp.11.rgs -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.cram /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.4.cram | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -G /build/bcftools-Mlf9dV/bcftools-1.21/test/mplp.11.rgs -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.sam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -G /build/bcftools-Mlf9dV/bcftools-1.21/test/mplp.11.rgs -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.sam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.4.sam | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -G /build/bcftools-Mlf9dV/bcftools-1.21/test/mplp.11.rgs -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.bam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -G /build/bcftools-Mlf9dV/bcftools-1.21/test/mplp.11.rgs -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.bam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.4.bam | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -G /build/bcftools-Mlf9dV/bcftools-1.21/test/mplp.11.rgs -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.cram /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -G /build/bcftools-Mlf9dV/bcftools-1.21/test/mplp.11.rgs -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.3.cram /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup.4.cram | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a AD -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/indel-AD.1.fa /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/indel-AD.1.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a AD -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/indel-AD.1.fa -Ob /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/indel-AD.1.sam | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a AD -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/indel-AD.1.fa /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/indel-AD.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a AD -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/indel-AD.1.fa -Ob /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/indel-AD.1.bam | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a AD -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/indel-AD.1.fa /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/indel-AD.1.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a AD -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/indel-AD.1.fa -Ob /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/indel-AD.1.cram | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a AD --indels-cns -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/indel-AD.1.fa /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/indel-AD.1.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a AD --indels-cns -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/indel-AD.1.fa -Ob /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/indel-AD.1.sam | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a AD --indels-cns -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/indel-AD.1.fa /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/indel-AD.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a AD --indels-cns -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/indel-AD.1.fa -Ob /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/indel-AD.1.bam | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a AD --indels-cns -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/indel-AD.1.fa /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/indel-AD.1.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a AD --indels-cns -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/indel-AD.1.fa -Ob /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/indel-AD.1.cram | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a AD -r 11:75 -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/indel-AD.2.fa /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a AD -r 11:75 -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/indel-AD.2.fa -Ob /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/indel-AD.2.bam | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a AD -r 11:75 -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/indel-AD.2.fa /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a AD -r 11:75 -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/indel-AD.2.fa -Ob /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/indel-AD.2.cram | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/indel-AD.2.fa /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/indel-AD.2.fa -Ob /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/indel-AD.2.bam | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/indel-AD.2.fa /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/indel-AD.2.fa -Ob /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/indel-AD.2.cram | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/indel-AD.2.fa /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/indel-AD.2.fa -Ob /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/indel-AD.2.bam | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/indel-AD.2.fa /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/indel-AD.2.fa -Ob /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/indel-AD.2.cram | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD,INFO/SCR,FMT/SCR -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup-SCR.fa /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup-SCR.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD,INFO/SCR,FMT/SCR -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup-SCR.fa -Ob /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup-SCR.bam | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD,INFO/SCR,FMT/SCR -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup-SCR.fa /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup-SCR.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD,INFO/SCR,FMT/SCR -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup-SCR.fa -Ob /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup-SCR.cram | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -t 1:100 --skip-all-set PAIRED,PROPER_PAIR,MREVERSE -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup-SCR.fa /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -t 1:100 --skip-all-set PAIRED,PROPER_PAIR,MREVERSE -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup-SCR.fa -Ob /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup-filter.sam | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -t 1:100 --skip-any-set READ1 -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup-SCR.fa /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -t 1:100 --skip-any-set READ1 -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup-SCR.fa -Ob /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup-filter.sam | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -t 1:100 --skip-all-unset READ1 -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup-SCR.fa /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -t 1:100 --skip-all-unset READ1 -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup-SCR.fa -Ob /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup-filter.sam | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -t 1:100 --skip-any-unset READ1 -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup-SCR.fa /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD -t 1:100 --skip-any-unset READ1 -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup-SCR.fa -Ob /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/mpileup-filter.sam | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD,INFO/NMBZ -r chr19:69-99 -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/annot-NMBZ.1.fa /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/annot-NMBZ.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD,INFO/NMBZ -r chr19:69-99 -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/annot-NMBZ.1.fa -Ob /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/annot-NMBZ.1.bam | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD,INFO/NMBZ -r chr6:75 -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/annot-NMBZ.2.fa /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/annot-NMBZ.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD,INFO/NMBZ -r chr6:75 -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/annot-NMBZ.2.fa -Ob /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/annot-NMBZ.2.bam | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD,INFO/NMBZ -r chr16:75 -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/annot-NMBZ.3.fa /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/annot-NMBZ.3.1.bam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/annot-NMBZ.3.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools mpileup -a -AD,INFO/NMBZ -r chr16:75 -f /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/annot-NMBZ.3.fa -Ob /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/annot-NMBZ.3.1.bam /build/bcftools-Mlf9dV/bcftools-1.21/test/mpileup/annot-NMBZ.3.2.bam | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_csq: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq.gff3 /build/bcftools-Mlf9dV/bcftools-1.21/test/csq.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq.chr.gff3 /build/bcftools-Mlf9dV/bcftools-1.21/test/csq.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq.2.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq.2.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq.2.gff --ncsq 64 /build/bcftools-Mlf9dV/bcftools-1.21/test/csq.2.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq.nchr.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq.nchr.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq.nchr.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq.ychr.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq.nchr.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq.nchr.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq.nchr.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq.ychr.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq.nchr.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq.ychr.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq.ychr.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq.nchr.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq.ychr.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq.ychr.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq.ychr.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq.ychr.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq.nchr.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq.ychr.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq.nchr.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq.ychr.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq.ychr.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq.nchr.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq.nchr.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq.ychr.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000373833/ENST00000373833.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000373833/ENST00000373833.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000373833/boundary-insertion.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -l -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000373833/ENST00000373833.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000373833/ENST00000373833.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000373833/boundary-insertion.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000422159 && /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f ENST00000422159.fa -g ENST00000422159.gff multiallelic.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS\t%REF\t%ALT\t%GT\t%TBCSQ\n]' | ../sort-csq -q ; echo ; /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f ENST00000422159.fa -g short.gff multiallelic.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS\t%REF\t%ALT\t%GT\t%TBCSQ\n]' | ../sort-csq -q .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000378322/ENST00000378322.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000378322/ENST00000378322.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000378322/end-overlap-tscript.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -l -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000378322/ENST00000378322.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000378322/ENST00000378322.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000378322/end-overlap-tscript.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000263103-INS/ENST00000263103-INS.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000263103-INS/ENST00000263103-INS.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000263103-INS/insertions.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000269081/ENST00000269081.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000269081/ENST00000269081.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000269081/stop-gained-not-inframe-insertion.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000420190/ENST00000420190.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000420190/ENST00000420190.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000420190/abort-in-csq-push.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000329454/ENST00000329454.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000329454/ENST00000329454.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000329454/boundary-deletion.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -l -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000329454/ENST00000329454.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000329454/ENST00000329454.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000329454/boundary-deletion.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000294661/ENST00000294661.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000294661/ENST00000294661.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000294661/non-coding-boundary.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -l -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000294661/ENST00000294661.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000294661/ENST00000294661.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000294661/non-coding-boundary.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000285021/ENST00000285021.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000285021/ENST00000285021.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000285021/stop-gained-inframe-indel.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000381157/ENST00000381157.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000381157/ENST00000381157.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000381157/haploid-diploid.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n' .. ok test_csq_real: cd /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000410009 && /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -lb -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000410009 && /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -B 5 -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000410009 && /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -b -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000410009/ENST00000410009.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000410009/ENST00000410009.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000410009/frameshift.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENSMUST00000133836 && /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f ENSMUST00000133836.fa -g ENSMUST00000133836.gff filter-problem.vcf -i 'FILTER="PASS"' --phase m | ../sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/EMN908947 && /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f EMN908947.fa -g ribosomal-slippage.gff ribosomal-slippage.vcf --force | ../sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/EMN908947 && /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f EMN908947.fa -g simple.gff simple.vcf | ../sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000519442/ENST00000519442.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000519442/ENST00000519442.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000519442/synon-splice-region-del.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000557788/ENST00000557788.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000557788/ENST00000557788.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000557788/long-overlap-del.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENSMUST00000121418 && /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25105' --phase m | ../sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENSMUST00000121418 && /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25500' --phase m | ../sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENSMUST00000121418 && /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25496' --phase m | ../sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000420670/ENST00000420670.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000420670/ENST00000420670.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000420670/start-stop-lost.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000420670/ENST00000420670.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000420670/ENST00000420670.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000420670/segfault.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000409523/ENST00000409523.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000409523/ENST00000409523.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000409523/long-overlapping-del.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000520795/ENST00000520795.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000520795/ENST00000520795.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000520795/long-inside-del.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -l -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000520795/ENST00000520795.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000520795/ENST00000520795.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000520795/long-inside-del.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000382647/ENST00000382647.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000382647/ENST00000382647.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000382647/synon-splice-region-insert.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000545279/ENST00000545279.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000545279/ENST00000545279.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000545279/splice-region-insert.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000528237/ENST00000528237.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000528237/ENST00000528237.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000528237/retained-stop-incomplete-cds.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000379416 && /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.del-snp.vcf | ../sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-del.vcf | ../sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-ins.vcf | ../sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-snp.vcf | ../sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff single.vcf | ../sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000400151/ENST00000400151.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000400151/ENST00000400151.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000400151/long-del.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000624631/ENST00000624631.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000624631/ENST00000624631.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000624631/ambiguous.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000218032/ENST00000218032.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000218032/ENST00000218032.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000218032/start-lost-del.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000218032/ENST00000218032.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000218032/ENST00000218032.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000218032/start-lost.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -l -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000218032/ENST00000218032.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000218032/ENST00000218032.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000218032/start-lost.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000542803/ENST00000542803.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000542803/ENST00000542803.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000542803/splice-region.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -l -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000542803/ENST00000542803.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000542803/ENST00000542803.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000542803/splice-region.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000543077/ENST00000543077.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000543077/ENST00000543077.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000543077/not-a-start-lost.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -l -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000543077/ENST00000543077.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000543077/ENST00000543077.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000543077/not-a-start-lost.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -l -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -l -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -l -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/frame3.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -l -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/frame3.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -l -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -l -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -l -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/frame2.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -l -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/frame2.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/not-a-start-lost.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -l -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/not-a-start-lost.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/frame1.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -l -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/frame1.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -l -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -l -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -l -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000536784/ENST00000536784.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000536784/ENST00000536784.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000536784/not-a-start-lost.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -l -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000536784/ENST00000536784.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000536784/ENST00000536784.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000536784/not-a-start-lost.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/EDUMMY0003/EDUMMY0003.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/EDUMMY0003/EDUMMY0003.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/EDUMMY0003/long-del.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000000000 && /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -p a -f ENST00000000000.fa -g ENST00000000000.gff upstream-stop.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'[%POS\t%REF\t%ALT\t%SAMPLE\t%GT\t%TBCSQ\n]' | ../sort-csq -q .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000448695/ENST00000448695.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000448695/ENST00000448695.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000448695/syn-and-splice-reg.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/EDUMMY0002/EDUMMY0002.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/EDUMMY0002/EDUMMY0002.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/EDUMMY0002/boundaries.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000318249/ENST00000318249.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000318249/ENST00000318249.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000318249/start-lost.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -l -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000318249/ENST00000318249.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000318249/ENST00000318249.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000318249/start-lost.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000580206 && /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.ins-snv.vcf | ../sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g short.gff compound.ins-snv.vcf | ../sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff single.ins-snv.vcf | ../sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g short.gff single.ins-snv.vcf | ../sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.del-snv.vcf | ../sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g short.gff compound.del-snv.vcf | ../sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g short.gff single.del-snv.vcf | ../sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.del-ins.vcf | ../sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g short.gff compound.del-ins.vcf | ../sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f ENST00000580206.fa -g short.gff single.del-ins.vcf | ../sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000520868/ENST00000520868.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000520868/ENST00000520868.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000520868/long-deletion.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000413103/ENST00000413103.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000413103/ENST00000413103.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000413103/long-deletion.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENSG00000173376/ENSG00000173376.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENSG00000173376/ENSG00000173376.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENSG00000173376/synon.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000571540/ENST00000571540.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000571540/ENST00000571540.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000571540/nmd.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000227471/ENST00000227471.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000227471/ENST00000227471.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000227471/insert-splice-vs-frameshift.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000271583/ENST00000271583.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000271583/ENST00000271583.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000271583/splice-acceptor.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000368801/ENST00000368801.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000368801/ENST00000368801.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000368801/compound-lost.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000301246/ENST00000301246.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000301246/ENST00000301246.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000301246/15bp-insert.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000318249.2/ENST00000318249.2.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000318249.2/ENST00000318249.2.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000318249.2/synonymous-start-lost.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/EDUMMY0001/EDUMMY0001.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/EDUMMY0001/EDUMMY0001.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/EDUMMY0001/starts-with-1.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -l -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/EDUMMY0001/EDUMMY0001.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/EDUMMY0001/EDUMMY0001.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/EDUMMY0001/starts-with-1.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000295641/ENST00000295641.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000295641/ENST00000295641.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000295641/not-a-start-lost.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -l -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000295641/ENST00000295641.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000295641/ENST00000295641.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000295641/not-a-start-lost.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000479739/ENST00000479739.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000479739/ENST00000479739.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000479739/short-cds-start-lost.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -l -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000479739/ENST00000479739.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000479739/ENST00000479739.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000479739/short-cds-start-lost.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000436063/ENST00000436063.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000436063/ENST00000436063.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000436063/insert-before-utr.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000573035-bt2212/ENST00000573035-bt2212.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000573035-bt2212/ENST00000573035-bt2212.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000573035-bt2212/complex-event.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000518414/ENST00000518414.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000518414/ENST00000518414.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000518414/incorrect-inframe-del.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000368801.2/ENST00000368801.2.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000368801.2/ENST00000368801.2.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000368801.2/start-lost.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000518414-ENST00000521270/valgrind.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000423372/snps.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -l -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000423372/snps.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000423372/insert3.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -l -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000423372/ENST00000423372.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000423372/insert3.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000303039/ENST00000303039.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000303039/ENST00000303039.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000303039/not-a-stop.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -l -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000303039/ENST00000303039.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000303039/ENST00000303039.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000303039/not-a-stop.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000256452/ENST00000256452.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000256452/ENST00000256452.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000256452/intron.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000357367/ENST00000357367.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000357367/ENST00000357367.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000357367/stop-retained.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000375992/ENST00000375992.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000375992/ENST00000375992.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000375992/incorrect-synon-del-not-start-lost.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000593942/ENST00000593942.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000593942/ENST00000593942.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000593942/last-codon-deletion.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000360372/ENST00000360372.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000360372/ENST00000360372.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000360372/mnp.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000230048/ENST00000230048.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000230048/ENST00000230048.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000230048/start-del.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000573314/ENST00000573314.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000573314/ENST00000573314.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -l -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000573314/ENST00000573314.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000573314/ENST00000573314.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools csq -f /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000390520/ENST00000390520.fa -g /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000390520/ENST00000390520.gff /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/ENST00000390520/deletion-overlap.vcf | /build/bcftools-Mlf9dV/bcftools-1.21/test/csq/sort-csq | /build/bcftools-Mlf9dV/bcftools-1.21/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_roh: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools roh /build/bcftools-Mlf9dV/bcftools-1.21/test/roh.1.vcf.gz -Or -G30 --AF-dflt 0.4| grep -v ^# .. ok test_roh: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools roh /build/bcftools-Mlf9dV/bcftools-1.21/test/roh.1.vcf.gz -Or -G30 --AF-file /build/bcftools-Mlf9dV/bcftools-1.21/test/roh.1.tab.gz| grep -v ^# .. ok test_roh: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools roh /build/bcftools-Mlf9dV/bcftools-1.21/test/roh.1.vcf.gz -Or -G30 --AF-file /build/bcftools-Mlf9dV/bcftools-1.21/test/roh.1.tab.gz --ignore-homref| grep -v ^# .. ok test_roh: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools roh /build/bcftools-Mlf9dV/bcftools-1.21/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245| grep -v ^# .. ok test_roh: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools roh /build/bcftools-Mlf9dV/bcftools-1.21/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --ignore-homref| grep -v ^# .. ok test_roh: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools roh /build/bcftools-Mlf9dV/bcftools-1.21/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --ignore-homref --include-noalt| grep -v ^# .. ok test_roh: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools roh /build/bcftools-Mlf9dV/bcftools-1.21/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --include-noalt| grep -v ^# .. ok test_gtcheck: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools gtcheck -e 0 --no-HWE-prob /tmp/MadjcxLl4P/gtcheck.1.vcf.gz -g /tmp/MadjcxLl4P/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools gtcheck -e 0 /tmp/MadjcxLl4P/gtcheck.1.vcf.gz -g /tmp/MadjcxLl4P/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools gtcheck -e 0 -u GT,GT /tmp/MadjcxLl4P/gtcheck.1.vcf.gz -g /tmp/MadjcxLl4P/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools gtcheck -e 0 -u GT,PL /tmp/MadjcxLl4P/gtcheck.1.vcf.gz -g /tmp/MadjcxLl4P/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools gtcheck -e 0 -u PL,GT /tmp/MadjcxLl4P/gtcheck.1.vcf.gz -g /tmp/MadjcxLl4P/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools gtcheck -e 0 -u PL,PL /tmp/MadjcxLl4P/gtcheck.1.vcf.gz -g /tmp/MadjcxLl4P/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools gtcheck -e 0 -p s1,s1 /tmp/MadjcxLl4P/gtcheck.1.vcf.gz -g /tmp/MadjcxLl4P/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools gtcheck -e 0 /tmp/MadjcxLl4P/gtcheck.2.vcf.gz -g /tmp/MadjcxLl4P/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools gtcheck -e 0 /tmp/MadjcxLl4P/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools gtcheck -e 0 -p B,A,C,A,C,B,D,A,D,B,D,C,E,A,E,B,E,C,E,D /tmp/MadjcxLl4P/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools gtcheck -e 0 -P /build/bcftools-Mlf9dV/bcftools-1.21/test/gtcheck.3.pairs /tmp/MadjcxLl4P/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools gtcheck -e 0 -u PL /tmp/MadjcxLl4P/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools gtcheck -e 0 --n-matches 4 /tmp/MadjcxLl4P/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO | sort .. ok test_gtcheck: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools gtcheck -e 0 -s qry:E,D,C /tmp/MadjcxLl4P/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools gtcheck -e 0 -s qry:E,D,C -u PL /tmp/MadjcxLl4P/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools gtcheck -e 0 -s qry:B -s gt:D /tmp/MadjcxLl4P/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools gtcheck -e 0 -s qry:B -s gt:D -u PL /tmp/MadjcxLl4P/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools gtcheck -e 0 -s qry:B -s gt:D,C /tmp/MadjcxLl4P/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools gtcheck -e 0 -p B,C,B,D /tmp/MadjcxLl4P/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools gtcheck -e 0 -u GT,GT -H /tmp/MadjcxLl4P/gtcheck.1.vcf.gz -g /tmp/MadjcxLl4P/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools gtcheck -e 0 -u GT,PL -H /tmp/MadjcxLl4P/gtcheck.1.vcf.gz -g /tmp/MadjcxLl4P/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools gtcheck -e 0 -u PL,GT -H /tmp/MadjcxLl4P/gtcheck.1.vcf.gz -g /tmp/MadjcxLl4P/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools gtcheck -e 0 -u PL,PL -H /tmp/MadjcxLl4P/gtcheck.1.vcf.gz -g /tmp/MadjcxLl4P/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools gtcheck -e 0 -P /build/bcftools-Mlf9dV/bcftools-1.21/test/gtcheck.4.pairs --distinctive-sites 3 /tmp/MadjcxLl4P/gtcheck.4.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools gtcheck -e 0 -P /build/bcftools-Mlf9dV/bcftools-1.21/test/gtcheck.4.pairs --distinctive-sites 3,1 /tmp/MadjcxLl4P/gtcheck.4.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools gtcheck -u GT -e 30 /tmp/MadjcxLl4P/gtcheck.1.vcf.gz -g /tmp/MadjcxLl4P/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools gtcheck -u GT -e 30 -p s1,s1 /tmp/MadjcxLl4P/gtcheck.1.vcf.gz -g /tmp/MadjcxLl4P/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools gtcheck -u GT -e 300 /tmp/MadjcxLl4P/gtcheck.1.vcf.gz -g /tmp/MadjcxLl4P/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools gtcheck -u PL -e 30 /tmp/MadjcxLl4P/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools gtcheck /tmp/MadjcxLl4P/gtcheck.ntop.vcf.gz -g /tmp/MadjcxLl4P/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools gtcheck --n-matches 2 /tmp/MadjcxLl4P/gtcheck.ntop.vcf.gz -g /tmp/MadjcxLl4P/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools gtcheck /tmp/MadjcxLl4P/gtcheck.5.vcf.gz -g /tmp/MadjcxLl4P/gtcheck.5.gts.vcf.gz | grep -v ^# | grep -v Time .. ok test_gtcheck: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools gtcheck -p A,B,B,C /tmp/MadjcxLl4P/gtcheck.6.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-Mlf9dV/bcftools-1.21/bcftools gtcheck -t 11:33 -p A,D,A,E,D,E -u GT -e 10 /tmp/MadjcxLl4P/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok Number of tests: total .. 1805 passed .. 1805 failed .. 0 make[2]: Leaving directory '/build/bcftools-Mlf9dV/bcftools-1.21' make[1]: Leaving directory '/build/bcftools-Mlf9dV/bcftools-1.21' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/bcftools/ make -j2 install DESTDIR=/build/bcftools-Mlf9dV/bcftools-1.21/debian/bcftools AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/bcftools-Mlf9dV/bcftools-1.21' mkdir -p -m 755 /build/bcftools-Mlf9dV/bcftools-1.21/debian/bcftools/usr/bin /build/bcftools-Mlf9dV/bcftools-1.21/debian/bcftools/usr/share/man/man1 /build/bcftools-Mlf9dV/bcftools-1.21/debian/bcftools/usr/lib/x86_64-linux-gnu/bcftools install -p bcftools /build/bcftools-Mlf9dV/bcftools-1.21/debian/bcftools/usr/bin install -p misc/color-chrs.pl misc/gff2gff.py misc/guess-ploidy.py misc/plot-vcfstats misc/plot-roh.py misc/run-roh.pl misc/vcfutils.pl /build/bcftools-Mlf9dV/bcftools-1.21/debian/bcftools/usr/bin install -p -m 644 doc/bcftools.1 /build/bcftools-Mlf9dV/bcftools-1.21/debian/bcftools/usr/share/man/man1 install -p plugins/*.so /build/bcftools-Mlf9dV/bcftools-1.21/debian/bcftools/usr/lib/x86_64-linux-gnu/bcftools make[1]: Leaving directory '/build/bcftools-Mlf9dV/bcftools-1.21' debian/rules override_dh_install make[1]: Entering directory '/build/bcftools-Mlf9dV/bcftools-1.21' dh_install # Fix Perl interpreter PATH for pscript in `grep -Rl '#!/usr/bin/env \+perl' debian/*` ; do \ sed -i '1s?#!/usr/bin/env \+perl?#!/usr/bin/perl?' ${pscript} ; \ done make[1]: Leaving directory '/build/bcftools-Mlf9dV/bcftools-1.21' dh_installdocs dh_installchangelogs debian/rules override_dh_installman make[1]: Entering directory '/build/bcftools-Mlf9dV/bcftools-1.21' dh_installman --language=C make[1]: Leaving directory '/build/bcftools-Mlf9dV/bcftools-1.21' dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dpkg-gencontrol: warning: package bcftools: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package bcftools: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'bcftools' in '../bcftools_1.21-1_amd64.deb'. dpkg-deb: building package 'bcftools-dbgsym' in '../bcftools-dbgsym_1.21-1_amd64.deb'. dpkg-genbuildinfo -O../bcftools_1.21-1_amd64.buildinfo dpkg-genchanges -O../bcftools_1.21-1_amd64.changes dpkg-genchanges: info: including full source code in upload dpkg-source -Zxz --after-build . dpkg-buildpackage: info: full upload (original source is included) -------------------------------------------------------------------------------- Build finished at 2025-06-30T04:18:46Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Mon, 30 Jun 2025 04:18:46 +0000 | +------------------------------------------------------------------------------+ bcftools_1.21-1_amd64.changes: ------------------------------ Format: 1.8 Date: Thu, 13 Feb 2025 21:42:57 +0100 Source: bcftools Binary: bcftools bcftools-dbgsym Architecture: source amd64 Version: 1.21-1 Distribution: perl-5.40-throwaway Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: bcftools - genomic variant calling and manipulation of VCF/BCF files Changes: bcftools (1.21-1) unstable; urgency=medium . * New upstream version 1.21 * d/copyright: update copyright year. * skip_new_test_failing_on_32bit.patch: unfuzz. * tests-pluginpath.patch: delete: hunk inhibited upstream. * d/patches/*: normalise Last-Update timestamp. * d/rules: activate hardening. Checksums-Sha1: 6a38e1e0014f7bc1196c43da01b74b14098a91ce 1242 bcftools_1.21-1.dsc 7f367e0f03d4f56ca88d5f3a79435f196591fbce 3665160 bcftools_1.21.orig.tar.gz 4df0cc69dacce808b43d3516e542197da60ab309 7500 bcftools_1.21-1.debian.tar.xz 9ec1690c0206d6cb0b4a310eb21cdb45420fe7ce 2229324 bcftools-dbgsym_1.21-1_amd64.deb 70a5d525411fe7e00b44cecd47e9cf20e5aa08b4 7426 bcftools_1.21-1_amd64.buildinfo 687680739d528c87b6b57378cdcef4774032faca 784124 bcftools_1.21-1_amd64.deb Checksums-Sha256: 51dd5c18612732034ef2be5bd19f48fdc697412bff52e4a24a58a36c2cd42e94 1242 bcftools_1.21-1.dsc 7484695c5d833fb1a89c2b886ec302db0514ba3c8e5ef7397b9302fa8bd37f8d 3665160 bcftools_1.21.orig.tar.gz 10b8964c10a3a4d8bd65d0e568eeb6fe7040e1fd33e0ac2bf5012670aed5a39e 7500 bcftools_1.21-1.debian.tar.xz 64cfff7f511b48eb1d00177a9abe417191a1514f6957ded8848f3b3150d1befe 2229324 bcftools-dbgsym_1.21-1_amd64.deb b04eb22d2f66665e2706e6ef39c3d4a6a75f46ba3c784b6b0de22607acd810f0 7426 bcftools_1.21-1_amd64.buildinfo ddb46db7df9be7c328281cbb13c7ccee9730c60b81a773f60c7056c87628cbe5 784124 bcftools_1.21-1_amd64.deb Files: 6835b0b13b376ba4edc1a14e1764b90a 1242 science optional bcftools_1.21-1.dsc e144a5777c606c69eb643ae8ff613dbb 3665160 science optional bcftools_1.21.orig.tar.gz d02793361bfdb9a259bf61335780f39c 7500 science optional bcftools_1.21-1.debian.tar.xz f3bafde10985c0f25ab09eec407eb362 2229324 debug optional bcftools-dbgsym_1.21-1_amd64.deb aa7e7ba118518a39a7b94326ca281048 7426 science optional bcftools_1.21-1_amd64.buildinfo 1ee550e6bd54e595be0b56e65a87acaf 784124 science optional bcftools_1.21-1_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo Mon, 30 Jun 2025 04:18:47 +0000 | +------------------------------------------------------------------------------+ Format: 1.0 Source: bcftools Binary: bcftools bcftools-dbgsym Architecture: amd64 source Version: 1.21-1 Checksums-Md5: 6835b0b13b376ba4edc1a14e1764b90a 1242 bcftools_1.21-1.dsc f3bafde10985c0f25ab09eec407eb362 2229324 bcftools-dbgsym_1.21-1_amd64.deb 1ee550e6bd54e595be0b56e65a87acaf 784124 bcftools_1.21-1_amd64.deb Checksums-Sha1: 6a38e1e0014f7bc1196c43da01b74b14098a91ce 1242 bcftools_1.21-1.dsc 9ec1690c0206d6cb0b4a310eb21cdb45420fe7ce 2229324 bcftools-dbgsym_1.21-1_amd64.deb 687680739d528c87b6b57378cdcef4774032faca 784124 bcftools_1.21-1_amd64.deb Checksums-Sha256: 51dd5c18612732034ef2be5bd19f48fdc697412bff52e4a24a58a36c2cd42e94 1242 bcftools_1.21-1.dsc 64cfff7f511b48eb1d00177a9abe417191a1514f6957ded8848f3b3150d1befe 2229324 bcftools-dbgsym_1.21-1_amd64.deb ddb46db7df9be7c328281cbb13c7ccee9730c60b81a773f60c7056c87628cbe5 784124 bcftools_1.21-1_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Mon, 30 Jun 2025 04:18:46 +0000 Build-Path: /build/bcftools-Mlf9dV/bcftools-1.21 Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: autoconf (= 2.72-3.1), automake (= 1:1.17-4), autopoint (= 0.23.1-2), autotools-dev (= 20240727.1), base-files (= 13.8), base-passwd (= 3.6.7), bash (= 5.2.37-2+b3), binutils (= 2.44-3), binutils-common (= 2.44-3), binutils-x86-64-linux-gnu (= 2.44-3), bsdextrautils (= 2.41-5), bsdutils (= 1:2.41-5), build-essential (= 12.12), bzip2 (= 1.0.8-6), comerr-dev (= 2.1-1.47.2-3+b1), coreutils (= 9.7-3), cpp (= 4:14.2.0-1), cpp-13 (= 13.4.0-1), cpp-13-x86-64-linux-gnu (= 13.4.0-1), cpp-14 (= 14.2.0-19), cpp-14-x86-64-linux-gnu (= 14.2.0-19), cpp-x86-64-linux-gnu (= 4:14.2.0-1), dash (= 0.5.12-12), debconf (= 1.5.91), debhelper (= 13.24.2), debianutils (= 5.23.1), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.14.1-2), diffutils (= 1:3.10-4), dpkg (= 1.22.20), dpkg-dev (= 1.22.20), dwz (= 0.15-1+b1), file (= 1:5.46-5), findutils (= 4.10.0-3), g++ (= 4:14.2.0-1), g++-14 (= 14.2.0-19), g++-14-x86-64-linux-gnu (= 14.2.0-19), g++-x86-64-linux-gnu (= 4:14.2.0-1), gcc (= 4:14.2.0-1), gcc-13 (= 13.4.0-1), gcc-13-base (= 13.4.0-1), gcc-13-x86-64-linux-gnu (= 13.4.0-1), gcc-14 (= 14.2.0-19), gcc-14-base (= 14.2.0-19), gcc-14-x86-64-linux-gnu (= 14.2.0-19), gcc-x86-64-linux-gnu (= 4:14.2.0-1), gettext (= 0.23.1-2), gettext-base (= 0.23.1-2), grep (= 3.11-4), groff-base (= 1.23.0-9), gzip (= 1.13-1), hostname (= 3.25), init-system-helpers (= 1.68), intltool-debian (= 0.35.0+20060710.6), krb5-multidev (= 1.21.3-5), libacl1 (= 2.3.2-2+b1), libarchive-zip-perl (= 1.68-1), libasan8 (= 14.2.0-19), libatomic1 (= 14.2.0-19), libattr1 (= 1:2.5.2-3), libaudit-common (= 1:4.0.2-2), libaudit1 (= 1:4.0.2-2+b2), libbinutils (= 2.44-3), libblkid1 (= 2.41-5), libbrotli-dev (= 1.1.0-2+b7), libbrotli1 (= 1.1.0-2+b7), libbz2-1.0 (= 1.0.8-6), libbz2-dev (= 1.0.8-6), libc-bin (= 2.41-9), libc-dev-bin (= 2.41-9), libc6 (= 2.41-9), libc6-dev (= 2.41-9), libcap-ng0 (= 0.8.5-4+b1), libcap2 (= 1:2.75-9), libcc1-0 (= 14.2.0-19), libcom-err2 (= 1.47.2-3+b1), libcrypt-dev (= 1:4.4.38-1), libcrypt1 (= 1:4.4.38-1), libctf-nobfd0 (= 2.44-3), libctf0 (= 2.44-3), libcurl3t64-gnutls (= 8.14.1-2), libcurl4-gnutls-dev (= 8.14.1-2), libdb5.3t64 (= 5.3.28+dfsg2-9), libdebconfclient0 (= 0.279), libdebhelper-perl (= 13.24.2), libdeflate-dev (= 1.23-2), libdeflate0 (= 1.23-2), libdpkg-perl (= 1.22.20), libelf1t64 (= 0.192-4), libevent-2.1-7t64 (= 2.1.12-stable-10+b1), libffi8 (= 3.4.8-2), libfile-stripnondeterminism-perl (= 1.14.1-2), libgcc-13-dev (= 13.4.0-1), libgcc-14-dev (= 14.2.0-19), libgcc-s1 (= 14.2.0-19), libgdbm-compat4t64 (= 1.24-2), libgdbm6t64 (= 1.24-2), libgmp-dev (= 2:6.3.0+dfsg-3), libgmp10 (= 2:6.3.0+dfsg-3), libgmpxx4ldbl (= 2:6.3.0+dfsg-3), libgnutls-dane0t64 (= 3.8.9-2), libgnutls-openssl27t64 (= 3.8.9-2), libgnutls28-dev (= 3.8.9-2), libgnutls30t64 (= 3.8.9-2), libgomp1 (= 14.2.0-19), libgprofng0 (= 2.44-3), libgsl-dev (= 2.8+dfsg-5), libgsl28 (= 2.8+dfsg-5), libgslcblas0 (= 2.8+dfsg-5), libgssapi-krb5-2 (= 1.21.3-5), libgssrpc4t64 (= 1.21.3-5), libhogweed6t64 (= 3.10.1-1), libhts-dev (= 1.21+ds-1), libhts3t64 (= 1.21+ds-1), libhtscodecs2 (= 1.6.1-2), libhwasan0 (= 14.2.0-19), libidn2-0 (= 2.3.8-2), libidn2-dev (= 2.3.8-2), libio-pty-perl (= 1:1.20-1+b4), libisl23 (= 0.27-1), libitm1 (= 14.2.0-19), libjansson4 (= 2.14-2+b3), libk5crypto3 (= 1.21.3-5), libkadm5clnt-mit12 (= 1.21.3-5), libkadm5srv-mit12 (= 1.21.3-5), libkdb5-10t64 (= 1.21.3-5), libkeyutils1 (= 1.6.3-6), libkrb5-3 (= 1.21.3-5), libkrb5-dev (= 1.21.3-5), libkrb5support0 (= 1.21.3-5), liblastlog2-2 (= 2.41-5), libldap-dev (= 2.6.10+dfsg-1+b1), libldap2 (= 2.6.10+dfsg-1+b1), liblsan0 (= 14.2.0-19), liblzma-dev (= 5.8.1-1), liblzma5 (= 5.8.1-1), libmagic-mgc (= 1:5.46-5), libmagic1t64 (= 1:5.46-5), libmd0 (= 1.1.0-2+b1), libmount1 (= 2.41-5), libmpc3 (= 1.3.1-1+b3), libmpfr6 (= 4.2.2-1), libnettle8t64 (= 3.10.1-1), libnghttp2-14 (= 1.64.0-1.1), libnghttp2-dev (= 1.64.0-1.1), libnghttp3-9 (= 1.8.0-1), libnghttp3-dev (= 1.8.0-1), libngtcp2-16 (= 1.11.0-1), libngtcp2-crypto-gnutls-dev (= 1.11.0-1), libngtcp2-crypto-gnutls8 (= 1.11.0-1), libngtcp2-dev (= 1.11.0-1), libp11-kit-dev (= 0.25.5-3), libp11-kit0 (= 0.25.5-3), libpam-modules (= 1.7.0-5), libpam-modules-bin (= 1.7.0-5), libpam-runtime (= 1.7.0-5), libpam0g (= 1.7.0-5), libpcre2-8-0 (= 10.45-1), libperl5.40 (= 5.40.1-4), libpipeline1 (= 1.5.8-1), libpkgconf3 (= 1.8.1-4), libpsl-dev (= 0.21.2-1.1+b1), libpsl5t64 (= 0.21.2-1.1+b1), libquadmath0 (= 14.2.0-19), librtmp-dev (= 2.4+20151223.gitfa8646d.1-2+b5), librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b5), libsasl2-2 (= 2.1.28+dfsg1-9), libsasl2-modules-db (= 2.1.28+dfsg1-9), libseccomp2 (= 2.6.0-2), libselinux1 (= 3.8.1-1), libsframe1 (= 2.44-3), libsmartcols1 (= 2.41-5), libsqlite3-0 (= 3.46.1-6), libssh2-1-dev (= 1.11.1-1), libssh2-1t64 (= 1.11.1-1), libssl-dev (= 3.5.0-2), libssl3t64 (= 3.5.0-2), libstdc++-14-dev (= 14.2.0-19), libstdc++6 (= 14.2.0-19), libsystemd0 (= 257.7-1), libtasn1-6 (= 4.20.0-2), libtasn1-6-dev (= 4.20.0-2), libtinfo6 (= 6.5+20250216-2), libtool (= 2.5.4-4), libtsan2 (= 14.2.0-19), libubsan1 (= 14.2.0-19), libuchardet0 (= 0.0.8-1+b2), libudev1 (= 257.7-1), libunbound8 (= 1.22.0-1+b1), libunistring5 (= 1.3-2), libuuid1 (= 2.41-5), libxml2 (= 2.12.7+dfsg+really2.9.14-1), libzstd-dev (= 1.5.7+dfsg-1), libzstd1 (= 1.5.7+dfsg-1), linux-libc-dev (= 6.12.33-1), m4 (= 1.4.19-8), make (= 4.4.1-2), man-db (= 2.13.1-1), mawk (= 1.3.4.20250131-1), ncurses-base (= 6.5+20250216-2), ncurses-bin (= 6.5+20250216-2), nettle-dev (= 3.10.1-1), openssl-provider-legacy (= 3.5.0-2), patch (= 2.8-2), perl (= 5.40.1-4), perl-base (= 5.40.1-4), perl-modules-5.40 (= 5.40.1-4), pkgconf (= 1.8.1-4), pkgconf-bin (= 1.8.1-4), po-debconf (= 1.0.21+nmu1), rpcsvc-proto (= 1.4.3-1), sed (= 4.9-2), sensible-utils (= 0.0.25), sysvinit-utils (= 3.14-4), tabix (= 1.21+ds-1), tar (= 1.35+dfsg-3.1), util-linux (= 2.41-5), xz-utils (= 5.8.1-1), zlib1g (= 1:1.3.dfsg+really1.3.1-1+b1), zlib1g-dev (= 1:1.3.dfsg+really1.3.1-1+b1) Environment: DEB_BUILD_OPTIONS="parallel=2" LANG="C.UTF-8" LC_COLLATE="C.UTF-8" LC_CTYPE="C.UTF-8" 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Installed-Size: 2716 Depends: libc6 (>= 2.34), libhts3t64 (>= 1.17) 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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+------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup Mon, 30 Jun 2025 04:18:48 +0000 | +------------------------------------------------------------------------------+ Purging /build/bcftools-Mlf9dV Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Mon, 30 Jun 2025 04:18:49 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 52780 Build-Time: 153 Distribution: perl-5.40-throwaway Host Architecture: amd64 Install-Time: 11 Job: /srv/debomatic/incoming/bcftools_1.21-1.dsc Machine Architecture: amd64 Package: bcftools Package-Time: 176 Source-Version: 1.21-1 Space: 52780 Status: successful Version: 1.21-1 -------------------------------------------------------------------------------- Finished at 2025-06-30T04:18:46Z Build needed 00:02:56, 52780k disk space