sbuild (Debian sbuild) 0.91.10 (27 June 2026) on carme.larted.org.uk +==============================================================================+ | bcftools 1.24-1 (amd64) Tue, 22 Sep 2026 07:20:13 +0000 | +==============================================================================+ Package: bcftools Version: 1.24-1 Source Version: 1.24-1 Distribution: perl-5.44-throwaway Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: full I: Setting up the chroot... I: Creating chroot session... I: Setting up log color... +------------------------------------------------------------------------------+ | Chroot Setup Commands Tue, 22 Sep 2026 07:20:15 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup bcftools_1.24-1 perl-5.44-throwaway amd64 ---------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup bcftools_1.24-1 perl-5.44-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: Setting up apt archive... +------------------------------------------------------------------------------+ | Update chroot Tue, 22 Sep 2026 07:20:15 +0000 | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.44 InRelease [3042 B] Get:1 file:/srv/reprepro perl-5.44 InRelease [3042 B] Get:2 file:/srv/reprepro perl-5.44/main amd64 Packages [606 kB] Hit:3 http://deb.debian.org/debian unstable InRelease Hit:4 http://deb.debian.org/debian sid InRelease 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 Tue, 22 Sep 2026 07:20:22 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/bcftools_1.24-1.dsc exists in /srv/debomatic/incoming; copying to chroot +------------------------------------------------------------------------------+ | Install package build dependencies Tue, 22 Sep 2026 07:20:23 +0000 | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 14), zlib1g-dev, libbz2-dev, liblzma-dev, libhts-dev (>= 1.24), libgsl-dev, tabix, libio-pty-perl, build-essential Filtered Build-Depends: debhelper-compat (= 14), zlib1g-dev, libbz2-dev, liblzma-dev, libhts-dev (>= 1.24), libgsl-dev, tabix, libio-pty-perl, build-essential dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/build/bcftools-qI88Pr/resolver-rYlGD7/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/build/bcftools-qI88Pr/resolver-rYlGD7/apt_archive ./ InRelease Get:2 copy:/build/bcftools-qI88Pr/resolver-rYlGD7/apt_archive ./ Release [609 B] Ign:3 copy:/build/bcftools-qI88Pr/resolver-rYlGD7/apt_archive ./ Release.gpg Get:4 copy:/build/bcftools-qI88Pr/resolver-rYlGD7/apt_archive ./ Sources [716 B] Get:5 copy:/build/bcftools-qI88Pr/resolver-rYlGD7/apt_archive ./ Packages [733 B] Fetched 2058 B in 0s (136 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... Solving dependencies... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils comerr-dev debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian krb5-multidev libarchive-zip-perl libbrotli-dev libbrotli1 libbz2-dev libcom-err2 libcurl4-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libelf1t64 libevent-2.1-7t64 libfile-stripnondeterminism-perl libgmp-dev libgmpxx4ldbl libgnutls-dane0t64 libgnutls28-dev libgsl-dev libgsl28 libgslcblas0 libgssapi-krb5-2 libgssrpc4t64 libhts-dev libhts3t64 libhtscodecs2 libidn2-dev libio-pty-perl libk5crypto3 libkadm5clnt-mit12 libkadm5srv-mit12 libkdb5-10t64 libkeyutils1 libkrb5-3 libkrb5-dev libkrb5support0 libldap-dev liblzma-dev libmagic-mgc libmagic1t64 libnghttp2-14 libnghttp2-dev libnghttp3-9 libnghttp3-dev libngtcp2-16 libngtcp2-crypto-gnutls-dev libngtcp2-crypto-gnutls8 libngtcp2-dev libp11-kit-dev libpipeline1 libpkgconf7 libpsl-dev libpsl5t64 librtmp-dev librtmp1 libssh2-1-dev libssh2-1t64 libssl-dev libtasn1-6-dev libtool libuchardet0 libunbound8 libunistring-dev libxml2-16 libzstd-dev m4 man-db nettle-dev pkgconf pkgconf-bin po-debconf sensible-utils tabix zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc doc-base dh-make gettext-doc libasprintf-dev libgettextpo-dev gnulib-l10n groff krb5-doc libcurl4-doc libidn-dev gmp-doc libgmp10-doc libmpfr-dev dns-root-data gnutls-bin gnutls-doc gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html krb5-user liblzma-doc libnghttp2-doc p11-kit-doc libssl-doc libtool-doc gfortran | fortran95-compiler m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx python3:any python3-requests 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 libcurl4-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libelf1t64 libevent-2.1-7t64 libfile-stripnondeterminism-perl libgmp-dev libgmpxx4ldbl libgnutls-dane0t64 libgnutls28-dev libgsl-dev libgsl28 libgslcblas0 libgssapi-krb5-2 libgssrpc4t64 libhts-dev libhts3t64 libhtscodecs2 libidn2-dev libio-pty-perl libk5crypto3 libkadm5clnt-mit12 libkadm5srv-mit12 libkdb5-10t64 libkeyutils1 libkrb5-3 libkrb5-dev libkrb5support0 libldap-dev liblzma-dev libmagic-mgc libmagic1t64 libnghttp2-14 libnghttp2-dev libnghttp3-9 libnghttp3-dev libngtcp2-16 libngtcp2-crypto-gnutls-dev libngtcp2-crypto-gnutls8 libngtcp2-dev libp11-kit-dev libpipeline1 libpkgconf7 libpsl-dev libpsl5t64 librtmp-dev librtmp1 libssh2-1-dev libssh2-1t64 libssl-dev libtasn1-6-dev libtool libuchardet0 libunbound8 libunistring-dev libxml2-16 libzstd-dev m4 man-db nettle-dev pkgconf pkgconf-bin po-debconf sbuild-build-depends-main-dummy sensible-utils tabix zlib1g-dev 0 upgraded, 90 newly installed, 0 to remove and 0 not upgraded. Need to get 33.1 MB/33.4 MB of archives. After this operation, 136 MB of additional disk space will be used. Get:1 file:/srv/reprepro perl-5.44/main amd64 libldap-dev amd64 2.6.14+dfsg-2+b1 [321 kB] Get:2 copy:/build/bcftools-qI88Pr/resolver-rYlGD7/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [908 B] Get:3 file:/srv/reprepro perl-5.44/main amd64 libio-pty-perl amd64 1:1.31-1+b2 [38.2 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.47-4 [345 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.47-4 [111 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.47-4 [43.0 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 1.0-5 [334 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2+b2 [69.0 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.24.1-1 [1336 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.42.3-1 [102 kB] Get:12 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-3 [49.2 kB] Get:13 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get:14 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.21-1 [332 kB] Get:15 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.73-2 [516 kB] Get:16 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1+nmu1 [60.0 kB] Get:17 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.19-2 [891 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 autopoint all 1.0-5 [820 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.4-1+b1 [19.5 kB] Get:20 http://deb.debian.org/debian unstable/main amd64 comerr-dev amd64 2.1-1.47.4-1+b1 [51.2 kB] Get:21 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 14.5 [77.7 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 libtool all 2.6.2-3 [552 kB] Get:23 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 23 [12.7 kB] Get:24 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:25 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.1-1 [17.1 kB] Get:26 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.1-1 [6020 B] Get:27 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.196-1 [61.2 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.17-1 [109 kB] Get:29 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.15.4+dfsg-1 [683 kB] Get:30 http://deb.debian.org/debian unstable/main amd64 gettext amd64 1.0-5 [2704 kB] Get:31 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:32 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.22 [216 kB] Get:33 http://deb.debian.org/debian unstable/main amd64 debhelper all 14.5 [944 kB] Get:34 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.22.1-3 [31.1 kB] Get:35 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.22.1-3 [79.0 kB] Get:36 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6+b2 [9348 B] Get:37 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.22.1-3 [335 kB] Get:38 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.22.1-3 [137 kB] Get:39 http://deb.debian.org/debian unstable/main amd64 libgssrpc4t64 amd64 1.22.1-3 [58.3 kB] Get:40 http://deb.debian.org/debian unstable/main amd64 libkadm5clnt-mit12 amd64 1.22.1-3 [40.3 kB] Get:41 http://deb.debian.org/debian unstable/main amd64 libkdb5-10t64 amd64 1.22.1-3 [41.3 kB] Get:42 http://deb.debian.org/debian unstable/main amd64 libkadm5srv-mit12 amd64 1.22.1-3 [54.1 kB] Get:43 http://deb.debian.org/debian unstable/main amd64 krb5-multidev amd64 1.22.1-3 [125 kB] Get:44 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.2.0-4+b1 [312 kB] Get:45 http://deb.debian.org/debian unstable/main amd64 libbrotli-dev amd64 1.2.0-4+b1 [324 kB] Get:46 http://deb.debian.org/debian unstable/main amd64 libbz2-dev amd64 1.0.8-6+b2 [33.6 kB] Get:47 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.17.0-1 [68.1 kB] Get:48 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.24.0-1 [145 kB] Get:49 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.70.0-1 [92.7 kB] Get:50 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.24.0-1 [23.9 kB] Get:51 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.23.3-1 [61.7 kB] Get:52 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-6 [253 kB] Get:53 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls amd64 8.22.0-1 [457 kB] Get:54 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.13-stable-1 [183 kB] Get:55 http://deb.debian.org/debian unstable/main amd64 libunbound8 amd64 1.26.1-1 [664 kB] Get:56 http://deb.debian.org/debian unstable/main amd64 libgnutls-dane0t64 amd64 3.8.13-1 [496 kB] Get:57 http://deb.debian.org/debian unstable/main amd64 libidn2-dev amd64 2.3.8-5 [102 kB] Get:58 http://deb.debian.org/debian unstable/main amd64 libp11-kit-dev amd64 0.26.5-1 [226 kB] Get:59 http://deb.debian.org/debian unstable/main amd64 libtasn1-6-dev amd64 4.21.0-2+b1 [98.6 kB] Get:60 http://deb.debian.org/debian unstable/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-5+b2 [328 kB] Get:61 http://deb.debian.org/debian unstable/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-5+b2 [641 kB] Get:62 http://deb.debian.org/debian unstable/main amd64 nettle-dev amd64 3.10.2-1+b1 [1321 kB] Get:63 http://deb.debian.org/debian unstable/main amd64 libgnutls28-dev amd64 3.8.13-1 [1479 kB] Get:64 http://deb.debian.org/debian unstable/main amd64 libkrb5-dev amd64 1.22.1-3 [14.0 kB] Get:65 http://deb.debian.org/debian unstable/main amd64 libpkgconf7 amd64 2.5.1-4 [47.8 kB] Get:66 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 2.5.1-4 [35.9 kB] Get:67 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 2.5.1-4 [33.6 kB] Get:68 http://deb.debian.org/debian unstable/main amd64 libnghttp2-dev amd64 1.70.0-1 [131 kB] Get:69 http://deb.debian.org/debian unstable/main amd64 libnghttp3-dev amd64 1.17.0-1 [96.3 kB] Get:70 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.24.0-1 [24.0 kB] Get:71 http://deb.debian.org/debian unstable/main amd64 libngtcp2-dev amd64 1.24.0-1 [204 kB] Get:72 http://deb.debian.org/debian unstable/main amd64 libunistring-dev amd64 1.4.2-1 [651 kB] Get:73 http://deb.debian.org/debian unstable/main amd64 libpsl-dev amd64 0.23.3-1 [30.1 kB] Get:74 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.6-1 [60.3 kB] Get:75 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.2-3 [918 kB] Get:76 http://deb.debian.org/debian unstable/main amd64 librtmp-dev amd64 2.6-1 [69.7 kB] Get:77 http://deb.debian.org/debian unstable/main amd64 libssl-dev amd64 3.6.4-1 [3156 kB] Get:78 http://deb.debian.org/debian unstable/main amd64 libssh2-1-dev amd64 1.11.1-6 [402 kB] Get:79 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.7+dfsg-4 [371 kB] Get:80 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls-dev amd64 8.22.0-1 [590 kB] Get:81 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.25-1 [48.0 kB] Get:82 http://deb.debian.org/debian unstable/main amd64 libdeflate-dev amd64 1.25-1 [56.7 kB] Get:83 http://deb.debian.org/debian unstable/main amd64 libgslcblas0 amd64 2.8+dfsg-6+b1 [131 kB] Get:84 http://deb.debian.org/debian unstable/main amd64 libgsl28 amd64 2.8+dfsg-6+b1 [1002 kB] Get:85 http://deb.debian.org/debian unstable/main amd64 libgsl-dev amd64 2.8+dfsg-6+b1 [1248 kB] Get:86 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.7-1 [102 kB] Get:87 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.24-2 [506 kB] Get:88 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.8.4-1 [391 kB] Get:89 http://deb.debian.org/debian unstable/main amd64 libhts-dev amd64 1.24-2 [1917 kB] Get:90 http://deb.debian.org/debian unstable/main amd64 tabix amd64 1.24-2 [533 kB] Preconfiguring packages ... Fetched 33.1 MB in 0s (105 MB/s) Selecting previously unselected package sensible-utils. (Reading database ... 15721 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.47-4_amd64.deb ... Unpacking libmagic-mgc (1:5.47-4) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.47-4_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.47-4) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.47-4_amd64.deb ... Unpacking file (1:5.47-4) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_1.0-5_amd64.deb ... Unpacking gettext-base (1.0-5) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-2+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-2+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.24.1-1_amd64.deb ... Unpacking groff-base (1.24.1-1) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.42.3-1_amd64.deb ... Unpacking bsdextrautils (2.42.3-1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.8-3_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-3) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.1-1_amd64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.21-1_amd64.deb ... Unpacking m4 (1.4.21-1) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.73-2_all.deb ... Unpacking autoconf (2.73-2) ... Selecting previously unselected package autotools-dev. 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Setting up libpkgconf7:amd64 (2.5.1-4) ... Setting up libmagic1t64:amd64 (1:5.47-4) ... Setting up libpsl5t64:amd64 (0.23.3-1) ... Setting up libnghttp2-14:amd64 (1.70.0-1) ... Setting up libdeflate0:amd64 (1.25-1) ... Setting up gettext-base (1.0-5) ... Setting up m4 (1.4.21-1) ... Setting up libevent-2.1-7t64:amd64 (2.1.13-stable-1) ... Setting up libcom-err2:amd64 (1.47.4-1+b1) ... Setting up file (1:5.47-4) ... Setting up libelf1t64:amd64 (0.196-1) ... Setting up libkrb5support0:amd64 (1.22.1-3) ... Setting up autotools-dev (20240727.1+nmu1) ... Setting up libunbound8:amd64 (1.26.1-1) ... Setting up libgmpxx4ldbl:amd64 (2:6.3.0+dfsg-5+b2) ... Setting up libgnutls-dane0t64:amd64 (3.8.13-1) ... Setting up librtmp1:amd64 (2.6-1) ... Setting up libldap-dev:amd64 (2.6.14+dfsg-2+b1) ... Setting up comerr-dev:amd64 (2.1-1.47.4-1+b1) ... Setting up libssl-dev:amd64 (3.6.4-1) ... Setting up autopoint (1.0-5) ... Setting up pkgconf-bin (2.5.1-4) ... Setting up libk5crypto3:amd64 (1.22.1-3) ... Setting up libidn2-dev:amd64 (2.3.8-5) ... Setting up autoconf (2.73-2) ... Setting up libnghttp3-9:amd64 (1.17.0-1) ... Setting up libnghttp3-dev:amd64 (1.17.0-1) ... Setting up liblzma-dev:amd64 (5.8.4-1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.2-3) ... Setting up dwz (0.17-1) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:amd64 (0.0.8-2+b2) ... Setting up libngtcp2-16:amd64 (1.24.0-1) ... Setting up libkrb5-3:amd64 (1.22.1-3) ... Setting up libssh2-1t64:amd64 (1.11.1-6) ... Setting up libgsl28:amd64 (2.8+dfsg-6+b1) ... Setting up libtasn1-6-dev:amd64 (4.21.0-2+b1) ... Setting up libdeflate-dev:amd64 (1.25-1) ... Setting up tabix (1.24-2) ... Setting up libbrotli-dev:amd64 (1.2.0-4+b1) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.24.0-1) ... Setting up libp11-kit-dev:amd64 (0.26.5-1) ... Setting up libbz2-dev:amd64 (1.0.8-6+b2) ... Setting up automake (1:1.19-2) ... update-alternatives: using /usr/bin/automake-1.19 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.1-1) ... Setting up gettext (1.0-5) ... Setting up libgsl-dev (2.8+dfsg-6+b1) ... Setting up libgmp-dev:amd64 (2:6.3.0+dfsg-5+b2) ... Setting up nettle-dev:amd64 (3.10.2-1+b1) ... Setting up libtool (2.6.2-3) ... Setting up libngtcp2-crypto-gnutls-dev:amd64 (1.24.0-1) ... Setting up libngtcp2-dev:amd64 (1.24.0-1) ... Setting up pkgconf:amd64 (2.5.1-4) ... Setting up libpsl-dev:amd64 (0.23.3-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (23) ... Setting up libgssapi-krb5-2:amd64 (1.22.1-3) ... Setting up libssh2-1-dev:amd64 (1.11.1-6) ... Setting up dh-strip-nondeterminism (1.15.1-1) ... Setting up groff-base (1.24.1-1) ... Setting up libgnutls28-dev:amd64 (3.8.13-1) ... Setting up libcurl4-gnutls:amd64 (8.22.0-1) ... Setting up libnghttp2-dev:amd64 (1.70.0-1) ... Setting up po-debconf (1.0.22) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libgssrpc4t64:amd64 (1.22.1-3) ... Setting up librtmp-dev:amd64 (2.6-1) ... Setting up libhts3t64:amd64 (1.24-2) ... Setting up libkadm5clnt-mit12:amd64 (1.22.1-3) ... Setting up libkdb5-10t64:amd64 (1.22.1-3) ... Setting up debhelper (14.5) ... Setting up libkadm5srv-mit12:amd64 (1.22.1-3) ... Setting up krb5-multidev:amd64 (1.22.1-3) ... Setting up libkrb5-dev:amd64 (1.22.1-3) ... Setting up libcurl4-gnutls-dev:amd64 (8.22.0-1) ... Setting up libhts-dev:amd64 (1.24-2) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.43-6) ... +------------------------------------------------------------------------------+ | Check architectures Tue, 22 Sep 2026 07:20:36 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Build environment Tue, 22 Sep 2026 07:20:36 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 7.0.10+deb14-amd64 #1 SMP PREEMPT_DYNAMIC Debian 7.0.10-1 (2026-05-27) amd64 (x86_64) Toolchain package versions: binutils_2.47-6 dpkg-dev_1.23.11 g++-15_15.3.0-4 g++-16_16.2.0-3 gcc-15_15.3.0-4 gcc-16_16.2.0-3 libc6-dev_2.43-6 libstdc++-15-dev_15.3.0-4 libstdc++-16-dev_16.2.0-3 libstdc++6_16.2.0-3 linux-libc-dev_7.2.6-1 Package versions: apt_3.3.3 autoconf_2.73-2 automake_1:1.19-2 autopoint_1.0-5 autotools-dev_20240727.1+nmu1 base-files_14.2 base-passwd_3.6.8 bash_5.3-4 binutils_2.47-6 binutils-common_2.47-6 binutils-x86-64-linux-gnu_2.47-6 bsdextrautils_2.42.3-1 build-essential_12.12 bzip2_1.0.8-6+b2 comerr-dev_2.1-1.47.4-1+b1 coreutils_9.10-1 cpp_4:16.1.0-3 cpp-15_15.3.0-4 cpp-15-x86-64-linux-gnu_15.3.0-4 cpp-16_16.2.0-3 cpp-16-x86-64-linux-gnu_16.2.0-3 cpp-x86-64-linux-gnu_4:16.1.0-3 dash_0.5.12-12 debconf_1.5.92 debhelper_14.5 debian-archive-keyring_2025.1 debianutils_5.24 dh-autoreconf_23 dh-strip-nondeterminism_1.15.1-1 diffutils_1:3.12-1 dirmngr_2.4.9-7+b1 dpkg_1.23.11 dpkg-dev_1.23.11 dwz_0.17-1 eatmydata_131-2 file_1:5.47-4 findutils_4.11.0-2 g++_4:16.1.0-3 g++-15_15.3.0-4 g++-15-x86-64-linux-gnu_15.3.0-4 g++-16_16.2.0-3 g++-16-x86-64-linux-gnu_16.2.0-3 g++-x86-64-linux-gnu_4:16.1.0-3 gcc_4:16.1.0-3 gcc-15_15.3.0-4 gcc-15-base_15.3.0-4 gcc-15-x86-64-linux-gnu_15.3.0-4 gcc-16_16.2.0-3 gcc-16-base_16.2.0-3 gcc-16-x86-64-linux-gnu_16.2.0-3 gcc-x86-64-linux-gnu_4:16.1.0-3 gettext_1.0-5 gettext-base_1.0-5 gnupg_2.4.9-7 gnupg-l10n_2.4.9-7 gpg_2.4.9-7+b1 gpg-agent_2.4.9-7+b1 gpgconf_2.4.9-7+b1 gpgsm_2.4.9-7+b1 grep_3.12-1 groff-base_1.24.1-1 gzip_1.14-1 hostname_3.25 init-system-helpers_1.69+nmu2 intltool-debian_0.35.0+20060710.6 krb5-multidev_1.22.1-3 libacl1_2.4.0-1 libapt-pkg7.0_3.3.3 libarchive-zip-perl_1.68-1 libasan8_16.2.0-3 libassuan9_3.0.2-2+b2 libatomic1_16.2.0-3 libattr1_1:2.6.0-1 libaudit-common_1:4.2.1-1 libaudit1_1:4.2.1-1 libbinutils_2.47-6 libblkid1_2.42.3-1 libbrotli-dev_1.2.0-4+b1 libbrotli1_1.2.0-4+b1 libbz2-1.0_1.0.8-6+b2 libbz2-dev_1.0.8-6+b2 libc-bin_2.43-6 libc-dev-bin_2.43-6 libc-gconv-modules-extra_2.43-6 libc6_2.43-6 libc6-dev_2.43-6 libcap-ng0_0.9.6-1 libcc1-0_16.2.0-3 libcom-err2_1.47.4-1+b1 libcrypt1_1:4.5.2+20251210-1 libctf-nobfd0_2.47-6 libctf0_2.47-6 libcurl4-gnutls_8.22.0-1 libcurl4-gnutls-dev_8.22.0-1 libdb5.3t64_5.3.28+dfsg2-11+b1 libdebconfclient0_0.283 libdebhelper-perl_14.5 libdeflate-dev_1.25-1 libdeflate0_1.25-1 libdpkg-perl_1.23.11 libeatmydata1_131-2+b2 libelf1t64_0.196-1 libevent-2.1-7t64_2.1.13-stable-1 libffi8_3.8.0-2 libfile-stripnondeterminism-perl_1.15.1-1 libgcc-15-dev_15.3.0-4 libgcc-16-dev_16.2.0-3 libgcc-s1_16.2.0-3 libgcrypt20_1.12.3-2 libgdbm-compat4t64_1.26-1+b2 libgdbm6t64_1.26-1+b2 libgmp-dev_2:6.3.0+dfsg-5+b2 libgmp10_2:6.3.0+dfsg-5+b2 libgmpxx4ldbl_2:6.3.0+dfsg-5+b2 libgnutls-dane0t64_3.8.13-1 libgnutls28-dev_3.8.13-1 libgnutls30t64_3.8.13-1 libgomp1_16.2.0-3 libgpg-error0_1.61-5 libgprofng0_2.47-6 libgsl-dev_2.8+dfsg-6+b1 libgsl28_2.8+dfsg-6+b1 libgslcblas0_2.8+dfsg-6+b1 libgssapi-krb5-2_1.22.1-3 libgssrpc4t64_1.22.1-3 libhogweed6t64_3.10.2-1+b1 libhts-dev_1.24-2 libhts3t64_1.24-2 libhtscodecs2_1.6.7-1 libhwasan0_16.2.0-3 libidn2-0_2.3.8-5 libidn2-dev_2.3.8-5 libio-pty-perl_1:1.31-1+b2 libisl23_0.28-1 libitm1_16.2.0-3 libjansson4_2.15.1-1 libk5crypto3_1.22.1-3 libkadm5clnt-mit12_1.22.1-3 libkadm5srv-mit12_1.22.1-3 libkdb5-10t64_1.22.1-3 libkeyutils1_1.6.3-6+b2 libkrb5-3_1.22.1-3 libkrb5-dev_1.22.1-3 libkrb5support0_1.22.1-3 libksba8_1.8.1-1 libldap-dev_2.6.14+dfsg-2+b1 libldap2_2.6.14+dfsg-2+b1 liblsan0_16.2.0-3 liblz4-1_1.10.0-10 liblzma-dev_5.8.4-1 liblzma5_5.8.4-1 libmagic-mgc_1:5.47-4 libmagic1t64_1:5.47-4 libmd0_1.2.0-2 libmount1_2.42.3-1 libmpc3_1.3.1-3 libmpfr6_4.2.2-3 libncursesw6_6.6+20260608-2 libnettle8t64_3.10.2-1+b1 libnghttp2-14_1.70.0-1 libnghttp2-dev_1.70.0-1 libnghttp3-9_1.17.0-1 libnghttp3-dev_1.17.0-1 libngtcp2-16_1.24.0-1 libngtcp2-crypto-gnutls-dev_1.24.0-1 libngtcp2-crypto-gnutls8_1.24.0-1 libngtcp2-dev_1.24.0-1 libnpth0t64_1.8-4 libp11-kit-dev_0.26.5-1 libp11-kit0_0.26.5-1 libpam-modules_1.7.0-8 libpam-modules-bin_1.7.0-8 libpam-runtime_1.7.0-8 libpam0g_1.7.0-8 libpcre2-8-0_10.48-3 libperl5.40_5.40.1-8 libperl5.44_5.44.0-1 libpipeline1_1.5.8-3 libpkgconf7_2.5.1-4 libpsl-dev_0.23.3-1 libpsl5t64_0.23.3-1 libquadmath0_16.2.0-3 libreadline8t64_8.3-4 librtmp-dev_2.6-1 librtmp1_2.6-1 libsasl2-2_2.1.28+dfsg1-11 libsasl2-modules-db_2.1.28+dfsg1-11 libseccomp2_2.6.1-1+b1 libselinux1_3.11-2 libsframe3_2.47-6 libsmartcols1_2.42.3-1 libsqlite3-0_3.53.4-2 libssh2-1-dev_1.11.1-6 libssh2-1t64_1.11.1-6 libssl-dev_3.6.4-1 libssl3t64_3.6.4-1 libstdc++-15-dev_15.3.0-4 libstdc++-16-dev_16.2.0-3 libstdc++6_16.2.0-3 libsystemd0_262~rc3-1 libtasn1-6_4.21.0-2+b1 libtasn1-6-dev_4.21.0-2+b1 libtinfo6_6.6+20260608-2 libtool_2.6.2-3 libtsan2_16.2.0-3 libtss2-mu-4.0.1-0t64_4.1.3-7 libtss2-rc0t64_4.1.3-7 libtss2-sys1t64_4.1.3-7 libtss2-tcti-device0t64_4.1.3-7 libtss2-tcti-mssim0t64_4.1.3-7 libtss2-tcti-swtpm0t64_4.1.3-7 libubsan1_16.2.0-3 libuchardet0_0.0.8-2+b2 libudev1_262~rc3-1 libunbound8_1.26.1-1 libunistring-dev_1.4.2-1 libunistring5_1.4.2-1 libuuid1_2.42.3-1 libxml2-16_2.15.4+dfsg-1 libxxhash0_0.8.3-2+b2 libzstd-dev_1.5.7+dfsg-4 libzstd1_1.5.7+dfsg-4 linux-libc-dev_7.2.6-1 m4_1.4.21-1 make_4.4.1-3 man-db_2.13.1-1 mawk_1.3.4.20260302-1 mount_2.42.3-1 ncurses-base_6.6+20260608-2 ncurses-bin_6.6+20260608-2 nettle-dev_3.10.2-1+b1 openssl-provider-legacy_3.6.4-1 patch_2.8-2 perl_5.44.0-1 perl-base_5.44.0-1 perl-modules-5.40_5.40.1-8 perl-modules-5.44_5.44.0-1 pinentry-curses_1.3.3-3 pkgconf_2.5.1-4 pkgconf-bin_2.5.1-4 po-debconf_1.0.22 readline-common_8.3-4 rpcsvc-proto_1.4.4-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-3 sensible-utils_0.0.26 sqv_1.5.0-1 sysvinit-utils_3.18-1 tabix_1.24-2 tar_1.35+dfsg-6 util-linux_2.42.3-1 xz-utils_5.8.4-1 zlib1g_1:1.3.dfsg+really1.3.2-3 zlib1g-dev_1:1.3.dfsg+really1.3.2-3 +------------------------------------------------------------------------------+ | Build Tue, 22 Sep 2026 07:20:36 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: bcftools Binary: bcftools Architecture: any Version: 1.24-1 Maintainer: Debian Med Packaging Team Uploaders: Michael R. Crusoe , Étienne Mollier Homepage: https://samtools.github.io/bcftools/ Standards-Version: 4.7.4 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 (= 14), zlib1g-dev, libbz2-dev, liblzma-dev, libhts-dev (>= 1.24), libgsl-dev, tabix , libio-pty-perl Package-List: bcftools deb science optional arch=any Checksums-Sha1: 4d6bfd6e59e2fddc6a6094f34ba52ebfb3687a58 3800401 bcftools_1.24.orig.tar.gz aff4011dc6e2680f96e8b77b3e11558020b85ec0 8912 bcftools_1.24-1.debian.tar.xz Checksums-Sha256: 8e0492098682634d29f20105c0c026139122ef0cf9f09f444f1e8a3ae35a0f64 3800401 bcftools_1.24.orig.tar.gz 2e9474623c538722fabd7d9ef2ad7d4ba29226c814d7273a4646188a4f8d8e40 8912 bcftools_1.24-1.debian.tar.xz Files: f9debbe1e479d70adeca100dbf673231 3800401 bcftools_1.24.orig.tar.gz 1364f9f2bb10c9c31e867d8a37eaf22b 8912 bcftools_1.24-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmqxBTURHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtEiKQ/6Araf+rNW6f0YAsozdppfO5ORrZgIzqr6 KKkBaNQG6RbAzCD8hiLAPnmXuSHPCLxIJEWxwtj+FwlNPMNquS+ngzeBV5KjOi1D CHDzGwh4FmCb0CL2L54Y6JqV8hXCDpRkXcnnQCGYBVxCC5v7SePVh7Yaiyi5imhm WCdyr1P4YVTX1Rmvb4wqjNyap/NpyAnqxxKVnsBDDM/63jX7hAQT05WVNlNsDl5G 75atFZcHi3DaG8YIoNbyY8qKOh1WG6x7QkZYulAxlSfOVWaKhwJBkeAfgA67LhRR uyx41NTaMpODKdjAyV1gDgZ7KuUFeoCRDj9YTUvIzQc1VI6PiV1LDSzroSnvyNTM zlZmoci3gMUiAW9+225EvJgKHJJwv0HsXNZxTcZQYIlkS7TIFlolb4z8khNX2ECj C41ftmW0FufB6pizhtovW/+UPpVEStTnDGE7cKzWm695/2D5QmeM3nZAr44GxsaZ 839us9Jm5ckvHSAqa4UGtOeDXscXv4zAfBTV8E4qYBxJOkMwDOjY64s9/ikT0NNC nQOo2l1hzAJgPtGGE+6Zq6D6lGdYAsIWuiTPA+Pe/E7pGLkARSIxmH2ntUf1hMJy 2WRkIQClazUrz1tRjqf1Rs0zg3kAnzNf54YATYUPAvvppY5mkuCRh6CIvD5pEUvd 3ANQuGSjuDM= =Sobp -----END PGP SIGNATURE----- dpkg-source: warning: cannot verify inline signature for ./bcftools_1.24-1.dsc: missing OpenPGP keyrings dpkg-source: info: verifying ./bcftools_1.24-1.dsc dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-keyring.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-tag2upload.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-nonupload.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-maintainers.pgp dpkg-source: info: extracting bcftools in /build/bcftools-qI88Pr/bcftools-1.24 dpkg-source: info: unpacking bcftools_1.24.orig.tar.gz dpkg-source: info: unpacking bcftools_1.24-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying skip_new_test_failing_on_32bit.patch dpkg-source: info: applying 2to3.patch clean up apt cache ------------------ Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Time Build Commands Tue, 22 Sep 2026 07:20:38 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network bcftools_1.24-1 perl-5.44-throwaway amd64 ---------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network bcftools_1.24-1 perl-5.44-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANGUAGE=en_GB:en LC_ALL=C.UTF-8 LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so LOGNAME=debomatic PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games PWD=/build/bcftools-qI88Pr/bcftools-1.24 SCHROOT_ALIAS_NAME=perl-5.44-throwaway-amd64-debomatic SCHROOT_CHROOT_NAME=perl-5.44-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=110 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=perl-5.44-amd64-debomatic-ec9f40bd-281c-4c03-b903-47b413d567fc 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 1.24-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source -Zxz --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean rm -f config.mk && touch config.mk dh clean dh: warning: Implicitly activating single-binary dh addon for backwards compatibility. In compat 15+, dh: warning: this fallback will *not* happen automatically. The dh_auto_install tool will instead use a dh: warning: different default for --destdir unless the single-binary add-on is active, dh: warning: which can cause the source to produce an empty binary package dh: warning: dh: warning: To keep the existing behaviour (compat 13), please activate the single-binary addon explicitly. dh: warning: This can be done by adding "dh-sequence-single-binary" to Build-Depends or passing dh: warning: --with=single-binary to dh. dh: warning: dh: warning: If you have solved this issue differently (e.g., by passing --destdir explicitly to dh: warning: dh_auto_install or not using dh_auto_install at all) and want to silence this warning dh: warning: without activating the addon, you can do that by passing --without=single-binary to dh dh: warning: to explicitly acknowledge the change. dh: warning: dh: warning: Please see the description of the "single-binary" in "man dh" for more details of what dh: warning: it does and why this is changing from implicit behaviour to explicitly opt-in. debian/rules override_dh_auto_clean make[1]: Entering directory '/build/bcftools-qI88Pr/bcftools-1.24' dh_auto_clean make -j2 distclean make[2]: Entering directory '/build/bcftools-qI88Pr/bcftools-1.24' 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 mpileup2/*.o *.a *~ bcftools version.h rm -rf *.dSYM test/*.dSYM rm -f config.cache config.h config.log config.mk config.status rm -rf autom4te.cache rm -f TAGS make[2]: Leaving directory '/build/bcftools-qI88Pr/bcftools-1.24' 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-qI88Pr/bcftools-1.24' dh_clean dpkg-source -Zxz -b . dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building bcftools using existing ../bcftools_1.24.orig.tar.gz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: building bcftools in ../bcftools_1.24-1.debian.tar.xz dpkg-source: info: building bcftools in ../bcftools_1.24-1.dsc debian/rules binary dh binary dh: warning: Implicitly activating single-binary dh addon for backwards compatibility. In compat 15+, dh: warning: this fallback will *not* happen automatically. The dh_auto_install tool will instead use a dh: warning: different default for --destdir unless the single-binary add-on is active, dh: warning: which can cause the source to produce an empty binary package dh: warning: dh: warning: To keep the existing behaviour (compat 13), please activate the single-binary addon explicitly. dh: warning: This can be done by adding "dh-sequence-single-binary" to Build-Depends or passing dh: warning: --with=single-binary to dh. dh: warning: dh: warning: If you have solved this issue differently (e.g., by passing --destdir explicitly to dh: warning: dh_auto_install or not using dh_auto_install at all) and want to silence this warning dh: warning: without activating the addon, you can do that by passing --without=single-binary to dh dh: warning: to explicitly acknowledge the change. dh: warning: dh: warning: Please see the description of the "single-binary" in "man dh" for more details of what dh: warning: it does and why this is changing from implicit behaviour to explicitly opt-in. dh_update_autotools_config debian/rules override_dh_autoreconf make[1]: Entering directory '/build/bcftools-qI88Pr/bcftools-1.24' rm -f config.mk && touch config.mk export MAKEFLAGS="-s"; dh_autoreconf autoreconf: export WARNINGS= autoreconf: Entering directory '.' autoreconf: configure.ac: no obvious need to run autopoint autoreconf: running: aclocal --force autoreconf: configure.ac: tracing autoreconf: configure.ac: subdirectory $HTSDIR not present autoreconf: configure.ac: not using Libtool autoreconf: configure.ac: not using Intltool autoreconf: configure.ac: not using Gtkdoc autoreconf: configure.ac: no need to run autopoint (confirmed) autoreconf: running: /usr/bin/autoconf --force configure.ac:94: warning: _AC_CONFIG_SUBDIRS: you should use literals ./lib/autoconf/status.m4:1100: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:94: the top level autoreconf: running: /usr/bin/autoheader --force autoreconf: configure.ac: not using Automake autoreconf: configure.ac: not running make: --make not given autoreconf: Leaving directory '.' make[1]: Leaving directory '/build/bcftools-qI88Pr/bcftools-1.24' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/bcftools-qI88Pr/bcftools-1.24' dh_auto_configure -- \ --with-htslib=system \ --enable-gsl \ --with-cblas=gslcblas \ --with-bcf-plugin-dir=/usr/lib/x86_64-linux-gnu/bcftools ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system --enable-gsl --with-cblas=gslcblas --with-bcf-plugin-dir=/usr/lib/x86_64-linux-gnu/bcftools checking for gcc... x86_64-linux-gnu-gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether x86_64-linux-gnu-gcc accepts -g... yes checking for x86_64-linux-gnu-gcc option to enable C23 features... none needed checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking for x86_64-linux-gnu-gcc option to support large files... none needed checking for htslib/sam.h... yes checking for hts_version in -lhts... yes checking shared library type... plain .so checking for library containing dlopen... none required checking if the compiler accepts -rdynamic... yes checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing regcomp... none required configure: creating ./config.status config.status: creating config.mk config.status: creating config.h make[1]: Leaving directory '/build/bcftools-qI88Pr/bcftools-1.24' dh_auto_build make -j2 make[1]: Entering directory '/build/bcftools-qI88Pr/bcftools-1.24' x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -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 echo '#define BCFTOOLS_VERSION "1.24"' > version.h x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tabix.o tabix.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfstats.o vcfstats.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfisec.o vcfisec.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfmerge.o vcfmerge.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfquery.o vcfquery.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcffilter.o vcffilter.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o filter.o filter.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfsom.o vcfsom.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfnorm.o vcfnorm.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfgtcheck.o vcfgtcheck.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfview.o vcfview.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfannotate.o vcfannotate.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfroh.o vcfroh.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfconcat.o vcfconcat.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcall.o vcfcall.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mcall.o mcall.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcmp.o vcmp.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gvcf.o gvcf.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o reheader.o reheader.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o convert.o convert.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfconvert.o vcfconvert.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tsv2vcf.o tsv2vcf.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcnv.o vcfcnv.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfhead.o vcfhead.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o HMM.o HMM.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o consensus.o consensus.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ploidy.o ploidy.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bin.o bin.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hclust.o hclust.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o version.o version.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o regidx.o regidx.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o smpl_ilist.o smpl_ilist.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o csq.o csq.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfbuf.o vcfbuf.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mpileup.o mpileup.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_iaux.o bam2bcf_iaux.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_edlib.o bam2bcf_edlib.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o read_consensus.o read_consensus.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sample.o bam_sample.c bam_sample.c: In function ‘bam_smpl_add_bam’: bam_sample.c:172:21: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 172 | char *eol = strchr(q + 3, '\n'); | ^~~~~~ x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfsort.o vcfsort.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cols.o cols.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o extsort.o extsort.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dist.o dist.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o abuf.o abuf.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ccall.o ccall.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o em.o em.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o prob1.o prob1.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kmin.o kmin.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o str_finder.o str_finder.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gff.o gff.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o edlib.o edlib.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mpileup2/mpileup.o mpileup2/mpileup.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DPLUGINPATH='"/usr/lib/x86_64-linux-gnu/bcftools"' -c -o vcfplugin.o vcfplugin.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -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 x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -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 x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -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 x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -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 x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -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 x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -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 x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/af-dist.so bin.c version.c plugins/af-dist.c x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/allele-length.so version.c plugins/allele-length.c x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/check-ploidy.so version.c plugins/check-ploidy.c x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/check-sparsity.so version.c plugins/check-sparsity.c x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/color-chrs.so HMM.c version.c plugins/color-chrs.c x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/contrast.so version.c plugins/contrast.c x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/counts.so version.c plugins/counts.c x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/dosage.so version.c plugins/dosage.c x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/fill-AN-AC.so version.c plugins/fill-AN-AC.c x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/fill-from-fasta.so filter.c version.c plugins/fill-from-fasta.c x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/fill-tags.so version.c plugins/fill-tags.c x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/fixploidy.so ploidy.c regidx.c version.c plugins/fixploidy.c x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/fixref.so version.c plugins/fixref.c x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/frameshifts.so version.c plugins/frameshifts.c x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/guess-ploidy.so version.c plugins/guess-ploidy.c x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/gvcfz.so version.c plugins/gvcfz.c x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/impute-info.so version.c plugins/impute-info.c x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/indel-stats.so version.c plugins/indel-stats.c x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/isecGT.so smpl_ilist.c version.c plugins/isecGT.c x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/mendelian2.so version.c plugins/mendelian2.c x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/missing2ref.so version.c plugins/missing2ref.c x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/parental-origin.so version.c plugins/parental-origin.c x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/prune.so version.c plugins/prune.c x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/remove-overlaps.so version.c plugins/remove-overlaps.c x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/scatter.so version.c plugins/scatter.c x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/setGT.so version.c plugins/setGT.c x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/smpl-stats.so version.c plugins/smpl-stats.c x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/split-vep.so version.c plugins/split-vep.c x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/split.so version.c plugins/split.c x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/tag2tag.so version.c plugins/tag2tag.c x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -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-dnm3.so version.c plugins/trio-dnm3.c x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/trio-stats.so version.c plugins/trio-stats.c x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/trio-switch-rate.so version.c plugins/trio-switch-rate.c x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/variant-distance.so version.c plugins/variant-distance.c x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/variantkey-hex.so version.c plugins/variantkey-hex.c x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/vcf2table.so version.c plugins/vcf2table.c plugins/vcf2table.c: In function ‘process’: plugins/vcf2table.c:1066:18: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 1066 | char* eq = strchr(info, '='); | ^~~~~~ x86_64-linux-gnu-gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o plugins/vrfs.so version.c plugins/vrfs.c x86_64-linux-gnu-gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/bcftools-qI88Pr/bcftools-1.24=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o main.o main.c x86_64-linux-gnu-gcc -Wl,-z,relro -Wl,-z,now -o test/test-rbuf test/test-rbuf.o -lz x86_64-linux-gnu-gcc -Wl,-z,relro -Wl,-z,now -o test/test-regidx test/test-regidx.o regidx.o -lhts -lpthread -lz x86_64-linux-gnu-gcc -rdynamic -Wl,-z,relro -Wl,-z,now -o bcftools main.o vcfindex.o tabix.o vcfstats.o vcfisec.o vcfmerge.o vcfquery.o vcffilter.o filter.o vcfsom.o vcfnorm.o vcfgtcheck.o vcfview.o vcfannotate.o vcfroh.o vcfconcat.o vcfcall.o mcall.o vcmp.o gvcf.o reheader.o convert.o vcfconvert.o tsv2vcf.o vcfcnv.o vcfhead.o HMM.o consensus.o ploidy.o bin.o hclust.o version.o regidx.o smpl_ilist.o csq.o vcfbuf.o mpileup.o bam2bcf.o bam2bcf_indel.o bam2bcf_iaux.o bam2bcf_edlib.o read_consensus.o bam_sample.o vcfsort.o cols.o extsort.o dist.o abuf.o ccall.o em.o prob1.o kmin.o str_finder.o gff.o edlib.o mpileup2/mpileup.o vcfplugin.o -lhts -lm -lz -lpthread make[1]: Leaving directory '/build/bcftools-qI88Pr/bcftools-1.24' debian/rules override_dh_auto_test make[1]: Entering directory '/build/bcftools-qI88Pr/bcftools-1.24' make test-no-plugins VERBOSE=1 make[2]: Entering directory '/build/bcftools-qI88Pr/bcftools-1.24' ./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/iaQXJX5nkE/merge.a.vcf.gz 2:3199812-3199812 .. ok test_tabix: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -H /tmp/iaQXJX5nkE/merge.a.bcf 2:3199812-3199812 .. ok test_tabix: tabix /tmp/iaQXJX5nkE/merge.a.vcf.gz 1:3000151-3000151 .. ok test_tabix: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -H /tmp/iaQXJX5nkE/merge.a.bcf 1:3000151-3000151 .. ok test_index: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -H /tmp/iaQXJX5nkE/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -H /tmp/iaQXJX5nkE/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -H /tmp/iaQXJX5nkE/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -H /tmp/iaQXJX5nkE/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -H /tmp/iaQXJX5nkE/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -H /tmp/iaQXJX5nkE/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -H /tmp/iaQXJX5nkE/large_chrom_csi_limit.bcf chr20 .. ok test_index: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -H /tmp/iaQXJX5nkE/large_chrom_csi_limit.bcf chr20 .. ok test_index: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -H /tmp/iaQXJX5nkE/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -H /tmp/iaQXJX5nkE/large_chrom_csi_limit.bcf chr20 .. ok test_vcf_idxstats: /build/bcftools-qI88Pr/bcftools-1.24/bcftools index -s /tmp/iaQXJX5nkE/idx.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-qI88Pr/bcftools-1.24/bcftools index -s /tmp/iaQXJX5nkE/idx.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-qI88Pr/bcftools-1.24/bcftools index -s /tmp/iaQXJX5nkE/idx.bcf .. ok test_vcf_idxstats: /build/bcftools-qI88Pr/bcftools-1.24/bcftools index -n /tmp/iaQXJX5nkE/idx.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-qI88Pr/bcftools-1.24/bcftools index -n /tmp/iaQXJX5nkE/idx.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-qI88Pr/bcftools-1.24/bcftools index -n /tmp/iaQXJX5nkE/idx.vcf.gz.csi .. ok test_vcf_idxstats: /build/bcftools-qI88Pr/bcftools-1.24/bcftools index -n /tmp/iaQXJX5nkE/idx.bcf .. ok test_vcf_idxstats: /build/bcftools-qI88Pr/bcftools-1.24/bcftools index -n /tmp/iaQXJX5nkE/idx.bcf.csi .. ok test_vcf_idxstats: /build/bcftools-qI88Pr/bcftools-1.24/bcftools index -s /tmp/iaQXJX5nkE/empty.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-qI88Pr/bcftools-1.24/bcftools index -s /tmp/iaQXJX5nkE/empty.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-qI88Pr/bcftools-1.24/bcftools index -s /tmp/iaQXJX5nkE/empty.bcf .. ok test_vcf_idxstats: /build/bcftools-qI88Pr/bcftools-1.24/bcftools index -n /tmp/iaQXJX5nkE/empty.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-qI88Pr/bcftools-1.24/bcftools index -n /tmp/iaQXJX5nkE/empty.vcf.gz .. ok test_vcf_idxstats: /build/bcftools-qI88Pr/bcftools-1.24/bcftools index -n /tmp/iaQXJX5nkE/empty.vcf.gz.csi .. ok test_vcf_idxstats: /build/bcftools-qI88Pr/bcftools-1.24/bcftools index -n /tmp/iaQXJX5nkE/empty.bcf .. ok test_vcf_idxstats: /build/bcftools-qI88Pr/bcftools-1.24/bcftools index -n /tmp/iaQXJX5nkE/empty.bcf.csi .. ok test_vcf_check: /build/bcftools-qI88Pr/bcftools-1.24/bcftools stats -s - /tmp/iaQXJX5nkE/check.vcf.gz | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/check.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools stats -s - | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check_merge: /build/bcftools-qI88Pr/bcftools-1.24/misc/plot-vcfstats -m /tmp/iaQXJX5nkE/check.1.chk /tmp/iaQXJX5nkE/check.2.chk /tmp/iaQXJX5nkE/check.3.chk /tmp/iaQXJX5nkE/check.4.chk | grep -v 'plot-vcfstats' | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_stats: /build/bcftools-qI88Pr/bcftools-1.24/bcftools stats -s A,B /tmp/iaQXJX5nkE/stats-smpl-order.vcf.gz | grep -v '^#' | grep -v '^ID ' | LC_ALL=C sort .. ok test_vcf_stats: /build/bcftools-qI88Pr/bcftools-1.24/bcftools stats -s B,A /tmp/iaQXJX5nkE/stats-smpl-order.vcf.gz | grep -v '^#' | grep -v '^ID ' | LC_ALL=C sort .. ok test_vcf_stats: /build/bcftools-qI88Pr/bcftools-1.24/bcftools stats -s - /tmp/iaQXJX5nkE/stats.a.vcf.gz /tmp/iaQXJX5nkE/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/bcftools-qI88Pr/bcftools-1.24/bcftools stats -s B /tmp/iaQXJX5nkE/stats.a.vcf.gz /tmp/iaQXJX5nkE/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/bcftools-qI88Pr/bcftools-1.24/bcftools stats -s - /tmp/iaQXJX5nkE/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/bcftools-qI88Pr/bcftools-1.24/bcftools stats -s - -i 'type="snp"' /tmp/iaQXJX5nkE/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /build/bcftools-qI88Pr/bcftools-1.24/bcftools stats -s - /tmp/iaQXJX5nkE/stats.vaf.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_isec: /build/bcftools-qI88Pr/bcftools-1.24/bcftools isec -n =2 -w 2 --no-version /tmp/iaQXJX5nkE/isec.match-id.1.1.vcf.gz /tmp/iaQXJX5nkE/isec.match-id.1.2.vcf.gz .. ok test_vcf_isec: /build/bcftools-qI88Pr/bcftools-1.24/bcftools isec -n =2 -w 2 -c id --no-version /tmp/iaQXJX5nkE/isec.match-id.1.1.vcf.gz /tmp/iaQXJX5nkE/isec.match-id.1.2.vcf.gz .. ok test_vcf_isec: /build/bcftools-qI88Pr/bcftools-1.24/bcftools isec -n =2 /tmp/iaQXJX5nkE/isec.a.vcf.gz /tmp/iaQXJX5nkE/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-qI88Pr/bcftools-1.24/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/iaQXJX5nkE/isec.a.vcf.gz /tmp/iaQXJX5nkE/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-qI88Pr/bcftools-1.24/bcftools isec -n =2 -c both /tmp/iaQXJX5nkE/isec.a.vcf.gz /tmp/iaQXJX5nkE/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-qI88Pr/bcftools-1.24/bcftools isec -n =2 -c any /tmp/iaQXJX5nkE/isec.a.vcf.gz /tmp/iaQXJX5nkE/isec.b.vcf.gz .. ok test_vcf_isec: /build/bcftools-qI88Pr/bcftools-1.24/bcftools isec -C -c any /tmp/iaQXJX5nkE/isec.a.vcf.gz /tmp/iaQXJX5nkE/isec.b.vcf.gz .. ok test_vcf_isec2: /build/bcftools-qI88Pr/bcftools-1.24/bcftools isec --no-version -T /tmp/iaQXJX5nkE/isec.tab.gz /tmp/iaQXJX5nkE/isec.a.vcf.gz .. ok test_vcf_isec2: /build/bcftools-qI88Pr/bcftools-1.24/bcftools isec -Ob -T /tmp/iaQXJX5nkE/isec.tab.gz /tmp/iaQXJX5nkE/isec.a.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_isec: /build/bcftools-qI88Pr/bcftools-1.24/bcftools isec -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/iaQXJX5nkE/isec-miss.1.1.vcf.gz /tmp/iaQXJX5nkE/isec-miss.1.2.vcf.gz /tmp/iaQXJX5nkE/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /build/bcftools-qI88Pr/bcftools-1.24/bcftools isec -R /build/bcftools-qI88Pr/bcftools-1.24/test/isec-miss.1.regs.txt -n +1 /tmp/iaQXJX5nkE/isec-miss.1.1.vcf.gz /tmp/iaQXJX5nkE/isec-miss.1.2.vcf.gz /tmp/iaQXJX5nkE/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /build/bcftools-qI88Pr/bcftools-1.24/bcftools isec -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/iaQXJX5nkE/isec-miss.2.1.vcf.gz /tmp/iaQXJX5nkE/isec-miss.2.2.vcf.gz /tmp/iaQXJX5nkE/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /build/bcftools-qI88Pr/bcftools-1.24/bcftools isec -R /build/bcftools-qI88Pr/bcftools-1.24/test/isec-miss.1.regs.txt -n +1 /tmp/iaQXJX5nkE/isec-miss.2.1.vcf.gz /tmp/iaQXJX5nkE/isec-miss.2.2.vcf.gz /tmp/iaQXJX5nkE/isec-miss.2.3.vcf.gz .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version /tmp/iaQXJX5nkE/merge.exact.a.vcf.gz /tmp/iaQXJX5nkE/merge.exact.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob /tmp/iaQXJX5nkE/merge.exact.a.vcf.gz /tmp/iaQXJX5nkE/merge.exact.b.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version /tmp/iaQXJX5nkE/merge.exact.a.bcf /tmp/iaQXJX5nkE/merge.exact.b.bcf .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob /tmp/iaQXJX5nkE/merge.exact.a.bcf /tmp/iaQXJX5nkE/merge.exact.b.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -m exact /tmp/iaQXJX5nkE/merge.exact.a.vcf.gz /tmp/iaQXJX5nkE/merge.exact.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob -m exact /tmp/iaQXJX5nkE/merge.exact.a.vcf.gz /tmp/iaQXJX5nkE/merge.exact.b.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -m exact /tmp/iaQXJX5nkE/merge.exact.a.bcf /tmp/iaQXJX5nkE/merge.exact.b.bcf .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob -m exact /tmp/iaQXJX5nkE/merge.exact.a.bcf /tmp/iaQXJX5nkE/merge.exact.b.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version /tmp/iaQXJX5nkE/merge.broken-gvcf.a.vcf.gz /tmp/iaQXJX5nkE/merge.broken-gvcf.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob /tmp/iaQXJX5nkE/merge.broken-gvcf.a.vcf.gz /tmp/iaQXJX5nkE/merge.broken-gvcf.b.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version /tmp/iaQXJX5nkE/merge.broken-gvcf.a.bcf /tmp/iaQXJX5nkE/merge.broken-gvcf.b.bcf .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob /tmp/iaQXJX5nkE/merge.broken-gvcf.a.bcf /tmp/iaQXJX5nkE/merge.broken-gvcf.b.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version /tmp/iaQXJX5nkE/merge.symbolic.1.a.vcf.gz /tmp/iaQXJX5nkE/merge.symbolic.1.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob /tmp/iaQXJX5nkE/merge.symbolic.1.a.vcf.gz /tmp/iaQXJX5nkE/merge.symbolic.1.b.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version /tmp/iaQXJX5nkE/merge.symbolic.1.a.bcf /tmp/iaQXJX5nkE/merge.symbolic.1.b.bcf .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob /tmp/iaQXJX5nkE/merge.symbolic.1.a.bcf /tmp/iaQXJX5nkE/merge.symbolic.1.b.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --merge none /tmp/iaQXJX5nkE/merge.multiallelics.1.a.vcf.gz /tmp/iaQXJX5nkE/merge.multiallelics.1.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --merge none /tmp/iaQXJX5nkE/merge.multiallelics.1.a.vcf.gz /tmp/iaQXJX5nkE/merge.multiallelics.1.b.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --merge none /tmp/iaQXJX5nkE/merge.multiallelics.1.a.bcf /tmp/iaQXJX5nkE/merge.multiallelics.1.b.bcf .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --merge none /tmp/iaQXJX5nkE/merge.multiallelics.1.a.bcf /tmp/iaQXJX5nkE/merge.multiallelics.1.b.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --merge both /tmp/iaQXJX5nkE/merge.multiallelics.1.a.vcf.gz /tmp/iaQXJX5nkE/merge.multiallelics.1.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --merge both /tmp/iaQXJX5nkE/merge.multiallelics.1.a.vcf.gz /tmp/iaQXJX5nkE/merge.multiallelics.1.b.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --merge both /tmp/iaQXJX5nkE/merge.multiallelics.1.a.bcf /tmp/iaQXJX5nkE/merge.multiallelics.1.b.bcf .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --merge both /tmp/iaQXJX5nkE/merge.multiallelics.1.a.bcf /tmp/iaQXJX5nkE/merge.multiallelics.1.b.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --merge none /tmp/iaQXJX5nkE/merge.12.a.vcf.gz /tmp/iaQXJX5nkE/merge.12.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --merge none /tmp/iaQXJX5nkE/merge.12.a.vcf.gz /tmp/iaQXJX5nkE/merge.12.b.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --merge none /tmp/iaQXJX5nkE/merge.12.a.bcf /tmp/iaQXJX5nkE/merge.12.b.bcf .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --merge none /tmp/iaQXJX5nkE/merge.12.a.bcf /tmp/iaQXJX5nkE/merge.12.b.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --merge both /tmp/iaQXJX5nkE/merge.12.a.vcf.gz /tmp/iaQXJX5nkE/merge.12.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --merge both /tmp/iaQXJX5nkE/merge.12.a.vcf.gz /tmp/iaQXJX5nkE/merge.12.b.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --merge both /tmp/iaQXJX5nkE/merge.12.a.bcf /tmp/iaQXJX5nkE/merge.12.b.bcf .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --merge both /tmp/iaQXJX5nkE/merge.12.a.bcf /tmp/iaQXJX5nkE/merge.12.b.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version /tmp/iaQXJX5nkE/merge.phased.1.a.vcf.gz /tmp/iaQXJX5nkE/merge.phased.1.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob /tmp/iaQXJX5nkE/merge.phased.1.a.vcf.gz /tmp/iaQXJX5nkE/merge.phased.1.b.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version /tmp/iaQXJX5nkE/merge.phased.1.a.bcf /tmp/iaQXJX5nkE/merge.phased.1.b.bcf .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob /tmp/iaQXJX5nkE/merge.phased.1.a.bcf /tmp/iaQXJX5nkE/merge.phased.1.b.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version /tmp/iaQXJX5nkE/merge.11.a.vcf.gz /tmp/iaQXJX5nkE/merge.11.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob /tmp/iaQXJX5nkE/merge.11.a.vcf.gz /tmp/iaQXJX5nkE/merge.11.b.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version /tmp/iaQXJX5nkE/merge.11.a.bcf /tmp/iaQXJX5nkE/merge.11.b.bcf .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob /tmp/iaQXJX5nkE/merge.11.a.bcf /tmp/iaQXJX5nkE/merge.11.b.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -i AF:join /tmp/iaQXJX5nkE/merge.join.a.vcf.gz /tmp/iaQXJX5nkE/merge.join.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob -i AF:join /tmp/iaQXJX5nkE/merge.join.a.vcf.gz /tmp/iaQXJX5nkE/merge.join.b.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -i AF:join /tmp/iaQXJX5nkE/merge.join.a.bcf /tmp/iaQXJX5nkE/merge.join.b.bcf .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob -i AF:join /tmp/iaQXJX5nkE/merge.join.a.bcf /tmp/iaQXJX5nkE/merge.join.b.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --force-single /tmp/iaQXJX5nkE/merge.LPL.a.vcf.gz .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --force-single /tmp/iaQXJX5nkE/merge.LPL.a.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --force-single /tmp/iaQXJX5nkE/merge.LPL.a.bcf .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --force-single /tmp/iaQXJX5nkE/merge.LPL.a.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --force-samples /tmp/iaQXJX5nkE/merge.LPL.a.vcf.gz /tmp/iaQXJX5nkE/merge.LPL.b.vcf.gz /tmp/iaQXJX5nkE/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --force-samples /tmp/iaQXJX5nkE/merge.LPL.a.vcf.gz /tmp/iaQXJX5nkE/merge.LPL.b.vcf.gz /tmp/iaQXJX5nkE/merge.LPL.c.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --force-samples /tmp/iaQXJX5nkE/merge.LPL.a.bcf /tmp/iaQXJX5nkE/merge.LPL.b.bcf /tmp/iaQXJX5nkE/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --force-samples /tmp/iaQXJX5nkE/merge.LPL.a.bcf /tmp/iaQXJX5nkE/merge.LPL.b.bcf /tmp/iaQXJX5nkE/merge.LPL.c.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --force-samples -L 1 /tmp/iaQXJX5nkE/merge.LPL.a.vcf.gz /tmp/iaQXJX5nkE/merge.LPL.b.vcf.gz /tmp/iaQXJX5nkE/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --force-samples -L 1 /tmp/iaQXJX5nkE/merge.LPL.a.vcf.gz /tmp/iaQXJX5nkE/merge.LPL.b.vcf.gz /tmp/iaQXJX5nkE/merge.LPL.c.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --force-samples -L 1 /tmp/iaQXJX5nkE/merge.LPL.a.bcf /tmp/iaQXJX5nkE/merge.LPL.b.bcf /tmp/iaQXJX5nkE/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --force-samples -L 1 /tmp/iaQXJX5nkE/merge.LPL.a.bcf /tmp/iaQXJX5nkE/merge.LPL.b.bcf /tmp/iaQXJX5nkE/merge.LPL.c.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --force-samples -L 2 /tmp/iaQXJX5nkE/merge.LPL.a.vcf.gz /tmp/iaQXJX5nkE/merge.LPL.b.vcf.gz /tmp/iaQXJX5nkE/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --force-samples -L 2 /tmp/iaQXJX5nkE/merge.LPL.a.vcf.gz /tmp/iaQXJX5nkE/merge.LPL.b.vcf.gz /tmp/iaQXJX5nkE/merge.LPL.c.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --force-samples -L 2 /tmp/iaQXJX5nkE/merge.LPL.a.bcf /tmp/iaQXJX5nkE/merge.LPL.b.bcf /tmp/iaQXJX5nkE/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --force-samples -L 2 /tmp/iaQXJX5nkE/merge.LPL.a.bcf /tmp/iaQXJX5nkE/merge.LPL.b.bcf /tmp/iaQXJX5nkE/merge.LPL.c.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --force-samples -L 3 /tmp/iaQXJX5nkE/merge.LPL.a.vcf.gz /tmp/iaQXJX5nkE/merge.LPL.b.vcf.gz /tmp/iaQXJX5nkE/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --force-samples -L 3 /tmp/iaQXJX5nkE/merge.LPL.a.vcf.gz /tmp/iaQXJX5nkE/merge.LPL.b.vcf.gz /tmp/iaQXJX5nkE/merge.LPL.c.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --force-samples -L 3 /tmp/iaQXJX5nkE/merge.LPL.a.bcf /tmp/iaQXJX5nkE/merge.LPL.b.bcf /tmp/iaQXJX5nkE/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --force-samples -L 3 /tmp/iaQXJX5nkE/merge.LPL.a.bcf /tmp/iaQXJX5nkE/merge.LPL.b.bcf /tmp/iaQXJX5nkE/merge.LPL.c.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --force-samples -L 4 /tmp/iaQXJX5nkE/merge.LPL.a.vcf.gz /tmp/iaQXJX5nkE/merge.LPL.b.vcf.gz /tmp/iaQXJX5nkE/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --force-samples -L 4 /tmp/iaQXJX5nkE/merge.LPL.a.vcf.gz /tmp/iaQXJX5nkE/merge.LPL.b.vcf.gz /tmp/iaQXJX5nkE/merge.LPL.c.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --force-samples -L 4 /tmp/iaQXJX5nkE/merge.LPL.a.bcf /tmp/iaQXJX5nkE/merge.LPL.b.bcf /tmp/iaQXJX5nkE/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --force-samples -L 4 /tmp/iaQXJX5nkE/merge.LPL.a.bcf /tmp/iaQXJX5nkE/merge.LPL.b.bcf /tmp/iaQXJX5nkE/merge.LPL.c.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --force-samples -L 5 /tmp/iaQXJX5nkE/merge.LPL.a.vcf.gz /tmp/iaQXJX5nkE/merge.LPL.b.vcf.gz /tmp/iaQXJX5nkE/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --force-samples -L 5 /tmp/iaQXJX5nkE/merge.LPL.a.vcf.gz /tmp/iaQXJX5nkE/merge.LPL.b.vcf.gz /tmp/iaQXJX5nkE/merge.LPL.c.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --force-samples -L 5 /tmp/iaQXJX5nkE/merge.LPL.a.bcf /tmp/iaQXJX5nkE/merge.LPL.b.bcf /tmp/iaQXJX5nkE/merge.LPL.c.bcf .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --force-samples -L 5 /tmp/iaQXJX5nkE/merge.LPL.a.bcf /tmp/iaQXJX5nkE/merge.LPL.b.bcf /tmp/iaQXJX5nkE/merge.LPL.c.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --force-samples /tmp/iaQXJX5nkE/merge.a.vcf.gz /tmp/iaQXJX5nkE/merge.b.vcf.gz /tmp/iaQXJX5nkE/merge.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --force-samples /tmp/iaQXJX5nkE/merge.a.vcf.gz /tmp/iaQXJX5nkE/merge.b.vcf.gz /tmp/iaQXJX5nkE/merge.c.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --force-samples /tmp/iaQXJX5nkE/merge.a.bcf /tmp/iaQXJX5nkE/merge.b.bcf /tmp/iaQXJX5nkE/merge.c.bcf .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --force-samples /tmp/iaQXJX5nkE/merge.a.bcf /tmp/iaQXJX5nkE/merge.b.bcf /tmp/iaQXJX5nkE/merge.c.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --force-samples -Fx /tmp/iaQXJX5nkE/merge.a.vcf.gz /tmp/iaQXJX5nkE/merge.b.vcf.gz /tmp/iaQXJX5nkE/merge.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --force-samples -Fx /tmp/iaQXJX5nkE/merge.a.vcf.gz /tmp/iaQXJX5nkE/merge.b.vcf.gz /tmp/iaQXJX5nkE/merge.c.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --force-samples -Fx /tmp/iaQXJX5nkE/merge.a.bcf /tmp/iaQXJX5nkE/merge.b.bcf /tmp/iaQXJX5nkE/merge.c.bcf .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --force-samples -Fx /tmp/iaQXJX5nkE/merge.a.bcf /tmp/iaQXJX5nkE/merge.b.bcf /tmp/iaQXJX5nkE/merge.c.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --force-samples -0 /tmp/iaQXJX5nkE/merge.a.vcf.gz /tmp/iaQXJX5nkE/merge.b.vcf.gz /tmp/iaQXJX5nkE/merge.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --force-samples -0 /tmp/iaQXJX5nkE/merge.a.vcf.gz /tmp/iaQXJX5nkE/merge.b.vcf.gz /tmp/iaQXJX5nkE/merge.c.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --force-samples -0 /tmp/iaQXJX5nkE/merge.a.bcf /tmp/iaQXJX5nkE/merge.b.bcf /tmp/iaQXJX5nkE/merge.c.bcf .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --force-samples -0 /tmp/iaQXJX5nkE/merge.a.bcf /tmp/iaQXJX5nkE/merge.b.bcf /tmp/iaQXJX5nkE/merge.c.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --force-samples -m none /tmp/iaQXJX5nkE/merge.2.a.vcf.gz /tmp/iaQXJX5nkE/merge.2.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --force-samples -m none /tmp/iaQXJX5nkE/merge.2.a.vcf.gz /tmp/iaQXJX5nkE/merge.2.b.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --force-samples -m none /tmp/iaQXJX5nkE/merge.2.a.bcf /tmp/iaQXJX5nkE/merge.2.b.bcf .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --force-samples -m none /tmp/iaQXJX5nkE/merge.2.a.bcf /tmp/iaQXJX5nkE/merge.2.b.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --force-samples -m both /tmp/iaQXJX5nkE/merge.2.a.vcf.gz /tmp/iaQXJX5nkE/merge.2.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --force-samples -m both /tmp/iaQXJX5nkE/merge.2.a.vcf.gz /tmp/iaQXJX5nkE/merge.2.b.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --force-samples -m both /tmp/iaQXJX5nkE/merge.2.a.bcf /tmp/iaQXJX5nkE/merge.2.b.bcf .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --force-samples -m both /tmp/iaQXJX5nkE/merge.2.a.bcf /tmp/iaQXJX5nkE/merge.2.b.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --force-samples -m all /tmp/iaQXJX5nkE/merge.2.a.vcf.gz /tmp/iaQXJX5nkE/merge.2.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --force-samples -m all /tmp/iaQXJX5nkE/merge.2.a.vcf.gz /tmp/iaQXJX5nkE/merge.2.b.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --force-samples -m all /tmp/iaQXJX5nkE/merge.2.a.bcf /tmp/iaQXJX5nkE/merge.2.b.bcf .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --force-samples -m all /tmp/iaQXJX5nkE/merge.2.a.bcf /tmp/iaQXJX5nkE/merge.2.b.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/iaQXJX5nkE/merge.3.a.vcf.gz /tmp/iaQXJX5nkE/merge.3.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/iaQXJX5nkE/merge.3.a.vcf.gz /tmp/iaQXJX5nkE/merge.3.b.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/iaQXJX5nkE/merge.3.a.bcf /tmp/iaQXJX5nkE/merge.3.b.bcf .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/iaQXJX5nkE/merge.3.a.bcf /tmp/iaQXJX5nkE/merge.3.b.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --force-samples -m id /tmp/iaQXJX5nkE/merge.4.a.vcf.gz /tmp/iaQXJX5nkE/merge.4.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --force-samples -m id /tmp/iaQXJX5nkE/merge.4.a.vcf.gz /tmp/iaQXJX5nkE/merge.4.b.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --force-samples -m id /tmp/iaQXJX5nkE/merge.4.a.bcf /tmp/iaQXJX5nkE/merge.4.b.bcf .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --force-samples -m id /tmp/iaQXJX5nkE/merge.4.a.bcf /tmp/iaQXJX5nkE/merge.4.b.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --gvcf - /tmp/iaQXJX5nkE/gvcf.merge.1.vcf.gz /tmp/iaQXJX5nkE/gvcf.merge.2.vcf.gz /tmp/iaQXJX5nkE/gvcf.merge.3.vcf.gz .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --gvcf - /tmp/iaQXJX5nkE/gvcf.merge.1.vcf.gz /tmp/iaQXJX5nkE/gvcf.merge.2.vcf.gz /tmp/iaQXJX5nkE/gvcf.merge.3.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --gvcf - /tmp/iaQXJX5nkE/gvcf.merge.1.bcf /tmp/iaQXJX5nkE/gvcf.merge.2.bcf /tmp/iaQXJX5nkE/gvcf.merge.3.bcf .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --gvcf - /tmp/iaQXJX5nkE/gvcf.merge.1.bcf /tmp/iaQXJX5nkE/gvcf.merge.2.bcf /tmp/iaQXJX5nkE/gvcf.merge.3.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --gvcf - /tmp/iaQXJX5nkE/merge.gvcf.2.a.vcf.gz /tmp/iaQXJX5nkE/merge.gvcf.2.b.vcf.gz /tmp/iaQXJX5nkE/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --gvcf - /tmp/iaQXJX5nkE/merge.gvcf.2.a.vcf.gz /tmp/iaQXJX5nkE/merge.gvcf.2.b.vcf.gz /tmp/iaQXJX5nkE/merge.gvcf.2.c.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --gvcf - -m both,* /tmp/iaQXJX5nkE/merge.gvcf.2.a.vcf.gz /tmp/iaQXJX5nkE/merge.gvcf.2.b.vcf.gz /tmp/iaQXJX5nkE/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --gvcf - -m both,* /tmp/iaQXJX5nkE/merge.gvcf.2.a.vcf.gz /tmp/iaQXJX5nkE/merge.gvcf.2.b.vcf.gz /tmp/iaQXJX5nkE/merge.gvcf.2.c.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --gvcf - -m both,** /tmp/iaQXJX5nkE/merge.gvcf.2.a.vcf.gz /tmp/iaQXJX5nkE/merge.gvcf.2.b.vcf.gz /tmp/iaQXJX5nkE/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --gvcf - -m both,** /tmp/iaQXJX5nkE/merge.gvcf.2.a.vcf.gz /tmp/iaQXJX5nkE/merge.gvcf.2.b.vcf.gz /tmp/iaQXJX5nkE/merge.gvcf.2.c.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --gvcf - -i SRC:join /tmp/iaQXJX5nkE/merge.gvcf.3.a.vcf.gz /tmp/iaQXJX5nkE/merge.gvcf.3.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --gvcf - -i SRC:join /tmp/iaQXJX5nkE/merge.gvcf.3.a.vcf.gz /tmp/iaQXJX5nkE/merge.gvcf.3.b.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --gvcf - /tmp/iaQXJX5nkE/merge.gvcf.4.a.vcf.gz /tmp/iaQXJX5nkE/merge.gvcf.4.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --gvcf - /tmp/iaQXJX5nkE/merge.gvcf.4.a.vcf.gz /tmp/iaQXJX5nkE/merge.gvcf.4.b.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --gvcf - /tmp/iaQXJX5nkE/merge.gvcf.4.a.bcf /tmp/iaQXJX5nkE/merge.gvcf.4.b.bcf .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --gvcf - /tmp/iaQXJX5nkE/merge.gvcf.4.a.bcf /tmp/iaQXJX5nkE/merge.gvcf.4.b.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version /tmp/iaQXJX5nkE/merge.5.a.vcf.gz /tmp/iaQXJX5nkE/merge.5.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob /tmp/iaQXJX5nkE/merge.5.a.vcf.gz /tmp/iaQXJX5nkE/merge.5.b.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version /tmp/iaQXJX5nkE/merge.5.a.bcf /tmp/iaQXJX5nkE/merge.5.b.bcf .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob /tmp/iaQXJX5nkE/merge.5.a.bcf /tmp/iaQXJX5nkE/merge.5.b.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version /tmp/iaQXJX5nkE/merge.6.a.vcf.gz /tmp/iaQXJX5nkE/merge.6.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob /tmp/iaQXJX5nkE/merge.6.a.vcf.gz /tmp/iaQXJX5nkE/merge.6.b.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version /tmp/iaQXJX5nkE/merge.6.a.bcf /tmp/iaQXJX5nkE/merge.6.b.bcf .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob /tmp/iaQXJX5nkE/merge.6.a.bcf /tmp/iaQXJX5nkE/merge.6.b.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --gvcf - /tmp/iaQXJX5nkE/merge.gvcf.7.a.vcf.gz /tmp/iaQXJX5nkE/merge.gvcf.7.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --gvcf - /tmp/iaQXJX5nkE/merge.gvcf.7.a.vcf.gz /tmp/iaQXJX5nkE/merge.gvcf.7.b.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --gvcf - /tmp/iaQXJX5nkE/merge.gvcf.7.a.bcf /tmp/iaQXJX5nkE/merge.gvcf.7.b.bcf .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --gvcf - /tmp/iaQXJX5nkE/merge.gvcf.7.a.bcf /tmp/iaQXJX5nkE/merge.gvcf.7.b.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --gvcf - /tmp/iaQXJX5nkE/merge.gvcf.8.a.vcf.gz /tmp/iaQXJX5nkE/merge.gvcf.8.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --gvcf - /tmp/iaQXJX5nkE/merge.gvcf.8.a.vcf.gz /tmp/iaQXJX5nkE/merge.gvcf.8.b.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --gvcf - /tmp/iaQXJX5nkE/merge.gvcf.8.a.bcf /tmp/iaQXJX5nkE/merge.gvcf.8.b.bcf .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --gvcf - /tmp/iaQXJX5nkE/merge.gvcf.8.a.bcf /tmp/iaQXJX5nkE/merge.gvcf.8.b.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --force-samples /tmp/iaQXJX5nkE/merge.7.a.vcf.gz /tmp/iaQXJX5nkE/merge.7.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --force-samples /tmp/iaQXJX5nkE/merge.7.a.vcf.gz /tmp/iaQXJX5nkE/merge.7.b.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --force-samples /tmp/iaQXJX5nkE/merge.7.a.bcf /tmp/iaQXJX5nkE/merge.7.b.bcf .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --force-samples /tmp/iaQXJX5nkE/merge.7.a.bcf /tmp/iaQXJX5nkE/merge.7.b.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --gvcf /build/bcftools-qI88Pr/bcftools-1.24/test/gvcf.fa /tmp/iaQXJX5nkE/merge.gvcf.9a.vcf.gz /tmp/iaQXJX5nkE/merge.gvcf.9b.vcf.gz /tmp/iaQXJX5nkE/merge.gvcf.9c.vcf.gz /tmp/iaQXJX5nkE/merge.gvcf.9d.vcf.gz .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --gvcf /build/bcftools-qI88Pr/bcftools-1.24/test/gvcf.fa /tmp/iaQXJX5nkE/merge.gvcf.9a.vcf.gz /tmp/iaQXJX5nkE/merge.gvcf.9b.vcf.gz /tmp/iaQXJX5nkE/merge.gvcf.9c.vcf.gz /tmp/iaQXJX5nkE/merge.gvcf.9d.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --gvcf /build/bcftools-qI88Pr/bcftools-1.24/test/gvcf.fa /tmp/iaQXJX5nkE/merge.gvcf.9a.bcf /tmp/iaQXJX5nkE/merge.gvcf.9b.bcf /tmp/iaQXJX5nkE/merge.gvcf.9c.bcf /tmp/iaQXJX5nkE/merge.gvcf.9d.bcf .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --gvcf /build/bcftools-qI88Pr/bcftools-1.24/test/gvcf.fa /tmp/iaQXJX5nkE/merge.gvcf.9a.bcf /tmp/iaQXJX5nkE/merge.gvcf.9b.bcf /tmp/iaQXJX5nkE/merge.gvcf.9c.bcf /tmp/iaQXJX5nkE/merge.gvcf.9d.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --gvcf /build/bcftools-qI88Pr/bcftools-1.24/test/gvcf.fa -r 22:21-23 /tmp/iaQXJX5nkE/merge.gvcf.9a.vcf.gz /tmp/iaQXJX5nkE/merge.gvcf.9b.vcf.gz /tmp/iaQXJX5nkE/merge.gvcf.9c.vcf.gz /tmp/iaQXJX5nkE/merge.gvcf.9d.vcf.gz .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --gvcf /build/bcftools-qI88Pr/bcftools-1.24/test/gvcf.fa -r 22:21-23 /tmp/iaQXJX5nkE/merge.gvcf.9a.vcf.gz /tmp/iaQXJX5nkE/merge.gvcf.9b.vcf.gz /tmp/iaQXJX5nkE/merge.gvcf.9c.vcf.gz /tmp/iaQXJX5nkE/merge.gvcf.9d.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --gvcf /build/bcftools-qI88Pr/bcftools-1.24/test/gvcf.fa -r 22:21-23 /tmp/iaQXJX5nkE/merge.gvcf.9a.bcf /tmp/iaQXJX5nkE/merge.gvcf.9b.bcf /tmp/iaQXJX5nkE/merge.gvcf.9c.bcf /tmp/iaQXJX5nkE/merge.gvcf.9d.bcf .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --gvcf /build/bcftools-qI88Pr/bcftools-1.24/test/gvcf.fa -r 22:21-23 /tmp/iaQXJX5nkE/merge.gvcf.9a.bcf /tmp/iaQXJX5nkE/merge.gvcf.9b.bcf /tmp/iaQXJX5nkE/merge.gvcf.9c.bcf /tmp/iaQXJX5nkE/merge.gvcf.9d.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --gvcf /build/bcftools-qI88Pr/bcftools-1.24/test/gvcf.fa /tmp/iaQXJX5nkE/merge.gvcf.9a.vcf.gz /tmp/iaQXJX5nkE/merge.gvcf.9b.vcf.gz /tmp/iaQXJX5nkE/merge.gvcf.9c.vcf.gz /tmp/iaQXJX5nkE/merge.gvcf.9d.vcf.gz /tmp/iaQXJX5nkE/merge.gvcf.9e.vcf.gz .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --gvcf /build/bcftools-qI88Pr/bcftools-1.24/test/gvcf.fa /tmp/iaQXJX5nkE/merge.gvcf.9a.vcf.gz /tmp/iaQXJX5nkE/merge.gvcf.9b.vcf.gz /tmp/iaQXJX5nkE/merge.gvcf.9c.vcf.gz /tmp/iaQXJX5nkE/merge.gvcf.9d.vcf.gz /tmp/iaQXJX5nkE/merge.gvcf.9e.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --gvcf /build/bcftools-qI88Pr/bcftools-1.24/test/gvcf.fa /tmp/iaQXJX5nkE/merge.gvcf.9a.bcf /tmp/iaQXJX5nkE/merge.gvcf.9b.bcf /tmp/iaQXJX5nkE/merge.gvcf.9c.bcf /tmp/iaQXJX5nkE/merge.gvcf.9d.bcf /tmp/iaQXJX5nkE/merge.gvcf.9e.bcf .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --gvcf /build/bcftools-qI88Pr/bcftools-1.24/test/gvcf.fa /tmp/iaQXJX5nkE/merge.gvcf.9a.bcf /tmp/iaQXJX5nkE/merge.gvcf.9b.bcf /tmp/iaQXJX5nkE/merge.gvcf.9c.bcf /tmp/iaQXJX5nkE/merge.gvcf.9d.bcf /tmp/iaQXJX5nkE/merge.gvcf.9e.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --gvcf /build/bcftools-qI88Pr/bcftools-1.24/test/gvcf.fa -r 22:21-23 /tmp/iaQXJX5nkE/merge.gvcf.9a.vcf.gz /tmp/iaQXJX5nkE/merge.gvcf.9b.vcf.gz /tmp/iaQXJX5nkE/merge.gvcf.9c.vcf.gz /tmp/iaQXJX5nkE/merge.gvcf.9d.vcf.gz /tmp/iaQXJX5nkE/merge.gvcf.9e.vcf.gz .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --gvcf /build/bcftools-qI88Pr/bcftools-1.24/test/gvcf.fa -r 22:21-23 /tmp/iaQXJX5nkE/merge.gvcf.9a.vcf.gz /tmp/iaQXJX5nkE/merge.gvcf.9b.vcf.gz /tmp/iaQXJX5nkE/merge.gvcf.9c.vcf.gz /tmp/iaQXJX5nkE/merge.gvcf.9d.vcf.gz /tmp/iaQXJX5nkE/merge.gvcf.9e.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --gvcf /build/bcftools-qI88Pr/bcftools-1.24/test/gvcf.fa -r 22:21-23 /tmp/iaQXJX5nkE/merge.gvcf.9a.bcf /tmp/iaQXJX5nkE/merge.gvcf.9b.bcf /tmp/iaQXJX5nkE/merge.gvcf.9c.bcf /tmp/iaQXJX5nkE/merge.gvcf.9d.bcf /tmp/iaQXJX5nkE/merge.gvcf.9e.bcf .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --gvcf /build/bcftools-qI88Pr/bcftools-1.24/test/gvcf.fa -r 22:21-23 /tmp/iaQXJX5nkE/merge.gvcf.9a.bcf /tmp/iaQXJX5nkE/merge.gvcf.9b.bcf /tmp/iaQXJX5nkE/merge.gvcf.9c.bcf /tmp/iaQXJX5nkE/merge.gvcf.9d.bcf /tmp/iaQXJX5nkE/merge.gvcf.9e.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version /tmp/iaQXJX5nkE/merge.gvcf.10.a.vcf.gz /tmp/iaQXJX5nkE/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob /tmp/iaQXJX5nkE/merge.gvcf.10.a.vcf.gz /tmp/iaQXJX5nkE/merge.gvcf.10.b.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version /tmp/iaQXJX5nkE/merge.gvcf.10.a.bcf /tmp/iaQXJX5nkE/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob /tmp/iaQXJX5nkE/merge.gvcf.10.a.bcf /tmp/iaQXJX5nkE/merge.gvcf.10.b.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -m none /tmp/iaQXJX5nkE/merge.gvcf.10.a.vcf.gz /tmp/iaQXJX5nkE/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob -m none /tmp/iaQXJX5nkE/merge.gvcf.10.a.vcf.gz /tmp/iaQXJX5nkE/merge.gvcf.10.b.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -m none /tmp/iaQXJX5nkE/merge.gvcf.10.a.bcf /tmp/iaQXJX5nkE/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob -m none /tmp/iaQXJX5nkE/merge.gvcf.10.a.bcf /tmp/iaQXJX5nkE/merge.gvcf.10.b.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -g /build/bcftools-qI88Pr/bcftools-1.24/test/merge.gvcf.10.fa /tmp/iaQXJX5nkE/merge.gvcf.10.a.vcf.gz /tmp/iaQXJX5nkE/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob -g /build/bcftools-qI88Pr/bcftools-1.24/test/merge.gvcf.10.fa /tmp/iaQXJX5nkE/merge.gvcf.10.a.vcf.gz /tmp/iaQXJX5nkE/merge.gvcf.10.b.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -g /build/bcftools-qI88Pr/bcftools-1.24/test/merge.gvcf.10.fa /tmp/iaQXJX5nkE/merge.gvcf.10.a.bcf /tmp/iaQXJX5nkE/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob -g /build/bcftools-qI88Pr/bcftools-1.24/test/merge.gvcf.10.fa /tmp/iaQXJX5nkE/merge.gvcf.10.a.bcf /tmp/iaQXJX5nkE/merge.gvcf.10.b.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -g /build/bcftools-qI88Pr/bcftools-1.24/test/merge.gvcf.10.fa -m none /tmp/iaQXJX5nkE/merge.gvcf.10.a.vcf.gz /tmp/iaQXJX5nkE/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob -g /build/bcftools-qI88Pr/bcftools-1.24/test/merge.gvcf.10.fa -m none /tmp/iaQXJX5nkE/merge.gvcf.10.a.vcf.gz /tmp/iaQXJX5nkE/merge.gvcf.10.b.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -g /build/bcftools-qI88Pr/bcftools-1.24/test/merge.gvcf.10.fa -m none /tmp/iaQXJX5nkE/merge.gvcf.10.a.bcf /tmp/iaQXJX5nkE/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob -g /build/bcftools-qI88Pr/bcftools-1.24/test/merge.gvcf.10.fa -m none /tmp/iaQXJX5nkE/merge.gvcf.10.a.bcf /tmp/iaQXJX5nkE/merge.gvcf.10.b.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version /tmp/iaQXJX5nkE/merge.noidx.a.vcf.gz /tmp/iaQXJX5nkE/merge.noidx.b.vcf.gz /tmp/iaQXJX5nkE/merge.noidx.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob /tmp/iaQXJX5nkE/merge.noidx.a.vcf.gz /tmp/iaQXJX5nkE/merge.noidx.b.vcf.gz /tmp/iaQXJX5nkE/merge.noidx.c.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version /tmp/iaQXJX5nkE/merge.noidx.a.bcf /tmp/iaQXJX5nkE/merge.noidx.b.bcf /tmp/iaQXJX5nkE/merge.noidx.c.bcf .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob /tmp/iaQXJX5nkE/merge.noidx.a.bcf /tmp/iaQXJX5nkE/merge.noidx.b.bcf /tmp/iaQXJX5nkE/merge.noidx.c.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --no-index /build/bcftools-qI88Pr/bcftools-1.24/test/merge.noidx.a.vcf /build/bcftools-qI88Pr/bcftools-1.24/test/merge.noidx.b.vcf /build/bcftools-qI88Pr/bcftools-1.24/test/merge.noidx.c.vcf .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --no-index /build/bcftools-qI88Pr/bcftools-1.24/test/merge.noidx.a.vcf /build/bcftools-qI88Pr/bcftools-1.24/test/merge.noidx.b.vcf /build/bcftools-qI88Pr/bcftools-1.24/test/merge.noidx.c.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --no-index /tmp/iaQXJX5nkE/merge.noidx.a.bcf /tmp/iaQXJX5nkE/merge.noidx.b.bcf /tmp/iaQXJX5nkE/merge.noidx.c.bcf .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --no-index /tmp/iaQXJX5nkE/merge.noidx.a.bcf /tmp/iaQXJX5nkE/merge.noidx.b.bcf /tmp/iaQXJX5nkE/merge.noidx.c.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version /tmp/iaQXJX5nkE/merge.8.a.vcf.gz /tmp/iaQXJX5nkE/merge.8.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob /tmp/iaQXJX5nkE/merge.8.a.vcf.gz /tmp/iaQXJX5nkE/merge.8.b.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version /tmp/iaQXJX5nkE/merge.8.a.bcf /tmp/iaQXJX5nkE/merge.8.b.bcf .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob /tmp/iaQXJX5nkE/merge.8.a.bcf /tmp/iaQXJX5nkE/merge.8.b.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -i AN:sum,AC:sum /tmp/iaQXJX5nkE/merge.8.a.vcf.gz /tmp/iaQXJX5nkE/merge.8.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/iaQXJX5nkE/merge.8.a.vcf.gz /tmp/iaQXJX5nkE/merge.8.b.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -i AN:sum,AC:sum /tmp/iaQXJX5nkE/merge.8.a.bcf /tmp/iaQXJX5nkE/merge.8.b.bcf .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/iaQXJX5nkE/merge.8.a.bcf /tmp/iaQXJX5nkE/merge.8.b.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version /tmp/iaQXJX5nkE/merge.9.a.vcf.gz /tmp/iaQXJX5nkE/merge.9.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob /tmp/iaQXJX5nkE/merge.9.a.vcf.gz /tmp/iaQXJX5nkE/merge.9.b.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version /tmp/iaQXJX5nkE/merge.9.a.bcf /tmp/iaQXJX5nkE/merge.9.b.bcf .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob /tmp/iaQXJX5nkE/merge.9.a.bcf /tmp/iaQXJX5nkE/merge.9.b.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -i AN:sum,AC:sum /tmp/iaQXJX5nkE/merge.9.a.vcf.gz /tmp/iaQXJX5nkE/merge.9.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/iaQXJX5nkE/merge.9.a.vcf.gz /tmp/iaQXJX5nkE/merge.9.b.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -i AN:sum,AC:sum /tmp/iaQXJX5nkE/merge.9.a.bcf /tmp/iaQXJX5nkE/merge.9.b.bcf .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/iaQXJX5nkE/merge.9.a.bcf /tmp/iaQXJX5nkE/merge.9.b.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -m none /tmp/iaQXJX5nkE/merge.10.a.vcf.gz /tmp/iaQXJX5nkE/merge.10.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob -m none /tmp/iaQXJX5nkE/merge.10.a.vcf.gz /tmp/iaQXJX5nkE/merge.10.b.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -m none /tmp/iaQXJX5nkE/merge.10.a.bcf /tmp/iaQXJX5nkE/merge.10.b.bcf .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob -m none /tmp/iaQXJX5nkE/merge.10.a.bcf /tmp/iaQXJX5nkE/merge.10.b.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -m both /tmp/iaQXJX5nkE/merge.10.a.vcf.gz /tmp/iaQXJX5nkE/merge.10.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob -m both /tmp/iaQXJX5nkE/merge.10.a.vcf.gz /tmp/iaQXJX5nkE/merge.10.b.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -m both /tmp/iaQXJX5nkE/merge.10.a.bcf /tmp/iaQXJX5nkE/merge.10.b.bcf .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob -m both /tmp/iaQXJX5nkE/merge.10.a.bcf /tmp/iaQXJX5nkE/merge.10.b.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -m snp-ins-del /tmp/iaQXJX5nkE/merge.10.a.vcf.gz /tmp/iaQXJX5nkE/merge.10.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob -m snp-ins-del /tmp/iaQXJX5nkE/merge.10.a.vcf.gz /tmp/iaQXJX5nkE/merge.10.b.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -m snp-ins-del /tmp/iaQXJX5nkE/merge.10.a.bcf /tmp/iaQXJX5nkE/merge.10.b.bcf .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob -m snp-ins-del /tmp/iaQXJX5nkE/merge.10.a.bcf /tmp/iaQXJX5nkE/merge.10.b.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --gvcf - /tmp/iaQXJX5nkE/merge.mrules.1.a.vcf.gz /tmp/iaQXJX5nkE/merge.mrules.1.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --gvcf - /tmp/iaQXJX5nkE/merge.mrules.1.a.vcf.gz /tmp/iaQXJX5nkE/merge.mrules.1.b.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --gvcf - /tmp/iaQXJX5nkE/merge.mrules.1.a.bcf /tmp/iaQXJX5nkE/merge.mrules.1.b.bcf .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --gvcf - /tmp/iaQXJX5nkE/merge.mrules.1.a.bcf /tmp/iaQXJX5nkE/merge.mrules.1.b.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --gvcf - -M AD:.,PL:. /tmp/iaQXJX5nkE/merge.mrules.1.a.vcf.gz /tmp/iaQXJX5nkE/merge.mrules.1.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --gvcf - -M AD:.,PL:. /tmp/iaQXJX5nkE/merge.mrules.1.a.vcf.gz /tmp/iaQXJX5nkE/merge.mrules.1.b.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --gvcf - -M AD:.,PL:. /tmp/iaQXJX5nkE/merge.mrules.1.a.bcf /tmp/iaQXJX5nkE/merge.mrules.1.b.bcf .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --gvcf - -M AD:.,PL:. /tmp/iaQXJX5nkE/merge.mrules.1.a.bcf /tmp/iaQXJX5nkE/merge.mrules.1.b.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --gvcf - /tmp/iaQXJX5nkE/merge.gvcf.5.a.vcf.gz /tmp/iaQXJX5nkE/merge.gvcf.5.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --gvcf - /tmp/iaQXJX5nkE/merge.gvcf.5.a.vcf.gz /tmp/iaQXJX5nkE/merge.gvcf.5.b.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --gvcf - /tmp/iaQXJX5nkE/merge.gvcf.5.a.bcf /tmp/iaQXJX5nkE/merge.gvcf.5.b.bcf .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --gvcf - /tmp/iaQXJX5nkE/merge.gvcf.5.a.bcf /tmp/iaQXJX5nkE/merge.gvcf.5.b.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --gvcf - --merge none /tmp/iaQXJX5nkE/merge.gvcf.5.a.vcf.gz /tmp/iaQXJX5nkE/merge.gvcf.5.b.vcf.gz .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --gvcf - --merge none /tmp/iaQXJX5nkE/merge.gvcf.5.a.vcf.gz /tmp/iaQXJX5nkE/merge.gvcf.5.b.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --gvcf - --merge none /tmp/iaQXJX5nkE/merge.gvcf.5.a.bcf /tmp/iaQXJX5nkE/merge.gvcf.5.b.bcf .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --gvcf - --merge none /tmp/iaQXJX5nkE/merge.gvcf.5.a.bcf /tmp/iaQXJX5nkE/merge.gvcf.5.b.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --gvcf - /tmp/iaQXJX5nkE/merge.gvcf.11.a.vcf.gz /tmp/iaQXJX5nkE/merge.gvcf.11.b.vcf.gz /tmp/iaQXJX5nkE/merge.gvcf.11.c.vcf.gz .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --gvcf - /tmp/iaQXJX5nkE/merge.gvcf.11.a.vcf.gz /tmp/iaQXJX5nkE/merge.gvcf.11.b.vcf.gz /tmp/iaQXJX5nkE/merge.gvcf.11.c.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version --gvcf - /tmp/iaQXJX5nkE/merge.gvcf.11.a.bcf /tmp/iaQXJX5nkE/merge.gvcf.11.b.bcf /tmp/iaQXJX5nkE/merge.gvcf.11.c.bcf .. ok test_vcf_merge: /build/bcftools-qI88Pr/bcftools-1.24/bcftools merge --no-version -Ob --gvcf - /tmp/iaQXJX5nkE/merge.gvcf.11.a.bcf /tmp/iaQXJX5nkE/merge.gvcf.11.b.bcf /tmp/iaQXJX5nkE/merge.gvcf.11.c.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '[%CHROM\t%POS\t%GT\t%LAA\t%smpl_count(FMT/LAA)\n]\n' /tmp/iaQXJX5nkE/smpl-count.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/smpl-count.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '[%CHROM\t%POS\t%GT\t%LAA\t%smpl_count(FMT/LAA)\n]\n' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '[%CHROM\t%POS\t%GT\t%LAA\t%smpl_count(FMT/LAA)\n]\n' -i'smpl_count(LAA)==1' /tmp/iaQXJX5nkE/smpl-count.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/smpl-count.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '[%CHROM\t%POS\t%GT\t%LAA\t%smpl_count(FMT/LAA)\n]\n' -i'smpl_count(LAA)==1' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '[%CHROM\t%POS\t%GT\t%LAA\t%smpl_count(FMT/LAA)\n]\n' -i'smpl_count(LAA)==1 & GT="hom"' /tmp/iaQXJX5nkE/smpl-count.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/smpl-count.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '[%CHROM\t%POS\t%GT\t%LAA\t%smpl_count(FMT/LAA)\n]\n' -i'smpl_count(LAA)==1 & GT="hom"' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '[%CHROM\t%POS\t%GT\t%LAA\t%smpl_count(FMT/LAA)\n]\n' -i'GT="hom" & smpl_count(LAA)==1' /tmp/iaQXJX5nkE/smpl-count.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/smpl-count.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '[%CHROM\t%POS\t%GT\t%LAA\t%smpl_count(FMT/LAA)\n]\n' -i'GT="hom" & smpl_count(LAA)==1' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%TAG' -i 'TAG[*]="."' /tmp/iaQXJX5nkE/query.filter.15.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.filter.15.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%TAG' -i 'TAG[*]="."' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%TAG' -i 'TAG[*]~"\."' /tmp/iaQXJX5nkE/query.filter.15.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.filter.15.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%TAG' -i 'TAG[*]~"\."' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%TAG' -i 'TAG[*]!="."' /tmp/iaQXJX5nkE/query.filter.15.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.filter.15.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%TAG' -i 'TAG[*]!="."' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%TAG' -i 'TAG[*]!~"\."' /tmp/iaQXJX5nkE/query.filter.15.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.filter.15.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%TAG' -i 'TAG[*]!~"\."' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%CHROM %POS %ID %REF %ALT %QUAL %FILTER \t %INFO/CHROM %INFO/POS %INFO/ID %INFO/REF %INFO/ALT %INFO/QUAL %INFO/FILTER' /tmp/iaQXJX5nkE/query.3.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.3.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%CHROM %POS %ID %REF %ALT %QUAL %FILTER \t %INFO/CHROM %INFO/POS %INFO/ID %INFO/REF %INFO/ALT %INFO/QUAL %INFO/FILTER' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '[ %CHROM] \t [ %POS] \t [ %ID] \t [ %REF] \t [ %ALT] \t [ %QUAL] \t [ %FILTER]' /tmp/iaQXJX5nkE/query.3.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.3.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '[ %CHROM] \t [ %POS] \t [ %ID] \t [ %REF] \t [ %ALT] \t [ %QUAL] \t [ %FILTER]' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '[ %/CHROM] \t [ %/POS] \t [ %/ID] \t [ %/REF] \t [ %/ALT] \t [ %/QUAL] \t [ %/FILTER]' /tmp/iaQXJX5nkE/query.3.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.3.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '[ %/CHROM] \t [ %/POS] \t [ %/ID] \t [ %/REF] \t [ %/ALT] \t [ %/QUAL] \t [ %/FILTER]' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%CHROM:%POS [ %SAMPLE %GT]' /tmp/iaQXJX5nkE/query.filter.14.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.filter.14.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%CHROM:%POS [ %SAMPLE %GT]' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%CHROM:%POS [ %SAMPLE %GT]' -i'GT="."' /tmp/iaQXJX5nkE/query.filter.14.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.filter.14.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%CHROM:%POS [ %SAMPLE %GT]' -i'GT="."' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%CHROM:%POS [ %SAMPLE %GT]' -i'GT="0|1"' /tmp/iaQXJX5nkE/query.filter.14.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.filter.14.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%CHROM:%POS [ %SAMPLE %GT]' -i'GT="0|1"' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%CHROM:%POS\t%INFO/AD\t%SUM(INFO/AD)' /tmp/iaQXJX5nkE/query.func.1.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.func.1.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%CHROM:%POS\t%INFO/AD\t%SUM(INFO/AD)' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%CHROM:%POS\t[%AD ]\t%SUM(FORMAT/AD)' /tmp/iaQXJX5nkE/query.func.1.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.func.1.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%CHROM:%POS\t[%AD ]\t%SUM(FORMAT/AD)' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%CHROM:%POS\t[%AD ]\t[ %SUM(FORMAT/AD)]' /tmp/iaQXJX5nkE/query.func.1.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.func.1.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%CHROM:%POS\t[%AD ]\t[ %SUM(FORMAT/AD)]' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%CHROM:%POS\t[%AD ]\t[ %sSUM(FORMAT/AD)]' /tmp/iaQXJX5nkE/query.func.1.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.func.1.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%CHROM:%POS\t[%AD ]\t[ %sSUM(FORMAT/AD)]' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided,_conflicting_interpretations"' /tmp/iaQXJX5nkE/query.string.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.string.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided,_conflicting_interpretations"' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" || CLNREVSTAT="_conflicting_interpretations"' /tmp/iaQXJX5nkE/query.string.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.string.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" || CLNREVSTAT="_conflicting_interpretations"' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" && CLNREVSTAT="_conflicting_interpretations"' /tmp/iaQXJX5nkE/query.string.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.string.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" && CLNREVSTAT="_conflicting_interpretations"' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%CHROM\t%POS\t%INFO/STR\n' -i'INFO/STR=@/build/bcftools-qI88Pr/bcftools-1.24/test/query.string.2.1.txt' /tmp/iaQXJX5nkE/query.string.2.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.string.2.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%CHROM\t%POS\t%INFO/STR\n' -i'INFO/STR=@/build/bcftools-qI88Pr/bcftools-1.24/test/query.string.2.1.txt' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%CHROM\t%POS[\t%STR]\n' -i'FMT/STR=@/build/bcftools-qI88Pr/bcftools-1.24/test/query.string.2.2.txt' /tmp/iaQXJX5nkE/query.string.2.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.string.2.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%CHROM\t%POS[\t%STR]\n' -i'FMT/STR=@/build/bcftools-qI88Pr/bcftools-1.24/test/query.string.2.2.txt' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' /tmp/iaQXJX5nkE/query.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/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-qI88Pr/bcftools-1.24/bcftools query -f '%RSX\t%VKX\n' /tmp/iaQXJX5nkE/query.variantkey.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.variantkey.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%RSX\t%VKX\n' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%XRI\n' -i'XRI[*]>1111' /tmp/iaQXJX5nkE/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/view.filter.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%XRI\n' -i'XRI[*]>1111' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' /tmp/iaQXJX5nkE/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/view.filter.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' /tmp/iaQXJX5nkE/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/view.filter.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' /tmp/iaQXJX5nkE/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/view.filter.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' /tmp/iaQXJX5nkE/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/view.filter.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' /tmp/iaQXJX5nkE/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/view.filter.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' /tmp/iaQXJX5nkE/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/view.filter.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' /tmp/iaQXJX5nkE/query.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' /tmp/iaQXJX5nkE/query.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' /tmp/iaQXJX5nkE/query.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' /tmp/iaQXJX5nkE/query.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' /tmp/iaQXJX5nkE/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/view.filter.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' /tmp/iaQXJX5nkE/query.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' /tmp/iaQXJX5nkE/query.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' /tmp/iaQXJX5nkE/query.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' /tmp/iaQXJX5nkE/query.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/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/iaQXJX5nkE/view.vectors.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/view.vectors.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/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-qI88Pr/bcftools-1.24/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' /tmp/iaQXJX5nkE/query.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.filter.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' /tmp/iaQXJX5nkE/query.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.filter.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' /tmp/iaQXJX5nkE/query.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.filter.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' /tmp/iaQXJX5nkE/query.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.filter.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' /tmp/iaQXJX5nkE/query.2.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.2.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -i'IINT="."' -f'%POS %IINT\n' /tmp/iaQXJX5nkE/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/missing.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -i'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -i'IINT!="."' -f'%POS %IINT\n' /tmp/iaQXJX5nkE/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/missing.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -i'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -e'IINT!="."' -f'%POS %IINT\n' /tmp/iaQXJX5nkE/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/missing.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -e'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -e'IINT="."' -f'%POS %IINT\n' /tmp/iaQXJX5nkE/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/missing.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -e'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' /tmp/iaQXJX5nkE/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/missing.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' /tmp/iaQXJX5nkE/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/missing.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' /tmp/iaQXJX5nkE/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/missing.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' /tmp/iaQXJX5nkE/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/missing.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' /tmp/iaQXJX5nkE/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/missing.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' /tmp/iaQXJX5nkE/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/missing.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' /tmp/iaQXJX5nkE/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/missing.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' /tmp/iaQXJX5nkE/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/missing.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' /tmp/iaQXJX5nkE/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/missing.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -i'FILTER="A"' -f'%POS %FILTER\n' /tmp/iaQXJX5nkE/filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/filter.11.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -i'FILTER="A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -i'FILTER!="A"' -f'%POS %FILTER\n' /tmp/iaQXJX5nkE/filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/filter.11.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -i'FILTER!="A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -i'FILTER~"A"' -f'%POS %FILTER\n' /tmp/iaQXJX5nkE/filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/filter.11.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -i'FILTER~"A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n' /tmp/iaQXJX5nkE/filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/filter.11.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%LINE' /tmp/iaQXJX5nkE/query.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%LINE' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' /tmp/iaQXJX5nkE/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.filter-type.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' /tmp/iaQXJX5nkE/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.filter-type.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' /tmp/iaQXJX5nkE/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.filter-type.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' /tmp/iaQXJX5nkE/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.filter-type.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\n' -i'INFO/TYPE="xxx"' /tmp/iaQXJX5nkE/query.filter-type.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.filter-type.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\n' -i'INFO/TYPE="xxx"' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/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/iaQXJX5nkE/filter-missing-floats.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/filter-missing-floats.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/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-qI88Pr/bcftools-1.24/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/iaQXJX5nkE/filter-missing-floats.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/filter-missing-floats.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/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-qI88Pr/bcftools-1.24/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' /tmp/iaQXJX5nkE/missing.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/missing.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' /tmp/iaQXJX5nkE/query.filter.2.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.filter.2.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' /tmp/iaQXJX5nkE/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/view.filter.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' /tmp/iaQXJX5nkE/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/view.filter.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' /tmp/iaQXJX5nkE/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/view.filter.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' /tmp/iaQXJX5nkE/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/view.filter.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' /tmp/iaQXJX5nkE/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/view.filter.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' /tmp/iaQXJX5nkE/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/view.filter.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' /tmp/iaQXJX5nkE/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/view.filter.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' /tmp/iaQXJX5nkE/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/view.filter.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' /tmp/iaQXJX5nkE/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/view.filter.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' /tmp/iaQXJX5nkE/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/view.filter.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' /tmp/iaQXJX5nkE/filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/filter.5.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' /tmp/iaQXJX5nkE/filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/filter.5.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' /tmp/iaQXJX5nkE/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/view.filter.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' /tmp/iaQXJX5nkE/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/view.filter.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' /tmp/iaQXJX5nkE/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/view.filter.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' /tmp/iaQXJX5nkE/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/view.filter.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' /tmp/iaQXJX5nkE/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/view.filter.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 & FMT/GQ=589' /tmp/iaQXJX5nkE/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/view.filter.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 & FMT/GQ=589' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' /tmp/iaQXJX5nkE/view.filter.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/view.filter.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' /tmp/iaQXJX5nkE/query.filter.3.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.filter.3.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"' /tmp/iaQXJX5nkE/query.filter.3.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.filter.3.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' /tmp/iaQXJX5nkE/query.filter.3.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.filter.3.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS %SAMPLE %AD\n]\n' -i'AD[:0]+AD[:1] > 12' /tmp/iaQXJX5nkE/filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/filter.5.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS %SAMPLE %AD\n]\n' -i'AD[:0]+AD[:1] > 12' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' /tmp/iaQXJX5nkE/query.filter.4.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.filter.4.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%ID\n' -i 'ID=@/build/bcftools-qI88Pr/bcftools-1.24/test/query.56.out' /tmp/iaQXJX5nkE/view.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/view.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%ID\n' -i 'ID=@/build/bcftools-qI88Pr/bcftools-1.24/test/query.56.out' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD)>0.01' /tmp/iaQXJX5nkE/query.filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.filter.5.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/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-qI88Pr/bcftools-1.24/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD[:0],FMT/AD[:1])>0.01' /tmp/iaQXJX5nkE/query.filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.filter.5.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/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-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%AD\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01' /tmp/iaQXJX5nkE/query.filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.filter.5.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%AD\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[GT]==10' /tmp/iaQXJX5nkE/query.filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.filter.5.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[GT]==10' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'sSUM(FMT/AD[GT])==210' /tmp/iaQXJX5nkE/query.filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.filter.5.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'sSUM(FMT/AD[GT])==210' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[0:GT]==30' /tmp/iaQXJX5nkE/query.filter.5.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.filter.5.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[0:GT]==30' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TF[:GT]==1 && FMT/TF[:GT]==2' /tmp/iaQXJX5nkE/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.gtidx.1.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TF[:GT]==1 && FMT/TF[:GT]==2' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TI[:GT]==1 && FMT/TF[:GT]==2' /tmp/iaQXJX5nkE/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.gtidx.1.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TI[:GT]==1 && FMT/TF[:GT]==2' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TS[:GT]=="BB" && FMT/TS[:GT]=="CC"' /tmp/iaQXJX5nkE/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.gtidx.1.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TS[:GT]=="BB" && FMT/TS[:GT]=="CC"' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TC[:GT]=="B" && FMT/TC[:GT]=="C"' /tmp/iaQXJX5nkE/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.gtidx.1.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TC[:GT]=="B" && FMT/TC[:GT]=="C"' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%GT %TI\n]' -i'FMT/TI[:GT]=="."' /tmp/iaQXJX5nkE/query.gtidx.1.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.gtidx.1.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%GT %TI\n]' -i'FMT/TI[:GT]=="."' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%CHROM %POS\n' -i'CHROM="4"' /tmp/iaQXJX5nkE/query.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%CHROM %POS\n' -i'CHROM="4"' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%TAG1\n' -i'(TAG1>=-129 && TAG1<=-120) || (TAG1>=-32769 && TAG1<=-32760)' /tmp/iaQXJX5nkE/query.negative.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.negative.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%TAG1\n' -i'(TAG1>=-129 && TAG1<=-120) || (TAG1>=-32769 && TAG1<=-32760)' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%TAGV1\n' -i'(TAGV1>=-129 && TAGV1<=-120) || (TAGV1>=-32769 && TAGV1<=-32760)' /tmp/iaQXJX5nkE/query.negative.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.negative.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%TAGV1\n' -i'(TAGV1>=-129 && TAGV1<=-120) || (TAGV1>=-32769 && TAGV1<=-32760)' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%TAG2\n' -i'(TAG2>=-129 && TAG2<=-120) || (TAG2>=-32769 && TAG2<=-32760)' /tmp/iaQXJX5nkE/query.negative.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.negative.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%TAG2\n' -i'(TAG2>=-129 && TAG2<=-120) || (TAG2>=-32769 && TAG2<=-32760)' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%TAGV2\n' -i'(TAGV2>=-129 && TAGV2<=-120) || (TAGV2>=-32769 && TAGV2<=-32760)' /tmp/iaQXJX5nkE/query.negative.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.negative.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%TAGV2\n' -i'(TAGV2>=-129 && TAGV2<=-120) || (TAGV2>=-32769 && TAGV2<=-32760)' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS\t%SAMPLE\t%GQ\n]' -i'N_PASS(GQ<20)==1' /tmp/iaQXJX5nkE/query.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS\t%SAMPLE\t%GQ\n]' -i'N_PASS(GQ<20)==1' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")==1' /tmp/iaQXJX5nkE/query.filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.filter.11.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")==1' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")!=1' /tmp/iaQXJX5nkE/query.filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.filter.11.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")!=1' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")==1' /tmp/iaQXJX5nkE/query.filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.filter.11.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")==1' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")!=1' /tmp/iaQXJX5nkE/query.filter.11.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.filter.11.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")!=1' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%CHROM\t%POS\t%INFO\t%FORMAT\n' -s D,C /tmp/iaQXJX5nkE/query.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%CHROM\t%POS\t%INFO\t%FORMAT\n' -s D,C .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\n' -i'POS==16777217 || POS==33554432 || POS=118673904' /tmp/iaQXJX5nkE/query.filter.6.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.filter.6.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\n' -i'POS==16777217 || POS==33554432 || POS=118673904' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(II)==6' /tmp/iaQXJX5nkE/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.filter.7.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(II)==6' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(FORMAT/FI)==7' /tmp/iaQXJX5nkE/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.filter.7.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(FORMAT/FI)==7' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(II)==2' /tmp/iaQXJX5nkE/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.filter.7.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(II)==2' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(FORMAT/FI)==1.75' /tmp/iaQXJX5nkE/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.filter.7.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(FORMAT/FI)==1.75' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(II)==2' /tmp/iaQXJX5nkE/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.filter.7.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(II)==2' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(FORMAT/FI)==1.75' /tmp/iaQXJX5nkE/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.filter.7.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(FORMAT/FI)==1.75' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(II)==2' /tmp/iaQXJX5nkE/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.filter.7.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(II)==2' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(FORMAT/FI)==1.5' /tmp/iaQXJX5nkE/query.filter.7.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.filter.7.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(FORMAT/FI)==1.5' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'%ILEN==1' /tmp/iaQXJX5nkE/query.filter.8.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.filter.8.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'%ILEN==1' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'ILEN==1' /tmp/iaQXJX5nkE/query.filter.8.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.filter.8.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'ILEN==1' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] < FMT/AD[:1]' /tmp/iaQXJX5nkE/query.filter.9.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.filter.9.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] < FMT/AD[:1]' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] > FMT/AD[:1]' /tmp/iaQXJX5nkE/query.filter.9.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.filter.9.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] > FMT/AD[:1]' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[ %AD\n]' -i'AD[:1] / sum(AD[*]) > 0.5' /tmp/iaQXJX5nkE/query.filter.13.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.filter.13.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[ %AD\n]' -i'AD[:1] / sum(AD[*]) > 0.5' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS %NUM_TAG\n' -i'COUNT(INFO/NUM_TAG)=2' /tmp/iaQXJX5nkE/query.filter.10.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.filter.10.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS %NUM_TAG\n' -i'COUNT(INFO/NUM_TAG)=2' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2' /tmp/iaQXJX5nkE/query.filter.10.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.filter.10.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%CHROM:%POS\t%N_PASS(GT="alt" & GQ>110)\t[\t%GT]\t[\t%GQ]\n' /tmp/iaQXJX5nkE/query.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/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-qI88Pr/bcftools-1.24/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 1,3,0 /tmp/iaQXJX5nkE/query.filter.12.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.filter.12.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 1,3,0 .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 0,1,3 /tmp/iaQXJX5nkE/query.filter.12.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.filter.12.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 0,1,3 .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f "[%SAMPLE %GT\n]" -S /build/bcftools-qI88Pr/bcftools-1.24/test/query.smpl.11.txt /tmp/iaQXJX5nkE/query.smpl.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.smpl.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f "[%SAMPLE %GT\n]" -S /build/bcftools-qI88Pr/bcftools-1.24/test/query.smpl.11.txt .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -l -S /build/bcftools-qI88Pr/bcftools-1.24/test/query.smpl.11.txt /tmp/iaQXJX5nkE/query.smpl.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.smpl.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -l -S /build/bcftools-qI88Pr/bcftools-1.24/test/query.smpl.11.txt .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f "[%SAMPLE %GT\n]" -S ^/build/bcftools-qI88Pr/bcftools-1.24/test/query.smpl.11.txt /tmp/iaQXJX5nkE/query.smpl.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.smpl.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f "[%SAMPLE %GT\n]" -S ^/build/bcftools-qI88Pr/bcftools-1.24/test/query.smpl.11.txt .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -l -S ^/build/bcftools-qI88Pr/bcftools-1.24/test/query.smpl.11.txt /tmp/iaQXJX5nkE/query.smpl.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.smpl.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -l -S ^/build/bcftools-qI88Pr/bcftools-1.24/test/query.smpl.11.txt .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f "[%SAMPLE %GT\n]" -S /build/bcftools-qI88Pr/bcftools-1.24/test/query.smpl.txt /tmp/iaQXJX5nkE/query.smpl.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.smpl.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f "[%SAMPLE %GT\n]" -S /build/bcftools-qI88Pr/bcftools-1.24/test/query.smpl.txt .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -l -S /build/bcftools-qI88Pr/bcftools-1.24/test/query.smpl.txt /tmp/iaQXJX5nkE/query.smpl.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.smpl.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -l -S /build/bcftools-qI88Pr/bcftools-1.24/test/query.smpl.txt .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%ID\n' -i'ID~"s12"' /tmp/iaQXJX5nkE/query.filter.id.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.filter.id.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%ID\n' -i'ID~"s12"' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%ID\n' -i'ID="rs123"' /tmp/iaQXJX5nkE/query.filter.id.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.filter.id.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%ID\n' -i'ID="rs123"' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%ID\n' -i'ID="abc"' /tmp/iaQXJX5nkE/query.filter.id.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.filter.id.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%ID\n' -i'ID="abc"' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%ID\n' -i'ID=@/build/bcftools-qI88Pr/bcftools-1.24/test/query.filter.id.3.txt' /tmp/iaQXJX5nkE/query.filter.id.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.filter.id.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%ID\n' -i'ID=@/build/bcftools-qI88Pr/bcftools-1.24/test/query.filter.id.3.txt' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%ID\n' -i'ID!="abc"' /tmp/iaQXJX5nkE/query.filter.id.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.filter.id.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%ID\n' -i'ID!="abc"' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%ID\n' -i'ID!=@/build/bcftools-qI88Pr/bcftools-1.24/test/query.filter.id.3.txt' /tmp/iaQXJX5nkE/query.filter.id.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.filter.id.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%ID\n' -i'ID!=@/build/bcftools-qI88Pr/bcftools-1.24/test/query.filter.id.3.txt' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -i'FILTER="A"' -f'%FILTER\n' /tmp/iaQXJX5nkE/filter.12.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/filter.12.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -i'FILTER="A"' -f'%FILTER\n' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -i'FILTER~"A"' -f'%FILTER\n' /tmp/iaQXJX5nkE/filter.12.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/filter.12.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -i'FILTER~"A"' -f'%FILTER\n' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -i'FILTER="A;B"' -f'%FILTER\n' /tmp/iaQXJX5nkE/filter.12.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/filter.12.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -i'FILTER="A;B"' -f'%FILTER\n' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -i'FILTER!="A;B"' -f'%FILTER\n' /tmp/iaQXJX5nkE/filter.12.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/filter.12.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -i'FILTER!="A;B"' -f'%FILTER\n' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -i'FILTER~"A;B"' -f'%FILTER\n' /tmp/iaQXJX5nkE/filter.12.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/filter.12.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -i'FILTER~"A;B"' -f'%FILTER\n' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -i'FILTER!~"A;B"' -f'%FILTER\n' /tmp/iaQXJX5nkE/filter.12.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/filter.12.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -i'FILTER!~"A;B"' -f'%FILTER\n' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -i'DP%10==2' -f'[ %DP]\n' /tmp/iaQXJX5nkE/filter.10.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/filter.10.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -i'DP%10==2' -f'[ %DP]\n' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -i'REF="N"' -f'%CHROM %POS %REF %ALT %QUAL\n' /tmp/iaQXJX5nkE/filter.13.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/filter.13.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -i'REF="N"' -f'%CHROM %POS %REF %ALT %QUAL\n' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -H -f'[%CHROM %POS %SAMPLE %DP %GT\n]' /tmp/iaQXJX5nkE/query.header.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.header.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -H -f'[%CHROM %POS %SAMPLE %DP %GT\n]' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -H -f'[%CHROM %POS %SAMPLE %DP %GT\t]\n' /tmp/iaQXJX5nkE/query.header.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.header.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -H -f'[%CHROM %POS %SAMPLE %DP %GT\t]\n' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]\n' /tmp/iaQXJX5nkE/query.header.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.header.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]\n' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]' /tmp/iaQXJX5nkE/query.header.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.header.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]\n' /tmp/iaQXJX5nkE/query.header.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.header.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]\n' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]' /tmp/iaQXJX5nkE/query.header.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.header.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -HH -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]' /tmp/iaQXJX5nkE/query.header.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.header.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -HH -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%SAMPLE %DP\n]' -i'DP=1 || DP=2' /tmp/iaQXJX5nkE/query.filter-or.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.filter-or.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%SAMPLE %DP\n]' -i'DP=1 || DP=2' .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%SAMPLE %DP\n]' -i'DP=1 | DP=2' /tmp/iaQXJX5nkE/query.filter-or.vcf.gz .. ok test_vcf_query: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/query.filter-or.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%SAMPLE %DP\n]' -i'DP=1 | DP=2' .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -c s /tmp/iaQXJX5nkE/norm.dup-end.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/norm.dup-end.fa .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -c s /tmp/iaQXJX5nkE/norm.dup-end.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/norm.dup-end.fa -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -c s -N10 /tmp/iaQXJX5nkE/norm.dup-end.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/norm.dup-end.fa .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -c s -N10 /tmp/iaQXJX5nkE/norm.dup-end.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/norm.dup-end.fa -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -c s -N /tmp/iaQXJX5nkE/norm.dup-end.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/norm.dup-end.fa .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -c s -N /tmp/iaQXJX5nkE/norm.dup-end.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/norm.dup-end.fa -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -c s -N0 /tmp/iaQXJX5nkE/norm.dup-end.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/norm.dup-end.fa .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -c s -N0 /tmp/iaQXJX5nkE/norm.dup-end.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/norm.dup-end.fa -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -c s -N3 /tmp/iaQXJX5nkE/norm.dup-end.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/norm.dup-end.fa .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -c s -N3 /tmp/iaQXJX5nkE/norm.dup-end.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/norm.dup-end.fa -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -c s -e 'type~"other"' /tmp/iaQXJX5nkE/norm.dup-end.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/norm.dup-end.fa .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -c s -e 'type~"other"' /tmp/iaQXJX5nkE/norm.dup-end.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/norm.dup-end.fa -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -c s /tmp/iaQXJX5nkE/norm.check-ref.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/norm.check-ref.fa .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -c s /tmp/iaQXJX5nkE/norm.check-ref.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/norm.check-ref.fa -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m +both -i 'ID=@/build/bcftools-qI88Pr/bcftools-1.24/test/norm.filter.txt' /tmp/iaQXJX5nkE/norm.filter.vcf.gz .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m +both -i 'ID=@/build/bcftools-qI88Pr/bcftools-1.24/test/norm.filter.txt' /tmp/iaQXJX5nkE/norm.filter.vcf.gz -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m +both -i 'ALT!="C"' /tmp/iaQXJX5nkE/norm.filter.vcf.gz .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m +both -i 'ALT!="C"' /tmp/iaQXJX5nkE/norm.filter.vcf.gz -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -d both -i 'ID=@/build/bcftools-qI88Pr/bcftools-1.24/test/norm.filter.txt' /tmp/iaQXJX5nkE/norm.filter.vcf.gz .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -d both -i 'ID=@/build/bcftools-qI88Pr/bcftools-1.24/test/norm.filter.txt' /tmp/iaQXJX5nkE/norm.filter.vcf.gz -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -d both -i 'ALT!="C"' /tmp/iaQXJX5nkE/norm.filter.vcf.gz .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -d both -i 'ALT!="C"' /tmp/iaQXJX5nkE/norm.filter.vcf.gz -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -c e /tmp/iaQXJX5nkE/norm.6.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/norm.2.fa .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -c e /tmp/iaQXJX5nkE/norm.6.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/norm.2.fa -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m - /tmp/iaQXJX5nkE/norm.breakend.1.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/norm.breakend.1.fa .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m - /tmp/iaQXJX5nkE/norm.breakend.1.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/norm.breakend.1.fa -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m - /tmp/iaQXJX5nkE/norm.sort.vcf.gz .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m - /tmp/iaQXJX5nkE/norm.sort.vcf.gz -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m - -S lex /tmp/iaQXJX5nkE/norm.sort.vcf.gz .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m - -S lex /tmp/iaQXJX5nkE/norm.sort.vcf.gz -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m +both /tmp/iaQXJX5nkE/norm.join-missing-ploidy.vcf.gz .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m +both /tmp/iaQXJX5nkE/norm.join-missing-ploidy.vcf.gz -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m - --multi-overlaps . /tmp/iaQXJX5nkE/norm.split.5.vcf.gz .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m - --multi-overlaps . /tmp/iaQXJX5nkE/norm.split.5.vcf.gz -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version /tmp/iaQXJX5nkE/norm.symbolic.3.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/norm.symbolic.3.fa .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version /tmp/iaQXJX5nkE/norm.symbolic.3.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/norm.symbolic.3.fa -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -cx /tmp/iaQXJX5nkE/norm.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/norm.fa .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -cx /tmp/iaQXJX5nkE/norm.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/norm.fa -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m- /tmp/iaQXJX5nkE/norm.split.vcf.gz .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m- /tmp/iaQXJX5nkE/norm.split.vcf.gz -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m- -a /tmp/iaQXJX5nkE/norm.split.vcf.gz .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m- -a /tmp/iaQXJX5nkE/norm.split.vcf.gz -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m- /tmp/iaQXJX5nkE/norm.split.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m- /tmp/iaQXJX5nkE/norm.split.2.vcf.gz -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m- --force /tmp/iaQXJX5nkE/norm.split.3.vcf.gz .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m- --force /tmp/iaQXJX5nkE/norm.split.3.vcf.gz -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m- /tmp/iaQXJX5nkE/norm.split.4.vcf.gz .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m- /tmp/iaQXJX5nkE/norm.split.4.vcf.gz -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m- --keep-sum AD /tmp/iaQXJX5nkE/norm.split.4.vcf.gz .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m- --keep-sum AD /tmp/iaQXJX5nkE/norm.split.4.vcf.gz -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m- /tmp/iaQXJX5nkE/norm.split.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/norm.fa .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m- /tmp/iaQXJX5nkE/norm.split.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/norm.fa -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m+ /tmp/iaQXJX5nkE/norm.merge.vcf.gz .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m+ /tmp/iaQXJX5nkE/norm.merge.vcf.gz -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m+ /tmp/iaQXJX5nkE/norm.merge.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m+ /tmp/iaQXJX5nkE/norm.merge.2.vcf.gz -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m+ /tmp/iaQXJX5nkE/norm.merge.3.vcf.gz .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m+ /tmp/iaQXJX5nkE/norm.merge.3.vcf.gz -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m+ -s /tmp/iaQXJX5nkE/norm.merge.vcf.gz .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m+ -s /tmp/iaQXJX5nkE/norm.merge.vcf.gz -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -N -c s /tmp/iaQXJX5nkE/norm.setref.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/norm.fa .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -N -c s /tmp/iaQXJX5nkE/norm.setref.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/norm.fa -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version /tmp/iaQXJX5nkE/norm.telomere.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/norm.fa .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version /tmp/iaQXJX5nkE/norm.telomere.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/norm.fa -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -d snps /tmp/iaQXJX5nkE/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -d snps /tmp/iaQXJX5nkE/norm.rmdup.vcf.gz -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -d indels /tmp/iaQXJX5nkE/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -d indels /tmp/iaQXJX5nkE/norm.rmdup.vcf.gz -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -d both /tmp/iaQXJX5nkE/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -d both /tmp/iaQXJX5nkE/norm.rmdup.vcf.gz -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -d all /tmp/iaQXJX5nkE/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -d all /tmp/iaQXJX5nkE/norm.rmdup.vcf.gz -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -d none /tmp/iaQXJX5nkE/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -d none /tmp/iaQXJX5nkE/norm.rmdup.vcf.gz -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -d exact /tmp/iaQXJX5nkE/norm.rmdup.vcf.gz .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -d exact /tmp/iaQXJX5nkE/norm.rmdup.vcf.gz -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -d none /tmp/iaQXJX5nkE/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -d none /tmp/iaQXJX5nkE/norm.rmdup.2.vcf.gz -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -d exact /tmp/iaQXJX5nkE/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -d exact /tmp/iaQXJX5nkE/norm.rmdup.2.vcf.gz -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -d indels /tmp/iaQXJX5nkE/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -d indels /tmp/iaQXJX5nkE/norm.rmdup.2.vcf.gz -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -d any /tmp/iaQXJX5nkE/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -d any /tmp/iaQXJX5nkE/norm.rmdup.2.vcf.gz -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -d both /tmp/iaQXJX5nkE/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -d both /tmp/iaQXJX5nkE/norm.rmdup.2.vcf.gz -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -d snps /tmp/iaQXJX5nkE/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -d snps /tmp/iaQXJX5nkE/norm.rmdup.2.vcf.gz -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -d exact /tmp/iaQXJX5nkE/norm.rmdup.3.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/norm.rmdup.3.fa .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -d exact /tmp/iaQXJX5nkE/norm.rmdup.3.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/norm.rmdup.3.fa -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -d all /tmp/iaQXJX5nkE/norm.rmdup.3.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/norm.rmdup.3.fa .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -d all /tmp/iaQXJX5nkE/norm.rmdup.3.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/norm.rmdup.3.fa -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -c s -a --old-rec-tag XX /tmp/iaQXJX5nkE/norm.2.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/norm.2.fa .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -c s -a --old-rec-tag XX /tmp/iaQXJX5nkE/norm.2.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/norm.2.fa -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -c s --old-rec-tag XX /tmp/iaQXJX5nkE/norm.iupac.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/norm.iupac.fa .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -c s --old-rec-tag XX /tmp/iaQXJX5nkE/norm.iupac.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/norm.iupac.fa -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -c s --old-rec-tag XX /tmp/iaQXJX5nkE/norm.iupac.2.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/norm.iupac.2.fa .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -c s --old-rec-tag XX /tmp/iaQXJX5nkE/norm.iupac.2.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/norm.iupac.2.fa -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -c s --old-rec-tag XX /tmp/iaQXJX5nkE/norm.3.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/norm.3.fa .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -c s --old-rec-tag XX /tmp/iaQXJX5nkE/norm.3.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/norm.3.fa -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -c s -i'alt="N"' --old-rec-tag XX /tmp/iaQXJX5nkE/norm.3.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/norm.3.fa .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -c s -i'alt="N"' --old-rec-tag XX /tmp/iaQXJX5nkE/norm.3.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/norm.3.fa -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -a --old-rec-tag OLD_REC /tmp/iaQXJX5nkE/atomize.split.1.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m -any --force .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -a --old-rec-tag OLD_REC /tmp/iaQXJX5nkE/atomize.split.1.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m -any --force -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m -any --old-rec-tag OLD_REC --force /tmp/iaQXJX5nkE/atomize.split.1.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -a .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m -any --old-rec-tag OLD_REC --force /tmp/iaQXJX5nkE/atomize.split.1.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -a -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m -any --old-rec-tag OLD_REC --force -a /tmp/iaQXJX5nkE/atomize.split.1.vcf.gz .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m -any --old-rec-tag OLD_REC --force -a /tmp/iaQXJX5nkE/atomize.split.1.vcf.gz -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/iaQXJX5nkE/atomize.split.1.vcf.gz .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/iaQXJX5nkE/atomize.split.1.vcf.gz -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/iaQXJX5nkE/atomize.split.1.vcf.gz .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/iaQXJX5nkE/atomize.split.1.vcf.gz -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/iaQXJX5nkE/atomize.split.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/iaQXJX5nkE/atomize.split.2.vcf.gz -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/iaQXJX5nkE/atomize.split.2.vcf.gz .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/iaQXJX5nkE/atomize.split.2.vcf.gz -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version --atomize --atom-overlaps . /tmp/iaQXJX5nkE/atomize.split.3.vcf.gz .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version --atomize --atom-overlaps . /tmp/iaQXJX5nkE/atomize.split.3.vcf.gz -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/iaQXJX5nkE/atomize.split.4.vcf.gz .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/iaQXJX5nkE/atomize.split.4.vcf.gz -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC -i 'ILEN=0' /tmp/iaQXJX5nkE/atomize.split.4.vcf.gz .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC -i 'ILEN=0' /tmp/iaQXJX5nkE/atomize.split.4.vcf.gz -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version --atomize --old-rec-tag OLD_REC --atom-overlaps . /tmp/iaQXJX5nkE/atomize.split.5.vcf.gz .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version --atomize --old-rec-tag OLD_REC --atom-overlaps . /tmp/iaQXJX5nkE/atomize.split.5.vcf.gz -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/iaQXJX5nkE/atomize.split.5.vcf.gz .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/iaQXJX5nkE/atomize.split.5.vcf.gz -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m +both /tmp/iaQXJX5nkE/norm.4.vcf.gz .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m +both /tmp/iaQXJX5nkE/norm.4.vcf.gz -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m +any /tmp/iaQXJX5nkE/norm.4.vcf.gz .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m +any /tmp/iaQXJX5nkE/norm.4.vcf.gz -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m - --multi-overlaps 0 /tmp/iaQXJX5nkE/norm.5.vcf.gz .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m - --multi-overlaps 0 /tmp/iaQXJX5nkE/norm.5.vcf.gz -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m - --multi-overlaps . /tmp/iaQXJX5nkE/norm.5.vcf.gz .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m - --multi-overlaps . /tmp/iaQXJX5nkE/norm.5.vcf.gz -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m -any /tmp/iaQXJX5nkE/norm.m-any.vcf.gz .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m -any /tmp/iaQXJX5nkE/norm.m-any.vcf.gz -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m -any /tmp/iaQXJX5nkE/norm.phased-split.vcf.gz .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m -any /tmp/iaQXJX5nkE/norm.phased-split.vcf.gz -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m +any /tmp/iaQXJX5nkE/norm.phased-join.vcf.gz .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m +any /tmp/iaQXJX5nkE/norm.phased-join.vcf.gz -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version --old-rec-tag ORI /tmp/iaQXJX5nkE/norm.symbolic.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/norm.symbolic.fa .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version --old-rec-tag ORI /tmp/iaQXJX5nkE/norm.symbolic.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/norm.symbolic.fa -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version --old-rec-tag ORI /tmp/iaQXJX5nkE/norm.symbolic.2.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/norm.symbolic.fa .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version --old-rec-tag ORI /tmp/iaQXJX5nkE/norm.symbolic.2.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/norm.symbolic.fa -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version --old-rec-tag ORI /tmp/iaQXJX5nkE/norm.right-align.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/norm.right-align.fa .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version --old-rec-tag ORI /tmp/iaQXJX5nkE/norm.right-align.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/norm.right-align.fa -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version --old-rec-tag ORI -g /build/bcftools-qI88Pr/bcftools-1.24/test/norm.right-align.gff /tmp/iaQXJX5nkE/norm.right-align.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/norm.right-align.fa .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version --old-rec-tag ORI -g /build/bcftools-qI88Pr/bcftools-1.24/test/norm.right-align.gff /tmp/iaQXJX5nkE/norm.right-align.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/norm.right-align.fa -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version --old-rec-tag ORI -a -m -any /tmp/iaQXJX5nkE/norm.atom-split-norm.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/norm.atom-split-norm.fa .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version --old-rec-tag ORI -a -m -any /tmp/iaQXJX5nkE/norm.atom-split-norm.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/norm.atom-split-norm.fa -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m -any /tmp/iaQXJX5nkE/norm.string-tags.vcf.gz .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m -any /tmp/iaQXJX5nkE/norm.string-tags.vcf.gz -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m - /tmp/iaQXJX5nkE/norm.split.merge.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m +both .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m - /tmp/iaQXJX5nkE/norm.split.merge.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m +both -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m - /tmp/iaQXJX5nkE/norm.split.merge.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m +indels .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m - /tmp/iaQXJX5nkE/norm.split.merge.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m +indels -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m - /tmp/iaQXJX5nkE/norm.split.merge.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m +snps .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m - /tmp/iaQXJX5nkE/norm.split.merge.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m +snps -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m - /tmp/iaQXJX5nkE/norm.split.merge.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m +snps .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m - /tmp/iaQXJX5nkE/norm.split.merge.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m +snps -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m - /tmp/iaQXJX5nkE/norm.split.merge.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m +any .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m - /tmp/iaQXJX5nkE/norm.split.merge.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m +any -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m - -i 'type="snp"' /tmp/iaQXJX5nkE/norm.split.merge.vcf.gz .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m - -i 'type="snp"' /tmp/iaQXJX5nkE/norm.split.merge.vcf.gz -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m +any /tmp/iaQXJX5nkE/norm.merge.4.vcf.gz .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m +any /tmp/iaQXJX5nkE/norm.merge.4.vcf.gz -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m +both /tmp/iaQXJX5nkE/norm.merge.4.vcf.gz .. ok test_vcf_norm: /build/bcftools-qI88Pr/bcftools-1.24/bcftools norm --no-version -m +both /tmp/iaQXJX5nkE/norm.merge.4.vcf.gz -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -Hv ref /tmp/iaQXJX5nkE/view.types.vcf.gz .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -Hv snps /tmp/iaQXJX5nkE/view.types.vcf.gz .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -Hv mnps /tmp/iaQXJX5nkE/view.types.vcf.gz .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -Hv indels /tmp/iaQXJX5nkE/view.types.vcf.gz .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -Hv other /tmp/iaQXJX5nkE/view.types.vcf.gz .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -Hv bnd /tmp/iaQXJX5nkE/view.types.vcf.gz .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -Hv overlap /tmp/iaQXJX5nkE/view.types.vcf.gz .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -Hi 'MAC>=2' /tmp/iaQXJX5nkE/filter.mac.vcf.gz .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -Hi 'MAF>=0.09' /tmp/iaQXJX5nkE/filter.mac.vcf.gz .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -Hi 'MAF*AN>=2' /tmp/iaQXJX5nkE/filter.mac.vcf.gz .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -i 'INFO/TAG=@/build/bcftools-qI88Pr/bcftools-1.24/test/filter.string.1.txt' /tmp/iaQXJX5nkE/filter.string.1.vcf.gz .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob -i 'INFO/TAG=@/build/bcftools-qI88Pr/bcftools-1.24/test/filter.string.1.txt' /tmp/iaQXJX5nkE/filter.string.1.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -i 'FMT/TAG=@/build/bcftools-qI88Pr/bcftools-1.24/test/filter.string.1.txt' /tmp/iaQXJX5nkE/filter.string.1.vcf.gz .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob -i 'FMT/TAG=@/build/bcftools-qI88Pr/bcftools-1.24/test/filter.string.1.txt' /tmp/iaQXJX5nkE/filter.string.1.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -HA /tmp/iaQXJX5nkE/merge.gvcf.2.a.vcf.gz .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -HAA /tmp/iaQXJX5nkE/merge.gvcf.2.a.vcf.gz .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version /tmp/iaQXJX5nkE/weird-chr-names.vcf.gz -r 1 .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/weird-chr-names.vcf.gz -r 1 | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version /tmp/iaQXJX5nkE/weird-chr-names.vcf.gz -r 1:1-2 .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/weird-chr-names.vcf.gz -r 1:1-2 | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version /tmp/iaQXJX5nkE/weird-chr-names.vcf.gz -r 1:1,1:2 .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/weird-chr-names.vcf.gz -r 1:1,1:2 | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version /tmp/iaQXJX5nkE/weird-chr-names.vcf.gz -r 1:1-1 .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/weird-chr-names.vcf.gz -r 1:1-1 | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version /tmp/iaQXJX5nkE/weird-chr-names.vcf.gz -r {1:1} .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/weird-chr-names.vcf.gz -r {1:1} | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version /tmp/iaQXJX5nkE/weird-chr-names.vcf.gz -r {1:1}:1-2 .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/weird-chr-names.vcf.gz -r {1:1}:1-2 | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version /tmp/iaQXJX5nkE/weird-chr-names.vcf.gz -r {1:1}:1,{1:1}:2 .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/weird-chr-names.vcf.gz -r {1:1}:1,{1:1}:2 | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version /tmp/iaQXJX5nkE/weird-chr-names.vcf.gz -r {1:1}:1-1 .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/weird-chr-names.vcf.gz -r {1:1}:1-1 | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version /tmp/iaQXJX5nkE/weird-chr-names.vcf.gz -r {1:1-1} .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/weird-chr-names.vcf.gz -r {1:1-1} | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version /tmp/iaQXJX5nkE/weird-chr-names.vcf.gz -r {1:1-1}:1-2 .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/weird-chr-names.vcf.gz -r {1:1-1}:1-2 | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version /tmp/iaQXJX5nkE/weird-chr-names.vcf.gz -r {1:1-1}:1,{1:1-1}:2 .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/weird-chr-names.vcf.gz -r {1:1-1}:1,{1:1-1}:2 | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version /tmp/iaQXJX5nkE/weird-chr-names.vcf.gz -r {1:1-1}:1-1 .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/weird-chr-names.vcf.gz -r {1:1-1}:1-1 | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version /tmp/iaQXJX5nkE/weird-chr-names.vcf.gz -r {1:1-1}-2 .. ok, expected non-zero status test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/weird-chr-names.vcf.gz -r {1:1-1}-2 | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok, expected non-zero status test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -aUc1 -C1 -s NA00002 -v snps /tmp/iaQXJX5nkE/view.vcf.gz .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/iaQXJX5nkE/view.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -f PASS -Xks NA00003 /tmp/iaQXJX5nkE/view.vcf.gz -r20,Y .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob -f PASS -Xks NA00003 /tmp/iaQXJX5nkE/view.vcf.gz -r20,Y | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -xs NA00003 /tmp/iaQXJX5nkE/view.vcf.gz .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob -xs NA00003 /tmp/iaQXJX5nkE/view.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/iaQXJX5nkE/view.vcf.gz .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/iaQXJX5nkE/view.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -p /tmp/iaQXJX5nkE/view.vcf.gz .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob -p /tmp/iaQXJX5nkE/view.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -P /tmp/iaQXJX5nkE/view.vcf.gz .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob -P /tmp/iaQXJX5nkE/view.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -hm2 -M2 -q0.3 -Q0.7 /tmp/iaQXJX5nkE/view.vcf.gz .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/iaQXJX5nkE/view.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -Hu /tmp/iaQXJX5nkE/view.vcf.gz .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -GVsnps /tmp/iaQXJX5nkE/view.vcf.gz .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob -GVsnps /tmp/iaQXJX5nkE/view.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -ne 'INDEL=1 || PV4[0]<0.006' /tmp/iaQXJX5nkE/view.vcf.gz .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/iaQXJX5nkE/view.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -s ^NA00003 /tmp/iaQXJX5nkE/view.vcf.gz .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob -s ^NA00003 /tmp/iaQXJX5nkE/view.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version /tmp/iaQXJX5nkE/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/view.omitgenotypes.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -G /tmp/iaQXJX5nkE/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob -G /tmp/iaQXJX5nkE/view.omitgenotypes.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -HG /tmp/iaQXJX5nkE/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -a /tmp/iaQXJX5nkE/many.alleles.vcf.gz .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob -a /tmp/iaQXJX5nkE/many.alleles.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -asA /tmp/iaQXJX5nkE/view.vectors.vcf.gz .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob -asA /tmp/iaQXJX5nkE/view.vectors.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -asB /tmp/iaQXJX5nkE/view.vectors.vcf.gz .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob -asB /tmp/iaQXJX5nkE/view.vectors.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -asA /tmp/iaQXJX5nkE/view.vectors.2.vcf.gz .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob -asA /tmp/iaQXJX5nkE/view.vectors.2.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -H -i'FMT/FGS[*:0]="AAAAAA"' /tmp/iaQXJX5nkE/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -H -i'FMT/FGS[*:2]="C"' /tmp/iaQXJX5nkE/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -H -i'FMT/FGS[*:4]="EE"' /tmp/iaQXJX5nkE/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -H -i'FMT/FRS[*:1]="BB"' /tmp/iaQXJX5nkE/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -H -i'TXT0="text"' /tmp/iaQXJX5nkE/view.filter.vcf.gz .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -T /build/bcftools-qI88Pr/bcftools-1.24/test/view.chrs.tab /tmp/iaQXJX5nkE/view.chrs.vcf.gz .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob -T /build/bcftools-qI88Pr/bcftools-1.24/test/view.chrs.tab /tmp/iaQXJX5nkE/view.chrs.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -i 'POS>=3062917' /tmp/iaQXJX5nkE/filter.2.vcf.gz 1:3062917-3157410 .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob -i 'POS>=3062917' /tmp/iaQXJX5nkE/filter.2.vcf.gz 1:3062917-3157410 | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -H -r 1:10,1:12,1:10 /tmp/iaQXJX5nkE/idx.1.vcf.gz .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -H -r 1:1172777-1172804,1:1172806-1172808 /tmp/iaQXJX5nkE/idx.2.vcf.gz .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -H -R /build/bcftools-qI88Pr/bcftools-1.24/test/idx.2.bed /tmp/iaQXJX5nkE/idx.2.vcf.gz .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -H -R /build/bcftools-qI88Pr/bcftools-1.24/test/idx.3.bed /tmp/iaQXJX5nkE/idx.3.vcf.gz .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -H -R /build/bcftools-qI88Pr/bcftools-1.24/test/idx.4.bed /tmp/iaQXJX5nkE/idx.4.vcf.gz .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -Ht 2 /tmp/iaQXJX5nkE/view-t.vcf.gz .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -Ht 3 /tmp/iaQXJX5nkE/view-t.vcf.gz .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 0 /tmp/iaQXJX5nkE/overlap.vcf.gz .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 1 /tmp/iaQXJX5nkE/overlap.vcf.gz .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 2 /tmp/iaQXJX5nkE/overlap.vcf.gz .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 0 /tmp/iaQXJX5nkE/overlap.vcf.gz .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 1 /tmp/iaQXJX5nkE/overlap.vcf.gz .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 2 /tmp/iaQXJX5nkE/overlap.vcf.gz .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 0 /tmp/iaQXJX5nkE/overlap.vcf.gz .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 1 /tmp/iaQXJX5nkE/overlap.vcf.gz .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 2 /tmp/iaQXJX5nkE/overlap.vcf.gz .. ok test_vcf_64bit: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view /build/bcftools-qI88Pr/bcftools-1.24/test/view64bit.1.vcf -H .. ok test_vcf_64bit: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view /build/bcftools-qI88Pr/bcftools-1.24/test/view64bit.1.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view /build/bcftools-qI88Pr/bcftools-1.24/test/view64bit.1.vcf -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view /build/bcftools-qI88Pr/bcftools-1.24/test/view64bit.2.vcf -H .. ok test_vcf_64bit: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view /build/bcftools-qI88Pr/bcftools-1.24/test/view64bit.2.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view /build/bcftools-qI88Pr/bcftools-1.24/test/view64bit.2.vcf -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view /build/bcftools-qI88Pr/bcftools-1.24/test/view64bit.3.vcf -H .. ok test_vcf_64bit: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view /build/bcftools-qI88Pr/bcftools-1.24/test/view64bit.3.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view /build/bcftools-qI88Pr/bcftools-1.24/test/view64bit.4.vcf -H .. ok test_vcf_64bit: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view /build/bcftools-qI88Pr/bcftools-1.24/test/view64bit.4.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view /build/bcftools-qI88Pr/bcftools-1.24/test/view64bit.4.vcf -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view /build/bcftools-qI88Pr/bcftools-1.24/test/view64bit.5.vcf -H .. ok test_vcf_64bit: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view /build/bcftools-qI88Pr/bcftools-1.24/test/view64bit.5.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -H .. ok test_vcf_64bit: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view /build/bcftools-qI88Pr/bcftools-1.24/test/view64bit.5.vcf -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -H .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -H -C5:nonmajor /tmp/iaQXJX5nkE/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -H -c6:nonmajor /tmp/iaQXJX5nkE/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -H -q0.3:major /tmp/iaQXJX5nkE/view.minmaxac.vcf.gz .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/iaQXJX5nkE/view.filter.annovar.vcf.gz .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -H -i 'Gene.refGene~"NOD"' /tmp/iaQXJX5nkE/view.filter.annovar.vcf.gz .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -H -i 'LJB2_MutationTaster=="0.291000"' /tmp/iaQXJX5nkE/view.filter.annovar.vcf.gz .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -H -a /tmp/iaQXJX5nkE/view-a.vcf.gz .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -T /build/bcftools-qI88Pr/bcftools-1.24/test/view.sites.txt /tmp/iaQXJX5nkE/view.sites.vcf.gz .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob -T /build/bcftools-qI88Pr/bcftools-1.24/test/view.sites.txt /tmp/iaQXJX5nkE/view.sites.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -T /build/bcftools-qI88Pr/bcftools-1.24/test/view.sites.txt.gz /tmp/iaQXJX5nkE/view.sites.vcf.gz .. ok test_vcf_view: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob -T /build/bcftools-qI88Pr/bcftools-1.24/test/view.sites.txt.gz /tmp/iaQXJX5nkE/view.sites.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_head: /build/bcftools-qI88Pr/bcftools-1.24/bcftools head /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.2.vcf .. ok test_vcf_head: /build/bcftools-qI88Pr/bcftools-1.24/bcftools head -h 0 /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.2.vcf .. ok test_vcf_head: /build/bcftools-qI88Pr/bcftools-1.24/bcftools head -h 1 /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.2.vcf .. ok test_vcf_head: /build/bcftools-qI88Pr/bcftools-1.24/bcftools head -h 5 /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.2.vcf .. ok test_vcf_head: /build/bcftools-qI88Pr/bcftools-1.24/bcftools head -h 22 /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.2.vcf .. ok test_vcf_head: /build/bcftools-qI88Pr/bcftools-1.24/bcftools head -h 23 /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.2.vcf .. ok test_vcf_head: /build/bcftools-qI88Pr/bcftools-1.24/bcftools head -n 0 /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.2.vcf .. ok test_vcf_head: /build/bcftools-qI88Pr/bcftools-1.24/bcftools head -n 1 /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.2.vcf .. ok test_vcf_head: /build/bcftools-qI88Pr/bcftools-1.24/bcftools head -n 5 /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.2.vcf .. ok test_vcf_head: /build/bcftools-qI88Pr/bcftools-1.24/bcftools head -h 5 -n 5 < /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.2.vcf .. ok test_vcf_head2: /build/bcftools-qI88Pr/bcftools-1.24/bcftools head -s0 /tmp/iaQXJX5nkE/mpileup.2.vcf.gz .. ok test_vcf_head2: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -Ob /tmp/iaQXJX5nkE/mpileup.2.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools head -s0 .. ok test_vcf_head2: /build/bcftools-qI88Pr/bcftools-1.24/bcftools head -s1 /tmp/iaQXJX5nkE/mpileup.2.vcf.gz .. ok test_vcf_head2: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -Ob /tmp/iaQXJX5nkE/mpileup.2.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools head -s1 .. ok test_vcf_head2: /build/bcftools-qI88Pr/bcftools-1.24/bcftools head -s2 -h2 /tmp/iaQXJX5nkE/mpileup.2.vcf.gz .. ok test_vcf_head2: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version -Ob /tmp/iaQXJX5nkE/mpileup.2.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools head -s2 -h2 .. ok test_vcf_call: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call --no-version -m -s sample1 /build/bcftools-qI88Pr/bcftools-1.24/test/samples.vcf .. ok test_vcf_call: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call -Ob -m -s sample1 /build/bcftools-qI88Pr/bcftools-1.24/test/samples.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call --no-version -m -s ^sample2,sample3 /build/bcftools-qI88Pr/bcftools-1.24/test/samples.vcf .. ok test_vcf_call: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call -Ob -m -s ^sample2,sample3 /build/bcftools-qI88Pr/bcftools-1.24/test/samples.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call --no-version -m -s sample3 /build/bcftools-qI88Pr/bcftools-1.24/test/samples.vcf .. ok test_vcf_call: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call -Ob -m -s sample3 /build/bcftools-qI88Pr/bcftools-1.24/test/samples.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call --no-version -m -s ^sample1,sample2 /build/bcftools-qI88Pr/bcftools-1.24/test/samples.vcf .. ok test_vcf_call: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call -Ob -m -s ^sample1,sample2 /build/bcftools-qI88Pr/bcftools-1.24/test/samples.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call --no-version -m --ploidy-file /build/bcftools-qI88Pr/bcftools-1.24/test/call-ploidy.1.txt -S /build/bcftools-qI88Pr/bcftools-1.24/test/call-ploidy.1.ped /build/bcftools-qI88Pr/bcftools-1.24/test/call-ploidy.1.vcf .. ok test_vcf_call: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call -Ob -m --ploidy-file /build/bcftools-qI88Pr/bcftools-1.24/test/call-ploidy.1.txt -S /build/bcftools-qI88Pr/bcftools-1.24/test/call-ploidy.1.ped /build/bcftools-qI88Pr/bcftools-1.24/test/call-ploidy.1.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call --no-version -mv /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.vcf .. ok test_vcf_call: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call -Ob -mv /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call --no-version -mg0 /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.vcf .. ok test_vcf_call: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call -Ob -mg0 /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call --no-version -mv -S /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.3.samples /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.vcf .. ok test_vcf_call: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call -Ob -mv -S /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.3.samples /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call --no-version -mv -S /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.4.samples /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.vcf .. ok test_vcf_call: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call -Ob -mv -S /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.4.samples /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call --no-version -mv -S /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.5.samples /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.vcf .. ok test_vcf_call: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call -Ob -mv -S /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.5.samples /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call --no-version -mv --ploidy-file /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.ploidy -S /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.samples /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.X.vcf .. ok test_vcf_call: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call -Ob -mv --ploidy-file /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.ploidy -S /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.samples /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.X.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call --no-version -mv --ploidy-file /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.ploidy -S /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.ped /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.X.vcf .. ok test_vcf_call: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call -Ob -mv --ploidy-file /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.ploidy -S /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.ped /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.X.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call --no-version -mv --ploidy-file /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.ploidy -S /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.2.samples /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.X.vcf .. ok test_vcf_call: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call -Ob -mv --ploidy-file /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.ploidy -S /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.2.samples /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.X.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call --no-version -mv /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.NA19213.NA19129.vcf .. ok test_vcf_call: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call -Ob -mv /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.NA19213.NA19129.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call --no-version -mv -G - --group-samples-tag AD /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.NA19213.NA19129.vcf .. ok test_vcf_call: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call -Ob -mv -G - --group-samples-tag AD /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.NA19213.NA19129.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call --no-version -mv /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.hwe.vcf .. ok test_vcf_call: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call -Ob -mv /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.hwe.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call --no-version -mv -G - --group-samples-tag AD /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.hwe.vcf .. ok test_vcf_call: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call -Ob -mv -G - --group-samples-tag AD /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.hwe.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call --no-version -mv -G /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.hwe.samples --group-samples-tag AD /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.hwe.vcf .. ok test_vcf_call: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call -Ob -mv -G /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.hwe.samples --group-samples-tag AD /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.hwe.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call --no-version -mA -C alleles -T /tmp/iaQXJX5nkE/mpileup.tab.gz /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.vcf .. ok test_vcf_call_cAls: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call -Ob -mA -C alleles -T /tmp/iaQXJX5nkE/mpileup.tab.gz /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call --no-version -mA -C alleles -T /tmp/iaQXJX5nkE/mpileup.2.tab.gz /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.2.vcf .. ok test_vcf_call_cAls: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call -Ob -mA -C alleles -T /tmp/iaQXJX5nkE/mpileup.2.tab.gz /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.2.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call --no-version -mA -C alleles -T /tmp/iaQXJX5nkE/mpileup.3.tab.gz -i /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call -Ob -mA -C alleles -T /tmp/iaQXJX5nkE/mpileup.3.tab.gz -i /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.3.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call --no-version -mA -C alleles -T /tmp/iaQXJX5nkE/mpileup.4.tab.gz -i /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call -Ob -mA -C alleles -T /tmp/iaQXJX5nkE/mpileup.4.tab.gz -i /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.3.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call --no-version -mA -C alleles -T /tmp/iaQXJX5nkE/mpileup.5.tab.gz -i /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call -Ob -mA -C alleles -T /tmp/iaQXJX5nkE/mpileup.5.tab.gz -i /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.3.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call --no-version -mA -C alleles -T /tmp/iaQXJX5nkE/mpileup.6.tab.gz -i /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.4.vcf .. ok test_vcf_call_cAls: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call -Ob -mA -C alleles -T /tmp/iaQXJX5nkE/mpileup.6.tab.gz -i /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.4.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call --no-version -mA -C alleles -T /tmp/iaQXJX5nkE/mpileup.7.tab.gz -i /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.5.vcf .. ok test_vcf_call_cAls: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call -Ob -mA -C alleles -T /tmp/iaQXJX5nkE/mpileup.7.tab.gz -i /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.5.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call --no-version -mA -C alleles -T /tmp/iaQXJX5nkE/mpileup.cals.1.tab.gz /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.cals.1.vcf .. ok test_vcf_call_cAls: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call -Ob -mA -C alleles -T /tmp/iaQXJX5nkE/mpileup.cals.1.tab.gz /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.cals.1.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call --no-version -mA -C alleles -T /tmp/iaQXJX5nkE/mpileup.cals.2.tab.gz /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.cals.2.vcf .. ok test_vcf_call_cAls: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call -Ob -mA -C alleles -T /tmp/iaQXJX5nkE/mpileup.cals.2.tab.gz /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.cals.2.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call --no-version -cv /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.c.vcf .. ok test_vcf_call: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call -Ob -cv /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.c.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call --no-version -cv --ploidy-file /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.ploidy -S /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.samples /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.c.X.vcf .. ok test_vcf_call: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call -Ob -cv --ploidy-file /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.ploidy -S /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.samples /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.c.X.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call --no-version -cv --ploidy-file /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.ploidy -S /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.ped /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.c.X.vcf .. ok test_vcf_call: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call -Ob -cv --ploidy-file /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.ploidy -S /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.ped /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.c.X.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call --no-version -cv --ploidy-file /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.ploidy -S /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.2.samples /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.c.X.vcf .. ok test_vcf_call: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call -Ob -cv --ploidy-file /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.ploidy -S /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.2.samples /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup.c.X.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call --no-version -mv /build/bcftools-qI88Pr/bcftools-1.24/test/call-G.vcf .. ok test_vcf_call: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call -Ob -mv /build/bcftools-qI88Pr/bcftools-1.24/test/call-G.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call --no-version -mv -G - --group-samples-tag AD /build/bcftools-qI88Pr/bcftools-1.24/test/call-G.vcf .. ok test_vcf_call: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call -Ob -mv -G - --group-samples-tag AD /build/bcftools-qI88Pr/bcftools-1.24/test/call-G.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call --no-version -mv -F AN_POP,AC_POP /build/bcftools-qI88Pr/bcftools-1.24/test/call-G.2.vcf .. ok test_vcf_call: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call -Ob -mv -F AN_POP,AC_POP /build/bcftools-qI88Pr/bcftools-1.24/test/call-G.2.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call --no-version -m /build/bcftools-qI88Pr/bcftools-1.24/test/call.af-fixation.vcf .. ok test_vcf_call: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call -Ob -m /build/bcftools-qI88Pr/bcftools-1.24/test/call.af-fixation.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call --no-version -m -G /build/bcftools-qI88Pr/bcftools-1.24/test/call.af-fixation.txt /build/bcftools-qI88Pr/bcftools-1.24/test/call.af-fixation.vcf .. ok test_vcf_call: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call -Ob -m -G /build/bcftools-qI88Pr/bcftools-1.24/test/call.af-fixation.txt /build/bcftools-qI88Pr/bcftools-1.24/test/call.af-fixation.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call --no-version -m -G /build/bcftools-qI88Pr/bcftools-1.24/test/call.af-fixation.txt -a GP,GQ /build/bcftools-qI88Pr/bcftools-1.24/test/call.af-fixation.vcf .. ok test_vcf_call: /build/bcftools-qI88Pr/bcftools-1.24/bcftools call -Ob -m -G /build/bcftools-qI88Pr/bcftools-1.24/test/call.af-fixation.txt -a GP,GQ /build/bcftools-qI88Pr/bcftools-1.24/test/call.af-fixation.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -S. -e'TXT0="text"' /build/bcftools-qI88Pr/bcftools-1.24/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -S. -e'TXT0="text"' /build/bcftools-qI88Pr/bcftools-1.24/test/view.filter.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -S. -e'FMT/FRS[*:1]="BB"' /build/bcftools-qI88Pr/bcftools-1.24/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -S. -e'FMT/FRS[*:1]="BB"' /build/bcftools-qI88Pr/bcftools-1.24/test/view.filter.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -S. -e'FMT/FGS[*:0]="AAAAAA"' /build/bcftools-qI88Pr/bcftools-1.24/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -S. -e'FMT/FGS[*:0]="AAAAAA"' /build/bcftools-qI88Pr/bcftools-1.24/test/view.filter.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -S. -e'FMT/FGS[*:1]="BBB"' /build/bcftools-qI88Pr/bcftools-1.24/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -S. -e'FMT/FGS[*:1]="BBB"' /build/bcftools-qI88Pr/bcftools-1.24/test/view.filter.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -S. -e'FMT/FGS[*:4]="EE"' /build/bcftools-qI88Pr/bcftools-1.24/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -S. -e'FMT/FGS[*:4]="EE"' /build/bcftools-qI88Pr/bcftools-1.24/test/view.filter.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -S. -e'FMT/STR="XX"' /build/bcftools-qI88Pr/bcftools-1.24/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -S. -e'FMT/STR="XX"' /build/bcftools-qI88Pr/bcftools-1.24/test/view.filter.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -S. -e'FMT/FILTER="aaa"' /build/bcftools-qI88Pr/bcftools-1.24/test/view.filter.2.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -S. -e'FMT/FILTER="aaa"' /build/bcftools-qI88Pr/bcftools-1.24/test/view.filter.2.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -mx -g2 -G2 /build/bcftools-qI88Pr/bcftools-1.24/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -mx -g2 -G2 /build/bcftools-qI88Pr/bcftools-1.24/test/filter.1.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /build/bcftools-qI88Pr/bcftools-1.24/test/filter.2.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /build/bcftools-qI88Pr/bcftools-1.24/test/filter.2.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -e'INFO/DP=19' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.3.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -e'INFO/DP=19' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.3.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -e'INFO/DP=19' -s XX /build/bcftools-qI88Pr/bcftools-1.24/test/filter.3.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -e'INFO/DP=19' -s XX /build/bcftools-qI88Pr/bcftools-1.24/test/filter.3.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -e'INFO/DP=19' -s XX -m+ /build/bcftools-qI88Pr/bcftools-1.24/test/filter.3.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+ /build/bcftools-qI88Pr/bcftools-1.24/test/filter.3.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -e'INFO/DP=19' -s XX -mx /build/bcftools-qI88Pr/bcftools-1.24/test/filter.3.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -e'INFO/DP=19' -s XX -mx /build/bcftools-qI88Pr/bcftools-1.24/test/filter.3.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -e'INFO/DP=19' -s XX -m+x /build/bcftools-qI88Pr/bcftools-1.24/test/filter.3.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+x /build/bcftools-qI88Pr/bcftools-1.24/test/filter.3.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -e'FMT/GT="0/2"' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.3.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -e'FMT/GT="0/2"' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.3.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -e'FMT/GT="0/2"' -s XX /build/bcftools-qI88Pr/bcftools-1.24/test/filter.3.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX /build/bcftools-qI88Pr/bcftools-1.24/test/filter.3.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -e'FMT/GT="0/2"' -s XX -m+ /build/bcftools-qI88Pr/bcftools-1.24/test/filter.3.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+ /build/bcftools-qI88Pr/bcftools-1.24/test/filter.3.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -e'FMT/GT="0/2"' -s XX -mx /build/bcftools-qI88Pr/bcftools-1.24/test/filter.3.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -mx /build/bcftools-qI88Pr/bcftools-1.24/test/filter.3.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -e'FMT/GT="0/2"' -s XX -m+x /build/bcftools-qI88Pr/bcftools-1.24/test/filter.3.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+x /build/bcftools-qI88Pr/bcftools-1.24/test/filter.3.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -i'FMT/GT="0/0" && AC[*]=2' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.2.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -i'FMT/GT="0/0" && AC[*]=2' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.2.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -i'AC[*]=2 && FMT/GT="0/0"' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.2.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -i'AC[*]=2 && FMT/GT="0/0"' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.2.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -i'ALT="."' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.2.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -i'ALT="."' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.2.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -S . -i 'FORMAT/TEST3<25' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.4.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -S . -i 'FORMAT/TEST3<25' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.4.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -S . -i 'FORMAT/TEST4<25' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.4.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -S . -i 'FORMAT/TEST4<25' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.4.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -i'GT="A"' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.2.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -i'GT="A"' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.2.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -i'GT="RR"' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.2.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -i'GT="RR"' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.2.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -i'GT="RA"' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.2.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -i'GT="RA"' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.2.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -i'GT="AR"' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.2.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -i'GT="AR"' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.2.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -i'GT="AA"' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.2.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -i'GT="AA"' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.2.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -i'GT="aA"' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.2.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -i'GT="aA"' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.2.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -i'GT="Aa"' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.2.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -i'GT="Aa"' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.2.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -i'GT="HOM"' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.2.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -i'GT="HOM"' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.2.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -i'GT="HET"' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.2.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -i'GT="HET"' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.2.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -i'GT="HAP"' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.2.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -i'GT="HAP"' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.2.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -i'AD[:1]=11' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.5.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -i'AD[:1]=11' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.5.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -i'AD[1:]=11' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.5.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -i'AD[1:]=11' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.5.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -i'FR[0:1]=11' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.5.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS[\t%FR]\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -i'FR[0:1]=11' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.5.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS[\t%FR]\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -i'AD[*]="."' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.5.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -i'AD[*]="."' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.5.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -i'AD[0:0]=="."' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.5.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -i'AD[0:0]=="."' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.5.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -i'AD[0:0]!="."' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.5.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -i'AD[0:0]!="."' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.5.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -i'QUAL=="."' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.5.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS\t%QUAL\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -i'QUAL=="."' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.5.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS\t%QUAL\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -i'N_PASS(DP>32)=1' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.2.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -i'N_PASS(DP>32)=1' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.2.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -i'F_PASS(DP>32)=0.5' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.2.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -i'F_PASS(DP>32)=0.5' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.2.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -i'F_MISSING>=1/5' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.6.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -i'F_MISSING>=1/5' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.6.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -i'F_MISSING>=0.2' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.6.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -i'F_MISSING>=0.2' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.6.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -i'F_PASS(GT=="mis")>=1/5' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.6.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -i'F_PASS(GT=="mis")>=1/5' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.6.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -i'F_PASS(GT=="mis")>=0.2' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.6.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -i'F_PASS(GT=="mis")>=0.2' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.6.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%POS\n' .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -mx -s + -g2:mnp,indel,other /build/bcftools-qI88Pr/bcftools-1.24/test/filter.7.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -mx -s + -g2:mnp,indel,other /build/bcftools-qI88Pr/bcftools-1.24/test/filter.7.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -S . -e 'FORMAT/AO==4' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -S . -e 'FORMAT/AO==4' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.8.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -S . -e 'MAX(FORMAT/AO[0:])==4' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -S . -e 'MAX(FORMAT/AO[0:])==4' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.8.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -S . -e 'MAX(FORMAT/AO)==4' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -S . -e 'MAX(FORMAT/AO)==4' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.8.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -S . -e 'MIN(FORMAT/AO[0:])==3' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO[0:])==3' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.8.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -S . -e 'MIN(FORMAT/AO)==2' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO)==2' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.8.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -S . -e 'MIN(FORMAT/AO[0:])==3' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO[0:])==3' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.8.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -S . -e 'AVG(FORMAT/AO[2:])==4' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -S . -e 'AVG(FORMAT/AO[2:])==4' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.8.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -S . -e 'MEDIAN(FORMAT/AO[2:])==4' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -S . -e 'MEDIAN(FORMAT/AO[2:])==4' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.8.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -S . -e 'STDEV(FORMAT/AO[0:])=0.5' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -S . -e 'STDEV(FORMAT/AO[0:])=0.5' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.8.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -S . -e 'SUM(FORMAT/AO[0:])=7' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -S . -e 'SUM(FORMAT/AO[0:])=7' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.8.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -S . -e 'SMPL_MAX(FORMAT/AO)==4' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -S . -e 'SMPL_MAX(FORMAT/AO)==4' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.8.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -S . -e 'sMIN(FORMAT/AO)==2' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -S . -e 'sMIN(FORMAT/AO)==2' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.8.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -S . -e 'ABS(sAVG(FORMAT/AO)-3.66666)<1e-5' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -S . -e 'ABS(sAVG(FORMAT/AO)-3.66666)<1e-5' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.8.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -S . -e 'sMEDIAN(FORMAT/AO)==4' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -S . -e 'sMEDIAN(FORMAT/AO)==4' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.8.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -S . -e 'ABS(sSTDEV(FORMAT/AO)-1.2472191)<1e-5' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -S . -e 'ABS(sSTDEV(FORMAT/AO)-1.2472191)<1e-5' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.8.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -S . -e 'sSUM(FORMAT/AO)==11' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -S . -e 'sSUM(FORMAT/AO)==11' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.8.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -i 'QUAL/FMT/AD==55' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.9.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -i 'QUAL/FMT/AD==55' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.9.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -i 'QUAL/INFO/AD==10' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.9.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -i 'QUAL/INFO/AD==10' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.9.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -S . -e 'ABS(SMPL_MAX(FORMAT/AO))=5' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -S . -e 'ABS(SMPL_MAX(FORMAT/AO))=5' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.8.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -S . -e 'PHRED(AO[1:])>-4' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -S . -e 'PHRED(AO[1:])>-4' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.8.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -S . -e 'ABS(AO[1:])==2' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -S . -e 'ABS(AO[1:])==2' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.8.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -i 'sum(AD[*]) > FORMAT/DP' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -i 'sum(AD[*]) > FORMAT/DP' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.10.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -i 'FORMAT/DP < sum(AD[*])' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -i 'FORMAT/DP < sum(AD[*])' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.10.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -i 'sum(AD[*]) < FORMAT/DP' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -i 'sum(AD[*]) < FORMAT/DP' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.10.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -i 'FORMAT/DP > sum(AD[*])' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob -i 'FORMAT/DP > sum(AD[*])' /build/bcftools-qI88Pr/bcftools-1.24/test/filter.10.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 0 /build/bcftools-qI88Pr/bcftools-1.24/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 0 /build/bcftools-qI88Pr/bcftools-1.24/test/filter.1.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 1 /build/bcftools-qI88Pr/bcftools-1.24/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 1 /build/bcftools-qI88Pr/bcftools-1.24/test/filter.1.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 2 /build/bcftools-qI88Pr/bcftools-1.24/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 2 /build/bcftools-qI88Pr/bcftools-1.24/test/filter.1.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter --soft-filter xxx --mask ^2:1005-1008 /build/bcftools-qI88Pr/bcftools-1.24/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /build/bcftools-qI88Pr/bcftools-1.24/bcftools filter -Ob --soft-filter xxx --mask ^2:1005-1008 /build/bcftools-qI88Pr/bcftools-1.24/test/filter.1.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_sort: /build/bcftools-qI88Pr/bcftools-1.24/bcftools sort -m 0 /build/bcftools-qI88Pr/bcftools-1.24/test/sort.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /build/bcftools-qI88Pr/bcftools-1.24/bcftools sort -Ob -m 0 /build/bcftools-qI88Pr/bcftools-1.24/test/sort.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /build/bcftools-qI88Pr/bcftools-1.24/bcftools sort -m 1000 /build/bcftools-qI88Pr/bcftools-1.24/test/sort.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /build/bcftools-qI88Pr/bcftools-1.24/bcftools sort -Ob -m 1000 /build/bcftools-qI88Pr/bcftools-1.24/test/sort.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_regions: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /build/bcftools-qI88Pr/bcftools-1.24/test/regions.tab /tmp/iaQXJX5nkE/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/regions.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /build/bcftools-qI88Pr/bcftools-1.24/test/regions.tab .. ok test_vcf_regions: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /build/bcftools-qI88Pr/bcftools-1.24/test/regions.tab /tmp/iaQXJX5nkE/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/iaQXJX5nkE/regions.tab.gz /tmp/iaQXJX5nkE/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/regions.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/iaQXJX5nkE/regions.tab.gz .. ok test_vcf_regions: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/iaQXJX5nkE/regions.tab.gz /tmp/iaQXJX5nkE/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/iaQXJX5nkE/regions.bed /tmp/iaQXJX5nkE/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/regions.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/iaQXJX5nkE/regions.bed .. ok test_vcf_regions: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/iaQXJX5nkE/regions.bed /tmp/iaQXJX5nkE/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/iaQXJX5nkE/regions.bed.gz /tmp/iaQXJX5nkE/regions.vcf.gz .. ok test_vcf_regions: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/regions.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/iaQXJX5nkE/regions.bed.gz .. ok test_vcf_regions: /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/iaQXJX5nkE/regions.bed.gz /tmp/iaQXJX5nkE/regions.vcf.gz .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annotate.pipes.tab.gz -c CHROM,POS,REF,ALT,SRC,FF,II /build/bcftools-qI88Pr/bcftools-1.24/test/annotate.pipes.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annotate.pipes.tab.gz -c CHROM,POS,REF,ALT,SRC,FF,II /build/bcftools-qI88Pr/bcftools-1.24/test/annotate.pipes.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annotate.pipes.tab.gz -c CHROM,POS,REF,ALT,SRC,FF,II -k -i 'SRC={SRC}' /build/bcftools-qI88Pr/bcftools-1.24/test/annotate.pipes.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annotate.pipes.tab.gz -c CHROM,POS,REF,ALT,SRC,FF,II -k -i 'SRC={SRC}' /build/bcftools-qI88Pr/bcftools-1.24/test/annotate.pipes.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annotate.AR.tab.gz -c CHROM,POS,REF,ALT,+INFO/IA,+INFO/FA,+INFO/IR,+INFO/FR /build/bcftools-qI88Pr/bcftools-1.24/test/annotate.AR.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annotate.AR.tab.gz -c CHROM,POS,REF,ALT,+INFO/IA,+INFO/FA,+INFO/IR,+INFO/FR /build/bcftools-qI88Pr/bcftools-1.24/test/annotate.AR.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annotate.AR.tab.gz -c CHROM,POS,REF,ALT,INFO/IA,INFO/FA,INFO/IR,INFO/FR /build/bcftools-qI88Pr/bcftools-1.24/test/annotate.AR.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annotate.AR.tab.gz -c CHROM,POS,REF,ALT,INFO/IA,INFO/FA,INFO/IR,INFO/FR /build/bcftools-qI88Pr/bcftools-1.24/test/annotate.AR.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annotate.int.src.vcf.gz -c +INFO/IA,+INFO/IR /tmp/iaQXJX5nkE/annotate.int.dst.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annotate.int.src.vcf.gz -c +INFO/IA,+INFO/IR /tmp/iaQXJX5nkE/annotate.int.dst.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -c INFO/ii:=INFO/XX /build/bcftools-qI88Pr/bcftools-1.24/test/annotate.rename.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -c INFO/ii:=INFO/XX /build/bcftools-qI88Pr/bcftools-1.24/test/annotate.rename.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -c FORMAT/ff:=FORMAT/XX /build/bcftools-qI88Pr/bcftools-1.24/test/annotate.rename.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -c FORMAT/ff:=FORMAT/XX /build/bcftools-qI88Pr/bcftools-1.24/test/annotate.rename.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annots36.bed.gz -c CHROM,POS,-,~X,-,AF,-,-,- -i'SVTYPE={X}' -k /build/bcftools-qI88Pr/bcftools-1.24/test/annotate36.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annots36.bed.gz -c CHROM,POS,-,~X,-,AF,-,-,- -i'SVTYPE={X}' -k /build/bcftools-qI88Pr/bcftools-1.24/test/annotate36.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annots36.bed.gz -c CHROM,BEG,END,~X,-,AF,-,-,- -i'SVTYPE={X}' -k /build/bcftools-qI88Pr/bcftools-1.24/test/annotate36.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annots36.bed.gz -c CHROM,BEG,END,~X,-,AF,-,-,- -i'SVTYPE={X}' -k /build/bcftools-qI88Pr/bcftools-1.24/test/annotate36.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annots35.vcf.gz -c CHROM,POS,~ID,REF,ALT,INFO/src /tmp/iaQXJX5nkE/annotate35.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annots35.vcf.gz -c CHROM,POS,~ID,REF,ALT,INFO/src /tmp/iaQXJX5nkE/annotate35.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annotate.escape.1.tab.gz -c CHROM,POS,ISTR,FMT/FSTR /build/bcftools-qI88Pr/bcftools-1.24/test/annotate.escape.1.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annotate.escape.1.tab.gz -c CHROM,POS,ISTR,FMT/FSTR /build/bcftools-qI88Pr/bcftools-1.24/test/annotate.escape.1.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annotate.match.1.tab.gz -c CHROM,POS,-,-,SCORE,~X,-,- -i'STR={X}' /build/bcftools-qI88Pr/bcftools-1.24/test/annotate.match.1.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annotate.match.1.tab.gz -c CHROM,POS,-,-,SCORE,~X,-,- -i'STR={X}' /build/bcftools-qI88Pr/bcftools-1.24/test/annotate.match.1.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annotate.match.1.tab.gz -c CHROM,POS,REF,ALT,SCORE,-,~X,- -i'INT={X}' /build/bcftools-qI88Pr/bcftools-1.24/test/annotate.match.1.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annotate.match.1.tab.gz -c CHROM,POS,REF,ALT,SCORE,-,~X,- -i'INT={X}' /build/bcftools-qI88Pr/bcftools-1.24/test/annotate.match.1.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annotate.match.1.tab.gz -c CHROM,POS,REF,ALT,SCORE,-,-,~X -i'FLT={X}' /build/bcftools-qI88Pr/bcftools-1.24/test/annotate.match.1.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annotate.match.1.tab.gz -c CHROM,POS,REF,ALT,SCORE,-,-,~X -i'FLT={X}' /build/bcftools-qI88Pr/bcftools-1.24/test/annotate.match.1.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annotate.tab.gz -h /build/bcftools-qI88Pr/bcftools-1.24/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /build/bcftools-qI88Pr/bcftools-1.24/test/annotate.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annotate.tab.gz -h /build/bcftools-qI88Pr/bcftools-1.24/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /build/bcftools-qI88Pr/bcftools-1.24/test/annotate.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annotate2.tab.gz -h /build/bcftools-qI88Pr/bcftools-1.24/test/annotate.hdr -c CHROM,POS,-,T_STR /build/bcftools-qI88Pr/bcftools-1.24/test/annotate.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annotate2.tab.gz -h /build/bcftools-qI88Pr/bcftools-1.24/test/annotate.hdr -c CHROM,POS,-,T_STR /build/bcftools-qI88Pr/bcftools-1.24/test/annotate.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annotate2.tab.gz -h /build/bcftools-qI88Pr/bcftools-1.24/test/annotate.hdr -c CHROM,FROM,TO,T_STR /build/bcftools-qI88Pr/bcftools-1.24/test/annotate.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annotate2.tab.gz -h /build/bcftools-qI88Pr/bcftools-1.24/test/annotate.hdr -c CHROM,FROM,TO,T_STR /build/bcftools-qI88Pr/bcftools-1.24/test/annotate.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/iaQXJX5nkE/annotate.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/iaQXJX5nkE/annotate.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/iaQXJX5nkE/annotate2.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/iaQXJX5nkE/annotate2.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/iaQXJX5nkE/annotate2.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/iaQXJX5nkE/annotate2.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/iaQXJX5nkE/annotate2.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/iaQXJX5nkE/annotate2.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/iaQXJX5nkE/annotate2.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/iaQXJX5nkE/annotate2.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/iaQXJX5nkE/annotate2.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/iaQXJX5nkE/annotate2.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /build/bcftools-qI88Pr/bcftools-1.24/test/annotate3.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /build/bcftools-qI88Pr/bcftools-1.24/test/annotate3.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -x FORMAT /build/bcftools-qI88Pr/bcftools-1.24/test/annotate3.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -x FORMAT /build/bcftools-qI88Pr/bcftools-1.24/test/annotate3.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annots4.vcf.gz -c +INFO /tmp/iaQXJX5nkE/annotate4.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annots4.vcf.gz -c +INFO /tmp/iaQXJX5nkE/annotate4.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annots4.tab.gz -h /build/bcftools-qI88Pr/bcftools-1.24/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /build/bcftools-qI88Pr/bcftools-1.24/test/annotate4.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annots4.tab.gz -h /build/bcftools-qI88Pr/bcftools-1.24/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /build/bcftools-qI88Pr/bcftools-1.24/test/annotate4.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annots10.tab.gz -h /build/bcftools-qI88Pr/bcftools-1.24/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /build/bcftools-qI88Pr/bcftools-1.24/test/annotate10.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annots10.tab.gz -h /build/bcftools-qI88Pr/bcftools-1.24/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /build/bcftools-qI88Pr/bcftools-1.24/test/annotate10.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/iaQXJX5nkE/annotate2.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/iaQXJX5nkE/annotate2.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /build/bcftools-qI88Pr/bcftools-1.24/test/annotate2.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /build/bcftools-qI88Pr/bcftools-1.24/test/annotate2.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/iaQXJX5nkE/annotate2.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/iaQXJX5nkE/annotate2.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/iaQXJX5nkE/annotate2.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/iaQXJX5nkE/annotate2.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/iaQXJX5nkE/annotate2.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/iaQXJX5nkE/annotate2.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annots11.vcf.gz -c FMT /tmp/iaQXJX5nkE/annotate11.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annots11.vcf.gz -c FMT /tmp/iaQXJX5nkE/annotate11.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annots2.vcf.gz -c FMT/newGT:=GT /tmp/iaQXJX5nkE/annotate2.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annots2.vcf.gz -c FMT/newGT:=GT /tmp/iaQXJX5nkE/annotate2.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annots12.vcf.gz -c FMT/GT:=newGT /tmp/iaQXJX5nkE/annotate2.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annots12.vcf.gz -c FMT/GT:=newGT /tmp/iaQXJX5nkE/annotate2.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annots13.tab.gz -h /build/bcftools-qI88Pr/bcftools-1.24/test/annotate13.hdr -c CHROM,BEG,END,ABC /build/bcftools-qI88Pr/bcftools-1.24/test/annotate13.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annots13.tab.gz -h /build/bcftools-qI88Pr/bcftools-1.24/test/annotate13.hdr -c CHROM,BEG,END,ABC /build/bcftools-qI88Pr/bcftools-1.24/test/annotate13.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annots13.tab.gz -h /build/bcftools-qI88Pr/bcftools-1.24/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:append /build/bcftools-qI88Pr/bcftools-1.24/test/annotate13.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annots13.tab.gz -h /build/bcftools-qI88Pr/bcftools-1.24/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:append /build/bcftools-qI88Pr/bcftools-1.24/test/annotate13.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annots13.tab.gz -h /build/bcftools-qI88Pr/bcftools-1.24/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:unique /build/bcftools-qI88Pr/bcftools-1.24/test/annotate13.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annots13.tab.gz -h /build/bcftools-qI88Pr/bcftools-1.24/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:unique /build/bcftools-qI88Pr/bcftools-1.24/test/annotate13.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -x FILTER/XX,INFO/XX --force /build/bcftools-qI88Pr/bcftools-1.24/test/annotate14.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -x FILTER/XX,INFO/XX --force /build/bcftools-qI88Pr/bcftools-1.24/test/annotate14.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annotate15.tab.gz -h /build/bcftools-qI88Pr/bcftools-1.24/test/annotate15.hdr -s SAMPLE1 -c CHROM,FROM,TO,FMT/FOO,BAR /build/bcftools-qI88Pr/bcftools-1.24/test/annotate15.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annotate15.tab.gz -h /build/bcftools-qI88Pr/bcftools-1.24/test/annotate15.hdr -s SAMPLE1 -c CHROM,FROM,TO,FMT/FOO,BAR /build/bcftools-qI88Pr/bcftools-1.24/test/annotate15.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annotate15.tab.gz -h /build/bcftools-qI88Pr/bcftools-1.24/test/annotate15.hdr -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR /build/bcftools-qI88Pr/bcftools-1.24/test/annotate15.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annotate15.tab.gz -h /build/bcftools-qI88Pr/bcftools-1.24/test/annotate15.hdr -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR /build/bcftools-qI88Pr/bcftools-1.24/test/annotate15.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annotate15.tab.gz -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR -H '##FORMAT=' -H '##INFO=' /build/bcftools-qI88Pr/bcftools-1.24/test/annotate15.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annotate15.tab.gz -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR -H '##FORMAT=' -H '##INFO=' /build/bcftools-qI88Pr/bcftools-1.24/test/annotate15.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -x FILTER /build/bcftools-qI88Pr/bcftools-1.24/test/annotate16.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -x FILTER /build/bcftools-qI88Pr/bcftools-1.24/test/annotate16.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/bcftools-qI88Pr/bcftools-1.24/test/annotate17.1.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/bcftools-qI88Pr/bcftools-1.24/test/annotate17.1.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/bcftools-qI88Pr/bcftools-1.24/test/annotate17.2.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/bcftools-qI88Pr/bcftools-1.24/test/annotate17.2.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annotate17.3.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/bcftools-qI88Pr/bcftools-1.24/test/annotate17.3.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annotate17.3.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /build/bcftools-qI88Pr/bcftools-1.24/test/annotate17.3.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/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-qI88Pr/bcftools-1.24/test/annotate18.1.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/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-qI88Pr/bcftools-1.24/test/annotate18.1.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/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-qI88Pr/bcftools-1.24/test/annotate18.2.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/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-qI88Pr/bcftools-1.24/test/annotate18.2.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/iaQXJX5nkE/annotate19.dst.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/iaQXJX5nkE/annotate19.dst.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/iaQXJX5nkE/annotate19.dst.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/iaQXJX5nkE/annotate19.dst.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/iaQXJX5nkE/annotate19.dst.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/iaQXJX5nkE/annotate19.dst.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -c INFO/FILTER:=FILTER /build/bcftools-qI88Pr/bcftools-1.24/test/annotate19.dst.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -c INFO/FILTER:=FILTER /build/bcftools-qI88Pr/bcftools-1.24/test/annotate19.dst.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER /tmp/iaQXJX5nkE/annotate19.dst.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER /tmp/iaQXJX5nkE/annotate19.dst.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER /tmp/iaQXJX5nkE/annotate19.dst.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER /tmp/iaQXJX5nkE/annotate19.dst.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER,FILTER /tmp/iaQXJX5nkE/annotate19.dst.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER,FILTER /tmp/iaQXJX5nkE/annotate19.dst.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=./FILTER /tmp/iaQXJX5nkE/annotate19.dst.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=./FILTER /tmp/iaQXJX5nkE/annotate19.dst.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annotate20.src.vcf.gz -c FMT/GT /tmp/iaQXJX5nkE/annotate20.dst.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annotate20.src.vcf.gz -c FMT/GT /tmp/iaQXJX5nkE/annotate20.dst.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annotate20.src.vcf.gz -c +FMT/GT /tmp/iaQXJX5nkE/annotate20.dst.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annotate20.src.vcf.gz -c +FMT/GT /tmp/iaQXJX5nkE/annotate20.dst.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annotate20.src.vcf.gz -c -FMT/GT /tmp/iaQXJX5nkE/annotate20.dst.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annotate20.src.vcf.gz -c -FMT/GT /tmp/iaQXJX5nkE/annotate20.dst.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annotate.multi.tab.gz -c CHROM,POS,REF,ALT,ANN -l ANN:append /build/bcftools-qI88Pr/bcftools-1.24/test/annotate.multi.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annotate.multi.tab.gz -c CHROM,POS,REF,ALT,ANN -l ANN:append /build/bcftools-qI88Pr/bcftools-1.24/test/annotate.multi.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/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-qI88Pr/bcftools-1.24/test/annotate.missing-append.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/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-qI88Pr/bcftools-1.24/test/annotate.missing-append.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /build/bcftools-qI88Pr/bcftools-1.24/test/annotate9.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /build/bcftools-qI88Pr/bcftools-1.24/test/annotate9.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate --rename-annots /build/bcftools-qI88Pr/bcftools-1.24/test/annotate21.txt /build/bcftools-qI88Pr/bcftools-1.24/test/annotate21.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob --rename-annots /build/bcftools-qI88Pr/bcftools-1.24/test/annotate21.txt /build/bcftools-qI88Pr/bcftools-1.24/test/annotate21.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/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-qI88Pr/bcftools-1.24/test/annotate21.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/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-qI88Pr/bcftools-1.24/test/annotate21.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/iaQXJX5nkE/annotate22.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/iaQXJX5nkE/annotate22.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annotate23.tab.gz -c CHROM,POS,~ID,REF,ALT,INFO/END /build/bcftools-qI88Pr/bcftools-1.24/test/annotate23.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annotate23.tab.gz -c CHROM,POS,~ID,REF,ALT,INFO/END /build/bcftools-qI88Pr/bcftools-1.24/test/annotate23.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annotate24.src.vcf.gz -c XX /tmp/iaQXJX5nkE/annotate24.dst.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annotate24.src.vcf.gz -c XX /tmp/iaQXJX5nkE/annotate24.dst.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annotate25.tab.gz -c CHROM,POS,ID,REF,ALT,~INFO/END /build/bcftools-qI88Pr/bcftools-1.24/test/annotate25.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annotate25.tab.gz -c CHROM,POS,ID,REF,ALT,~INFO/END /build/bcftools-qI88Pr/bcftools-1.24/test/annotate25.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annotate26.tab.gz -c CHROM,POS,-POS /build/bcftools-qI88Pr/bcftools-1.24/test/annotate26.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annotate26.tab.gz -c CHROM,POS,-POS /build/bcftools-qI88Pr/bcftools-1.24/test/annotate26.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,TSTR,TFLT,TINT /build/bcftools-qI88Pr/bcftools-1.24/test/annotate.missing.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,TSTR,TFLT,TINT /build/bcftools-qI88Pr/bcftools-1.24/test/annotate.missing.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.TSTR,.TFLT,.TINT /build/bcftools-qI88Pr/bcftools-1.24/test/annotate.missing.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.TSTR,.TFLT,.TINT /build/bcftools-qI88Pr/bcftools-1.24/test/annotate.missing.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.+TSTR,.+TFLT,.+TINT /build/bcftools-qI88Pr/bcftools-1.24/test/annotate.missing.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.+TSTR,.+TFLT,.+TINT /build/bcftools-qI88Pr/bcftools-1.24/test/annotate.missing.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,+TSTR,+TFLT,+TINT /build/bcftools-qI88Pr/bcftools-1.24/test/annotate.missing.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,+TSTR,+TFLT,+TINT /build/bcftools-qI88Pr/bcftools-1.24/test/annotate.missing.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.=TSTR,.=TFLT,.=TINT /build/bcftools-qI88Pr/bcftools-1.24/test/annotate.missing.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.=TSTR,.=TFLT,.=TINT /build/bcftools-qI88Pr/bcftools-1.24/test/annotate.missing.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,=TSTR,=TFLT,=TINT /build/bcftools-qI88Pr/bcftools-1.24/test/annotate.missing.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,=TSTR,=TFLT,=TINT /build/bcftools-qI88Pr/bcftools-1.24/test/annotate.missing.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique /build/bcftools-qI88Pr/bcftools-1.24/test/annotate.olap.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique /build/bcftools-qI88Pr/bcftools-1.24/test/annotate.olap.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique --min-overlap 0.4:0.5 -m XXX /build/bcftools-qI88Pr/bcftools-1.24/test/annotate.olap.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique --min-overlap 0.4:0.5 -m XXX /build/bcftools-qI88Pr/bcftools-1.24/test/annotate.olap.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annots.id.vcf.gz -c ALT /tmp/iaQXJX5nkE/annotate.id.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annots.id.vcf.gz -c ALT /tmp/iaQXJX5nkE/annotate.id.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annots.id.vcf.gz -c +ALT /tmp/iaQXJX5nkE/annotate.id.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annots.id.vcf.gz -c +ALT /tmp/iaQXJX5nkE/annotate.id.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annots.id.2.vcf.gz --pair-logic some -c +ID /tmp/iaQXJX5nkE/annotate.id.2.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annots.id.2.vcf.gz --pair-logic some -c +ID /tmp/iaQXJX5nkE/annotate.id.2.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annots.id.2.vcf.gz --pair-logic any -c +ID /tmp/iaQXJX5nkE/annotate.id.2.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annots.id.2.vcf.gz --pair-logic any -c +ID /tmp/iaQXJX5nkE/annotate.id.2.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annotate27.tab.gz -c CHROM,POS,REF,ALT,EVIDENCE /build/bcftools-qI88Pr/bcftools-1.24/test/annotate27.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annotate27.tab.gz -c CHROM,POS,REF,ALT,EVIDENCE /build/bcftools-qI88Pr/bcftools-1.24/test/annotate27.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1,smpl2 /build/bcftools-qI88Pr/bcftools-1.24/test/annotate28.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1,smpl2 /build/bcftools-qI88Pr/bcftools-1.24/test/annotate28.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2,smpl1 /build/bcftools-qI88Pr/bcftools-1.24/test/annotate28.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2,smpl1 /build/bcftools-qI88Pr/bcftools-1.24/test/annotate28.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1 /build/bcftools-qI88Pr/bcftools-1.24/test/annotate28.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1 /build/bcftools-qI88Pr/bcftools-1.24/test/annotate28.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2 /build/bcftools-qI88Pr/bcftools-1.24/test/annotate28.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2 /build/bcftools-qI88Pr/bcftools-1.24/test/annotate28.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -m XXX /build/bcftools-qI88Pr/bcftools-1.24/test/annotate.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -m XXX /build/bcftools-qI88Pr/bcftools-1.24/test/annotate.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annots34.tab.gz -c CHROM,FROM,TO,INFO/END -H '##INFO=' /build/bcftools-qI88Pr/bcftools-1.24/test/annotate34.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annots34.tab.gz -c CHROM,FROM,TO,INFO/END -H '##INFO=' /build/bcftools-qI88Pr/bcftools-1.24/test/annotate34.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -a /tmp/iaQXJX5nkE/annots-mark.bed.gz -c CHROM,FROM,TO -m TAG /build/bcftools-qI88Pr/bcftools-1.24/test/annots-mark.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate -Ob -a /tmp/iaQXJX5nkE/annots-mark.bed.gz -c CHROM,FROM,TO -m TAG /build/bcftools-qI88Pr/bcftools-1.24/test/annots-mark.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_trio_dnm3: export BCFTOOLS_PLUGINS=/build/bcftools-qI88Pr/bcftools-1.24/plugins; /build/bcftools-qI88Pr/bcftools-1.24/test/trio-dnm3/test.sh /build/bcftools-qI88Pr/bcftools-1.24/bcftools .. ok test_vcf_concat: /build/bcftools-qI88Pr/bcftools-1.24/bcftools concat --no-version -G /tmp/iaQXJX5nkE/concat.1.a.vcf.gz /tmp/iaQXJX5nkE/concat.1.b.vcf.gz .. ok test_vcf_concat: /build/bcftools-qI88Pr/bcftools-1.24/bcftools concat -Ob -G /tmp/iaQXJX5nkE/concat.1.a.vcf.gz /tmp/iaQXJX5nkE/concat.1.b.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-qI88Pr/bcftools-1.24/bcftools concat --no-version -G /build/bcftools-qI88Pr/bcftools-1.24/test/concat.1.a.vcf /build/bcftools-qI88Pr/bcftools-1.24/test/concat.1.b.vcf .. ok test_vcf_concat: /build/bcftools-qI88Pr/bcftools-1.24/bcftools concat --no-version /tmp/iaQXJX5nkE/concat.1.a.vcf.gz /tmp/iaQXJX5nkE/concat.1.b.vcf.gz .. ok test_vcf_concat: /build/bcftools-qI88Pr/bcftools-1.24/bcftools concat -Ob /tmp/iaQXJX5nkE/concat.1.a.vcf.gz /tmp/iaQXJX5nkE/concat.1.b.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-qI88Pr/bcftools-1.24/bcftools concat --no-version /build/bcftools-qI88Pr/bcftools-1.24/test/concat.1.a.vcf /build/bcftools-qI88Pr/bcftools-1.24/test/concat.1.b.vcf .. ok test_vcf_concat: /build/bcftools-qI88Pr/bcftools-1.24/bcftools concat --no-version /tmp/iaQXJX5nkE/concat.1.a.bcf /tmp/iaQXJX5nkE/concat.1.b.bcf .. ok test_vcf_concat: /build/bcftools-qI88Pr/bcftools-1.24/bcftools concat -Ob /tmp/iaQXJX5nkE/concat.1.a.bcf /tmp/iaQXJX5nkE/concat.1.b.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-qI88Pr/bcftools-1.24/bcftools concat --no-version -a /tmp/iaQXJX5nkE/concat.2.a.vcf.gz /tmp/iaQXJX5nkE/concat.2.b.vcf.gz .. ok test_vcf_concat: /build/bcftools-qI88Pr/bcftools-1.24/bcftools concat -Ob -a /tmp/iaQXJX5nkE/concat.2.a.vcf.gz /tmp/iaQXJX5nkE/concat.2.b.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-qI88Pr/bcftools-1.24/bcftools concat --no-version -a /tmp/iaQXJX5nkE/concat.2.a.bcf /tmp/iaQXJX5nkE/concat.2.b.bcf .. ok test_vcf_concat: /build/bcftools-qI88Pr/bcftools-1.24/bcftools concat -Ob -a /tmp/iaQXJX5nkE/concat.2.a.bcf /tmp/iaQXJX5nkE/concat.2.b.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-qI88Pr/bcftools-1.24/bcftools concat --no-version -aD /tmp/iaQXJX5nkE/concat.2.a.vcf.gz /tmp/iaQXJX5nkE/concat.2.b.vcf.gz .. ok test_vcf_concat: /build/bcftools-qI88Pr/bcftools-1.24/bcftools concat -Ob -aD /tmp/iaQXJX5nkE/concat.2.a.vcf.gz /tmp/iaQXJX5nkE/concat.2.b.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-qI88Pr/bcftools-1.24/bcftools concat --no-version -aD /tmp/iaQXJX5nkE/concat.2.a.bcf /tmp/iaQXJX5nkE/concat.2.b.bcf .. ok test_vcf_concat: /build/bcftools-qI88Pr/bcftools-1.24/bcftools concat -Ob -aD /tmp/iaQXJX5nkE/concat.2.a.bcf /tmp/iaQXJX5nkE/concat.2.b.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-qI88Pr/bcftools-1.24/bcftools concat --no-version -l --ligate-warn /tmp/iaQXJX5nkE/concat.3.a.vcf.gz /tmp/iaQXJX5nkE/concat.3.b.vcf.gz /tmp/iaQXJX5nkE/concat.3.0.vcf.gz /tmp/iaQXJX5nkE/concat.3.c.vcf.gz /tmp/iaQXJX5nkE/concat.3.d.vcf.gz /tmp/iaQXJX5nkE/concat.3.e.vcf.gz /tmp/iaQXJX5nkE/concat.3.f.vcf.gz .. ok test_vcf_concat: /build/bcftools-qI88Pr/bcftools-1.24/bcftools concat -Ob -l --ligate-warn /tmp/iaQXJX5nkE/concat.3.a.vcf.gz /tmp/iaQXJX5nkE/concat.3.b.vcf.gz /tmp/iaQXJX5nkE/concat.3.0.vcf.gz /tmp/iaQXJX5nkE/concat.3.c.vcf.gz /tmp/iaQXJX5nkE/concat.3.d.vcf.gz /tmp/iaQXJX5nkE/concat.3.e.vcf.gz /tmp/iaQXJX5nkE/concat.3.f.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-qI88Pr/bcftools-1.24/bcftools concat --no-version -l --ligate-warn /tmp/iaQXJX5nkE/concat.3.a.bcf /tmp/iaQXJX5nkE/concat.3.b.bcf /tmp/iaQXJX5nkE/concat.3.0.bcf /tmp/iaQXJX5nkE/concat.3.c.bcf /tmp/iaQXJX5nkE/concat.3.d.bcf /tmp/iaQXJX5nkE/concat.3.e.bcf /tmp/iaQXJX5nkE/concat.3.f.bcf .. ok test_vcf_concat: /build/bcftools-qI88Pr/bcftools-1.24/bcftools concat -Ob -l --ligate-warn /tmp/iaQXJX5nkE/concat.3.a.bcf /tmp/iaQXJX5nkE/concat.3.b.bcf /tmp/iaQXJX5nkE/concat.3.0.bcf /tmp/iaQXJX5nkE/concat.3.c.bcf /tmp/iaQXJX5nkE/concat.3.d.bcf /tmp/iaQXJX5nkE/concat.3.e.bcf /tmp/iaQXJX5nkE/concat.3.f.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ Random seed for test_naive_concat: 13402893971991729486 .. ok test_naive_concat: /build/bcftools-qI88Pr/bcftools-1.24/bcftools concat --naive-force /tmp/iaQXJX5nkE/naive_concat.0.bcf /tmp/iaQXJX5nkE/naive_concat.1.bcf /tmp/iaQXJX5nkE/naive_concat.2.bcf /tmp/iaQXJX5nkE/naive_concat.3.bcf /tmp/iaQXJX5nkE/naive_concat.4.bcf /tmp/iaQXJX5nkE/naive_concat.5.bcf /tmp/iaQXJX5nkE/naive_concat.6.bcf /tmp/iaQXJX5nkE/naive_concat.7.bcf /tmp/iaQXJX5nkE/naive_concat.8.bcf /tmp/iaQXJX5nkE/naive_concat.9.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -H .. ok test_naive_concat: /build/bcftools-qI88Pr/bcftools-1.24/bcftools concat --naive /tmp/iaQXJX5nkE/naive_concat.0.vcf.gz /tmp/iaQXJX5nkE/naive_concat.1.vcf.gz /tmp/iaQXJX5nkE/naive_concat.2.vcf.gz /tmp/iaQXJX5nkE/naive_concat.3.vcf.gz /tmp/iaQXJX5nkE/naive_concat.4.vcf.gz /tmp/iaQXJX5nkE/naive_concat.5.vcf.gz /tmp/iaQXJX5nkE/naive_concat.6.vcf.gz /tmp/iaQXJX5nkE/naive_concat.7.vcf.gz /tmp/iaQXJX5nkE/naive_concat.8.vcf.gz /tmp/iaQXJX5nkE/naive_concat.9.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -H .. ok test_vcf_concat: /build/bcftools-qI88Pr/bcftools-1.24/bcftools concat --no-version -l /tmp/iaQXJX5nkE/concat.4.a.vcf.gz /tmp/iaQXJX5nkE/concat.4.b.vcf.gz .. ok test_vcf_concat: /build/bcftools-qI88Pr/bcftools-1.24/bcftools concat -Ob -l /tmp/iaQXJX5nkE/concat.4.a.vcf.gz /tmp/iaQXJX5nkE/concat.4.b.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-qI88Pr/bcftools-1.24/bcftools concat --no-version -l /tmp/iaQXJX5nkE/concat.4.a.bcf /tmp/iaQXJX5nkE/concat.4.b.bcf .. ok test_vcf_concat: /build/bcftools-qI88Pr/bcftools-1.24/bcftools concat -Ob -l /tmp/iaQXJX5nkE/concat.4.a.bcf /tmp/iaQXJX5nkE/concat.4.b.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-qI88Pr/bcftools-1.24/bcftools concat --no-version -l --ligate-warn /tmp/iaQXJX5nkE/concat.5.a.vcf.gz /tmp/iaQXJX5nkE/concat.5.b.vcf.gz /tmp/iaQXJX5nkE/concat.5.c.vcf.gz .. ok test_vcf_concat: /build/bcftools-qI88Pr/bcftools-1.24/bcftools concat -Ob -l --ligate-warn /tmp/iaQXJX5nkE/concat.5.a.vcf.gz /tmp/iaQXJX5nkE/concat.5.b.vcf.gz /tmp/iaQXJX5nkE/concat.5.c.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-qI88Pr/bcftools-1.24/bcftools concat --no-version -l --ligate-warn /tmp/iaQXJX5nkE/concat.5.a.bcf /tmp/iaQXJX5nkE/concat.5.b.bcf /tmp/iaQXJX5nkE/concat.5.c.bcf .. ok test_vcf_concat: /build/bcftools-qI88Pr/bcftools-1.24/bcftools concat -Ob -l --ligate-warn /tmp/iaQXJX5nkE/concat.5.a.bcf /tmp/iaQXJX5nkE/concat.5.b.bcf /tmp/iaQXJX5nkE/concat.5.c.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-qI88Pr/bcftools-1.24/bcftools concat --no-version -l --ligate-force /tmp/iaQXJX5nkE/concat.5.a.bcf /tmp/iaQXJX5nkE/concat.5.b.bcf /tmp/iaQXJX5nkE/concat.5.c.bcf .. ok test_vcf_concat: /build/bcftools-qI88Pr/bcftools-1.24/bcftools concat -Ob -l --ligate-force /tmp/iaQXJX5nkE/concat.5.a.bcf /tmp/iaQXJX5nkE/concat.5.b.bcf /tmp/iaQXJX5nkE/concat.5.c.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-qI88Pr/bcftools-1.24/bcftools concat --no-version -G -a -D /tmp/iaQXJX5nkE/concat.5.a.vcf.gz /tmp/iaQXJX5nkE/concat.5.b.vcf.gz /tmp/iaQXJX5nkE/concat.5.c.vcf.gz .. ok test_vcf_concat: /build/bcftools-qI88Pr/bcftools-1.24/bcftools concat -Ob -G -a -D /tmp/iaQXJX5nkE/concat.5.a.vcf.gz /tmp/iaQXJX5nkE/concat.5.b.vcf.gz /tmp/iaQXJX5nkE/concat.5.c.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /build/bcftools-qI88Pr/bcftools-1.24/bcftools concat --no-version -G -a -D /tmp/iaQXJX5nkE/concat.5.a.bcf /tmp/iaQXJX5nkE/concat.5.b.bcf /tmp/iaQXJX5nkE/concat.5.c.bcf .. ok test_vcf_concat: /build/bcftools-qI88Pr/bcftools-1.24/bcftools concat -Ob -G -a -D /tmp/iaQXJX5nkE/concat.5.a.bcf /tmp/iaQXJX5nkE/concat.5.b.bcf /tmp/iaQXJX5nkE/concat.5.c.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_reheader: /build/bcftools-qI88Pr/bcftools-1.24/bcftools reheader -h /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.hdr /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools reheader -h /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.hdr | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-qI88Pr/bcftools-1.24/bcftools reheader -h /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.hdr /tmp/iaQXJX5nkE/reheader.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/iaQXJX5nkE/reheader.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools reheader -h /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.hdr | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-qI88Pr/bcftools-1.24/bcftools reheader -h /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.hdr /tmp/iaQXJX5nkE/reheader.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/iaQXJX5nkE/reheader.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools reheader -h /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.hdr | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-qI88Pr/bcftools-1.24/bcftools reheader -s /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.samples /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools reheader -s /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.samples | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-qI88Pr/bcftools-1.24/bcftools reheader -s /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.samples /tmp/iaQXJX5nkE/reheader.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/iaQXJX5nkE/reheader.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools reheader -s /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.samples | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-qI88Pr/bcftools-1.24/bcftools reheader -s /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.samples /tmp/iaQXJX5nkE/reheader.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/iaQXJX5nkE/reheader.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools reheader -s /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.samples | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-qI88Pr/bcftools-1.24/bcftools reheader -N /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.samples /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools reheader -N /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.samples | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-qI88Pr/bcftools-1.24/bcftools reheader -N /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.samples /tmp/iaQXJX5nkE/reheader.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/iaQXJX5nkE/reheader.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools reheader -N /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.samples | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-qI88Pr/bcftools-1.24/bcftools reheader -N /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.samples /tmp/iaQXJX5nkE/reheader.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/iaQXJX5nkE/reheader.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools reheader -N /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.samples | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-qI88Pr/bcftools-1.24/bcftools reheader -n AAA,BBB /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools reheader -n AAA,BBB | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-qI88Pr/bcftools-1.24/bcftools reheader -n AAA,BBB /tmp/iaQXJX5nkE/reheader.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/iaQXJX5nkE/reheader.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools reheader -n AAA,BBB | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-qI88Pr/bcftools-1.24/bcftools reheader -n AAA,BBB /tmp/iaQXJX5nkE/reheader.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/iaQXJX5nkE/reheader.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools reheader -n AAA,BBB | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-qI88Pr/bcftools-1.24/bcftools reheader -s /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.samples2 /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools reheader -s /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.samples2 | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-qI88Pr/bcftools-1.24/bcftools reheader -s /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.samples2 /tmp/iaQXJX5nkE/reheader.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/iaQXJX5nkE/reheader.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools reheader -s /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.samples2 | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-qI88Pr/bcftools-1.24/bcftools reheader -s /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.samples2 /tmp/iaQXJX5nkE/reheader.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/iaQXJX5nkE/reheader.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools reheader -s /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.samples2 | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-qI88Pr/bcftools-1.24/bcftools reheader -s /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.samples3 /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools reheader -s /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.samples3 | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-qI88Pr/bcftools-1.24/bcftools reheader -s /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.samples3 /tmp/iaQXJX5nkE/reheader.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/iaQXJX5nkE/reheader.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools reheader -s /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.samples3 | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-qI88Pr/bcftools-1.24/bcftools reheader -s /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.samples3 /tmp/iaQXJX5nkE/reheader.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/iaQXJX5nkE/reheader.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools reheader -s /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.samples3 | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-qI88Pr/bcftools-1.24/bcftools reheader -s /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.samples4 /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools reheader -s /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.samples4 | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-qI88Pr/bcftools-1.24/bcftools reheader -s /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.samples4 /tmp/iaQXJX5nkE/reheader.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/iaQXJX5nkE/reheader.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools reheader -s /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.samples4 | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-qI88Pr/bcftools-1.24/bcftools reheader -s /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.samples4 /tmp/iaQXJX5nkE/reheader.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/iaQXJX5nkE/reheader.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools reheader -s /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.samples4 | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-qI88Pr/bcftools-1.24/bcftools reheader -h /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.empty.hdr /build/bcftools-qI88Pr/bcftools-1.24/test/empty.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version .. ok test_vcf_reheader: cat /build/bcftools-qI88Pr/bcftools-1.24/test/empty.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools reheader -h /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.empty.hdr | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-qI88Pr/bcftools-1.24/bcftools reheader -h /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.empty.hdr /tmp/iaQXJX5nkE/empty.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/iaQXJX5nkE/empty.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools reheader -h /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.empty.hdr | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-qI88Pr/bcftools-1.24/bcftools reheader -h /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.empty.hdr /tmp/iaQXJX5nkE/empty.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/iaQXJX5nkE/empty.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools reheader -h /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.empty.hdr | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-qI88Pr/bcftools-1.24/bcftools reheader -f /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.fai /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.2.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-qI88Pr/bcftools-1.24/bcftools reheader -f /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.fai /tmp/iaQXJX5nkE/reheader.2.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-qI88Pr/bcftools-1.24/bcftools reheader -f /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.fai /tmp/iaQXJX5nkE/reheader.2.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-qI88Pr/bcftools-1.24/bcftools reheader -h /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.2.hdr -f /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.fai /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.2.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-qI88Pr/bcftools-1.24/bcftools reheader -h /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.2.hdr -f /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.fai /tmp/iaQXJX5nkE/reheader.2.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-qI88Pr/bcftools-1.24/bcftools reheader -h /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.2.hdr -f /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.fai /tmp/iaQXJX5nkE/reheader.2.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-qI88Pr/bcftools-1.24/bcftools reheader -f /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.3.fai /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.3.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-qI88Pr/bcftools-1.24/bcftools reheader -f /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.3.fai /tmp/iaQXJX5nkE/reheader.3.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version .. ok test_vcf_reheader: /build/bcftools-qI88Pr/bcftools-1.24/bcftools reheader -f /build/bcftools-qI88Pr/bcftools-1.24/test/reheader.3.fai /tmp/iaQXJX5nkE/reheader.3.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version .. ok test_rename_chrs: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate --rename-chrs /tmp/iaQXJX5nkE/rename.map -Ov /tmp/iaQXJX5nkE/annotate.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate --rename-chrs /tmp/iaQXJX5nkE/rename.map -Ob /tmp/iaQXJX5nkE/annotate.bcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate --rename-chrs /tmp/iaQXJX5nkE/rename.map -Ov /build/bcftools-qI88Pr/bcftools-1.24/test/annotate.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /build/bcftools-qI88Pr/bcftools-1.24/bcftools annotate --rename-chrs /tmp/iaQXJX5nkE/rename.map -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/annotate.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%CHROM\t%POS\n' .. ok test_vcf_convert: /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert -g -,. /tmp/iaQXJX5nkE/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/convert.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert -g -,. .. ok test_vcf_convert: /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert -g -,. --vcf-ids /tmp/iaQXJX5nkE/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/convert.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert -g -,. --vcf-ids .. ok test_vcf_convert: /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert -g -,. --vcf-ids --3N6 /tmp/iaQXJX5nkE/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/convert.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert -g -,. --vcf-ids --3N6 .. ok test_vcf_convert: /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert -g .,- /tmp/iaQXJX5nkE/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/convert.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert -g .,- .. ok test_vcf_convert_hs2vcf: /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert --vcf-ids -G /build/bcftools-qI88Pr/bcftools-1.24/test/convert.gs.gt.ids.gen,/build/bcftools-qI88Pr/bcftools-1.24/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert --vcf-ids -G /build/bcftools-qI88Pr/bcftools-1.24/test/convert.gs.gt.ids.gen,/build/bcftools-qI88Pr/bcftools-1.24/test/convert.gs.gt.samples -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert -G /build/bcftools-qI88Pr/bcftools-1.24/test/convert.gs.gt.ids.gen,/build/bcftools-qI88Pr/bcftools-1.24/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert -G /build/bcftools-qI88Pr/bcftools-1.24/test/convert.gs.gt.ids.gen,/build/bcftools-qI88Pr/bcftools-1.24/test/convert.gs.gt.samples -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert --3N6 -G /build/bcftools-qI88Pr/bcftools-1.24/test/convert.gs.gt.ids.3N6.gen,/build/bcftools-qI88Pr/bcftools-1.24/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert --3N6 -G /build/bcftools-qI88Pr/bcftools-1.24/test/convert.gs.gt.ids.3N6.gen,/build/bcftools-qI88Pr/bcftools-1.24/test/convert.gs.gt.samples -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert --vcf-ids -G /build/bcftools-qI88Pr/bcftools-1.24/test/convert.gs.gt.ids.gen.rev,/build/bcftools-qI88Pr/bcftools-1.24/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert --vcf-ids -G /build/bcftools-qI88Pr/bcftools-1.24/test/convert.gs.gt.ids.gen.rev,/build/bcftools-qI88Pr/bcftools-1.24/test/convert.gs.gt.samples -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert -G /build/bcftools-qI88Pr/bcftools-1.24/test/convert.gs.gt.ids.gen.rev,/build/bcftools-qI88Pr/bcftools-1.24/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert -G /build/bcftools-qI88Pr/bcftools-1.24/test/convert.gs.gt.ids.gen.rev,/build/bcftools-qI88Pr/bcftools-1.24/test/convert.gs.gt.samples -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^## .. ok test_vcf_convert: /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert -g -,. --tag PL /tmp/iaQXJX5nkE/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/convert.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert -g -,. --tag PL .. ok test_vcf_convert: /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert -g .,- --tag PL /tmp/iaQXJX5nkE/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/convert.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert -g .,- --tag PL .. ok test_vcf_convert: /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert -g -,. --vcf-ids /tmp/iaQXJX5nkE/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/check.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert -g -,. --vcf-ids .. ok test_vcf_convert: /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert -g .,- --vcf-ids /tmp/iaQXJX5nkE/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/check.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert -g .,- --vcf-ids .. ok test_vcf_convert: /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert -g -,. --3N6 /tmp/iaQXJX5nkE/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/check.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert -g -,. --3N6 .. ok test_vcf_convert: /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert -g .,- --3N6 /tmp/iaQXJX5nkE/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/check.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert -g .,- --3N6 .. ok test_vcf_convert: /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert -g -,. --3N6 --vcf-ids /tmp/iaQXJX5nkE/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/check.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert -g -,. --3N6 --vcf-ids .. ok test_vcf_convert: /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert -g .,- --3N6 --vcf-ids /tmp/iaQXJX5nkE/check.vcf.gz .. ok test_vcf_convert: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/check.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert -g .,- --3N6 --vcf-ids .. ok test_vcf_convert: /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert -h -,.,. /tmp/iaQXJX5nkE/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/convert.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert -h -,.,. .. ok test_vcf_convert: /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert -h .,-,. /tmp/iaQXJX5nkE/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/convert.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert -h .,-,. .. ok test_vcf_convert: /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert -h .,-,. --vcf-ids /tmp/iaQXJX5nkE/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/convert.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert -h .,-,. --vcf-ids .. ok test_vcf_convert: /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert -h .,.,- /tmp/iaQXJX5nkE/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/convert.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert -h .,.,- .. ok test_vcf_convert_hls2vcf: /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert -H /build/bcftools-qI88Pr/bcftools-1.24/test/convert.hls.gt.hap,/build/bcftools-qI88Pr/bcftools-1.24/test/convert.hls.gt.legend,/build/bcftools-qI88Pr/bcftools-1.24/test/convert.hls.gt.samples | grep -v ^## .. ok test_vcf_convert_hls2vcf: /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert -H /build/bcftools-qI88Pr/bcftools-1.24/test/convert.hls.gt.hap,/build/bcftools-qI88Pr/bcftools-1.24/test/convert.hls.gt.legend,/build/bcftools-qI88Pr/bcftools-1.24/test/convert.hls.gt.samples -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^## .. ok test_vcf_convert: /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert --haplegendsample -,.,. /tmp/iaQXJX5nkE/convert.hap-missing.vcf.gz .. ok test_vcf_convert: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/convert.hap-missing.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert --haplegendsample -,.,. .. ok test_vcf_convert: /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert --hapsample -,. /tmp/iaQXJX5nkE/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/convert.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert --hapsample -,. .. ok test_vcf_convert: /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert --hapsample -,. --vcf-ids /tmp/iaQXJX5nkE/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/convert.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert --hapsample -,. --vcf-ids .. ok test_vcf_convert: /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert --hapsample .,- /tmp/iaQXJX5nkE/convert.vcf.gz .. ok test_vcf_convert: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/convert.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert --hapsample .,- .. ok test_vcf_convert_hs2vcf: /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert --hapsample2vcf /build/bcftools-qI88Pr/bcftools-1.24/test/convert.hs.gt.hap,/build/bcftools-qI88Pr/bcftools-1.24/test/convert.hs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert --hapsample2vcf /build/bcftools-qI88Pr/bcftools-1.24/test/convert.hs.gt.hap,/build/bcftools-qI88Pr/bcftools-1.24/test/convert.hs.gt.samples -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert --vcf-ids --hapsample2vcf /build/bcftools-qI88Pr/bcftools-1.24/test/convert.hs.gt.ids.hap,/build/bcftools-qI88Pr/bcftools-1.24/test/convert.hs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert --vcf-ids --hapsample2vcf /build/bcftools-qI88Pr/bcftools-1.24/test/convert.hs.gt.ids.hap,/build/bcftools-qI88Pr/bcftools-1.24/test/convert.hs.gt.samples -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^## .. ok test_vcf_convert_gvcf: /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert --no-version --gvcf2vcf -i'FILTER="PASS"' -f /build/bcftools-qI88Pr/bcftools-1.24/test/gvcf.fa /tmp/iaQXJX5nkE/convert.gvcf.vcf.gz .. ok test_vcf_convert_gvcf: /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert --no-version --gvcf2vcf -i'FILTER="PASS"' -f /build/bcftools-qI88Pr/bcftools-1.24/test/gvcf.fa /tmp/iaQXJX5nkE/convert.gvcf.vcf.gz -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version .. ok test_vcf_convert_gvcf: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/convert.gvcf.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert --gvcf2vcf -i'FILTER="PASS"' -f /build/bcftools-qI88Pr/bcftools-1.24/test/gvcf.fa | grep -v ^##bcftools .. ok test_vcf_convert_gvcf: /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert --no-version --gvcf2vcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/gvcf.fa /tmp/iaQXJX5nkE/convert.gvcf.2.vcf.gz .. ok test_vcf_convert_gvcf: /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert --no-version --gvcf2vcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/gvcf.fa /tmp/iaQXJX5nkE/convert.gvcf.2.vcf.gz -Ou | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view --no-version .. ok test_vcf_convert_gvcf: /build/bcftools-qI88Pr/bcftools-1.24/bcftools view -Ob /tmp/iaQXJX5nkE/convert.gvcf.2.vcf.gz | /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert --gvcf2vcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/gvcf.fa | grep -v ^##bcftools .. ok test_vcf_convert_tsv2vcf: /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert --no-version -c ID,CHROM,POS,AA -s SAMPLE1 -f /build/bcftools-qI88Pr/bcftools-1.24/test/23andme.fa --tsv2vcf /build/bcftools-qI88Pr/bcftools-1.24/test/convert.23andme .. ok test_vcf_convert_tsv2vcf: /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert -Ou -c ID,CHROM,POS,AA -s SAMPLE1 -f /build/bcftools-qI88Pr/bcftools-1.24/test/23andme.fa --tsv2vcf /build/bcftools-qI88Pr/bcftools-1.24/test/convert.23andme | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_convert_tsv2vcf: /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert --no-version -c -,CHROM,POS,REF,ALT -f /build/bcftools-qI88Pr/bcftools-1.24/test/23andme.fa --tsv2vcf /build/bcftools-qI88Pr/bcftools-1.24/test/convert.tsv .. ok test_vcf_convert_tsv2vcf: /build/bcftools-qI88Pr/bcftools-1.24/bcftools convert -Ou -c -,CHROM,POS,REF,ALT -f /build/bcftools-qI88Pr/bcftools-1.24/test/23andme.fa --tsv2vcf /build/bcftools-qI88Pr/bcftools-1.24/test/convert.tsv | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.gvcf-missing.1.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.gvcf-missing.fa --missing N .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.gvcf-missing.1.bcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.gvcf-missing.fa --missing N .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.overlaps.1.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.overlaps.2.fa -s A .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.overlaps.1.bcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.overlaps.2.fa -s A .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.overlaps.1.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.overlaps.1.fa -s A .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.overlaps.1.bcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.overlaps.1.fa -s A .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.overlaps.1.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.overlaps.1.fa -s B .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.overlaps.1.bcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.overlaps.1.fa -s B .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.overlaps.1.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.overlaps.1.fa -s A -a N .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.overlaps.1.bcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.overlaps.1.fa -s A -a N .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.overlaps.1.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.overlaps.1.fa -s B -a N .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.overlaps.1.bcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.overlaps.1.fa -s B -a N .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.beyond.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.beyond.fa .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.beyond.bcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.beyond.fa .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.fa -s - -m /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.tab .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.bcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.fa -s - -m /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.tab .. ok test_vcf_consensus_chain: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.fa -s - -m /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.tab -c /tmp/iaQXJX5nkE/consensus.1.chain.new >/dev/null; cat /tmp/iaQXJX5nkE/consensus.1.chain.new .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.fa -H 1 -m /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.tab .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.bcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.fa -H 1 -m /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.tab .. ok test_vcf_consensus_chain: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.fa -H 1 -m /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.tab -c /tmp/iaQXJX5nkE/consensus.2.chain.new >/dev/null; cat /tmp/iaQXJX5nkE/consensus.2.chain.new .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.fa -I -s - -m /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.tab .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.bcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.fa -I -s - -m /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.tab .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.fa -s - -I -m /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.tab --mask-with X -m /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.tab --mask-with lc .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.bcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.fa -s - -I -m /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.tab --mask-with X -m /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.tab --mask-with lc .. ok test_vcf_consensus_chain: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.fa -I -m /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.tab -c /tmp/iaQXJX5nkE/consensus.3.chain.new >/dev/null; cat /tmp/iaQXJX5nkE/consensus.3.chain.new .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.fa -H 1 .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.bcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.fa -H 1 .. ok test_vcf_consensus_chain: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.fa -H 1 -c /tmp/iaQXJX5nkE/consensus.4.chain.new >/dev/null; cat /tmp/iaQXJX5nkE/consensus.4.chain.new .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus2.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus2.fa -H 1 .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus2.bcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus2.fa -H 1 .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus2.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus2.fa -H 2 .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus2.bcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus2.fa -H 2 .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/empty.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.fa -s - .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/empty.bcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.fa -s - .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus3.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus2.fa -H 2 -M "?" .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus3.bcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus2.fa -H 2 -M "?" .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus3.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus2.fa -H 2 -M "?" -p xx_ .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus3.bcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus2.fa -H 2 -M "?" -p xx_ .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus4.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus2.fa -s - .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus4.bcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus2.fa -s - .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus5.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus5.fa --haplotype LA .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus5.bcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus5.fa --haplotype LA .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus6.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus6.fa -s - .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus6.bcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus6.fa -s - .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus7.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus7.fa -H 2 .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus7.bcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus7.fa -H 2 .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus7.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus7.fa -H 4 .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus7.bcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus7.fa -H 4 .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus7.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus7.fa -H 2pIu .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus7.bcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus7.fa -H 2pIu .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus7.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus7.fa -H 4pIu .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus7.bcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus7.fa -H 4pIu .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus7.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus7.fa -H 1 .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus7.bcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus7.fa -H 1 .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus7.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus7.fa -H 3 .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus7.bcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus7.fa -H 3 .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus7.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus7.fa -H 1pIu .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus7.bcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus7.fa -H 1pIu .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus7.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus7.fa -H 3pIu .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus7.bcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus7.fa -H 3pIu .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus8.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.fa -s - .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus8.bcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.fa -s - .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus8.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.fa -s - -a . .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus8.bcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.fa -s - -a . .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus8.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.fa -s - -a . -i 'type="snp" || type="ref"' .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus8.bcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.fa -s - -a . -i 'type="snp" || type="ref"' .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus8.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.fa -s - -a . -i 'ALT!=""' .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus8.bcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.fa -s - -a . -i 'ALT!=""' .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus8.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.fa -s - -a . -e 'MinDP>15' .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus8.bcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.fa -s - -a . -e 'MinDP>15' .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus8.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.fa -s - -a . -e 'MinDP<15' .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus8.bcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.fa -s - -a . -e 'MinDP<15' .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.9.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.9.bcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.9.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.9.bcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.10.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.10.bcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.10.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.10.bcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.11.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.11.fa -s smpl .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.11.bcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.11.fa -s smpl .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.11.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.11.fa -s smpl -a N .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.11.bcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.11.fa -s smpl -a N .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.12.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.12.fa -s - .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.12.bcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.12.fa -s - .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.13.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.13.fa -s - .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.13.bcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.13.fa -s - .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.14.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.14.fa -s - .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.14.bcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.14.fa -s - .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.12.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.12.fa -s - --mark-del - --mark-ins uc --mark-snv uc .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.12.bcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.12.fa -s - --mark-del - --mark-ins uc --mark-snv uc .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.12.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.12.fa -s - --mark-del - --mark-ins + --mark-snv : .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.12.bcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.12.fa -s - --mark-del - --mark-ins + --mark-snv : .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.15.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.15.fa -H I --mark-ins lc --mark-snv lc .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.15.bcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.15.fa -H I --mark-ins lc --mark-snv lc .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.16.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.fa -s - -I .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.16.bcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.fa -s - -I .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.16.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.fa -H I .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.16.bcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.fa -H I .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.17.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus2.fa -s - -M N -m /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.17.bed .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.17.bcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus2.fa -s - -M N -m /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.17.bed .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.18.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.18.fa -s - .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.18.bcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.18.fa -s - .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.19.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.19.fa -s - .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.19.bcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.19.fa -s - .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.20.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.20.fa -s - .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.20.bcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.20.fa -s - .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.20.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.20.fa .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.20.bcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.20.fa .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.20.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.20.fa -M . -s b .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.20.bcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.20.fa -M . -s b .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.20.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.20.fa -M . -s a .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.20.bcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.20.fa -M . -s a .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.20.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.20.fa -M . -S /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.20.b.txt .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.20.bcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.20.fa -M . -S /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.20.b.txt .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.20.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.20.fa -M . -S /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.20.a.txt .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.20.bcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.20.fa -M . -S /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.20.a.txt .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.21.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.21.fa .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.21.bcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.21.fa .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.22.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.22.fa --regions-overlap 0 --mark-del . .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.22.bcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.22.fa --regions-overlap 0 --mark-del . .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.22.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.22.fa --regions-overlap 1 --mark-del . .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.22.bcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.22.fa --regions-overlap 1 --mark-del . .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.22.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.22.fa --regions-overlap 2 --mark-del . .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.22.bcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.22.fa --regions-overlap 2 --mark-del . .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.22.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.22.fa --regions-overlap 0 .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.22.bcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.22.fa --regions-overlap 0 .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.22.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.22.fa --regions-overlap 1 .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.22.bcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.22.fa --regions-overlap 1 .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.22.vcf.gz -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.22.fa --regions-overlap 2 .. ok test_vcf_consensus: /build/bcftools-qI88Pr/bcftools-1.24/bcftools consensus /tmp/iaQXJX5nkE/consensus.22.bcf -f /build/bcftools-qI88Pr/bcftools-1.24/test/consensus.22.fa --regions-overlap 2 .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -r 11:10-20 -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/iupac.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/iupac.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -r 11:10-20 -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/iupac.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/iupac.bam | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -r17:100-102,17:102-103,17:103-104,17:104-105,17:100-105 -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.1.bam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.2.bam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -r17:100-102,17:102-103,17:103-104,17:104-105,17:100-105 -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.1.bam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.2.bam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.bam | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -r17:100-102,17:102-103,17:103-104,17:104-105,17:100-105 -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa -b /tmp/iaQXJX5nkE/mpileup.bam.list --no-version | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -r17:100-102,17:102-103,17:103-104,17:104-105,17:100-105 -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa -Ob -b /tmp/iaQXJX5nkE/mpileup.bam.urllist | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -r17:100-102,17:102-103,17:103-104,17:104-105,17:100-105 -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.1.cram /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.2.cram /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -r17:100-102,17:102-103,17:103-104,17:104-105,17:100-105 -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.1.cram /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.2.cram /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.cram | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -r17:100-102,17:102-103,17:103-104,17:104-105,17:100-105 -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa -b /tmp/iaQXJX5nkE/mpileup.cram.list --no-version | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -r17:100-102,17:102-103,17:103-104,17:104-105,17:100-105 -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa -Ob -b /tmp/iaQXJX5nkE/mpileup.cram.urllist | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -r17:100-150 -a -AD -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.1.bam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.2.bam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -r17:100-150 -a -AD -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.1.bam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.2.bam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.bam | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -r17:100-150 -a -AD -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa -b /tmp/iaQXJX5nkE/mpileup.bam.list --no-version | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -r17:100-150 -a -AD -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa -Ob -b /tmp/iaQXJX5nkE/mpileup.bam.urllist | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -r17:100-150 -a -AD -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.1.cram /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.2.cram /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -r17:100-150 -a -AD -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.1.cram /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.2.cram /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.cram | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -r17:100-150 -a -AD -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa -b /tmp/iaQXJX5nkE/mpileup.cram.list --no-version | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -r17:100-150 -a -AD -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa -Ob -b /tmp/iaQXJX5nkE/mpileup.cram.urllist | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a DP,DV -r17:100-600 -a -AD -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.1.bam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.2.bam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a DP,DV -r17:100-600 -a -AD -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.1.bam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.2.bam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.bam | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a DP,DV -r17:100-600 -a -AD -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.1.cram /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.2.cram /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a DP,DV -r17:100-600 -a -AD -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.1.cram /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.2.cram /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.cram | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -a -AD -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -a -AD -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.1.bam | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -a -AD -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.1.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -a -AD -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.1.cram | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP,-AD -r17:100-600 -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.1.bam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.2.bam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP,-AD -r17:100-600 -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.1.bam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.2.bam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.bam | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP,-AD -r17:100-600 -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.1.cram /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.2.cram /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP,-AD -r17:100-600 -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.1.cram /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.2.cram /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.cram | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.1.bam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.2.bam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.1.bam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.2.bam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.bam | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.1.cram /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.2.cram /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.1.cram /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.2.cram /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.cram | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a DP,DV,-AD -r17:100-600 --gvcf 0,2,5 -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.1.bam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.2.bam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a DP,DV,-AD -r17:100-600 --gvcf 0,2,5 -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.1.bam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.2.bam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.bam | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a DP,DV,-AD -r17:100-600 --gvcf 0,2,5 -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.1.cram /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.2.cram /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a DP,DV,-AD -r17:100-600 --gvcf 0,2,5 -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.1.cram /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.2.cram /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.cram | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/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-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.1.bam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.2.bam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/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-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.1.bam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.2.bam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.bam | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/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-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.1.cram /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.2.cram /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/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-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.1.cram /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.2.cram /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.cram | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -r17:100-150 -s HG00101,HG00102 -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.1.bam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.2.bam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -r17:100-150 -s HG00101,HG00102 -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.1.bam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.2.bam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.bam | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -r17:100-150 -s HG00101,HG00102 -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.1.cram /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.2.cram /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -r17:100-150 -s HG00101,HG00102 -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.1.cram /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.2.cram /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.cram | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -r17:100-150 -S /build/bcftools-qI88Pr/bcftools-1.24/test/mplp.samples -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.1.bam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.2.bam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -r17:100-150 -S /build/bcftools-qI88Pr/bcftools-1.24/test/mplp.samples -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.1.bam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.2.bam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.bam | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -r17:100-150 -S /build/bcftools-qI88Pr/bcftools-1.24/test/mplp.samples -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.1.cram /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.2.cram /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -r17:100-150 -S /build/bcftools-qI88Pr/bcftools-1.24/test/mplp.samples -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.1.cram /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.2.cram /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.cram | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -r17:100-150 -s ^HG00101,HG00102 -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.1.bam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.2.bam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -r17:100-150 -s ^HG00101,HG00102 -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.1.bam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.2.bam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.bam | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -r17:100-150 -s ^HG00101,HG00102 -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.1.cram /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.2.cram /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -r17:100-150 -s ^HG00101,HG00102 -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.1.cram /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.2.cram /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.cram | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -r17:100-150 -S ^/build/bcftools-qI88Pr/bcftools-1.24/test/mplp.samples -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.1.bam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.2.bam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -r17:100-150 -S ^/build/bcftools-qI88Pr/bcftools-1.24/test/mplp.samples -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.1.bam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.2.bam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.bam | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -r17:100-150 -S ^/build/bcftools-qI88Pr/bcftools-1.24/test/mplp.samples -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.1.cram /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.2.cram /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -r17:100-150 -S ^/build/bcftools-qI88Pr/bcftools-1.24/test/mplp.samples -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.1.cram /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.2.cram /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.cram | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -t17:100-150 -S /build/bcftools-qI88Pr/bcftools-1.24/test/mplp.9.samples -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.1.sam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.2.sam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -t17:100-150 -S /build/bcftools-qI88Pr/bcftools-1.24/test/mplp.9.samples -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.1.sam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.2.sam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.sam | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -t17:100-150 -S /build/bcftools-qI88Pr/bcftools-1.24/test/mplp.9.samples -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.1.bam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.2.bam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -t17:100-150 -S /build/bcftools-qI88Pr/bcftools-1.24/test/mplp.9.samples -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.1.bam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.2.bam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.bam | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -t17:100-150 -S /build/bcftools-qI88Pr/bcftools-1.24/test/mplp.9.samples -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.1.cram /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.2.cram /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -t17:100-150 -S /build/bcftools-qI88Pr/bcftools-1.24/test/mplp.9.samples -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.1.cram /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.2.cram /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.cram | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -t17:100-150 -G /build/bcftools-qI88Pr/bcftools-1.24/test/mplp.10.samples -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.1.sam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.2.sam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -t17:100-150 -G /build/bcftools-qI88Pr/bcftools-1.24/test/mplp.10.samples -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.1.sam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.2.sam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.sam | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -t17:100-150 -G /build/bcftools-qI88Pr/bcftools-1.24/test/mplp.10.samples -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.1.bam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.2.bam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -t17:100-150 -G /build/bcftools-qI88Pr/bcftools-1.24/test/mplp.10.samples -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.1.bam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.2.bam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.bam | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -t17:100-150 -G /build/bcftools-qI88Pr/bcftools-1.24/test/mplp.10.samples -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.1.cram /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.2.cram /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -t17:100-150 -G /build/bcftools-qI88Pr/bcftools-1.24/test/mplp.10.samples -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.1.cram /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.2.cram /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.cram | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.sam | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.bam | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.cram | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -s HG00102 -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.sam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -s HG00102 -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.sam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.4.sam | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -s HG00102 -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.bam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -s HG00102 -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.bam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.4.bam | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -s HG00102 -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.cram /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -s HG00102 -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.cram /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.4.cram | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -s ^HG99999 -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.sam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -s ^HG99999 -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.sam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.4.sam | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -s ^HG99999 -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.bam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -s ^HG99999 -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.bam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.4.bam | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -s ^HG99999 -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.cram /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -s ^HG99999 -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.cram /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.4.cram | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -G /build/bcftools-qI88Pr/bcftools-1.24/test/mplp.11.rgs -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.sam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -G /build/bcftools-qI88Pr/bcftools-1.24/test/mplp.11.rgs -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.sam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.4.sam | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -G /build/bcftools-qI88Pr/bcftools-1.24/test/mplp.11.rgs -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.bam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -G /build/bcftools-qI88Pr/bcftools-1.24/test/mplp.11.rgs -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.bam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.4.bam | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -G /build/bcftools-qI88Pr/bcftools-1.24/test/mplp.11.rgs -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.cram /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -G /build/bcftools-qI88Pr/bcftools-1.24/test/mplp.11.rgs -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.cram /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.4.cram | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -G /build/bcftools-qI88Pr/bcftools-1.24/test/mplp.11.rgs -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.sam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -G /build/bcftools-qI88Pr/bcftools-1.24/test/mplp.11.rgs -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.sam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.4.sam | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -G /build/bcftools-qI88Pr/bcftools-1.24/test/mplp.11.rgs -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.bam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -G /build/bcftools-qI88Pr/bcftools-1.24/test/mplp.11.rgs -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.bam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.4.bam | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -G /build/bcftools-qI88Pr/bcftools-1.24/test/mplp.11.rgs -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.cram /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -G /build/bcftools-qI88Pr/bcftools-1.24/test/mplp.11.rgs -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.ref.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.3.cram /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup.4.cram | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a AD -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/indel-AD.1.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/indel-AD.1.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a AD -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/indel-AD.1.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/indel-AD.1.sam | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a AD -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/indel-AD.1.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/indel-AD.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a AD -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/indel-AD.1.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/indel-AD.1.bam | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a AD -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/indel-AD.1.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/indel-AD.1.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a AD -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/indel-AD.1.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/indel-AD.1.cram | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a AD --indels-cns -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/indel-AD.1.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/indel-AD.1.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a AD --indels-cns -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/indel-AD.1.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/indel-AD.1.sam | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a AD --indels-cns -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/indel-AD.1.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/indel-AD.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a AD --indels-cns -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/indel-AD.1.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/indel-AD.1.bam | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a AD --indels-cns -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/indel-AD.1.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/indel-AD.1.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a AD --indels-cns -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/indel-AD.1.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/indel-AD.1.cram | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a AD -r 11:75 -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/indel-AD.2.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a AD -r 11:75 -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/indel-AD.2.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/indel-AD.2.bam | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a AD -r 11:75 -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/indel-AD.2.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a AD -r 11:75 -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/indel-AD.2.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/indel-AD.2.cram | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/indel-AD.2.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/indel-AD.2.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/indel-AD.2.bam | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/indel-AD.2.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/indel-AD.2.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/indel-AD.2.cram | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/indel-AD.2.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/indel-AD.2.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/indel-AD.2.bam | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/indel-AD.2.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/indel-AD.2.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/indel-AD.2.cram | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD,INFO/SCR,FMT/SCR -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup-SCR.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup-SCR.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD,INFO/SCR,FMT/SCR -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup-SCR.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup-SCR.bam | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD,INFO/SCR,FMT/SCR -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup-SCR.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup-SCR.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD,INFO/SCR,FMT/SCR -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup-SCR.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup-SCR.cram | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -t 1:100 --skip-all-set PAIRED,PROPER_PAIR,MREVERSE -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup-SCR.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -t 1:100 --skip-all-set PAIRED,PROPER_PAIR,MREVERSE -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup-SCR.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup-filter.sam | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -t 1:100 --skip-any-set READ1 -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup-SCR.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -t 1:100 --skip-any-set READ1 -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup-SCR.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup-filter.sam | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -t 1:100 --skip-all-unset READ1 -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup-SCR.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -t 1:100 --skip-all-unset READ1 -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup-SCR.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup-filter.sam | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -t 1:100 --skip-any-unset READ1 -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup-SCR.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD -t 1:100 --skip-any-unset READ1 -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup-SCR.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/mpileup-filter.sam | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD,INFO/NMBZ -r chr19:69-99 -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/annot-NMBZ.1.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/annot-NMBZ.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD,INFO/NMBZ -r chr19:69-99 -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/annot-NMBZ.1.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/annot-NMBZ.1.bam | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD,INFO/NMBZ -r chr6:75 -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/annot-NMBZ.2.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/annot-NMBZ.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD,INFO/NMBZ -r chr6:75 -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/annot-NMBZ.2.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/annot-NMBZ.2.bam | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD,INFO/NMBZ -r chr16:75 -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/annot-NMBZ.3.fa /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/annot-NMBZ.3.1.bam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/annot-NMBZ.3.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /build/bcftools-qI88Pr/bcftools-1.24/bcftools mpileup -a -AD,INFO/NMBZ -r chr16:75 -f /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/annot-NMBZ.3.fa -Ob /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/annot-NMBZ.3.1.bam /build/bcftools-qI88Pr/bcftools-1.24/test/mpileup/annot-NMBZ.3.2.bam | /build/bcftools-qI88Pr/bcftools-1.24/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_csq: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq.greedy.1.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq.greedy.1.gff -pa /build/bcftools-qI88Pr/bcftools-1.24/test/csq.greedy.1.vcf | grep -v ^# .. ok test_csq: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq.greedy.1.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq.greedy.1.gff -pa -G1 /build/bcftools-qI88Pr/bcftools-1.24/test/csq.greedy.1.vcf | grep -v ^# .. ok test_csq: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq.greedy.1.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq.greedy.1.gff -pa -Ot /build/bcftools-qI88Pr/bcftools-1.24/test/csq.greedy.1.vcf | grep -v ^# .. ok test_csq: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq.greedy.1.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq.greedy.1.gff -pa -Ot -G1 /build/bcftools-qI88Pr/bcftools-1.24/test/csq.greedy.1.vcf | grep -v ^# .. ok test_csq: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq.greedy.2.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq.greedy.2.gff -pa /build/bcftools-qI88Pr/bcftools-1.24/test/csq.greedy.2.vcf | grep -v ^# .. ok test_csq: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq.greedy.2.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq.greedy.2.gff -pa -G1 /build/bcftools-qI88Pr/bcftools-1.24/test/csq.greedy.2.vcf | grep -v ^# .. ok test_csq: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq.greedy.2.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq.greedy.2.gff -pa -Ot /build/bcftools-qI88Pr/bcftools-1.24/test/csq.greedy.2.vcf | grep -v ^# .. ok test_csq: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq.greedy.2.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq.greedy.2.gff -pa -Ot -G1 /build/bcftools-qI88Pr/bcftools-1.24/test/csq.greedy.2.vcf | grep -v ^# .. ok test_csq: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq.ismpl.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq.ismpl.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq.ismpl.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%SAMPLE %GT %BCSQ %TBCSQ\n]' .. ok test_csq: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq.splice.issue-2543.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq.splice.issue-2543.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq.splice.issue-2543.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/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-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq.oob-codon.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq.oob-codon.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq.oob-codon.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/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-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq.gff3 /build/bcftools-qI88Pr/bcftools-1.24/test/csq.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/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-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq.chr.gff3 --unify-chr-names -,chr,- /build/bcftools-qI88Pr/bcftools-1.24/test/csq.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/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-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq.2.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq.2.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq.2.gff --ncsq 64 /build/bcftools-qI88Pr/bcftools-1.24/test/csq.2.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq.nchr.gff -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq.nchr.fa --unify-chr-names -,-,- /build/bcftools-qI88Pr/bcftools-1.24/test/csq.nchr.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq.nchr.gff -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq.ychr.fa --unify-chr-names -,-,chr /build/bcftools-qI88Pr/bcftools-1.24/test/csq.nchr.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq.ychr.gff -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq.nchr.fa --unify-chr-names -,chr,- /build/bcftools-qI88Pr/bcftools-1.24/test/csq.nchr.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq.ychr.gff -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq.ychr.fa --unify-chr-names -,chr,chr /build/bcftools-qI88Pr/bcftools-1.24/test/csq.nchr.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq.ychr.gff -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq.ychr.fa --unify-chr-names chr,chr,chr /build/bcftools-qI88Pr/bcftools-1.24/test/csq.ychr.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq.nchr.gff -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq.ychr.fa --unify-chr-names chr,-,chr /build/bcftools-qI88Pr/bcftools-1.24/test/csq.ychr.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq.ychr.gff -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq.nchr.fa --unify-chr-names chr,chr,- /build/bcftools-qI88Pr/bcftools-1.24/test/csq.ychr.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq.nchr.gff -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq.nchr.fa --unify-chr-names chr,-,- /build/bcftools-qI88Pr/bcftools-1.24/test/csq.ychr.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq.nchr.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq.ychr.gff --unify-chr-names Chromosome,chr,- /build/bcftools-qI88Pr/bcftools-1.24/test/csq.yychr.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000373833/ENST00000373833.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000373833/ENST00000373833.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000373833/boundary-insertion.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -l -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000373833/ENST00000373833.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000373833/ENST00000373833.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000373833/boundary-insertion.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/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-qI88Pr/bcftools-1.24/test/csq/ENST00000422159 && /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f ENST00000422159.fa -g ENST00000422159.gff multiallelic.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS\t%REF\t%ALT\t%GT\t%TBCSQ\n]' | ../sort-csq -q ; echo ; /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f ENST00000422159.fa -g short.gff multiallelic.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS\t%REF\t%ALT\t%GT\t%TBCSQ\n]' | ../sort-csq -q .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000378322/ENST00000378322.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000378322/ENST00000378322.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000378322/end-overlap-tscript.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -l -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000378322/ENST00000378322.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000378322/ENST00000378322.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000378322/end-overlap-tscript.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000263103-INS/ENST00000263103-INS.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000263103-INS/ENST00000263103-INS.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000263103-INS/insertions.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000269081/ENST00000269081.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000269081/ENST00000269081.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000269081/stop-gained-not-inframe-insertion.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000420190/ENST00000420190.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000420190/ENST00000420190.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000420190/abort-in-csq-push.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000329454/ENST00000329454.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000329454/ENST00000329454.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000329454/boundary-deletion.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -l -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000329454/ENST00000329454.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000329454/ENST00000329454.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000329454/boundary-deletion.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000294661/ENST00000294661.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000294661/ENST00000294661.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000294661/non-coding-boundary.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -l -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000294661/ENST00000294661.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000294661/ENST00000294661.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000294661/non-coding-boundary.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000285021/ENST00000285021.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000285021/ENST00000285021.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000285021/stop-gained-inframe-indel.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000381157/ENST00000381157.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000381157/ENST00000381157.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000381157/haploid-diploid.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n' .. ok test_csq_real: cd /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000410009 && /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -lb -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000410009 && /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -B 5 -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000410009 && /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -b -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000410009/ENST00000410009.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000410009/ENST00000410009.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000410009/frameshift.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/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-qI88Pr/bcftools-1.24/test/csq/ENSMUST00000133836 && /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f ENSMUST00000133836.fa -g ENSMUST00000133836.gff filter-problem.vcf -i 'FILTER="PASS"' --phase m | ../sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/bcftools-qI88Pr/bcftools-1.24/test/csq/EMN908947 && /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f EMN908947.fa -g ribosomal-slippage.gff ribosomal-slippage.vcf --force | ../sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/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-qI88Pr/bcftools-1.24/test/csq/EMN908947 && /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f EMN908947.fa -g simple.gff simple.vcf | ../sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000519442/ENST00000519442.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000519442/ENST00000519442.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000519442/synon-splice-region-del.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000557788/ENST00000557788.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000557788/ENST00000557788.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000557788/long-overlap-del.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/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-qI88Pr/bcftools-1.24/test/csq/ENSMUST00000121418 && /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25105' --phase m | ../sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENSMUST00000121418 && /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25500' --phase m | ../sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENSMUST00000121418 && /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25496' --phase m | ../sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000420670/ENST00000420670.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000420670/ENST00000420670.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000420670/start-stop-lost.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000420670/ENST00000420670.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000420670/ENST00000420670.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000420670/segfault.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000409523/ENST00000409523.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000409523/ENST00000409523.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000409523/long-overlapping-del.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000520795/ENST00000520795.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000520795/ENST00000520795.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000520795/long-inside-del.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -l -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000520795/ENST00000520795.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000520795/ENST00000520795.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000520795/long-inside-del.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000382647/ENST00000382647.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000382647/ENST00000382647.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000382647/synon-splice-region-insert.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000545279/ENST00000545279.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000545279/ENST00000545279.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000545279/splice-region-insert.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000528237/ENST00000528237.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000528237/ENST00000528237.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000528237/retained-stop-incomplete-cds.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/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-qI88Pr/bcftools-1.24/test/csq/ENST00000379416 && /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.del-snp.vcf | ../sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-del.vcf | ../sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-ins.vcf | ../sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-snp.vcf | ../sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff single.vcf | ../sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000400151/ENST00000400151.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000400151/ENST00000400151.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000400151/long-del.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000624631/ENST00000624631.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000624631/ENST00000624631.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000624631/ambiguous.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000218032/ENST00000218032.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000218032/ENST00000218032.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000218032/start-lost-del.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000218032/ENST00000218032.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000218032/ENST00000218032.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000218032/start-lost.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -l -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000218032/ENST00000218032.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000218032/ENST00000218032.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000218032/start-lost.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000542803/ENST00000542803.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000542803/ENST00000542803.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000542803/splice-region.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -l -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000542803/ENST00000542803.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000542803/ENST00000542803.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000542803/splice-region.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000543077/ENST00000543077.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000543077/ENST00000543077.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000543077/not-a-start-lost.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -l -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000543077/ENST00000543077.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000543077/ENST00000543077.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000543077/not-a-start-lost.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -l -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -l -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -l -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/frame3.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -l -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/frame3.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -l -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -l -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -l -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/frame2.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -l -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/frame2.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/not-a-start-lost.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -l -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/not-a-start-lost.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/frame1.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -l -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/frame1.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -l -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -l -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -l -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/ENST00000341065.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/ENST00000341065.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000536784/ENST00000536784.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000536784/ENST00000536784.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000536784/not-a-start-lost.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -l -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000536784/ENST00000536784.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000536784/ENST00000536784.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000536784/not-a-start-lost.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/EDUMMY0003/EDUMMY0003.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/EDUMMY0003/EDUMMY0003.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/EDUMMY0003/long-del.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/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-qI88Pr/bcftools-1.24/test/csq/ENST00000000000 && /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -p a -f ENST00000000000.fa -g ENST00000000000.gff upstream-stop.vcf | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'[%POS\t%REF\t%ALT\t%SAMPLE\t%GT\t%TBCSQ\n]' | ../sort-csq -q .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000448695/ENST00000448695.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000448695/ENST00000448695.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000448695/syn-and-splice-reg.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENSCAFT00000047742/ENSCAFT00000047742.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENSCAFT00000047742/ENSCAFT00000047742.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENSCAFT00000047742/test.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/EDUMMY0002/EDUMMY0002.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/EDUMMY0002/EDUMMY0002.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/EDUMMY0002/boundaries.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000318249/ENST00000318249.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000318249/ENST00000318249.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000318249/start-lost.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -l -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000318249/ENST00000318249.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000318249/ENST00000318249.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000318249/start-lost.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/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-qI88Pr/bcftools-1.24/test/csq/ENST00000580206 && /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.ins-snv.vcf | ../sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f ENST00000580206.fa -g short.gff compound.ins-snv.vcf | ../sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff single.ins-snv.vcf | ../sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f ENST00000580206.fa -g short.gff single.ins-snv.vcf | ../sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.del-snv.vcf | ../sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f ENST00000580206.fa -g short.gff compound.del-snv.vcf | ../sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f ENST00000580206.fa -g short.gff single.del-snv.vcf | ../sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.del-ins.vcf | ../sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f ENST00000580206.fa -g short.gff compound.del-ins.vcf | ../sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f ENST00000580206.fa -g short.gff single.del-ins.vcf | ../sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000520868/ENST00000520868.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000520868/ENST00000520868.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000520868/long-deletion.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000413103/ENST00000413103.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000413103/ENST00000413103.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000413103/long-deletion.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENSG00000173376/ENSG00000173376.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENSG00000173376/ENSG00000173376.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENSG00000173376/synon.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000571540/ENST00000571540.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000571540/ENST00000571540.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000571540/nmd.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000227471/ENST00000227471.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000227471/ENST00000227471.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000227471/insert-splice-vs-frameshift.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000271583/ENST00000271583.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000271583/ENST00000271583.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000271583/splice-acceptor.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000368801/ENST00000368801.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000368801/ENST00000368801.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000368801/compound-lost.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000301246/ENST00000301246.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000301246/ENST00000301246.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000301246/15bp-insert.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000318249.2/ENST00000318249.2.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000318249.2/ENST00000318249.2.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000318249.2/synonymous-start-lost.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/EDUMMY0001/EDUMMY0001.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/EDUMMY0001/EDUMMY0001.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/EDUMMY0001/starts-with-1.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -l -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/EDUMMY0001/EDUMMY0001.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/EDUMMY0001/EDUMMY0001.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/EDUMMY0001/starts-with-1.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/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-qI88Pr/bcftools-1.24/test/csq/ENST00000000001 && /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f ENST00000000001.fa -g ENST00000000001.gff test.vcf -p a -Ot | grep -v ^# .. ok test_csq_real: cd /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000000001 && /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f ENST00000000001.fa -g ENST00000000001.gff test.vcf -p a | ../sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000295641/ENST00000295641.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000295641/ENST00000295641.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000295641/not-a-start-lost.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -l -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000295641/ENST00000295641.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000295641/ENST00000295641.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000295641/not-a-start-lost.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000479739/ENST00000479739.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000479739/ENST00000479739.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000479739/short-cds-start-lost.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -l -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000479739/ENST00000479739.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000479739/ENST00000479739.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000479739/short-cds-start-lost.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000436063/ENST00000436063.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000436063/ENST00000436063.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000436063/insert-before-utr.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000573035-bt2212/ENST00000573035-bt2212.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000573035-bt2212/ENST00000573035-bt2212.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000573035-bt2212/complex-event.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000518414/ENST00000518414.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000518414/ENST00000518414.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000518414/incorrect-inframe-del.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/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-qI88Pr/bcftools-1.24/test/csq/ENST00000368801.2 && /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f ENST00000368801.2.fa -g ENST00000368801.2.gff alt-gencode.vcf -v 0 -C 1 | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%BCSQ\n' | ../sort-csq -q .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000368801.2/ENST00000368801.2.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000368801.2/ENST00000368801.2.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000368801.2/start-lost.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/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-qI88Pr/bcftools-1.24/test/csq/ENST00000368801.2 && /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f ENST00000368801.2.fa -g ENST00000368801.2.gff alt-gencode.vcf -v 0 -C 0 | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%BCSQ\n' | ../sort-csq -q .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000518414-ENST00000521270/valgrind.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000423372/ENST00000423372.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000423372/ENST00000423372.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000423372/snps.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -l -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000423372/ENST00000423372.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000423372/ENST00000423372.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000423372/snps.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000423372/ENST00000423372.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000423372/ENST00000423372.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000423372/insert3.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -l -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000423372/ENST00000423372.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000423372/ENST00000423372.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000423372/insert3.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000303039/ENST00000303039.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000303039/ENST00000303039.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000303039/not-a-stop.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -l -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000303039/ENST00000303039.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000303039/ENST00000303039.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000303039/not-a-stop.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000256452/ENST00000256452.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000256452/ENST00000256452.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000256452/intron.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000357367/ENST00000357367.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000357367/ENST00000357367.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000357367/stop-retained.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000375992/ENST00000375992.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000375992/ENST00000375992.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000375992/incorrect-synon-del-not-start-lost.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000593942/ENST00000593942.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000593942/ENST00000593942.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000593942/last-codon-deletion.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000360372/ENST00000360372.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000360372/ENST00000360372.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000360372/mnp.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000230048/ENST00000230048.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000230048/ENST00000230048.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000230048/start-del.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000573314/ENST00000573314.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000573314/ENST00000573314.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -l -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000573314/ENST00000573314.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000573314/ENST00000573314.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /build/bcftools-qI88Pr/bcftools-1.24/bcftools csq -f /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000390520/ENST00000390520.fa -g /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000390520/ENST00000390520.gff /build/bcftools-qI88Pr/bcftools-1.24/test/csq/ENST00000390520/deletion-overlap.vcf | /build/bcftools-qI88Pr/bcftools-1.24/test/csq/sort-csq | /build/bcftools-qI88Pr/bcftools-1.24/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-qI88Pr/bcftools-1.24/bcftools roh /build/bcftools-qI88Pr/bcftools-1.24/test/roh.1.vcf.gz -Or -G30 --AF-dflt 0.4| grep -v ^# .. ok test_roh: /build/bcftools-qI88Pr/bcftools-1.24/bcftools roh /build/bcftools-qI88Pr/bcftools-1.24/test/roh.1.vcf.gz -Or -G30 --AF-file /build/bcftools-qI88Pr/bcftools-1.24/test/roh.1.tab.gz| grep -v ^# .. ok test_roh: /build/bcftools-qI88Pr/bcftools-1.24/bcftools roh /build/bcftools-qI88Pr/bcftools-1.24/test/roh.1.vcf.gz -Or -G30 --AF-file /build/bcftools-qI88Pr/bcftools-1.24/test/roh.1.tab.gz --ignore-homref| grep -v ^# .. ok test_roh: /build/bcftools-qI88Pr/bcftools-1.24/bcftools roh /build/bcftools-qI88Pr/bcftools-1.24/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245| grep -v ^# .. ok test_roh: /build/bcftools-qI88Pr/bcftools-1.24/bcftools roh /build/bcftools-qI88Pr/bcftools-1.24/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --ignore-homref| grep -v ^# .. ok test_roh: /build/bcftools-qI88Pr/bcftools-1.24/bcftools roh /build/bcftools-qI88Pr/bcftools-1.24/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-qI88Pr/bcftools-1.24/bcftools roh /build/bcftools-qI88Pr/bcftools-1.24/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --include-noalt| grep -v ^# .. ok test_gtcheck: /build/bcftools-qI88Pr/bcftools-1.24/bcftools gtcheck --keep-refs /tmp/iaQXJX5nkE/gtcheck.gvcf.a.vcf.gz -g /tmp/iaQXJX5nkE/gtcheck.gvcf.b.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-qI88Pr/bcftools-1.24/bcftools gtcheck --keep-refs /tmp/iaQXJX5nkE/gtcheck.gvcf.b.vcf.gz -g /tmp/iaQXJX5nkE/gtcheck.gvcf.a.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-qI88Pr/bcftools-1.24/bcftools gtcheck /tmp/iaQXJX5nkE/gtcheck.gvcf.a.vcf.gz -g /tmp/iaQXJX5nkE/gtcheck.gvcf.b.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-qI88Pr/bcftools-1.24/bcftools gtcheck /tmp/iaQXJX5nkE/gtcheck.gvcf.b.vcf.gz -g /tmp/iaQXJX5nkE/gtcheck.gvcf.a.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-qI88Pr/bcftools-1.24/bcftools gtcheck -e 0 --no-HWE-prob /tmp/iaQXJX5nkE/gtcheck.1.vcf.gz -g /tmp/iaQXJX5nkE/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-qI88Pr/bcftools-1.24/bcftools gtcheck -e 0 /tmp/iaQXJX5nkE/gtcheck.1.vcf.gz -g /tmp/iaQXJX5nkE/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-qI88Pr/bcftools-1.24/bcftools gtcheck -e 0 -u GT,GT /tmp/iaQXJX5nkE/gtcheck.1.vcf.gz -g /tmp/iaQXJX5nkE/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-qI88Pr/bcftools-1.24/bcftools gtcheck -e 0 -u GT,PL /tmp/iaQXJX5nkE/gtcheck.1.vcf.gz -g /tmp/iaQXJX5nkE/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-qI88Pr/bcftools-1.24/bcftools gtcheck -e 0 -u PL,GT /tmp/iaQXJX5nkE/gtcheck.1.vcf.gz -g /tmp/iaQXJX5nkE/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-qI88Pr/bcftools-1.24/bcftools gtcheck -e 0 -u PL,PL /tmp/iaQXJX5nkE/gtcheck.1.vcf.gz -g /tmp/iaQXJX5nkE/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-qI88Pr/bcftools-1.24/bcftools gtcheck -e 0 -p s1,s1 /tmp/iaQXJX5nkE/gtcheck.1.vcf.gz -g /tmp/iaQXJX5nkE/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-qI88Pr/bcftools-1.24/bcftools gtcheck -e 0 /tmp/iaQXJX5nkE/gtcheck.2.vcf.gz -g /tmp/iaQXJX5nkE/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-qI88Pr/bcftools-1.24/bcftools gtcheck -e 0 /tmp/iaQXJX5nkE/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-qI88Pr/bcftools-1.24/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/iaQXJX5nkE/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-qI88Pr/bcftools-1.24/bcftools gtcheck -e 0 -P /build/bcftools-qI88Pr/bcftools-1.24/test/gtcheck.3.pairs /tmp/iaQXJX5nkE/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-qI88Pr/bcftools-1.24/bcftools gtcheck -e 0 -u PL /tmp/iaQXJX5nkE/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-qI88Pr/bcftools-1.24/bcftools gtcheck -e 0 --n-matches 4 /tmp/iaQXJX5nkE/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO | sort .. ok test_gtcheck: /build/bcftools-qI88Pr/bcftools-1.24/bcftools gtcheck -e 0 -s qry:E,D,C /tmp/iaQXJX5nkE/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-qI88Pr/bcftools-1.24/bcftools gtcheck -e 0 -s qry:E,D,C -u PL /tmp/iaQXJX5nkE/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-qI88Pr/bcftools-1.24/bcftools gtcheck -e 0 -s qry:B -s gt:D /tmp/iaQXJX5nkE/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-qI88Pr/bcftools-1.24/bcftools gtcheck -e 0 -s qry:B -s gt:D -u PL /tmp/iaQXJX5nkE/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-qI88Pr/bcftools-1.24/bcftools gtcheck -e 0 -s qry:B -s gt:D,C /tmp/iaQXJX5nkE/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-qI88Pr/bcftools-1.24/bcftools gtcheck -e 0 -p B,C,B,D /tmp/iaQXJX5nkE/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-qI88Pr/bcftools-1.24/bcftools gtcheck -e 0 -u GT,GT -H /tmp/iaQXJX5nkE/gtcheck.1.vcf.gz -g /tmp/iaQXJX5nkE/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-qI88Pr/bcftools-1.24/bcftools gtcheck -e 0 -u GT,PL -H /tmp/iaQXJX5nkE/gtcheck.1.vcf.gz -g /tmp/iaQXJX5nkE/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-qI88Pr/bcftools-1.24/bcftools gtcheck -e 0 -u PL,GT -H /tmp/iaQXJX5nkE/gtcheck.1.vcf.gz -g /tmp/iaQXJX5nkE/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-qI88Pr/bcftools-1.24/bcftools gtcheck -e 0 -u PL,PL -H /tmp/iaQXJX5nkE/gtcheck.1.vcf.gz -g /tmp/iaQXJX5nkE/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-qI88Pr/bcftools-1.24/bcftools gtcheck -e 0 -P /build/bcftools-qI88Pr/bcftools-1.24/test/gtcheck.4.pairs --distinctive-sites 3 /tmp/iaQXJX5nkE/gtcheck.4.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-qI88Pr/bcftools-1.24/bcftools gtcheck -e 0 -P /build/bcftools-qI88Pr/bcftools-1.24/test/gtcheck.4.pairs --distinctive-sites 3,1 /tmp/iaQXJX5nkE/gtcheck.4.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-qI88Pr/bcftools-1.24/bcftools gtcheck -u GT -e 30 /tmp/iaQXJX5nkE/gtcheck.1.vcf.gz -g /tmp/iaQXJX5nkE/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-qI88Pr/bcftools-1.24/bcftools gtcheck -u GT -e 30 -p s1,s1 /tmp/iaQXJX5nkE/gtcheck.1.vcf.gz -g /tmp/iaQXJX5nkE/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-qI88Pr/bcftools-1.24/bcftools gtcheck -u GT -e 300 /tmp/iaQXJX5nkE/gtcheck.1.vcf.gz -g /tmp/iaQXJX5nkE/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-qI88Pr/bcftools-1.24/bcftools gtcheck -u PL -e 30 /tmp/iaQXJX5nkE/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-qI88Pr/bcftools-1.24/bcftools gtcheck /tmp/iaQXJX5nkE/gtcheck.ntop.vcf.gz -g /tmp/iaQXJX5nkE/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-qI88Pr/bcftools-1.24/bcftools gtcheck --n-matches 2 /tmp/iaQXJX5nkE/gtcheck.ntop.vcf.gz -g /tmp/iaQXJX5nkE/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-qI88Pr/bcftools-1.24/bcftools gtcheck /tmp/iaQXJX5nkE/gtcheck.5.vcf.gz -g /tmp/iaQXJX5nkE/gtcheck.5.gts.vcf.gz | grep -v ^# | grep -v Time .. ok test_gtcheck: /build/bcftools-qI88Pr/bcftools-1.24/bcftools gtcheck -p A,B,B,C /tmp/iaQXJX5nkE/gtcheck.6.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /build/bcftools-qI88Pr/bcftools-1.24/bcftools gtcheck -t 11:33 -p A,D,A,E,D,E -u GT -e 10 /tmp/iaQXJX5nkE/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok Number of tests: total .. 2002 passed .. 2002 failed .. 0 make[2]: Leaving directory '/build/bcftools-qI88Pr/bcftools-1.24' make[1]: Leaving directory '/build/bcftools-qI88Pr/bcftools-1.24' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/bcftools/ make -j2 install DESTDIR=/build/bcftools-qI88Pr/bcftools-1.24/debian/bcftools AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/bcftools-qI88Pr/bcftools-1.24' mkdir -p -m 755 /build/bcftools-qI88Pr/bcftools-1.24/debian/bcftools/usr/bin /build/bcftools-qI88Pr/bcftools-1.24/debian/bcftools/usr/share/man/man1 /build/bcftools-qI88Pr/bcftools-1.24/debian/bcftools/usr/lib/x86_64-linux-gnu/bcftools install -p bcftools /build/bcftools-qI88Pr/bcftools-1.24/debian/bcftools/usr/bin install -p misc/color-chrs.pl misc/gff2gff misc/gff2gff.py misc/guess-ploidy.py misc/plot-vcfstats misc/plot-roh.py misc/roh-viz misc/run-roh.pl misc/vcfutils.pl misc/vrfs-variances /build/bcftools-qI88Pr/bcftools-1.24/debian/bcftools/usr/bin install -p -m 644 doc/bcftools.1 /build/bcftools-qI88Pr/bcftools-1.24/debian/bcftools/usr/share/man/man1 install -p plugins/*.so /build/bcftools-qI88Pr/bcftools-1.24/debian/bcftools/usr/lib/x86_64-linux-gnu/bcftools make[1]: Leaving directory '/build/bcftools-qI88Pr/bcftools-1.24' chmod -R u\+rwX /build/bcftools-qI88Pr/bcftools-1.24/debian/bcftools debian/rules override_dh_install make[1]: Entering directory '/build/bcftools-qI88Pr/bcftools-1.24' 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-qI88Pr/bcftools-1.24' dh_installdocs dh_installchangelogs debian/rules override_dh_installman make[1]: Entering directory '/build/bcftools-qI88Pr/bcftools-1.24' dh_installman --language=C make[1]: Leaving directory '/build/bcftools-qI88Pr/bcftools-1.24' dh_lintian dh_perl dh_link dh_missing dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_fixperms dh_strip_nondeterminism dh_compress dh_installdeb dh_computeautosubstvars dh_gencontrol dpkg-gencontrol: warning: Depends field of package bcftools: substitution variable ${misc:Depends} used, but is not defined dh_md5sums dh_builddeb dpkg-deb: building package 'bcftools' in '../bcftools_1.24-1_amd64.deb'. dpkg-deb: building package 'bcftools-dbgsym' in '../bcftools-dbgsym_1.24-1_amd64.deb'. dpkg-genbuildinfo -O../bcftools_1.24-1_amd64.buildinfo dpkg-genchanges -O../bcftools_1.24-1_amd64.changes dpkg-genchanges: info: including full source code in upload dpkg-source -Zxz --after-build . dpkg-buildpackage: info: full upload (original source is included) -------------------------------------------------------------------------------- Build finished at 2026-09-22T07:23:37Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Tue, 22 Sep 2026 07:23:37 +0000 | +------------------------------------------------------------------------------+ bcftools_1.24-1_amd64.changes: ------------------------------ Format: 1.8 Date: Mon, 21 Sep 2026 12:13:22 +0200 Source: bcftools Binary: bcftools bcftools-dbgsym Architecture: source amd64 Version: 1.24-1 Distribution: perl-5.44-throwaway Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: bcftools - genomic variant calling and manipulation of VCF/BCF files Closes: 1144268 Changes: bcftools (1.24-1) unstable; urgency=medium . * Team upload. * d/watch: version=5 * d/copyright: review * d/lrc.config: Exclude lots of false positives due to GPL only mentioned in LICENSE file * Do not depend on sse2-support since this is baseline now Closes: #1144268 * New upstream version * Standards-Version: 4.7.4 (routine-update) * Reflow Uploaders field (cme) * Remove Priority field (cme) * Drop 'Rules-Requires-Root: no' from d/control (routine-update) * Versioned Build-Depends: libhts-dev (>= 1.24) Checksums-Sha1: 82eb6674e483a00e84322660c212497f1ebce0d7 1242 bcftools_1.24-1.dsc 4d6bfd6e59e2fddc6a6094f34ba52ebfb3687a58 3800401 bcftools_1.24.orig.tar.gz aff4011dc6e2680f96e8b77b3e11558020b85ec0 8912 bcftools_1.24-1.debian.tar.xz ddd2559adeca4877688e2a66995e5a123811c442 2960568 bcftools-dbgsym_1.24-1_amd64.deb 0e7ab8fa4835c830b0051f2fa827c9dc2d099dee 7278 bcftools_1.24-1_amd64.buildinfo 360414f9612b2e6357da78a6565f3644ba2dbe72 881408 bcftools_1.24-1_amd64.deb Checksums-Sha256: cda43291d41c118449775d4f8305798421ae6b1b6d54341f5459f98d7735aeb3 1242 bcftools_1.24-1.dsc 8e0492098682634d29f20105c0c026139122ef0cf9f09f444f1e8a3ae35a0f64 3800401 bcftools_1.24.orig.tar.gz 2e9474623c538722fabd7d9ef2ad7d4ba29226c814d7273a4646188a4f8d8e40 8912 bcftools_1.24-1.debian.tar.xz f3136d506352625b48664747127a0210f1a058096e6a9ad05d238b5c095fcdb3 2960568 bcftools-dbgsym_1.24-1_amd64.deb e2fd7ce4d29881cbe03400792ce69f38827053565d3c1e278f7fe85b78abb3d6 7278 bcftools_1.24-1_amd64.buildinfo f2b98a50e79260a39c38ec5278e959f4b796ecdcf2931f42694a4cad3d367140 881408 bcftools_1.24-1_amd64.deb Files: 5b9fec077f74994e81f0af8ae50eb8b1 1242 science optional bcftools_1.24-1.dsc f9debbe1e479d70adeca100dbf673231 3800401 science optional bcftools_1.24.orig.tar.gz 1364f9f2bb10c9c31e867d8a37eaf22b 8912 science optional bcftools_1.24-1.debian.tar.xz 9abbf249e5eb83a325d42e02ed460539 2960568 debug optional bcftools-dbgsym_1.24-1_amd64.deb 804affa5e5ad51e827f948b0ff64f873 7278 science optional bcftools_1.24-1_amd64.buildinfo def334d2561ad0c32a0268da0c7d2d0b 881408 science optional bcftools_1.24-1_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo Tue, 22 Sep 2026 07:23:38 +0000 | +------------------------------------------------------------------------------+ Format: 1.0 Source: bcftools Binary: bcftools bcftools-dbgsym Architecture: amd64 source Version: 1.24-1 Checksums-Md5: 5b9fec077f74994e81f0af8ae50eb8b1 1242 bcftools_1.24-1.dsc 9abbf249e5eb83a325d42e02ed460539 2960568 bcftools-dbgsym_1.24-1_amd64.deb def334d2561ad0c32a0268da0c7d2d0b 881408 bcftools_1.24-1_amd64.deb Checksums-Sha1: 82eb6674e483a00e84322660c212497f1ebce0d7 1242 bcftools_1.24-1.dsc ddd2559adeca4877688e2a66995e5a123811c442 2960568 bcftools-dbgsym_1.24-1_amd64.deb 360414f9612b2e6357da78a6565f3644ba2dbe72 881408 bcftools_1.24-1_amd64.deb Checksums-Sha256: cda43291d41c118449775d4f8305798421ae6b1b6d54341f5459f98d7735aeb3 1242 bcftools_1.24-1.dsc f3136d506352625b48664747127a0210f1a058096e6a9ad05d238b5c095fcdb3 2960568 bcftools-dbgsym_1.24-1_amd64.deb f2b98a50e79260a39c38ec5278e959f4b796ecdcf2931f42694a4cad3d367140 881408 bcftools_1.24-1_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Tue, 22 Sep 2026 07:23:37 +0000 Build-Path: /build/bcftools-qI88Pr/bcftools-1.24 Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: autoconf (= 2.73-2), automake (= 1:1.19-2), autopoint (= 1.0-5), autotools-dev (= 20240727.1+nmu1), base-files (= 14.2), base-passwd (= 3.6.8), bash (= 5.3-4), binutils (= 2.47-6), binutils-common (= 2.47-6), binutils-x86-64-linux-gnu (= 2.47-6), bsdextrautils (= 2.42.3-1), build-essential (= 12.12), bzip2 (= 1.0.8-6+b2), comerr-dev (= 2.1-1.47.4-1+b1), coreutils (= 9.10-1), cpp (= 4:16.1.0-3), cpp-15 (= 15.3.0-4), cpp-15-x86-64-linux-gnu (= 15.3.0-4), cpp-16 (= 16.2.0-3), cpp-16-x86-64-linux-gnu (= 16.2.0-3), cpp-x86-64-linux-gnu (= 4:16.1.0-3), dash (= 0.5.12-12), debconf (= 1.5.92), debhelper (= 14.5), debianutils (= 5.24), dh-autoreconf (= 23), dh-strip-nondeterminism (= 1.15.1-1), diffutils (= 1:3.12-1), dpkg (= 1.23.11), dpkg-dev (= 1.23.11), dwz (= 0.17-1), file (= 1:5.47-4), findutils (= 4.11.0-2), g++ (= 4:16.1.0-3), g++-16 (= 16.2.0-3), g++-16-x86-64-linux-gnu (= 16.2.0-3), g++-x86-64-linux-gnu (= 4:16.1.0-3), gcc (= 4:16.1.0-3), gcc-15 (= 15.3.0-4), gcc-15-base (= 15.3.0-4), gcc-15-x86-64-linux-gnu (= 15.3.0-4), gcc-16 (= 16.2.0-3), gcc-16-base (= 16.2.0-3), gcc-16-x86-64-linux-gnu (= 16.2.0-3), gcc-x86-64-linux-gnu (= 4:16.1.0-3), gettext (= 1.0-5), gettext-base (= 1.0-5), grep (= 3.12-1), groff-base (= 1.24.1-1), gzip (= 1.14-1), hostname (= 3.25), init-system-helpers (= 1.69+nmu2), intltool-debian (= 0.35.0+20060710.6), krb5-multidev (= 1.22.1-3), libacl1 (= 2.4.0-1), libarchive-zip-perl (= 1.68-1), libasan8 (= 16.2.0-3), libatomic1 (= 16.2.0-3), libattr1 (= 1:2.6.0-1), libaudit-common (= 1:4.2.1-1), libaudit1 (= 1:4.2.1-1), libbinutils (= 2.47-6), libblkid1 (= 2.42.3-1), libbrotli-dev (= 1.2.0-4+b1), libbrotli1 (= 1.2.0-4+b1), libbz2-1.0 (= 1.0.8-6+b2), libbz2-dev (= 1.0.8-6+b2), libc-bin (= 2.43-6), libc-dev-bin (= 2.43-6), libc-gconv-modules-extra (= 2.43-6), libc6 (= 2.43-6), libc6-dev (= 2.43-6), libcap-ng0 (= 0.9.6-1), libcc1-0 (= 16.2.0-3), libcom-err2 (= 1.47.4-1+b1), libcrypt1 (= 1:4.5.2+20251210-1), libctf-nobfd0 (= 2.47-6), libctf0 (= 2.47-6), libcurl4-gnutls (= 8.22.0-1), libcurl4-gnutls-dev (= 8.22.0-1), libdb5.3t64 (= 5.3.28+dfsg2-11+b1), libdebconfclient0 (= 0.283), libdebhelper-perl (= 14.5), libdeflate-dev (= 1.25-1), libdeflate0 (= 1.25-1), libdpkg-perl (= 1.23.11), libelf1t64 (= 0.196-1), libevent-2.1-7t64 (= 2.1.13-stable-1), libffi8 (= 3.8.0-2), libfile-stripnondeterminism-perl (= 1.15.1-1), libgcc-15-dev (= 15.3.0-4), libgcc-16-dev (= 16.2.0-3), libgcc-s1 (= 16.2.0-3), libgdbm-compat4t64 (= 1.26-1+b2), libgdbm6t64 (= 1.26-1+b2), libgmp-dev (= 2:6.3.0+dfsg-5+b2), libgmp10 (= 2:6.3.0+dfsg-5+b2), libgmpxx4ldbl (= 2:6.3.0+dfsg-5+b2), libgnutls-dane0t64 (= 3.8.13-1), libgnutls28-dev (= 3.8.13-1), libgnutls30t64 (= 3.8.13-1), libgomp1 (= 16.2.0-3), libgprofng0 (= 2.47-6), libgsl-dev (= 2.8+dfsg-6+b1), libgsl28 (= 2.8+dfsg-6+b1), libgslcblas0 (= 2.8+dfsg-6+b1), libgssapi-krb5-2 (= 1.22.1-3), libgssrpc4t64 (= 1.22.1-3), libhogweed6t64 (= 3.10.2-1+b1), libhts-dev (= 1.24-2), libhts3t64 (= 1.24-2), libhtscodecs2 (= 1.6.7-1), libhwasan0 (= 16.2.0-3), libidn2-0 (= 2.3.8-5), libidn2-dev (= 2.3.8-5), libio-pty-perl (= 1:1.31-1+b2), libisl23 (= 0.28-1), libitm1 (= 16.2.0-3), libjansson4 (= 2.15.1-1), libk5crypto3 (= 1.22.1-3), libkadm5clnt-mit12 (= 1.22.1-3), libkadm5srv-mit12 (= 1.22.1-3), libkdb5-10t64 (= 1.22.1-3), libkeyutils1 (= 1.6.3-6+b2), libkrb5-3 (= 1.22.1-3), libkrb5-dev (= 1.22.1-3), libkrb5support0 (= 1.22.1-3), libldap-dev (= 2.6.14+dfsg-2+b1), libldap2 (= 2.6.14+dfsg-2+b1), liblsan0 (= 16.2.0-3), liblzma-dev (= 5.8.4-1), liblzma5 (= 5.8.4-1), libmagic-mgc (= 1:5.47-4), libmagic1t64 (= 1:5.47-4), libmd0 (= 1.2.0-2), libmount1 (= 2.42.3-1), libmpc3 (= 1.3.1-3), libmpfr6 (= 4.2.2-3), libnettle8t64 (= 3.10.2-1+b1), libnghttp2-14 (= 1.70.0-1), libnghttp2-dev (= 1.70.0-1), libnghttp3-9 (= 1.17.0-1), libnghttp3-dev (= 1.17.0-1), libngtcp2-16 (= 1.24.0-1), libngtcp2-crypto-gnutls-dev (= 1.24.0-1), libngtcp2-crypto-gnutls8 (= 1.24.0-1), libngtcp2-dev (= 1.24.0-1), libp11-kit-dev (= 0.26.5-1), libp11-kit0 (= 0.26.5-1), libpam-modules (= 1.7.0-8), libpam-modules-bin (= 1.7.0-8), libpam-runtime (= 1.7.0-8), libpam0g (= 1.7.0-8), libpcre2-8-0 (= 10.48-3), libperl5.44 (= 5.44.0-1), libpipeline1 (= 1.5.8-3), libpkgconf7 (= 2.5.1-4), libpsl-dev (= 0.23.3-1), libpsl5t64 (= 0.23.3-1), libquadmath0 (= 16.2.0-3), librtmp-dev (= 2.6-1), librtmp1 (= 2.6-1), libsasl2-2 (= 2.1.28+dfsg1-11), libsasl2-modules-db (= 2.1.28+dfsg1-11), libseccomp2 (= 2.6.1-1+b1), libselinux1 (= 3.11-2), libsframe3 (= 2.47-6), libsmartcols1 (= 2.42.3-1), libssh2-1-dev (= 1.11.1-6), libssh2-1t64 (= 1.11.1-6), libssl-dev (= 3.6.4-1), libssl3t64 (= 3.6.4-1), libstdc++-16-dev (= 16.2.0-3), libstdc++6 (= 16.2.0-3), libsystemd0 (= 262~rc3-1), libtasn1-6 (= 4.21.0-2+b1), libtasn1-6-dev (= 4.21.0-2+b1), libtinfo6 (= 6.6+20260608-2), libtool (= 2.6.2-3), libtsan2 (= 16.2.0-3), libubsan1 (= 16.2.0-3), libuchardet0 (= 0.0.8-2+b2), libudev1 (= 262~rc3-1), libunbound8 (= 1.26.1-1), libunistring-dev (= 1.4.2-1), libunistring5 (= 1.4.2-1), libuuid1 (= 2.42.3-1), libxml2-16 (= 2.15.4+dfsg-1), libzstd-dev (= 1.5.7+dfsg-4), libzstd1 (= 1.5.7+dfsg-4), linux-libc-dev (= 7.2.6-1), m4 (= 1.4.21-1), make (= 4.4.1-3), man-db (= 2.13.1-1), mawk (= 1.3.4.20260302-1), ncurses-base (= 6.6+20260608-2), ncurses-bin (= 6.6+20260608-2), nettle-dev (= 3.10.2-1+b1), openssl-provider-legacy (= 3.6.4-1), patch (= 2.8-2), perl (= 5.44.0-1), perl-base (= 5.44.0-1), perl-modules-5.44 (= 5.44.0-1), pkgconf (= 2.5.1-4), pkgconf-bin (= 2.5.1-4), po-debconf (= 1.0.22), sed (= 4.9-3), sensible-utils (= 0.0.26), sysvinit-utils (= 3.18-1), tabix (= 1.24-2), tar (= 1.35+dfsg-6), util-linux (= 2.42.3-1), xz-utils (= 5.8.4-1), zlib1g (= 1:1.3.dfsg+really1.3.2-3), zlib1g-dev (= 1:1.3.dfsg+really1.3.2-3) Environment: DEB_BUILD_OPTIONS="parallel=2" LANG="C.UTF-8" LANGUAGE="en_GB:en" LC_COLLATE="C.UTF-8" LC_CTYPE="C.UTF-8" LD_LIBRARY_PATH="/usr/lib/libeatmydata" 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amd64 Maintainer: Debian Med Packaging Team Installed-Size: 3035 Depends: libc6 (>= 2.43), libhts3t64 (>= 1.24), perl:any 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. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Commands: bcftools, color-chrs.pl, gff2gff, gff2gff.py, guess-ploidy.py, plot-roh.py, plot-vcfstats, roh-viz, run-roh.pl, vcfutils.pl, vrfs-variances drwxr-xr-x root/root 0 2026-09-21 10:13 ./ drwxr-xr-x root/root 0 2026-09-21 10:13 ./usr/ drwxr-xr-x root/root 0 2026-09-21 10:13 ./usr/bin/ -rwxr-xr-x root/root 1344136 2026-09-21 10:13 ./usr/bin/bcftools -rwxr-xr-x root/root 16949 2026-09-21 10:13 ./usr/bin/color-chrs.pl -rwxr-xr-x root/root 6456 2026-09-21 10:13 ./usr/bin/gff2gff -rwxr-xr-x root/root 7405 2026-07-09 09:42 ./usr/bin/gff2gff.py -rwxr-xr-x root/root 4325 2026-09-21 10:13 ./usr/bin/guess-ploidy.py -rwxr-xr-x root/root 15632 2026-07-09 09:42 ./usr/bin/plot-roh.py -rwxr-xr-x root/root 90352 2026-09-21 10:13 ./usr/bin/plot-vcfstats -rwxr-xr-x root/root 28007 2026-09-21 10:13 ./usr/bin/roh-viz -rwxr-xr-x root/root 13936 2026-09-21 10:13 ./usr/bin/run-roh.pl -rwxr-xr-x root/root 18202 2026-09-21 10:13 ./usr/bin/vcfutils.pl -rwxr-xr-x root/root 6704 2026-09-21 10:13 ./usr/bin/vrfs-variances drwxr-xr-x root/root 0 2026-09-21 10:13 ./usr/lib/ drwxr-xr-x root/root 0 2026-09-21 10:13 ./usr/lib/x86_64-linux-gnu/ drwxr-xr-x root/root 0 2026-09-21 10:13 ./usr/lib/x86_64-linux-gnu/bcftools/ -rw-r--r-- root/root 30744 2026-09-21 10:13 ./usr/lib/x86_64-linux-gnu/bcftools/GTisec.so -rw-r--r-- root/root 18392 2026-09-21 10:13 ./usr/lib/x86_64-linux-gnu/bcftools/GTsubset.so -rw-r--r-- root/root 84160 2026-09-21 10:13 ./usr/lib/x86_64-linux-gnu/bcftools/ad-bias.so -rw-r--r-- root/root 18272 2026-09-21 10:13 ./usr/lib/x86_64-linux-gnu/bcftools/add-variantkey.so -rw-r--r-- root/root 26680 2026-09-21 10:13 ./usr/lib/x86_64-linux-gnu/bcftools/af-dist.so -rw-r--r-- root/root 14176 2026-09-21 10:13 ./usr/lib/x86_64-linux-gnu/bcftools/allele-length.so -rw-r--r-- root/root 18360 2026-09-21 10:13 ./usr/lib/x86_64-linux-gnu/bcftools/check-ploidy.so -rw-r--r-- root/root 22552 2026-09-21 10:13 ./usr/lib/x86_64-linux-gnu/bcftools/check-sparsity.so -rw-r--r-- root/root 38904 2026-09-21 10:13 ./usr/lib/x86_64-linux-gnu/bcftools/color-chrs.so -rw-r--r-- root/root 35320 2026-09-21 10:13 ./usr/lib/x86_64-linux-gnu/bcftools/contrast.so -rw-r--r-- root/root 14176 2026-09-21 10:13 ./usr/lib/x86_64-linux-gnu/bcftools/counts.so -rw-r--r-- root/root 26552 2026-09-21 10:13 ./usr/lib/x86_64-linux-gnu/bcftools/dosage.so -rw-r--r-- root/root 14176 2026-09-21 10:13 ./usr/lib/x86_64-linux-gnu/bcftools/fill-AN-AC.so -rw-r--r-- root/root 129112 2026-09-21 10:13 ./usr/lib/x86_64-linux-gnu/bcftools/fill-from-fasta.so -rw-r--r-- root/root 51224 2026-09-21 10:13 ./usr/lib/x86_64-linux-gnu/bcftools/fill-tags.so -rw-r--r-- root/root 43064 2026-09-21 10:13 ./usr/lib/x86_64-linux-gnu/bcftools/fixploidy.so -rw-r--r-- root/root 35048 2026-09-21 10:13 ./usr/lib/x86_64-linux-gnu/bcftools/fixref.so -rw-r--r-- root/root 22456 2026-09-21 10:13 ./usr/lib/x86_64-linux-gnu/bcftools/frameshifts.so -rw-r--r-- root/root 31032 2026-09-21 10:13 ./usr/lib/x86_64-linux-gnu/bcftools/guess-ploidy.so -rw-r--r-- root/root 26808 2026-09-21 10:13 ./usr/lib/x86_64-linux-gnu/bcftools/gvcfz.so -rw-r--r-- root/root 22368 2026-09-21 10:13 ./usr/lib/x86_64-linux-gnu/bcftools/impute-info.so -rw-r--r-- root/root 35128 2026-09-21 10:13 ./usr/lib/x86_64-linux-gnu/bcftools/indel-stats.so -rw-r--r-- root/root 22680 2026-09-21 10:13 ./usr/lib/x86_64-linux-gnu/bcftools/isecGT.so -rw-r--r-- root/root 43520 2026-09-21 10:13 ./usr/lib/x86_64-linux-gnu/bcftools/mendelian2.so -rw-r--r-- root/root 18392 2026-09-21 10:13 ./usr/lib/x86_64-linux-gnu/bcftools/missing2ref.so -rw-r--r-- root/root 30904 2026-09-21 10:13 ./usr/lib/x86_64-linux-gnu/bcftools/parental-origin.so -rw-r--r-- root/root 35320 2026-09-21 10:13 ./usr/lib/x86_64-linux-gnu/bcftools/prune.so -rw-r--r-- root/root 27008 2026-09-21 10:13 ./usr/lib/x86_64-linux-gnu/bcftools/remove-overlaps.so -rw-r--r-- root/root 31256 2026-09-21 10:13 ./usr/lib/x86_64-linux-gnu/bcftools/scatter.so -rw-r--r-- root/root 30776 2026-09-21 10:13 ./usr/lib/x86_64-linux-gnu/bcftools/setGT.so -rw-r--r-- root/root 30872 2026-09-21 10:13 ./usr/lib/x86_64-linux-gnu/bcftools/smpl-stats.so -rw-r--r-- root/root 72536 2026-09-21 10:13 ./usr/lib/x86_64-linux-gnu/bcftools/split-vep.so -rw-r--r-- root/root 43416 2026-09-21 10:13 ./usr/lib/x86_64-linux-gnu/bcftools/split.so -rw-r--r-- root/root 30816 2026-09-21 10:13 ./usr/lib/x86_64-linux-gnu/bcftools/tag2tag.so -rw-r--r-- root/root 73080 2026-09-21 10:13 ./usr/lib/x86_64-linux-gnu/bcftools/trio-dnm3.so -rw-r--r-- root/root 35096 2026-09-21 10:13 ./usr/lib/x86_64-linux-gnu/bcftools/trio-stats.so -rw-r--r-- root/root 22456 2026-09-21 10:13 ./usr/lib/x86_64-linux-gnu/bcftools/trio-switch-rate.so -rw-r--r-- root/root 26968 2026-09-21 10:13 ./usr/lib/x86_64-linux-gnu/bcftools/variant-distance.so -rw-r--r-- root/root 22392 2026-09-21 10:13 ./usr/lib/x86_64-linux-gnu/bcftools/variantkey-hex.so -rw-r--r-- root/root 51232 2026-09-21 10:13 ./usr/lib/x86_64-linux-gnu/bcftools/vcf2table.so -rw-r--r-- root/root 39256 2026-09-21 10:13 ./usr/lib/x86_64-linux-gnu/bcftools/vrfs.so drwxr-xr-x root/root 0 2026-09-21 10:13 ./usr/share/ drwxr-xr-x root/root 0 2026-09-21 10:13 ./usr/share/doc/ drwxr-xr-x root/root 0 2026-09-21 10:13 ./usr/share/doc/bcftools/ -rw-r--r-- root/root 2192 2026-07-09 09:42 ./usr/share/doc/bcftools/README -rw-r--r-- root/root 1320 2026-09-21 10:13 ./usr/share/doc/bcftools/changelog.Debian.gz -rw-r--r-- root/root 3743 2026-09-21 10:13 ./usr/share/doc/bcftools/copyright drwxr-xr-x root/root 0 2026-09-21 10:13 ./usr/share/lintian/ drwxr-xr-x root/root 0 2026-09-21 10:13 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 119 2026-09-21 10:13 ./usr/share/lintian/overrides/bcftools drwxr-xr-x root/root 0 2026-09-21 10:13 ./usr/share/man/ drwxr-xr-x root/root 0 2026-09-21 10:13 ./usr/share/man/man1/ -rw-r--r-- root/root 52038 2026-09-21 10:13 ./usr/share/man/man1/bcftools.1.gz -rw-r--r-- root/root 253 2026-09-21 10:13 ./usr/share/man/man1/color-chrs.pl.1.gz -rw-r--r-- root/root 271 2026-09-21 10:13 ./usr/share/man/man1/plot-vcfstats.1.gz -rw-r--r-- root/root 208 2026-09-21 10:13 ./usr/share/man/man1/vcfutils.pl.1.gz +------------------------------------------------------------------------------+ | Post Build Tue, 22 Sep 2026 07:23:39 +0000 | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup Tue, 22 Sep 2026 07:23:39 +0000 | +------------------------------------------------------------------------------+ Purging /build/bcftools-qI88Pr Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Tue, 22 Sep 2026 07:23:40 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 58432 Build-Time: 179 Distribution: perl-5.44-throwaway Host Architecture: amd64 Install-Time: 13 Job: /srv/debomatic/incoming/bcftools_1.24-1.dsc Machine Architecture: amd64 Package: bcftools Package-Time: 204 Source-Version: 1.24-1 Space: 58432 Status: successful Version: 1.24-1 -------------------------------------------------------------------------------- Finished at 2026-09-22T07:23:37Z Build needed 00:03:24, 58432k disk space