https://launchpad.net/ubuntu/+source/bcftools/1.10.2-2/+build/19100310 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux riscv64-qemu-lcy01-102 5.3.0-13-generic #14+riscv64.5-Ubuntu SMP Wed Nov 13 20:10:41 UTC 2019 riscv64 Buildd toolchain package versions: launchpad-buildd_188 python-lpbuildd_188 sbuild_0.79.0-1ubuntu1 git_1:2.25.1-1ubuntu1 dpkg-dev_1.19.7ubuntu2 python-debian_0.1.36build1. Syncing the system clock with the buildd NTP service... 6 Apr 12:03:06 ntpdate[196201]: adjust time server 10.211.37.1 offset -0.000146 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=focal --arch=riscv64 PACKAGEBUILD-19100310 --image-type chroot /home/buildd/filecache-default/88ad86cb2b525f1abddded96eadf8014548f7845 Creating target for build PACKAGEBUILD-19100310 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=focal --arch=riscv64 PACKAGEBUILD-19100310 Starting target for build PACKAGEBUILD-19100310 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=focal --arch=riscv64 PACKAGEBUILD-19100310 'deb http://ftpmaster.internal/ubuntu focal main universe' Overriding sources.list in build-PACKAGEBUILD-19100310 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=focal --arch=riscv64 PACKAGEBUILD-19100310 Updating target for build PACKAGEBUILD-19100310 Ign:1 http://archive-team.internal/bootstrap/riscv64 focal InRelease Get:2 http://ftpmaster.internal/ubuntu focal InRelease [265 kB] Get:3 http://archive-team.internal/bootstrap/riscv64 focal Release [757 B] Ign:4 http://archive-team.internal/bootstrap/riscv64 focal Release.gpg Get:5 http://ftpmaster.internal/ubuntu focal-proposed InRelease [265 kB] Get:6 http://archive-team.internal/bootstrap/riscv64 focal/main riscv64 Packages [200 kB] Get:7 http://ftpmaster.internal/ubuntu focal/main riscv64 Packages [817 kB] Get:8 http://ftpmaster.internal/ubuntu focal/main Translation-en [501 kB] Get:9 http://ftpmaster.internal/ubuntu focal/universe riscv64 Packages [6704 kB] Get:10 http://ftpmaster.internal/ubuntu focal/universe Translation-en [5128 kB] Get:11 http://ftpmaster.internal/ubuntu focal-proposed/main riscv64 Packages [45.4 kB] Get:12 http://ftpmaster.internal/ubuntu focal-proposed/main Translation-en [36.1 kB] Get:13 http://ftpmaster.internal/ubuntu focal-proposed/restricted Translation-en [860 B] Get:14 http://ftpmaster.internal/ubuntu focal-proposed/universe riscv64 Packages [121 kB] Get:15 http://ftpmaster.internal/ubuntu focal-proposed/universe Translation-en [112 kB] Get:16 http://ftpmaster.internal/ubuntu focal-proposed/multiverse riscv64 Packages [1140 B] Fetched 14.2 MB in 31s (451 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: apt coreutils cpp-9 g++-9 gcc-8-base gcc-9 gcc-9-base libapt-pkg6.0 libc-bin libc-dev-bin libc6 libc6-dev libgcc-9-dev libgnutls30 liblocale-gettext-perl libperl5.30 libstdc++-9-dev libsystemd0 libtext-charwidth-perl libtext-iconv-perl libudev1 perl-base 22 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 39.4 MB of archives. After this operation, 329 kB disk space will be freed. Get:1 http://ftpmaster.internal/ubuntu focal/main riscv64 coreutils riscv64 8.30-3ubuntu2 [1158 kB] Get:2 http://ftpmaster.internal/ubuntu focal/main riscv64 perl-base riscv64 5.30.0-9build1 [1419 kB] Get:3 http://ftpmaster.internal/ubuntu focal/main riscv64 libc6-dev riscv64 2.31-0ubuntu7 [3659 kB] Get:4 http://ftpmaster.internal/ubuntu focal/main riscv64 libc-dev-bin riscv64 2.31-0ubuntu7 [62.5 kB] Get:5 http://ftpmaster.internal/ubuntu focal/main riscv64 libc6 riscv64 2.31-0ubuntu7 [2272 kB] Get:6 http://ftpmaster.internal/ubuntu focal/main riscv64 libc-bin riscv64 2.31-0ubuntu7 [505 kB] Get:7 http://ftpmaster.internal/ubuntu focal-proposed/main riscv64 libsystemd0 riscv64 245.2-1ubuntu3 [242 kB] Get:8 http://ftpmaster.internal/ubuntu focal-proposed/main riscv64 libudev1 riscv64 245.2-1ubuntu3 [69.0 kB] Get:9 http://ftpmaster.internal/ubuntu focal-proposed/main riscv64 libapt-pkg6.0 riscv64 2.0.1ubuntu1 [797 kB] Get:10 http://ftpmaster.internal/ubuntu focal-proposed/main riscv64 libgnutls30 riscv64 3.6.13-2ubuntu1 [720 kB] Get:11 http://ftpmaster.internal/ubuntu focal-proposed/main riscv64 apt riscv64 2.0.1ubuntu1 [1231 kB] Get:12 http://ftpmaster.internal/ubuntu focal/main riscv64 liblocale-gettext-perl riscv64 1.07-4 [16.5 kB] Get:13 http://ftpmaster.internal/ubuntu focal/main riscv64 libtext-charwidth-perl riscv64 0.04-10 [9460 B] Get:14 http://ftpmaster.internal/ubuntu focal/main riscv64 libtext-iconv-perl riscv64 1.7-7 [13.2 kB] Get:15 http://ftpmaster.internal/ubuntu focal/main riscv64 g++-9 riscv64 9.3.0-10ubuntu1 [6926 kB] Get:16 http://ftpmaster.internal/ubuntu focal/main riscv64 gcc-9 riscv64 9.3.0-10ubuntu1 [6788 kB] Get:17 http://ftpmaster.internal/ubuntu focal/main riscv64 libstdc++-9-dev riscv64 9.3.0-10ubuntu1 [3649 kB] Get:18 http://ftpmaster.internal/ubuntu focal/main riscv64 libgcc-9-dev riscv64 9.3.0-10ubuntu1 [404 kB] Get:19 http://ftpmaster.internal/ubuntu focal/main riscv64 cpp-9 riscv64 9.3.0-10ubuntu1 [6046 kB] Get:20 http://ftpmaster.internal/ubuntu focal/main riscv64 gcc-9-base riscv64 9.3.0-10ubuntu1 [19.2 kB] Get:21 http://ftpmaster.internal/ubuntu focal/universe riscv64 gcc-8-base riscv64 8.4.0-3ubuntu2 [18.4 kB] Get:22 http://ftpmaster.internal/ubuntu focal/main riscv64 libperl5.30 riscv64 5.30.0-9build1 [3422 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 39.4 MB in 9s (4502 kB/s) (Reading database ... 9818 files and directories currently installed.) Preparing to unpack .../coreutils_8.30-3ubuntu2_riscv64.deb ... Unpacking coreutils (8.30-3ubuntu2) over (8.30-3ubuntu2) ... Setting up coreutils (8.30-3ubuntu2) ... (Reading database ... 9818 files and directories currently installed.) Preparing to unpack .../perl-base_5.30.0-9build1_riscv64.deb ... Unpacking perl-base (5.30.0-9build1) over (5.30.0-9build1) ... Setting up perl-base (5.30.0-9build1) ... (Reading database ... 9818 files and directories currently installed.) Preparing to unpack .../libc6-dev_2.31-0ubuntu7_riscv64.deb ... Unpacking libc6-dev:riscv64 (2.31-0ubuntu7) over (2.31-0ubuntu6~riscv64.1) ... Preparing to unpack .../libc-dev-bin_2.31-0ubuntu7_riscv64.deb ... Unpacking libc-dev-bin (2.31-0ubuntu7) over (2.31-0ubuntu6~riscv64.1) ... Preparing to unpack .../libc6_2.31-0ubuntu7_riscv64.deb ... Unpacking libc6:riscv64 (2.31-0ubuntu7) over (2.31-0ubuntu6~riscv64.1) ... Setting up libc6:riscv64 (2.31-0ubuntu7) ... (Reading database ... 9818 files and directories currently installed.) Preparing to unpack .../libc-bin_2.31-0ubuntu7_riscv64.deb ... Unpacking libc-bin (2.31-0ubuntu7) over (2.31-0ubuntu6~riscv64.1) ... Setting up libc-bin (2.31-0ubuntu7) ... (Reading database ... 9818 files and directories currently installed.) Preparing to unpack .../libsystemd0_245.2-1ubuntu3_riscv64.deb ... Unpacking libsystemd0:riscv64 (245.2-1ubuntu3) over (244.3-1ubuntu1) ... Setting up libsystemd0:riscv64 (245.2-1ubuntu3) ... (Reading database ... 9818 files and directories currently installed.) Preparing to unpack .../libudev1_245.2-1ubuntu3_riscv64.deb ... Unpacking libudev1:riscv64 (245.2-1ubuntu3) over (244.3-1ubuntu1) ... Setting up libudev1:riscv64 (245.2-1ubuntu3) ... (Reading database ... 9818 files and directories currently installed.) Preparing to unpack .../libapt-pkg6.0_2.0.1ubuntu1_riscv64.deb ... Unpacking libapt-pkg6.0:riscv64 (2.0.1ubuntu1) over (2.0.1) ... Setting up libapt-pkg6.0:riscv64 (2.0.1ubuntu1) ... (Reading database ... 9818 files and directories currently installed.) Preparing to unpack .../libgnutls30_3.6.13-2ubuntu1_riscv64.deb ... Unpacking libgnutls30:riscv64 (3.6.13-2ubuntu1) over (3.6.11.1-2ubuntu2) ... Setting up libgnutls30:riscv64 (3.6.13-2ubuntu1) ... (Reading database ... 9818 files and directories currently installed.) Preparing to unpack .../apt_2.0.1ubuntu1_riscv64.deb ... Unpacking apt (2.0.1ubuntu1) over (2.0.1) ... Setting up apt (2.0.1ubuntu1) ... (Reading database ... 9818 files and directories currently installed.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-4_riscv64.deb ... Unpacking liblocale-gettext-perl (1.07-4) over (1.07-4) ... Preparing to unpack .../01-libtext-charwidth-perl_0.04-10_riscv64.deb ... Unpacking libtext-charwidth-perl (0.04-10) over (0.04-10) ... Preparing to unpack .../02-libtext-iconv-perl_1.7-7_riscv64.deb ... Unpacking libtext-iconv-perl (1.7-7) over (1.7-7) ... 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Preparing to unpack .../10-libperl5.30_5.30.0-9build1_riscv64.deb ... Unpacking libperl5.30:riscv64 (5.30.0-9build1) over (5.30.0-9build1) ... Setting up libtext-iconv-perl (1.7-7) ... Setting up libtext-charwidth-perl (0.04-10) ... Setting up gcc-8-base:riscv64 (8.4.0-3ubuntu2) ... Setting up libperl5.30:riscv64 (5.30.0-9build1) ... Setting up libc-dev-bin (2.31-0ubuntu7) ... Setting up liblocale-gettext-perl (1.07-4) ... Setting up gcc-9-base:riscv64 (9.3.0-10ubuntu1) ... Setting up libgcc-9-dev:riscv64 (9.3.0-10ubuntu1) ... Setting up cpp-9 (9.3.0-10ubuntu1) ... Setting up libc6-dev:riscv64 (2.31-0ubuntu7) ... Setting up gcc-9 (9.3.0-10ubuntu1) ... Setting up libstdc++-9-dev:riscv64 (9.3.0-10ubuntu1) ... Setting up g++-9 (9.3.0-10ubuntu1) ... Processing triggers for libc-bin (2.31-0ubuntu7) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-19100310 riscv64 focal -c chroot:build-PACKAGEBUILD-19100310 --arch=riscv64 --dist=focal --nolog bcftools_1.10.2-2.dsc Initiating build PACKAGEBUILD-19100310 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.3.0-13-generic #14+riscv64.5-Ubuntu SMP Wed Nov 13 20:10:41 UTC 2019 riscv64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on riscv64-qemu-lcy01-102 +==============================================================================+ | bcftools 1.10.2-2 (riscv64) Mon, 06 Apr 2020 12:07:04 +0000 | +==============================================================================+ Package: bcftools Version: 1.10.2-2 Source Version: 1.10.2-2 Distribution: focal Machine Architecture: riscv64 Host Architecture: riscv64 Build Architecture: riscv64 Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-19100310/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/bcftools-EVZ3cQ/resolver-FDfrpe' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- bcftools_1.10.2-2.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/bcftools-EVZ3cQ/bcftools-1.10.2' with '<>' I: NOTICE: Log filtering will replace 'build/bcftools-EVZ3cQ' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 12), zlib1g-dev, libbz2-dev, liblzma-dev, libhts-dev (>= 1.10), libgsl-dev, tabix, libio-pty-perl, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 12), zlib1g-dev, libbz2-dev, liblzma-dev, libhts-dev (>= 1.10), libgsl-dev, tabix, libio-pty-perl, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [430 B] Get:5 copy:/<>/apt_archive ./ Packages [503 B] Fetched 1890 B in 0s (5072 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following package was automatically installed and is no longer required: libgpm2 Use 'apt autoremove' to remove it. The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasn1-8-heimdal libbrotli1 libbsd0 libbz2-dev libcroco3 libcurl3-gnutls libdebhelper-perl libdeflate0 libelf1 libfile-stripnondeterminism-perl libglib2.0-0 libgsl-dev libgsl23 libgslcblas0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts3 libhx509-5-heimdal libicu66 libio-pty-perl libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libsub-override-perl libtool libuchardet0 libwind0-heimdal libxml2 m4 man-db po-debconf tabix tzdata zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html krb5-doc krb5-user liblzma-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx bzip2-doc libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasn1-8-heimdal libbrotli1 libbsd0 libbz2-dev libcroco3 libcurl3-gnutls libdebhelper-perl libdeflate0 libelf1 libfile-stripnondeterminism-perl libglib2.0-0 libgsl-dev libgsl23 libgslcblas0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts3 libhx509-5-heimdal libicu66 libio-pty-perl libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libsub-override-perl libtool libuchardet0 libwind0-heimdal libxml2 m4 man-db po-debconf sbuild-build-depends-main-dummy tabix tzdata zlib1g-dev 0 upgraded, 70 newly installed, 0 to remove and 0 not upgraded. Need to get 24.0 MB of archives. After this operation, 108 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [932 B] Get:2 http://ftpmaster.internal/ubuntu focal/main riscv64 libbsd0 riscv64 0.10.0-1 [42.0 kB] Get:3 http://archive-team.internal/bootstrap/riscv64 focal/main riscv64 libldap-2.4-2 riscv64 2.4.49+dfsg-2ubuntu1 [137 kB] Get:4 http://ftpmaster.internal/ubuntu focal/main riscv64 bsdmainutils riscv64 11.1.2ubuntu3 [176 kB] Get:5 http://ftpmaster.internal/ubuntu focal/main riscv64 libuchardet0 riscv64 0.0.6-3build1 [64.9 kB] Get:6 http://ftpmaster.internal/ubuntu focal/main riscv64 groff-base riscv64 1.22.4-4build1 [816 kB] Get:7 http://ftpmaster.internal/ubuntu focal/main riscv64 libpipeline1 riscv64 1.5.2-2build1 [23.9 kB] Get:8 http://ftpmaster.internal/ubuntu focal/main riscv64 man-db riscv64 2.9.1-1 [1075 kB] Get:9 http://ftpmaster.internal/ubuntu focal/main riscv64 libmagic-mgc riscv64 1:5.38-4 [218 kB] Get:10 http://ftpmaster.internal/ubuntu focal/main riscv64 libmagic1 riscv64 1:5.38-4 [70.5 kB] Get:11 http://ftpmaster.internal/ubuntu focal/main riscv64 file riscv64 1:5.38-4 [22.5 kB] Get:12 http://ftpmaster.internal/ubuntu focal/main riscv64 libelf1 riscv64 0.176-1.1build1 [41.8 kB] Get:13 http://ftpmaster.internal/ubuntu focal/main riscv64 libglib2.0-0 riscv64 2.64.1-1 [1122 kB] Get:14 http://ftpmaster.internal/ubuntu focal/main riscv64 tzdata all 2019c-3ubuntu1 [294 kB] Get:15 http://ftpmaster.internal/ubuntu focal/main riscv64 libicu66 riscv64 66.1-2ubuntu2 [8406 kB] Get:16 http://ftpmaster.internal/ubuntu focal/main riscv64 libxml2 riscv64 2.9.10+dfsg-4build1 [558 kB] Get:17 http://ftpmaster.internal/ubuntu focal/main riscv64 gettext-base riscv64 0.19.8.1-10build1 [47.4 kB] Get:18 http://ftpmaster.internal/ubuntu focal/main riscv64 libkrb5support0 riscv64 1.17-6ubuntu4 [28.3 kB] Get:19 http://ftpmaster.internal/ubuntu focal/main riscv64 libk5crypto3 riscv64 1.17-6ubuntu4 [91.8 kB] Get:20 http://ftpmaster.internal/ubuntu focal/main riscv64 libkeyutils1 riscv64 1.6-6ubuntu1 [9316 B] Get:21 http://ftpmaster.internal/ubuntu focal/main riscv64 libkrb5-3 riscv64 1.17-6ubuntu4 [295 kB] Get:22 http://ftpmaster.internal/ubuntu focal/main riscv64 libgssapi-krb5-2 riscv64 1.17-6ubuntu4 [107 kB] Get:23 http://ftpmaster.internal/ubuntu focal/main riscv64 libpsl5 riscv64 0.21.0-1ubuntu1 [50.5 kB] Get:24 http://ftpmaster.internal/ubuntu focal/main riscv64 libsigsegv2 riscv64 2.12-2 [13.0 kB] Get:25 http://ftpmaster.internal/ubuntu focal/main riscv64 m4 riscv64 1.4.18-4 [188 kB] Get:26 http://ftpmaster.internal/ubuntu focal/main riscv64 autoconf all 2.69-11.1 [321 kB] Get:27 http://ftpmaster.internal/ubuntu focal/main riscv64 autotools-dev all 20180224.1 [39.6 kB] Get:28 http://ftpmaster.internal/ubuntu focal/main riscv64 automake all 1:1.16.1-4ubuntu6 [522 kB] Get:29 http://ftpmaster.internal/ubuntu focal/main riscv64 autopoint all 0.19.8.1-10build1 [412 kB] Get:30 http://ftpmaster.internal/ubuntu focal/main riscv64 libtool all 2.4.6-13 [161 kB] Get:31 http://ftpmaster.internal/ubuntu focal/main riscv64 dh-autoreconf all 19 [16.1 kB] Get:32 http://ftpmaster.internal/ubuntu focal-proposed/main riscv64 libdebhelper-perl all 12.10ubuntu1 [62.1 kB] Get:33 http://ftpmaster.internal/ubuntu focal/main riscv64 libarchive-zip-perl all 1.67-2 [90.5 kB] Get:34 http://ftpmaster.internal/ubuntu focal/main riscv64 libsub-override-perl all 0.09-2 [9532 B] Get:35 http://ftpmaster.internal/ubuntu focal/main riscv64 libfile-stripnondeterminism-perl all 1.6.3-2 [16.0 kB] Get:36 http://ftpmaster.internal/ubuntu focal/main riscv64 dh-strip-nondeterminism all 1.6.3-2 [5228 B] Get:37 http://ftpmaster.internal/ubuntu focal/main riscv64 dwz riscv64 0.13-5 [147 kB] Get:38 http://ftpmaster.internal/ubuntu focal/main riscv64 libcroco3 riscv64 0.6.13-1 [71.1 kB] Get:39 http://ftpmaster.internal/ubuntu focal/main riscv64 gettext riscv64 0.19.8.1-10build1 [844 kB] Get:40 http://ftpmaster.internal/ubuntu focal/main riscv64 intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:41 http://ftpmaster.internal/ubuntu focal/main riscv64 po-debconf all 1.0.21 [233 kB] Get:42 http://ftpmaster.internal/ubuntu focal-proposed/main riscv64 debhelper all 12.10ubuntu1 [877 kB] Get:43 http://ftpmaster.internal/ubuntu focal/main riscv64 libroken18-heimdal riscv64 7.7.0+dfsg-1ubuntu1 [36.5 kB] Get:44 http://ftpmaster.internal/ubuntu focal/main riscv64 libasn1-8-heimdal riscv64 7.7.0+dfsg-1ubuntu1 [145 kB] Get:45 http://ftpmaster.internal/ubuntu focal/main riscv64 libbrotli1 riscv64 1.0.7-6build1 [279 kB] Get:46 http://ftpmaster.internal/ubuntu focal/main riscv64 libbz2-dev riscv64 1.0.8-2 [67.0 kB] Get:47 http://ftpmaster.internal/ubuntu focal/main riscv64 libheimbase1-heimdal riscv64 7.7.0+dfsg-1ubuntu1 [24.7 kB] Get:48 http://ftpmaster.internal/ubuntu focal/main riscv64 libhcrypto4-heimdal riscv64 7.7.0+dfsg-1ubuntu1 [86.5 kB] Get:49 http://ftpmaster.internal/ubuntu focal/main riscv64 libwind0-heimdal riscv64 7.7.0+dfsg-1ubuntu1 [47.0 kB] Get:50 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[50.8 kB] Get:59 http://ftpmaster.internal/ubuntu focal/main riscv64 libssh-4 riscv64 0.9.3-2ubuntu1 [147 kB] Get:60 http://ftpmaster.internal/ubuntu focal/main riscv64 libcurl3-gnutls riscv64 7.68.0-1ubuntu1 [205 kB] Get:61 http://ftpmaster.internal/ubuntu focal/universe riscv64 libdeflate0 riscv64 1.5-3 [52.1 kB] Get:62 http://ftpmaster.internal/ubuntu focal/universe riscv64 libgslcblas0 riscv64 2.5+dfsg-6build1 [69.1 kB] Get:63 http://ftpmaster.internal/ubuntu focal/universe riscv64 libgsl23 riscv64 2.5+dfsg-6build1 [818 kB] Get:64 http://ftpmaster.internal/ubuntu focal/universe riscv64 libgsl-dev riscv64 2.5+dfsg-6build1 [2516 kB] Get:65 http://ftpmaster.internal/ubuntu focal/universe riscv64 libhts3 riscv64 1.10.2-3 [328 kB] Get:66 http://ftpmaster.internal/ubuntu focal/main riscv64 liblzma-dev riscv64 5.2.4-1 [226 kB] Get:67 http://ftpmaster.internal/ubuntu focal/main riscv64 zlib1g-dev riscv64 1:1.2.11.dfsg-2ubuntu1 [207 kB] Get:68 http://ftpmaster.internal/ubuntu focal/universe riscv64 libhts-dev riscv64 1.10.2-3 [92.0 kB] Get:69 http://ftpmaster.internal/ubuntu focal/main riscv64 libio-pty-perl riscv64 1:1.12-1 [31.8 kB] Get:70 http://ftpmaster.internal/ubuntu focal/universe riscv64 tabix riscv64 1.10.2-3 [337 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 24.0 MB in 5s (4732 kB/s) Selecting previously unselected package libbsd0:riscv64. (Reading database ... 9816 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.10.0-1_riscv64.deb ... Unpacking libbsd0:riscv64 (0.10.0-1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2ubuntu3_riscv64.deb ... Unpacking bsdmainutils (11.1.2ubuntu3) ... Selecting previously unselected package libuchardet0:riscv64. Preparing to unpack .../02-libuchardet0_0.0.6-3build1_riscv64.deb ... Unpacking libuchardet0:riscv64 (0.0.6-3build1) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-4build1_riscv64.deb ... Unpacking groff-base (1.22.4-4build1) ... Selecting previously unselected package libpipeline1:riscv64. Preparing to unpack .../04-libpipeline1_1.5.2-2build1_riscv64.deb ... Unpacking libpipeline1:riscv64 (1.5.2-2build1) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.9.1-1_riscv64.deb ... 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Setting up libglib2.0-0:riscv64 (2.64.1-1) ... No schema files found: doing nothing. Setting up libdebhelper-perl (12.10ubuntu1) ... Setting up libbrotli1:riscv64 (1.0.7-6build1) ... Setting up libnghttp2-14:riscv64 (1.40.0-1build1) ... Setting up libmagic1:riscv64 (1:5.38-4) ... Setting up libdeflate0 (1.5-3) ... Setting up gettext-base (0.19.8.1-10build1) ... Setting up file (1:5.38-4) ... Setting up libldap-common (2.4.49+dfsg-2ubuntu1) ... Setting up libkrb5support0:riscv64 (1.17-6ubuntu4) ... Setting up libsasl2-modules-db:riscv64 (2.1.27+dfsg-2) ... Setting up tzdata (2019c-3ubuntu1) ... Current default time zone: 'Etc/UTC' Local time is now: Mon Apr 6 12:09:13 UTC 2020. Universal Time is now: Mon Apr 6 12:09:13 UTC 2020. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20180224.1) ... Setting up librtmp1:riscv64 (2.4+20151223.gitfa8646d.1-2build1) ... Setting up libgsl23:riscv64 (2.5+dfsg-6build1) ... Setting up libsigsegv2:riscv64 (2.12-2) ... Setting up autopoint (0.19.8.1-10build1) ... Setting up libk5crypto3:riscv64 (1.17-6ubuntu4) ... Setting up libsasl2-2:riscv64 (2.1.27+dfsg-2) ... Setting up libroken18-heimdal:riscv64 (7.7.0+dfsg-1ubuntu1) ... Setting up liblzma-dev:riscv64 (5.2.4-1) ... Setting up zlib1g-dev:riscv64 (1:1.2.11.dfsg-2ubuntu1) ... Setting up libuchardet0:riscv64 (0.0.6-3build1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libkrb5-3:riscv64 (1.17-6ubuntu4) ... Setting up libbsd0:riscv64 (0.10.0-1) ... Setting up libelf1:riscv64 (0.176-1.1build1) ... Setting up libheimbase1-heimdal:riscv64 (7.7.0+dfsg-1ubuntu1) ... Setting up libbz2-dev:riscv64 (1.0.8-2) ... Setting up libfile-stripnondeterminism-perl (1.6.3-2) ... Setting up libgsl-dev (2.5+dfsg-6build1) ... Setting up libtool (2.4.6-13) ... Setting up libicu66:riscv64 (66.1-2ubuntu2) ... Setting up libasn1-8-heimdal:riscv64 (7.7.0+dfsg-1ubuntu1) ... Setting up m4 (1.4.18-4) ... Setting up libhcrypto4-heimdal:riscv64 (7.7.0+dfsg-1ubuntu1) ... Setting up libwind0-heimdal:riscv64 (7.7.0+dfsg-1ubuntu1) ... Setting up bsdmainutils (11.1.2ubuntu3) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libgssapi-krb5-2:riscv64 (1.17-6ubuntu4) ... Setting up libssh-4:riscv64 (0.9.3-2ubuntu1) ... Setting up autoconf (2.69-11.1) ... Setting up dh-strip-nondeterminism (1.6.3-2) ... Setting up dwz (0.13-5) ... Setting up groff-base (1.22.4-4build1) ... Setting up libxml2:riscv64 (2.9.10+dfsg-4build1) ... Setting up automake (1:1.16.1-4ubuntu6) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libhx509-5-heimdal:riscv64 (7.7.0+dfsg-1ubuntu1) ... Setting up man-db (2.9.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libcroco3:riscv64 (0.6.13-1) ... Setting up libkrb5-26-heimdal:riscv64 (7.7.0+dfsg-1ubuntu1) ... Setting up gettext (0.19.8.1-10build1) ... Setting up libheimntlm0-heimdal:riscv64 (7.7.0+dfsg-1ubuntu1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libgssapi3-heimdal:riscv64 (7.7.0+dfsg-1ubuntu1) ... Setting up po-debconf (1.0.21) ... Setting up libldap-2.4-2:riscv64 (2.4.49+dfsg-2ubuntu1) ... Setting up libcurl3-gnutls:riscv64 (7.68.0-1ubuntu1) ... Setting up tabix (1.10.2-3) ... Setting up libhts3:riscv64 (1.10.2-3) ... Setting up libhts-dev:riscv64 (1.10.2-3) ... Setting up dh-autoreconf (19) ... Setting up debhelper (12.10ubuntu1) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.31-0ubuntu7) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (riscv64 included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.3.0-13-generic #14+riscv64.5-Ubuntu SMP Wed Nov 13 20:10:41 UTC 2019 riscv64 (riscv64) Toolchain package versions: binutils_2.34-5ubuntu1 dpkg-dev_1.19.7ubuntu3 g++-9_9.3.0-10ubuntu1 gcc-9_9.3.0-10ubuntu1 libc6-dev_2.31-0ubuntu7 libstdc++-9-dev_9.3.0-10ubuntu1 libstdc++6_10-20200324-1ubuntu1 linux-libc-dev_5.4.0-21.25 Package versions: adduser_3.118ubuntu1 advancecomp_2.1-2.1build1 apt_2.0.1ubuntu1 autoconf_2.69-11.1 automake_1:1.16.1-4ubuntu6 autopoint_0.19.8.1-10build1 autotools-dev_20180224.1 base-files_11ubuntu4 base-passwd_3.5.47 bash_5.0-6ubuntu1 binutils_2.34-5ubuntu1 binutils-common_2.34-5ubuntu1 binutils-riscv64-linux-gnu_2.34-5ubuntu1 bsdmainutils_11.1.2ubuntu3 bsdutils_1:2.34-0.1ubuntu8 build-essential_12.8ubuntu1 bzip2_1.0.8-2 ca-certificates_20190110ubuntu1 coreutils_8.30-3ubuntu2 cpp_4:9.3.0-1ubuntu2 cpp-9_9.3.0-10ubuntu1 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.10ubuntu1 debianutils_4.9.1 dh-autoreconf_19 dh-strip-nondeterminism_1.6.3-2 diffutils_1:3.7-3 dpkg_1.19.7ubuntu3 dpkg-dev_1.19.7ubuntu3 dwz_0.13-5 e2fsprogs_1.45.5-2ubuntu1 fakeroot_1.24-1 file_1:5.38-4 findutils_4.7.0-1ubuntu1 g++_4:9.3.0-1ubuntu2 g++-9_9.3.0-10ubuntu1 gcc_4:9.3.0-1ubuntu2 gcc-10-base_10-20200324-1ubuntu1 gcc-8-base_8.4.0-3ubuntu2 gcc-9_9.3.0-10ubuntu1 gcc-9-base_9.3.0-10ubuntu1 gettext_0.19.8.1-10build1 gettext-base_0.19.8.1-10build1 gpg_2.2.19-3ubuntu2 gpg-agent_2.2.19-3ubuntu2 gpgconf_2.2.19-3ubuntu2 gpgv_2.2.19-3ubuntu2 grep_3.4-1 groff-base_1.22.4-4build1 gzip_1.10-0ubuntu4 hostname_3.23 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libffi7_3.3-4 libfile-stripnondeterminism-perl_1.6.3-2 libgcc-9-dev_9.3.0-10ubuntu1 libgcc-s1_10-20200324-1ubuntu1 libgcc1_1:10-20200324-1ubuntu1 libgcrypt20_1.8.5-5ubuntu1 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.64.1-1 libgmp10_2:6.2.0+dfsg-4 libgnutls30_3.6.13-2ubuntu1 libgomp1_10-20200324-1ubuntu1 libgpg-error0_1.37-1 libgpm2_1.20.7-5 libgsl-dev_2.5+dfsg-6build1 libgsl23_2.5+dfsg-6build1 libgslcblas0_2.5+dfsg-6build1 libgssapi-krb5-2_1.17-6ubuntu4 libgssapi3-heimdal_7.7.0+dfsg-1ubuntu1 libhcrypto4-heimdal_7.7.0+dfsg-1ubuntu1 libheimbase1-heimdal_7.7.0+dfsg-1ubuntu1 libheimntlm0-heimdal_7.7.0+dfsg-1ubuntu1 libhogweed5_3.5.1+really3.5.1-2 libhts-dev_1.10.2-3 libhts3_1.10.2-3 libhx509-5-heimdal_7.7.0+dfsg-1ubuntu1 libicu66_66.1-2ubuntu2 libidn2-0_2.2.0-2 libio-pty-perl_1:1.12-1 libisl22_0.22.1-1 libk5crypto3_1.17-6ubuntu4 libkeyutils1_1.6-6ubuntu1 libkrb5-26-heimdal_7.7.0+dfsg-1ubuntu1 libkrb5-3_1.17-6ubuntu4 libkrb5support0_1.17-6ubuntu4 libldap-2.4-2_2.4.49+dfsg-2ubuntu1 libldap-common_2.4.49+dfsg-2ubuntu1 liblocale-gettext-perl_1.07-4 liblockfile-bin_1.16-1.1 liblockfile1_1.16-1.1 liblz4-1_1.9.2-2 liblzma-dev_5.2.4-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-4 libmagic1_1:5.38-4 libmount1_2.34-0.1ubuntu8 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libncursesw6_6.2-0ubuntu2 libnettle7_3.5.1+really3.5.1-2 libnghttp2-14_1.40.0-1build1 libnpth0_1.6-1 libp11-kit0_0.23.20-1build1 libpam-modules_1.3.1-5ubuntu4 libpam-modules-bin_1.3.1-5ubuntu4 libpam-runtime_1.3.1-5ubuntu4 libpam0g_1.3.1-5ubuntu4 libpcre2-8-0_10.34-7 libpcre3_2:8.39-12build1 libperl5.30_5.30.0-9build1 libpipeline1_1.5.2-2build1 libpng16-16_1.6.37-2 libpsl5_0.21.0-1ubuntu1 libreadline8_8.0-4 libroken18-heimdal_7.7.0+dfsg-1ubuntu1 librtmp1_2.4+20151223.gitfa8646d.1-2build1 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libselinux1_3.0-1build2 libsemanage-common_3.0-1build2 libsemanage1_3.0-1build2 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1ubuntu8 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policyrcd-script-zg2_0.1-3 readline-common_8.0-4 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-2.1ubuntu1 tabix_1.10.2-3 tar_1.30+dfsg-7 tzdata_2019c-3ubuntu1 ubuntu-keyring_2020.02.11.1 util-linux_2.34-0.1ubuntu8 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-2ubuntu1 zlib1g-dev_1:1.2.11.dfsg-2ubuntu1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: bcftools Binary: bcftools Architecture: any Version: 1.10.2-2 Maintainer: Debian Med Packaging Team Uploaders: Michael R. Crusoe Homepage: http://samtools.github.io/bcftools/ Standards-Version: 4.4.1 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 (= 12), zlib1g-dev, libbz2-dev, liblzma-dev, libhts-dev (>= 1.10), libgsl-dev, tabix , libio-pty-perl Package-List: bcftools deb science optional arch=any Checksums-Sha1: b19c9ba06b1c8e8f135c1e0ab0e4ff713a291bf4 2880994 bcftools_1.10.2.orig.tar.gz 22dd7fb5f9fcece42f164e49582983ad58b74283 6552 bcftools_1.10.2-2.debian.tar.xz Checksums-Sha256: 13277c17047152951e0bfe4467adc7768571b18e26610d206cab5560de5a395a 2880994 bcftools_1.10.2.orig.tar.gz 9abbc20d2f90a23895e224a45a1d8faed5a994563808a867b0976d94e850246e 6552 bcftools_1.10.2-2.debian.tar.xz Files: 6d1039729053e9bd5b946fdf9a71af1e 2880994 bcftools_1.10.2.orig.tar.gz c18dca20363baffa1817a47239cb8010 6552 bcftools_1.10.2-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- 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signature on ./bcftools_1.10.2-2.dsc dpkg-source: info: extracting bcftools in /<> dpkg-source: info: unpacking bcftools_1.10.2.orig.tar.gz dpkg-source: info: unpacking bcftools_1.10.2-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying tests-pluginpath.patch dpkg-source: info: applying skip_new_test_failing_on_32bit.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-19100310 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-19100310 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-19100310 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -mLaunchpad Build Daemon -B -rfakeroot dpkg-buildpackage: info: source package bcftools dpkg-buildpackage: info: source version 1.10.2-2 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture riscv64 fakeroot debian/rules clean rm -f config.mk && touch config.mk dh clean dh_auto_clean make -j4 distclean make[1]: Entering directory '/<>' rm -f test/*.o test/*~ test/test-rbuf test/test-regidx rm -f plugins/*.so plugins/*.P rm -rf plugins/*.dSYM rm -f test/*.hex rm -f gmon.out *.o *.a *~ bcftools version.h rm -rf *.dSYM test/*.dSYM rm -f config.cache config.h config.log config.mk config.status rm -rf autom4te.cache rm -f TAGS make[1]: Leaving directory '/<>' dh_clean debian/rules build-arch dh build-arch dh_update_autotools_config -a debian/rules override_dh_autoreconf make[1]: Entering directory '/<>' rm -f config.mk && touch config.mk export MAKEFLAGS="-s"; dh_autoreconf configure.ac:94: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:94: the top level configure.ac:94: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:94: the top level configure.ac:94: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:94: the top level configure.ac:94: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:94: the top level make[1]: Leaving directory '/<>' debian/rules override_dh_auto_configure make[1]: Entering directory '/<>' dh_auto_configure -- \ --with-htslib=system \ --enable-gsl \ --with-cblas=gslcblas \ --with-bcf-plugin-dir=/usr/lib/riscv64-linux-gnu/bcftools ./configure --build=riscv64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/riscv64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system --enable-gsl --with-cblas=gslcblas --with-bcf-plugin-dir=/usr/lib/riscv64-linux-gnu/bcftools checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for grep that handles long lines and -e... /bin/grep checking for C compiler warning flags... -Wall checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for htslib/sam.h... yes checking for hts_version in -lhts... yes checking shared library type... plain .so checking for library containing dlopen... -ldl checking if the compiler accepts -rdynamic... yes checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing regcomp... none required configure: creating ./config.status config.status: creating config.mk config.status: creating config.h make[1]: Leaving directory '/<>' dh_auto_build -a make -j4 make[1]: Entering directory '/<>' echo '#define BCFTOOLS_VERSION "1.10.2"' > version.h gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfindex.o vcfindex.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tabix.o tabix.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfstats.o vcfstats.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfisec.o vcfisec.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfmerge.o vcfmerge.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfquery.o vcfquery.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcffilter.o vcffilter.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o filter.o filter.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfsom.o vcfsom.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfnorm.o vcfnorm.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfgtcheck.o vcfgtcheck.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfview.o vcfview.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfannotate.o vcfannotate.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfroh.o vcfroh.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfconcat.o vcfconcat.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcall.o vcfcall.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mcall.o mcall.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcmp.o vcmp.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gvcf.o gvcf.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o reheader.o reheader.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o convert.o convert.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfconvert.o vcfconvert.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tsv2vcf.o tsv2vcf.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcnv.o vcfcnv.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o HMM.o HMM.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o consensus.o consensus.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ploidy.o ploidy.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bin.o bin.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hclust.o hclust.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o version.o version.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o regidx.o regidx.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o smpl_ilist.o smpl_ilist.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o csq.o csq.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfbuf.o vcfbuf.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mpileup.o mpileup.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sample.o bam_sample.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfsort.o vcfsort.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cols.o cols.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ccall.o ccall.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o em.o em.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o prob1.o prob1.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kmin.o kmin.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DPLUGINPATH='"/usr/lib/riscv64-linux-gnu/bcftools"' -c -o vcfplugin.o vcfplugin.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-rbuf.o test/test-rbuf.c gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-regidx.o test/test-regidx.c gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/parental-origin.so version.c plugins/parental-origin.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/ad-bias.so convert.c version.c plugins/ad-bias.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/smpl-stats.so version.c plugins/smpl-stats.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/setGT.so version.c plugins/setGT.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/add-variantkey.so version.c plugins/add-variantkey.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/trio-switch-rate.so version.c plugins/trio-switch-rate.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/remove-overlaps.so version.c plugins/remove-overlaps.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/tag2tag.so version.c plugins/tag2tag.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/fixploidy.so ploidy.c regidx.c version.c plugins/fixploidy.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/check-sparsity.so version.c plugins/check-sparsity.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/GTsubset.so version.c plugins/GTsubset.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/split.so version.c plugins/split.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/variantkey-hex.so version.c plugins/variantkey-hex.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/trio-stats.so version.c plugins/trio-stats.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/frameshifts.so version.c plugins/frameshifts.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/guess-ploidy.so version.c plugins/guess-ploidy.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/allele-length.so version.c plugins/allele-length.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/fill-tags.so version.c plugins/fill-tags.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/af-dist.so bin.c version.c plugins/af-dist.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/split-vep.so version.c plugins/split-vep.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/check-ploidy.so version.c plugins/check-ploidy.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/counts.so version.c plugins/counts.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/trio-dnm.so version.c plugins/trio-dnm.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/color-chrs.so HMM.c version.c plugins/color-chrs.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/isecGT.so smpl_ilist.c version.c plugins/isecGT.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/mendelian.so version.c plugins/mendelian.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/contrast.so version.c plugins/contrast.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/fixref.so version.c plugins/fixref.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/missing2ref.so version.c plugins/missing2ref.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/indel-stats.so version.c plugins/indel-stats.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/prune.so version.c plugins/prune.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/dosage.so version.c plugins/dosage.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/impute-info.so version.c plugins/impute-info.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/fill-AN-AC.so version.c plugins/fill-AN-AC.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/GTisec.so version.c plugins/GTisec.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/fill-from-fasta.so filter.c version.c plugins/fill-from-fasta.c -ldl gcc -fPIC -shared -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -o plugins/gvcfz.so version.c plugins/gvcfz.c -ldl gcc -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o main.o main.c gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -o test/test-rbuf test/test-rbuf.o -lz -ldl -ldl gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -o test/test-regidx test/test-regidx.o regidx.o -lhts -lpthread -lz -ldl -ldl gcc -rdynamic -pthread -Wl,-Bsymbolic-functions -Wl,-z,relro -o bcftools main.o vcfindex.o tabix.o vcfstats.o vcfisec.o vcfmerge.o vcfquery.o vcffilter.o filter.o vcfsom.o vcfnorm.o vcfgtcheck.o vcfview.o vcfannotate.o vcfroh.o vcfconcat.o vcfcall.o mcall.o vcmp.o gvcf.o reheader.o convert.o vcfconvert.o tsv2vcf.o vcfcnv.o HMM.o consensus.o ploidy.o bin.o hclust.o version.o regidx.o smpl_ilist.o csq.o vcfbuf.o mpileup.o bam2bcf.o bam2bcf_indel.o bam_sample.o vcfsort.o cols.o ccall.o em.o prob1.o kmin.o vcfplugin.o -lhts -lm -lz -ldl -ldl make[1]: Leaving directory '/<>' debian/rules override_dh_auto_test make[1]: Entering directory '/<>' make test-no-plugins VERBOSE=1 make[2]: Entering directory '/<>' ./test/test-rbuf Inserted 1-9 starting at offset 5: 5 6 7 8 9 0 1 2 3 1 2 3 4 5 6 7 8 9 4th is 4 Deleting 1-2: 7 8 9 0 1 2 3 3 4 5 6 7 8 9 Prepending 0-8: 8 9 0 1 2 3 4 5 6 7 8 7 6 5 4 3 2 1 0 3 Expanding: 8 9 10 11 12 13 14 15 16 17 8 7 6 5 4 3 2 1 0 3 ./test/test-regidx REF_PATH=: ./test/test.pl --exec bgzip= --exec tabix= --htsdir= ${TEST_OPTS:-} test_usage: bcftools .. ok test_usage_subcommand: bcftools index .. ok test_usage_subcommand: bcftools annotate .. ok test_usage_subcommand: bcftools concat .. ok test_usage_subcommand: bcftools convert .. ok test_usage_subcommand: bcftools isec .. ok test_usage_subcommand: bcftools merge .. ok test_usage_subcommand: bcftools norm .. ok test_usage_subcommand: bcftools plugin .. ok test_usage_subcommand: bcftools query .. ok test_usage_subcommand: bcftools reheader .. ok test_usage_subcommand: bcftools sort .. ok test_usage_subcommand: bcftools view .. ok test_usage_subcommand: bcftools call .. ok test_usage_subcommand: bcftools consensus .. ok test_usage_subcommand: bcftools cnv .. ok test_usage_subcommand: bcftools csq .. ok test_usage_subcommand: bcftools filter .. ok test_usage_subcommand: bcftools gtcheck .. ok test_usage_subcommand: bcftools mpileup .. ok test_usage_subcommand: bcftools roh .. ok test_usage_subcommand: bcftools stats .. ok test_tabix: tabix /tmp/eP2NabHXBR/merge.a.vcf.gz 2:3199812-3199812 .. ok test_tabix: /<>/bcftools view -H /tmp/eP2NabHXBR/merge.a.bcf 2:3199812-3199812 .. ok test_tabix: tabix /tmp/eP2NabHXBR/merge.a.vcf.gz 1:3000151-3000151 .. ok test_tabix: /<>/bcftools view -H /tmp/eP2NabHXBR/merge.a.bcf 1:3000151-3000151 .. ok test_index: /<>/bcftools view -H /tmp/eP2NabHXBR/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/eP2NabHXBR/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/eP2NabHXBR/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/eP2NabHXBR/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/eP2NabHXBR/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/eP2NabHXBR/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /<>/bcftools view -H /tmp/eP2NabHXBR/large_chrom_csi_limit.bcf chr20 .. ok test_index: /<>/bcftools view -H /tmp/eP2NabHXBR/large_chrom_csi_limit.bcf chr20 .. ok test_index: /<>/bcftools view -H /tmp/eP2NabHXBR/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /<>/bcftools view -H /tmp/eP2NabHXBR/large_chrom_csi_limit.bcf chr20 .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/eP2NabHXBR/idx.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/eP2NabHXBR/idx.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/eP2NabHXBR/idx.bcf .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/eP2NabHXBR/idx.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/eP2NabHXBR/idx.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/eP2NabHXBR/idx.bcf .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/eP2NabHXBR/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/eP2NabHXBR/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/eP2NabHXBR/empty.bcf .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/eP2NabHXBR/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/eP2NabHXBR/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/eP2NabHXBR/empty.bcf .. ok test_vcf_check: /<>/bcftools stats -s - /tmp/eP2NabHXBR/check.vcf.gz | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check: /<>/bcftools view -Ob /tmp/eP2NabHXBR/check.vcf.gz | /<>/bcftools stats -s - | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check_merge: /<>/misc/plot-vcfstats -m /tmp/eP2NabHXBR/check.1.chk /tmp/eP2NabHXBR/check.2.chk /tmp/eP2NabHXBR/check.3.chk /tmp/eP2NabHXBR/check.4.chk | grep -v 'plot-vcfstats' | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_stats: /<>/bcftools stats -s - /tmp/eP2NabHXBR/stats.a.vcf.gz /tmp/eP2NabHXBR/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /<>/bcftools stats -s B /tmp/eP2NabHXBR/stats.a.vcf.gz /tmp/eP2NabHXBR/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /<>/bcftools stats -s - /tmp/eP2NabHXBR/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_isec: /<>/bcftools isec -n =2 /tmp/eP2NabHXBR/isec.a.vcf.gz /tmp/eP2NabHXBR/isec.b.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 /tmp/eP2NabHXBR/isec.a.vcf.gz /tmp/eP2NabHXBR/isec.b.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/eP2NabHXBR/isec.a.vcf.gz /tmp/eP2NabHXBR/isec.b.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 -i"STRLEN(REF)==2" /tmp/eP2NabHXBR/isec.a.vcf.gz /tmp/eP2NabHXBR/isec.b.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -n =2 -c both /tmp/eP2NabHXBR/isec.a.vcf.gz /tmp/eP2NabHXBR/isec.b.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 -c both /tmp/eP2NabHXBR/isec.a.vcf.gz /tmp/eP2NabHXBR/isec.b.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -n =2 -c any /tmp/eP2NabHXBR/isec.a.vcf.gz /tmp/eP2NabHXBR/isec.b.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 -c any /tmp/eP2NabHXBR/isec.a.vcf.gz /tmp/eP2NabHXBR/isec.b.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -C -c any /tmp/eP2NabHXBR/isec.a.vcf.gz /tmp/eP2NabHXBR/isec.b.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -Ob -C -c any /tmp/eP2NabHXBR/isec.a.vcf.gz /tmp/eP2NabHXBR/isec.b.vcf.gz .. ok test_vcf_isec2: /<>/bcftools isec --no-version -T /tmp/eP2NabHXBR/isec.tab.gz /tmp/eP2NabHXBR/isec.a.vcf.gz .. ok test_vcf_isec2: /<>/bcftools isec -Ob -T /tmp/eP2NabHXBR/isec.tab.gz /tmp/eP2NabHXBR/isec.a.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_isec: /<>/bcftools isec -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/eP2NabHXBR/isec-miss.1.1.vcf.gz /tmp/eP2NabHXBR/isec-miss.1.2.vcf.gz /tmp/eP2NabHXBR/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -Ob -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/eP2NabHXBR/isec-miss.1.1.vcf.gz /tmp/eP2NabHXBR/isec-miss.1.2.vcf.gz /tmp/eP2NabHXBR/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -R /<>/test/isec-miss.1.regs.txt -n +1 /tmp/eP2NabHXBR/isec-miss.1.1.vcf.gz /tmp/eP2NabHXBR/isec-miss.1.2.vcf.gz /tmp/eP2NabHXBR/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -Ob -R /<>/test/isec-miss.1.regs.txt -n +1 /tmp/eP2NabHXBR/isec-miss.1.1.vcf.gz /tmp/eP2NabHXBR/isec-miss.1.2.vcf.gz /tmp/eP2NabHXBR/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/eP2NabHXBR/isec-miss.2.1.vcf.gz /tmp/eP2NabHXBR/isec-miss.2.2.vcf.gz /tmp/eP2NabHXBR/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -Ob -n +1 -r 20:100,20:140,12:55,20:140,20:100 /tmp/eP2NabHXBR/isec-miss.2.1.vcf.gz /tmp/eP2NabHXBR/isec-miss.2.2.vcf.gz /tmp/eP2NabHXBR/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -R /<>/test/isec-miss.1.regs.txt -n +1 /tmp/eP2NabHXBR/isec-miss.2.1.vcf.gz /tmp/eP2NabHXBR/isec-miss.2.2.vcf.gz /tmp/eP2NabHXBR/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -Ob -R /<>/test/isec-miss.1.regs.txt -n +1 /tmp/eP2NabHXBR/isec-miss.2.1.vcf.gz /tmp/eP2NabHXBR/isec-miss.2.2.vcf.gz /tmp/eP2NabHXBR/isec-miss.2.3.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples /tmp/eP2NabHXBR/merge.a.vcf.gz /tmp/eP2NabHXBR/merge.b.vcf.gz /tmp/eP2NabHXBR/merge.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples /tmp/eP2NabHXBR/merge.a.vcf.gz /tmp/eP2NabHXBR/merge.b.vcf.gz /tmp/eP2NabHXBR/merge.c.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -Fx /tmp/eP2NabHXBR/merge.a.vcf.gz /tmp/eP2NabHXBR/merge.b.vcf.gz /tmp/eP2NabHXBR/merge.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -Fx /tmp/eP2NabHXBR/merge.a.vcf.gz /tmp/eP2NabHXBR/merge.b.vcf.gz /tmp/eP2NabHXBR/merge.c.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -0 /tmp/eP2NabHXBR/merge.a.vcf.gz /tmp/eP2NabHXBR/merge.b.vcf.gz /tmp/eP2NabHXBR/merge.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -0 /tmp/eP2NabHXBR/merge.a.vcf.gz /tmp/eP2NabHXBR/merge.b.vcf.gz /tmp/eP2NabHXBR/merge.c.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -m none /tmp/eP2NabHXBR/merge.2.a.vcf.gz /tmp/eP2NabHXBR/merge.2.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -m none /tmp/eP2NabHXBR/merge.2.a.vcf.gz /tmp/eP2NabHXBR/merge.2.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -m both /tmp/eP2NabHXBR/merge.2.a.vcf.gz /tmp/eP2NabHXBR/merge.2.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -m both /tmp/eP2NabHXBR/merge.2.a.vcf.gz /tmp/eP2NabHXBR/merge.2.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -m all /tmp/eP2NabHXBR/merge.2.a.vcf.gz /tmp/eP2NabHXBR/merge.2.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -m all /tmp/eP2NabHXBR/merge.2.a.vcf.gz /tmp/eP2NabHXBR/merge.2.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/eP2NabHXBR/merge.3.a.vcf.gz /tmp/eP2NabHXBR/merge.3.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/eP2NabHXBR/merge.3.a.vcf.gz /tmp/eP2NabHXBR/merge.3.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -m id /tmp/eP2NabHXBR/merge.4.a.vcf.gz /tmp/eP2NabHXBR/merge.4.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -m id /tmp/eP2NabHXBR/merge.4.a.vcf.gz /tmp/eP2NabHXBR/merge.4.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/eP2NabHXBR/gvcf.merge.1.vcf.gz /tmp/eP2NabHXBR/gvcf.merge.2.vcf.gz /tmp/eP2NabHXBR/gvcf.merge.3.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --gvcf - /tmp/eP2NabHXBR/gvcf.merge.1.vcf.gz /tmp/eP2NabHXBR/gvcf.merge.2.vcf.gz /tmp/eP2NabHXBR/gvcf.merge.3.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/eP2NabHXBR/merge.gvcf.2.a.vcf.gz /tmp/eP2NabHXBR/merge.gvcf.2.b.vcf.gz /tmp/eP2NabHXBR/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --gvcf - /tmp/eP2NabHXBR/merge.gvcf.2.a.vcf.gz /tmp/eP2NabHXBR/merge.gvcf.2.b.vcf.gz /tmp/eP2NabHXBR/merge.gvcf.2.c.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - -i SRC:join /tmp/eP2NabHXBR/merge.gvcf.3.a.vcf.gz /tmp/eP2NabHXBR/merge.gvcf.3.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --gvcf - -i SRC:join /tmp/eP2NabHXBR/merge.gvcf.3.a.vcf.gz /tmp/eP2NabHXBR/merge.gvcf.3.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/eP2NabHXBR/merge.gvcf.4.a.vcf.gz /tmp/eP2NabHXBR/merge.gvcf.4.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --gvcf - /tmp/eP2NabHXBR/merge.gvcf.4.a.vcf.gz /tmp/eP2NabHXBR/merge.gvcf.4.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version /tmp/eP2NabHXBR/merge.5.a.vcf.gz /tmp/eP2NabHXBR/merge.5.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob /tmp/eP2NabHXBR/merge.5.a.vcf.gz /tmp/eP2NabHXBR/merge.5.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version /tmp/eP2NabHXBR/merge.6.a.vcf.gz /tmp/eP2NabHXBR/merge.6.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob /tmp/eP2NabHXBR/merge.6.a.vcf.gz /tmp/eP2NabHXBR/merge.6.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/eP2NabHXBR/merge.gvcf.7.a.vcf.gz /tmp/eP2NabHXBR/merge.gvcf.7.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --gvcf - /tmp/eP2NabHXBR/merge.gvcf.7.a.vcf.gz /tmp/eP2NabHXBR/merge.gvcf.7.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/eP2NabHXBR/merge.gvcf.8.a.vcf.gz /tmp/eP2NabHXBR/merge.gvcf.8.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --gvcf - /tmp/eP2NabHXBR/merge.gvcf.8.a.vcf.gz /tmp/eP2NabHXBR/merge.gvcf.8.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples /tmp/eP2NabHXBR/merge.7.a.vcf.gz /tmp/eP2NabHXBR/merge.7.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples /tmp/eP2NabHXBR/merge.7.a.vcf.gz /tmp/eP2NabHXBR/merge.7.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_query: /<>/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' /tmp/eP2NabHXBR/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/query.vcf.gz | /<>/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' .. ok test_vcf_query: /<>/bcftools query -f '%RSX\t%VKX\n' /tmp/eP2NabHXBR/query.variantkey.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/query.variantkey.vcf.gz | /<>/bcftools query -f '%RSX\t%VKX\n' .. ok test_vcf_query: /<>/bcftools query -f'%XRI\n' -i'XRI[*]>1111' /tmp/eP2NabHXBR/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/view.filter.vcf.gz | /<>/bcftools query -f'%XRI\n' -i'XRI[*]>1111' .. ok test_vcf_query: /<>/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' /tmp/eP2NabHXBR/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/view.filter.vcf.gz | /<>/bcftools query -f'%XRF\n' -i'XRF[*]=2e6' .. ok test_vcf_query: /<>/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' /tmp/eP2NabHXBR/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/view.filter.vcf.gz | /<>/bcftools query -f'%XGS\n' -i'XGS[5]="PQR"' .. ok test_vcf_query: /<>/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' /tmp/eP2NabHXBR/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/view.filter.vcf.gz | /<>/bcftools query -f'%XGS\n' -i'XGS[*]="GHI"' .. ok test_vcf_query: /<>/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' /tmp/eP2NabHXBR/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/view.filter.vcf.gz | /<>/bcftools query -f'%XGS\n' -i'XGS[2]~"H"' .. ok test_vcf_query: /<>/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' /tmp/eP2NabHXBR/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/view.filter.vcf.gz | /<>/bcftools query -f'%XGS\n' -i'XGS[3]!~"H" && XGS!="."' .. ok test_vcf_query: /<>/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' /tmp/eP2NabHXBR/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/view.filter.vcf.gz | /<>/bcftools query -f'%XGS\n' -i'XGS[*]~"H"' .. ok test_vcf_query: /<>/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' /tmp/eP2NabHXBR/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/query.vcf.gz | /<>/bcftools query -f'%POS %REF %ALT\n' -i'REF~"C" && ALT[*]~"CT"' .. ok test_vcf_query: /<>/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' /tmp/eP2NabHXBR/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/query.vcf.gz | /<>/bcftools query -f'%POS %REF %ALT\n' -i'N_ALT=2' .. ok test_vcf_query: /<>/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' /tmp/eP2NabHXBR/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/query.vcf.gz | /<>/bcftools query -f'%POS %AN\n' -i'AN!=2*N_SAMPLES' .. ok test_vcf_query: /<>/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' /tmp/eP2NabHXBR/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/query.vcf.gz | /<>/bcftools query -f'%POS[ %GL]\n' -i'min(abs(GL[*:0]))=10' .. ok test_vcf_query: /<>/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' /tmp/eP2NabHXBR/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/view.filter.vcf.gz | /<>/bcftools query -f'%POS %CIGAR\n' -i'strlen(CIGAR[*])=4' .. ok test_vcf_query: /<>/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' /tmp/eP2NabHXBR/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/query.vcf.gz | /<>/bcftools query -f'%POS[ %GT]\n' -i'AC[0]=3' .. ok test_vcf_query: /<>/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' /tmp/eP2NabHXBR/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/query.vcf.gz | /<>/bcftools query -f'%POS[ %GT]\n' -i'AF[0]=3/4' .. ok test_vcf_query: /<>/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' /tmp/eP2NabHXBR/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/query.vcf.gz | /<>/bcftools query -f'%POS[ %GT]\n' -i'MAC[0]=1' .. ok test_vcf_query: /<>/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' /tmp/eP2NabHXBR/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/query.vcf.gz | /<>/bcftools query -f'%POS[ %GT]\n' -i'MAF[0]=1/4' .. ok test_vcf_query: /<>/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/eP2NabHXBR/view.vectors.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/view.vectors.vcf.gz | /<>/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: /<>/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' /tmp/eP2NabHXBR/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/query.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT ="1"' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' /tmp/eP2NabHXBR/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/query.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT!="1"' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' /tmp/eP2NabHXBR/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/query.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT ="1"' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' /tmp/eP2NabHXBR/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/query.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %GT\n]' -e'GT!="1"' .. ok test_vcf_query: /<>/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' /tmp/eP2NabHXBR/query.2.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/query.2.vcf.gz | /<>/bcftools query -f'%XX_A %XX.A %XX.A0 %xx.a0\n' .. ok test_vcf_query: /<>/bcftools query -i'IINT="."' -f'%POS %IINT\n' /tmp/eP2NabHXBR/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/missing.vcf.gz | /<>/bcftools query -i'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /<>/bcftools query -i'IINT!="."' -f'%POS %IINT\n' /tmp/eP2NabHXBR/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/missing.vcf.gz | /<>/bcftools query -i'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /<>/bcftools query -e'IINT!="."' -f'%POS %IINT\n' /tmp/eP2NabHXBR/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/missing.vcf.gz | /<>/bcftools query -e'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /<>/bcftools query -e'IINT="."' -f'%POS %IINT\n' /tmp/eP2NabHXBR/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/missing.vcf.gz | /<>/bcftools query -e'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /<>/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' /tmp/eP2NabHXBR/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/missing.vcf.gz | /<>/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /<>/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' /tmp/eP2NabHXBR/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/missing.vcf.gz | /<>/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /<>/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' /tmp/eP2NabHXBR/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/missing.vcf.gz | /<>/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /<>/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' /tmp/eP2NabHXBR/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/missing.vcf.gz | /<>/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /<>/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' /tmp/eP2NabHXBR/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/missing.vcf.gz | /<>/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /<>/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' /tmp/eP2NabHXBR/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/missing.vcf.gz | /<>/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /<>/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' /tmp/eP2NabHXBR/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/missing.vcf.gz | /<>/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /<>/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' /tmp/eP2NabHXBR/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/missing.vcf.gz | /<>/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /<>/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' /tmp/eP2NabHXBR/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/missing.vcf.gz | /<>/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' .. ok test_vcf_query: /<>/bcftools query -f'%LINE' /tmp/eP2NabHXBR/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/query.vcf.gz | /<>/bcftools query -f'%LINE' .. ok test_vcf_query: /<>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' /tmp/eP2NabHXBR/query.filter-type.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/query.filter-type.vcf.gz | /<>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' .. ok test_vcf_query: /<>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' /tmp/eP2NabHXBR/query.filter-type.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/query.filter-type.vcf.gz | /<>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type~"snp"' .. ok test_vcf_query: /<>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' /tmp/eP2NabHXBR/query.filter-type.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/query.filter-type.vcf.gz | /<>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!="snp"' .. ok test_vcf_query: /<>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' /tmp/eP2NabHXBR/query.filter-type.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/query.filter-type.vcf.gz | /<>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type!~"snp"' .. ok test_vcf_query: /<>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'INFO/TYPE="xxx"' /tmp/eP2NabHXBR/query.filter-type.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/query.filter-type.vcf.gz | /<>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'INFO/TYPE="xxx"' .. ok test_vcf_query: /<>/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/eP2NabHXBR/filter-missing-floats.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/filter-missing-floats.vcf.gz | /<>/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: /<>/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/eP2NabHXBR/filter-missing-floats.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/filter-missing-floats.vcf.gz | /<>/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: /<>/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' /tmp/eP2NabHXBR/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/missing.vcf.gz | /<>/bcftools query -i'FMT/FINT!="."' -f'[\t%FINT]\n' .. ok test_vcf_query: /<>/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' /tmp/eP2NabHXBR/query.filter.2.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/query.filter.2.vcf.gz | /<>/bcftools query -f'[%GT]\n' -i'GT~"0/[1-9]" || GT~"[1-9]/0"' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' /tmp/eP2NabHXBR/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:1-2,4]="EE"' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' /tmp/eP2NabHXBR/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'"EE"=FGS[*:1-2,4]' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' /tmp/eP2NabHXBR/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]=6' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' /tmp/eP2NabHXBR/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'6=FGI[*:1-2,5]' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' /tmp/eP2NabHXBR/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %FGF\n]\n' -i'FGF[*:1-3,4]=5e-5' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' /tmp/eP2NabHXBR/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="EE"' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' /tmp/eP2NabHXBR/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]="."' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' /tmp/eP2NabHXBR/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %FGS\n]\n' -i'FGS[*:4]!="."' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' /tmp/eP2NabHXBR/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]="."' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' /tmp/eP2NabHXBR/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %FGI\n]\n' -i'FGI[*:1-2,5]!="."' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' /tmp/eP2NabHXBR/filter.5.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/filter.5.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP=2' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' /tmp/eP2NabHXBR/filter.5.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/filter.5.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=1 | FMT/DP="."' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' /tmp/eP2NabHXBR/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' /tmp/eP2NabHXBR/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 | FMT/DP="."' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' /tmp/eP2NabHXBR/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP=19 || FMT/DP="."' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' /tmp/eP2NabHXBR/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]=19' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' /tmp/eP2NabHXBR/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %DP\n]\n' -i'FMT/DP[0]!=19' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 & FMT/GQ=589' /tmp/eP2NabHXBR/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 & FMT/GQ=589' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' /tmp/eP2NabHXBR/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/view.filter.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %DP %GQ\n]\n' -i'FMT/DP=19 && FMT/GQ=1' .. ok test_vcf_query: /<>/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' /tmp/eP2NabHXBR/query.filter.3.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/query.filter.3.vcf.gz | /<>/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" && GT~"2"' .. ok test_vcf_query: /<>/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"' /tmp/eP2NabHXBR/query.filter.3.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/query.filter.3.vcf.gz | /<>/bcftools query -f'[\t%GT\n]\n' -i'GT~"1" & GT~"2"' .. ok test_vcf_query: /<>/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' /tmp/eP2NabHXBR/query.filter.3.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/query.filter.3.vcf.gz | /<>/bcftools query -f'%POS[\t%GT]\n' -i'COUNT(GT="het")=1' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %AD\n]\n' -i'AD[:0]+AD[:1] > 12' /tmp/eP2NabHXBR/filter.5.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/filter.5.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %AD\n]\n' -i'AD[:0]+AD[:1] > 12' .. ok test_vcf_query: /<>/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' /tmp/eP2NabHXBR/query.filter.4.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/query.filter.4.vcf.gz | /<>/bcftools query -f'%POS\t%REF\t%ALT[\t%GT]\n' -e'TYPE!="snp" || ALT="*"' .. ok test_vcf_query: /<>/bcftools query -f'%ID\n' -i 'ID=@/<>/test/query.56.out' /tmp/eP2NabHXBR/view.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/view.vcf.gz | /<>/bcftools query -f'%ID\n' -i 'ID=@/<>/test/query.56.out' .. ok test_vcf_query: /<>/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD)>0.01' /tmp/eP2NabHXBR/query.filter.5.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/query.filter.5.vcf.gz | /<>/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD)>0.01' .. ok test_vcf_query: /<>/bcftools query -f'[%POS\t%SAMPLE\t%GT\t%AD\n]' -i'GT="het" & binom(FMT/AD[:0],FMT/AD[:1])>0.01' /tmp/eP2NabHXBR/query.filter.5.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/query.filter.5.vcf.gz | /<>/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: /<>/bcftools query -f'%POS\t%AD\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01' /tmp/eP2NabHXBR/query.filter.5.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/query.filter.5.vcf.gz | /<>/bcftools query -f'%POS\t%AD\n' -i'binom(INFO/AD[0],INFO/AD[1])>0.01' .. ok test_vcf_query: /<>/bcftools query -f'%CHROM %POS\n' -i'CHROM="4"' /tmp/eP2NabHXBR/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/query.vcf.gz | /<>/bcftools query -f'%CHROM %POS\n' -i'CHROM="4"' .. ok test_vcf_query: /<>/bcftools query -f'%POS\t%TAG1\n' -i'(TAG1>=-129 && TAG1<=-120) || (TAG1>=-32769 && TAG1<=-32760)' /tmp/eP2NabHXBR/query.negative.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/query.negative.vcf.gz | /<>/bcftools query -f'%POS\t%TAG1\n' -i'(TAG1>=-129 && TAG1<=-120) || (TAG1>=-32769 && TAG1<=-32760)' .. ok test_vcf_query: /<>/bcftools query -f'%POS\t%TAGV1\n' -i'(TAGV1>=-129 && TAGV1<=-120) || (TAGV1>=-32769 && TAGV1<=-32760)' /tmp/eP2NabHXBR/query.negative.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/query.negative.vcf.gz | /<>/bcftools query -f'%POS\t%TAGV1\n' -i'(TAGV1>=-129 && TAGV1<=-120) || (TAGV1>=-32769 && TAGV1<=-32760)' .. ok test_vcf_query: /<>/bcftools query -f'%POS\t%TAG2\n' -i'(TAG2>=-129 && TAG2<=-120) || (TAG2>=-32769 && TAG2<=-32760)' /tmp/eP2NabHXBR/query.negative.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/query.negative.vcf.gz | /<>/bcftools query -f'%POS\t%TAG2\n' -i'(TAG2>=-129 && TAG2<=-120) || (TAG2>=-32769 && TAG2<=-32760)' .. ok test_vcf_query: /<>/bcftools query -f'%POS\t%TAGV2\n' -i'(TAGV2>=-129 && TAGV2<=-120) || (TAGV2>=-32769 && TAGV2<=-32760)' /tmp/eP2NabHXBR/query.negative.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/query.negative.vcf.gz | /<>/bcftools query -f'%POS\t%TAGV2\n' -i'(TAGV2>=-129 && TAGV2<=-120) || (TAGV2>=-32769 && TAGV2<=-32760)' .. ok test_vcf_query: /<>/bcftools query -f'[%POS\t%SAMPLE\t%GQ\n]' -i'N_PASS(GQ<20)==1' /tmp/eP2NabHXBR/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/query.vcf.gz | /<>/bcftools query -f'[%POS\t%SAMPLE\t%GQ\n]' -i'N_PASS(GQ<20)==1' .. ok test_vcf_query: /<>/bcftools query -f'%CHROM\t%POS\t%INFO\t%FORMAT\n' -s D,C /tmp/eP2NabHXBR/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/query.vcf.gz | /<>/bcftools query -f'%CHROM\t%POS\t%INFO\t%FORMAT\n' -s D,C .. ok test_vcf_query: /<>/bcftools query -f'%POS\n' -i'POS==16777217 || POS==33554432 || POS=118673904' /tmp/eP2NabHXBR/query.filter.6.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/query.filter.6.vcf.gz | /<>/bcftools query -f'%POS\n' -i'POS==16777217 || POS==33554432 || POS=118673904' .. ok test_vcf_query: /<>/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(II)==6' /tmp/eP2NabHXBR/query.filter.7.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/query.filter.7.vcf.gz | /<>/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(II)==6' .. ok test_vcf_query: /<>/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(FORMAT/FI)==7' /tmp/eP2NabHXBR/query.filter.7.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/query.filter.7.vcf.gz | /<>/bcftools query -f'%POS\t%II[\t%FI]\n' -i'sum(FORMAT/FI)==7' .. ok test_vcf_query: /<>/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(II)==2' /tmp/eP2NabHXBR/query.filter.7.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/query.filter.7.vcf.gz | /<>/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(II)==2' .. ok test_vcf_query: /<>/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(FORMAT/FI)==1.75' /tmp/eP2NabHXBR/query.filter.7.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/query.filter.7.vcf.gz | /<>/bcftools query -f'%POS\t%II[\t%FI]\n' -i'avg(FORMAT/FI)==1.75' .. ok test_vcf_query: /<>/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(II)==2' /tmp/eP2NabHXBR/query.filter.7.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/query.filter.7.vcf.gz | /<>/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(II)==2' .. ok test_vcf_query: /<>/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(FORMAT/FI)==1.75' /tmp/eP2NabHXBR/query.filter.7.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/query.filter.7.vcf.gz | /<>/bcftools query -f'%POS\t%II[\t%FI]\n' -i'mean(FORMAT/FI)==1.75' .. ok test_vcf_query: /<>/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(II)==2' /tmp/eP2NabHXBR/query.filter.7.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/query.filter.7.vcf.gz | /<>/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(II)==2' .. ok test_vcf_query: /<>/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(FORMAT/FI)==1.5' /tmp/eP2NabHXBR/query.filter.7.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/query.filter.7.vcf.gz | /<>/bcftools query -f'%POS\t%II[\t%FI]\n' -i'median(FORMAT/FI)==1.5' .. ok test_vcf_query: /<>/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'%ILEN==1' /tmp/eP2NabHXBR/query.filter.8.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/query.filter.8.vcf.gz | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'%ILEN==1' .. ok test_vcf_query: /<>/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'ILEN==1' /tmp/eP2NabHXBR/query.filter.8.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/query.filter.8.vcf.gz | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%ILEN\n' -i'ILEN==1' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] < FMT/AD[:1]' /tmp/eP2NabHXBR/query.filter.9.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/query.filter.9.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] < FMT/AD[:1]' .. ok test_vcf_query: /<>/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] > FMT/AD[:1]' /tmp/eP2NabHXBR/query.filter.9.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/query.filter.9.vcf.gz | /<>/bcftools query -f'[%POS %SAMPLE %AD\n]' -i'FMT/AD[:0] > FMT/AD[:1]' .. ok test_vcf_query: /<>/bcftools query -f'%POS %NUM_TAG\n' -i'COUNT(INFO/NUM_TAG)=2' /tmp/eP2NabHXBR/query.filter.10.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/query.filter.10.vcf.gz | /<>/bcftools query -f'%POS %NUM_TAG\n' -i'COUNT(INFO/NUM_TAG)=2' .. ok test_vcf_query: /<>/bcftools query -f'%POS %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2' /tmp/eP2NabHXBR/query.filter.10.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/eP2NabHXBR/query.filter.10.vcf.gz | /<>/bcftools query -f'%POS %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2' .. ok test_vcf_norm: /<>/bcftools norm --no-version -cx -f /<>/test/norm.fa /tmp/eP2NabHXBR/norm.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -cx -f /<>/test/norm.fa /tmp/eP2NabHXBR/norm.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- /tmp/eP2NabHXBR/norm.split.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -m- /tmp/eP2NabHXBR/norm.split.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- /tmp/eP2NabHXBR/norm.split.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -m- /tmp/eP2NabHXBR/norm.split.2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- --force /tmp/eP2NabHXBR/norm.split.3.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -m- --force /tmp/eP2NabHXBR/norm.split.3.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- -f /<>/test/norm.fa /tmp/eP2NabHXBR/norm.split.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -m- -f /<>/test/norm.fa /tmp/eP2NabHXBR/norm.split.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m+ /tmp/eP2NabHXBR/norm.merge.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -m+ /tmp/eP2NabHXBR/norm.merge.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m+ /tmp/eP2NabHXBR/norm.merge.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -m+ /tmp/eP2NabHXBR/norm.merge.2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m+ /tmp/eP2NabHXBR/norm.merge.3.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -m+ /tmp/eP2NabHXBR/norm.merge.3.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m+ -s /tmp/eP2NabHXBR/norm.merge.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -m+ -s /tmp/eP2NabHXBR/norm.merge.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -Nc s -f /<>/test/norm.fa /tmp/eP2NabHXBR/norm.setref.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -Nc s -f /<>/test/norm.fa /tmp/eP2NabHXBR/norm.setref.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -f /<>/test/norm.fa /tmp/eP2NabHXBR/norm.telomere.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -f /<>/test/norm.fa /tmp/eP2NabHXBR/norm.telomere.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d snps /tmp/eP2NabHXBR/norm.rmdup.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -d snps /tmp/eP2NabHXBR/norm.rmdup.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d indels /tmp/eP2NabHXBR/norm.rmdup.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -d indels /tmp/eP2NabHXBR/norm.rmdup.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d both /tmp/eP2NabHXBR/norm.rmdup.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -d both /tmp/eP2NabHXBR/norm.rmdup.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d all /tmp/eP2NabHXBR/norm.rmdup.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -d all /tmp/eP2NabHXBR/norm.rmdup.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d none /tmp/eP2NabHXBR/norm.rmdup.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -d none /tmp/eP2NabHXBR/norm.rmdup.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d exact /tmp/eP2NabHXBR/norm.rmdup.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -d exact /tmp/eP2NabHXBR/norm.rmdup.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d none /tmp/eP2NabHXBR/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -d none /tmp/eP2NabHXBR/norm.rmdup.2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d exact /tmp/eP2NabHXBR/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -d exact /tmp/eP2NabHXBR/norm.rmdup.2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d indels /tmp/eP2NabHXBR/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -d indels /tmp/eP2NabHXBR/norm.rmdup.2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d any /tmp/eP2NabHXBR/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -d any /tmp/eP2NabHXBR/norm.rmdup.2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d both /tmp/eP2NabHXBR/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -d both /tmp/eP2NabHXBR/norm.rmdup.2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d snps /tmp/eP2NabHXBR/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -d snps /tmp/eP2NabHXBR/norm.rmdup.2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -f /<>/test/norm.2.fa /tmp/eP2NabHXBR/norm.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -f /<>/test/norm.2.fa /tmp/eP2NabHXBR/norm.2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -aUc1 -C1 -s NA00002 -v snps /tmp/eP2NabHXBR/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/eP2NabHXBR/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -f PASS -Xks NA00003 /tmp/eP2NabHXBR/view.vcf.gz -r20,Y .. ok test_vcf_view: /<>/bcftools view -Ob -f PASS -Xks NA00003 /tmp/eP2NabHXBR/view.vcf.gz -r20,Y | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -xs NA00003 /tmp/eP2NabHXBR/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -xs NA00003 /tmp/eP2NabHXBR/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/eP2NabHXBR/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -i 'QUAL==999 && (FS<20 || FS>=41.02) && ICF>-0.1 && HWE*2>1.2' /tmp/eP2NabHXBR/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -p /tmp/eP2NabHXBR/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -p /tmp/eP2NabHXBR/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -P /tmp/eP2NabHXBR/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -P /tmp/eP2NabHXBR/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -hm2 -M2 -q0.3 -Q0.7 /tmp/eP2NabHXBR/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/eP2NabHXBR/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -Hu /tmp/eP2NabHXBR/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -GVsnps /tmp/eP2NabHXBR/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -GVsnps /tmp/eP2NabHXBR/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -ne 'INDEL=1 || PV4[0]<0.006' /tmp/eP2NabHXBR/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/eP2NabHXBR/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -s ^NA00003 /tmp/eP2NabHXBR/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -s ^NA00003 /tmp/eP2NabHXBR/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version /tmp/eP2NabHXBR/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob /tmp/eP2NabHXBR/view.omitgenotypes.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -G /tmp/eP2NabHXBR/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -G /tmp/eP2NabHXBR/view.omitgenotypes.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -HG /tmp/eP2NabHXBR/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -a /tmp/eP2NabHXBR/many.alleles.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -a /tmp/eP2NabHXBR/many.alleles.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -asA /tmp/eP2NabHXBR/view.vectors.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -asA /tmp/eP2NabHXBR/view.vectors.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -asB /tmp/eP2NabHXBR/view.vectors.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -asB /tmp/eP2NabHXBR/view.vectors.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -asA /tmp/eP2NabHXBR/view.vectors.2.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -asA /tmp/eP2NabHXBR/view.vectors.2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'FMT/FGS[*:0]="AAAAAA"' /tmp/eP2NabHXBR/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'FMT/FGS[*:2]="C"' /tmp/eP2NabHXBR/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'FMT/FGS[*:4]="EE"' /tmp/eP2NabHXBR/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'FMT/FRS[*:1]="BB"' /tmp/eP2NabHXBR/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'TXT0="text"' /tmp/eP2NabHXBR/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -T /<>/test/view.chrs.tab /tmp/eP2NabHXBR/view.chrs.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -T /<>/test/view.chrs.tab /tmp/eP2NabHXBR/view.chrs.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -i 'POS>=3062917' /tmp/eP2NabHXBR/filter.2.vcf.gz 1:3062917-3157410 .. ok test_vcf_view: /<>/bcftools view -Ob -i 'POS>=3062917' /tmp/eP2NabHXBR/filter.2.vcf.gz 1:3062917-3157410 | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -H -r 1:10,1:12,1:10 /tmp/eP2NabHXBR/idx.1.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -r 1:1172777-1172804,1:1172806-1172808 /tmp/eP2NabHXBR/idx.2.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -R /<>/test/idx.2.bed /tmp/eP2NabHXBR/idx.2.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -R /<>/test/idx.3.bed /tmp/eP2NabHXBR/idx.3.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -R /<>/test/idx.4.bed /tmp/eP2NabHXBR/idx.4.vcf.gz .. ok test_vcf_64bit: /<>/bcftools view /<>/test/view64bit.1.vcf -H .. ok test_vcf_64bit: /<>/bcftools view /<>/test/view64bit.1.vcf | /<>/bcftools view -H .. ok test_vcf_64bit: /<>/bcftools view /<>/test/view64bit.1.vcf -Ou | /<>/bcftools view -H .. ok test_vcf_64bit: /<>/bcftools view /<>/test/view64bit.2.vcf -H .. ok test_vcf_64bit: /<>/bcftools view /<>/test/view64bit.2.vcf | /<>/bcftools view -H .. ok test_vcf_64bit: /<>/bcftools view /<>/test/view64bit.2.vcf -Ou | /<>/bcftools view -H .. ok test_vcf_64bit: /<>/bcftools view /<>/test/view64bit.3.vcf -H .. ok test_vcf_64bit: /<>/bcftools view /<>/test/view64bit.3.vcf | /<>/bcftools view -H .. ok test_vcf_64bit: /<>/bcftools view /<>/test/view64bit.4.vcf -H .. ok test_vcf_64bit: /<>/bcftools view /<>/test/view64bit.4.vcf | /<>/bcftools view -H .. ok test_vcf_64bit: /<>/bcftools view /<>/test/view64bit.4.vcf -Ou | /<>/bcftools view -H .. ok test_vcf_64bit: /<>/bcftools view /<>/test/view64bit.5.vcf -H .. ok test_vcf_64bit: /<>/bcftools view /<>/test/view64bit.5.vcf | /<>/bcftools view -H .. ok test_vcf_64bit: /<>/bcftools view /<>/test/view64bit.5.vcf -Ou | /<>/bcftools view -H .. ok test_vcf_filter: /<>/bcftools filter -S. -e'TXT0="text"' /<>/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S. -e'TXT0="text"' /<>/test/view.filter.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S. -e'FMT/FRS[*:1]="BB"' /<>/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S. -e'FMT/FRS[*:1]="BB"' /<>/test/view.filter.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S. -e'FMT/FGS[*:0]="AAAAAA"' /<>/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S. -e'FMT/FGS[*:0]="AAAAAA"' /<>/test/view.filter.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S. -e'FMT/FGS[*:1]="BBB"' /<>/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S. -e'FMT/FGS[*:1]="BBB"' /<>/test/view.filter.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S. -e'FMT/FGS[*:4]="EE"' /<>/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S. -e'FMT/FGS[*:4]="EE"' /<>/test/view.filter.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S. -e'FMT/STR="XX"' /<>/test/view.filter.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S. -e'FMT/STR="XX"' /<>/test/view.filter.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S. -e'FMT/FILTER="aaa"' /<>/test/view.filter.2.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S. -e'FMT/FILTER="aaa"' /<>/test/view.filter.2.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -H -C5:nonmajor /tmp/eP2NabHXBR/view.minmaxac.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -c6:nonmajor /tmp/eP2NabHXBR/view.minmaxac.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -q0.3:major /tmp/eP2NabHXBR/view.minmaxac.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/eP2NabHXBR/view.filter.annovar.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i 'Gene.refGene~"NOD"' /tmp/eP2NabHXBR/view.filter.annovar.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i 'LJB2_MutationTaster=="0.291000"' /tmp/eP2NabHXBR/view.filter.annovar.vcf.gz .. ok test_vcf_call: /<>/bcftools call --no-version -mv /<>/test/mpileup.vcf .. ok test_vcf_call: /<>/bcftools call -Ob -mv /<>/test/mpileup.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /<>/bcftools call --no-version -mg0 /<>/test/mpileup.vcf .. ok test_vcf_call: /<>/bcftools call -Ob -mg0 /<>/test/mpileup.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /<>/bcftools call --no-version -mv -S /<>/test/mpileup.3.samples /<>/test/mpileup.vcf .. ok test_vcf_call: /<>/bcftools call -Ob -mv -S /<>/test/mpileup.3.samples /<>/test/mpileup.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /<>/bcftools call --no-version -mv -S /<>/test/mpileup.4.samples /<>/test/mpileup.vcf .. ok test_vcf_call: /<>/bcftools call -Ob -mv -S /<>/test/mpileup.4.samples /<>/test/mpileup.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /<>/bcftools call --no-version -mv -S /<>/test/mpileup.5.samples /<>/test/mpileup.vcf .. ok test_vcf_call: /<>/bcftools call -Ob -mv -S /<>/test/mpileup.5.samples /<>/test/mpileup.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /<>/bcftools call --no-version -mv --ploidy-file /<>/test/mpileup.ploidy -S /<>/test/mpileup.samples /<>/test/mpileup.X.vcf .. ok test_vcf_call: /<>/bcftools call -Ob -mv --ploidy-file /<>/test/mpileup.ploidy -S /<>/test/mpileup.samples /<>/test/mpileup.X.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /<>/bcftools call --no-version -mv --ploidy-file /<>/test/mpileup.ploidy -S /<>/test/mpileup.ped /<>/test/mpileup.X.vcf .. ok test_vcf_call: /<>/bcftools call -Ob -mv --ploidy-file /<>/test/mpileup.ploidy -S /<>/test/mpileup.ped /<>/test/mpileup.X.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /<>/bcftools call --no-version -mv --ploidy-file /<>/test/mpileup.ploidy -S /<>/test/mpileup.2.samples /<>/test/mpileup.X.vcf .. ok test_vcf_call: /<>/bcftools call -Ob -mv --ploidy-file /<>/test/mpileup.ploidy -S /<>/test/mpileup.2.samples /<>/test/mpileup.X.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /<>/bcftools call --no-version -mv /<>/test/mpileup.NA19213.NA19129.vcf .. ok test_vcf_call: /<>/bcftools call -Ob -mv /<>/test/mpileup.NA19213.NA19129.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /<>/bcftools call --no-version -mv -G - /<>/test/mpileup.NA19213.NA19129.vcf .. ok test_vcf_call: /<>/bcftools call -Ob -mv -G - /<>/test/mpileup.NA19213.NA19129.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /<>/bcftools call --no-version -mv /<>/test/mpileup.hwe.vcf .. ok test_vcf_call: /<>/bcftools call -Ob -mv /<>/test/mpileup.hwe.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /<>/bcftools call --no-version -mv -G - /<>/test/mpileup.hwe.vcf .. ok test_vcf_call: /<>/bcftools call -Ob -mv -G - /<>/test/mpileup.hwe.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /<>/bcftools call --no-version -mv -G /<>/test/mpileup.hwe.samples /<>/test/mpileup.hwe.vcf .. ok test_vcf_call: /<>/bcftools call -Ob -mv -G /<>/test/mpileup.hwe.samples /<>/test/mpileup.hwe.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /<>/bcftools call --no-version -mA -C alleles -T /tmp/eP2NabHXBR/mpileup.tab.gz /<>/test/mpileup.vcf .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/eP2NabHXBR/mpileup.tab.gz /<>/test/mpileup.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /<>/bcftools call --no-version -mA -C alleles -T /tmp/eP2NabHXBR/mpileup.2.tab.gz /<>/test/mpileup.2.vcf .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/eP2NabHXBR/mpileup.2.tab.gz /<>/test/mpileup.2.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /<>/bcftools call --no-version -mA -C alleles -T /tmp/eP2NabHXBR/mpileup.3.tab.gz -i /<>/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/eP2NabHXBR/mpileup.3.tab.gz -i /<>/test/mpileup.3.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /<>/bcftools call --no-version -mA -C alleles -T /tmp/eP2NabHXBR/mpileup.4.tab.gz -i /<>/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/eP2NabHXBR/mpileup.4.tab.gz -i /<>/test/mpileup.3.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /<>/bcftools call --no-version -mA -C alleles -T /tmp/eP2NabHXBR/mpileup.5.tab.gz -i /<>/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/eP2NabHXBR/mpileup.5.tab.gz -i /<>/test/mpileup.3.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /<>/bcftools call --no-version -mA -C alleles -T /tmp/eP2NabHXBR/mpileup.6.tab.gz -i /<>/test/mpileup.4.vcf .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/eP2NabHXBR/mpileup.6.tab.gz -i /<>/test/mpileup.4.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /<>/bcftools call --no-version -mA -C alleles -T /tmp/eP2NabHXBR/mpileup.7.tab.gz -i /<>/test/mpileup.5.vcf .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/eP2NabHXBR/mpileup.7.tab.gz -i /<>/test/mpileup.5.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /<>/bcftools call --no-version -mA -C alleles -T /tmp/eP2NabHXBR/mpileup.cals.1.tab.gz /<>/test/mpileup.cals.1.vcf .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/eP2NabHXBR/mpileup.cals.1.tab.gz /<>/test/mpileup.cals.1.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /<>/bcftools call --no-version -mA -C alleles -T /tmp/eP2NabHXBR/mpileup.cals.2.tab.gz /<>/test/mpileup.cals.2.vcf .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/eP2NabHXBR/mpileup.cals.2.tab.gz /<>/test/mpileup.cals.2.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /<>/bcftools call --no-version -cv /<>/test/mpileup.c.vcf .. ok test_vcf_call: /<>/bcftools call -Ob -cv /<>/test/mpileup.c.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /<>/bcftools call --no-version -cv --ploidy-file /<>/test/mpileup.ploidy -S /<>/test/mpileup.samples /<>/test/mpileup.c.X.vcf .. ok test_vcf_call: /<>/bcftools call -Ob -cv --ploidy-file /<>/test/mpileup.ploidy -S /<>/test/mpileup.samples /<>/test/mpileup.c.X.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /<>/bcftools call --no-version -cv --ploidy-file /<>/test/mpileup.ploidy -S /<>/test/mpileup.ped /<>/test/mpileup.c.X.vcf .. ok test_vcf_call: /<>/bcftools call -Ob -cv --ploidy-file /<>/test/mpileup.ploidy -S /<>/test/mpileup.ped /<>/test/mpileup.c.X.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /<>/bcftools call --no-version -cv --ploidy-file /<>/test/mpileup.ploidy -S /<>/test/mpileup.2.samples /<>/test/mpileup.c.X.vcf .. ok test_vcf_call: /<>/bcftools call -Ob -cv --ploidy-file /<>/test/mpileup.ploidy -S /<>/test/mpileup.2.samples /<>/test/mpileup.c.X.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -mx -g2 -G2 /<>/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -mx -g2 -G2 /<>/test/filter.1.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /<>/test/filter.2.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S. /<>/test/filter.2.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -e'INFO/DP=19' /<>/test/filter.3.vcf | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'INFO/DP=19' /<>/test/filter.3.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -e'INFO/DP=19' -s XX /<>/test/filter.3.vcf | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'INFO/DP=19' -s XX /<>/test/filter.3.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -e'INFO/DP=19' -s XX -m+ /<>/test/filter.3.vcf | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+ /<>/test/filter.3.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -e'INFO/DP=19' -s XX -mx /<>/test/filter.3.vcf | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'INFO/DP=19' -s XX -mx /<>/test/filter.3.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -e'INFO/DP=19' -s XX -m+x /<>/test/filter.3.vcf | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'INFO/DP=19' -s XX -m+x /<>/test/filter.3.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -e'FMT/GT="0/2"' /<>/test/filter.3.vcf | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'FMT/GT="0/2"' /<>/test/filter.3.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -e'FMT/GT="0/2"' -s XX /<>/test/filter.3.vcf | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX /<>/test/filter.3.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -e'FMT/GT="0/2"' -s XX -m+ /<>/test/filter.3.vcf | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+ /<>/test/filter.3.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -e'FMT/GT="0/2"' -s XX -mx /<>/test/filter.3.vcf | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -mx /<>/test/filter.3.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -e'FMT/GT="0/2"' -s XX -m+x /<>/test/filter.3.vcf | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -e'FMT/GT="0/2"' -s XX -m+x /<>/test/filter.3.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%FILTER\t%DP[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'FMT/GT="0/0" && AC[*]=2' /<>/test/filter.2.vcf | /<>/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'FMT/GT="0/0" && AC[*]=2' /<>/test/filter.2.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'AC[*]=2 && FMT/GT="0/0"' /<>/test/filter.2.vcf | /<>/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'AC[*]=2 && FMT/GT="0/0"' /<>/test/filter.2.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'ALT="."' /<>/test/filter.2.vcf | /<>/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'ALT="."' /<>/test/filter.2.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%AC[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -S . -i 'FORMAT/TEST3<25' /<>/test/filter.4.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S . -i 'FORMAT/TEST3<25' /<>/test/filter.4.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S . -i 'FORMAT/TEST4<25' /<>/test/filter.4.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S . -i 'FORMAT/TEST4<25' /<>/test/filter.4.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -i'GT="A"' /<>/test/filter.2.vcf | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'GT="A"' /<>/test/filter.2.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'GT="RR"' /<>/test/filter.2.vcf | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'GT="RR"' /<>/test/filter.2.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'GT="RA"' /<>/test/filter.2.vcf | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'GT="RA"' /<>/test/filter.2.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'GT="AR"' /<>/test/filter.2.vcf | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'GT="AR"' /<>/test/filter.2.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'GT="AA"' /<>/test/filter.2.vcf | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'GT="AA"' /<>/test/filter.2.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'GT="aA"' /<>/test/filter.2.vcf | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'GT="aA"' /<>/test/filter.2.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'GT="Aa"' /<>/test/filter.2.vcf | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'GT="Aa"' /<>/test/filter.2.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'GT="HOM"' /<>/test/filter.2.vcf | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'GT="HOM"' /<>/test/filter.2.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'GT="HET"' /<>/test/filter.2.vcf | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'GT="HET"' /<>/test/filter.2.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'GT="HAP"' /<>/test/filter.2.vcf | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'GT="HAP"' /<>/test/filter.2.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%GT]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'AD[:1]=11' /<>/test/filter.5.vcf | /<>/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'AD[:1]=11' /<>/test/filter.5.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'AD[1:]=11' /<>/test/filter.5.vcf | /<>/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'AD[1:]=11' /<>/test/filter.5.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'FR[0:1]=11' /<>/test/filter.5.vcf | /<>/bcftools query -f '%POS[\t%FR]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'FR[0:1]=11' /<>/test/filter.5.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%FR]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'AD[*]="."' /<>/test/filter.5.vcf | /<>/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'AD[*]="."' /<>/test/filter.5.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'AD[0:0]=="."' /<>/test/filter.5.vcf | /<>/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'AD[0:0]=="."' /<>/test/filter.5.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'AD[0:0]!="."' /<>/test/filter.5.vcf | /<>/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'AD[0:0]!="."' /<>/test/filter.5.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS[\t%AD]\n' .. ok test_vcf_filter: /<>/bcftools filter -i'QUAL=="."' /<>/test/filter.5.vcf | /<>/bcftools query -f '%POS\t%QUAL\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'QUAL=="."' /<>/test/filter.5.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\t%QUAL\n' .. ok test_vcf_filter: /<>/bcftools filter -i'N_PASS(DP>32)=1' /<>/test/filter.2.vcf | /<>/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'N_PASS(DP>32)=1' /<>/test/filter.2.vcf | /<>/bcftools view | /<>/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /<>/bcftools filter -i'F_PASS(DP>32)=0.5' /<>/test/filter.2.vcf | /<>/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'F_PASS(DP>32)=0.5' /<>/test/filter.2.vcf | /<>/bcftools view | /<>/bcftools query -f '[%POS\t%SAMPLE\t%DP\n]' .. ok test_vcf_filter: /<>/bcftools filter -i'F_MISSING>=1/5' /<>/test/filter.6.vcf | /<>/bcftools query -f '%POS\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'F_MISSING>=1/5' /<>/test/filter.6.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\n' .. ok test_vcf_filter: /<>/bcftools filter -i'F_MISSING>=0.2' /<>/test/filter.6.vcf | /<>/bcftools query -f '%POS\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'F_MISSING>=0.2' /<>/test/filter.6.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\n' .. ok test_vcf_filter: /<>/bcftools filter -i'F_PASS(GT=="mis")>=1/5' /<>/test/filter.6.vcf | /<>/bcftools query -f '%POS\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'F_PASS(GT=="mis")>=1/5' /<>/test/filter.6.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\n' .. ok test_vcf_filter: /<>/bcftools filter -i'F_PASS(GT=="mis")>=0.2' /<>/test/filter.6.vcf | /<>/bcftools query -f '%POS\n' .. ok test_vcf_filter: /<>/bcftools filter -Ob -i'F_PASS(GT=="mis")>=0.2' /<>/test/filter.6.vcf | /<>/bcftools view | /<>/bcftools query -f '%POS\n' .. ok test_vcf_sort: /<>/bcftools sort -m 0 /<>/test/sort.vcf | /<>/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /<>/bcftools sort -Ob -m 0 /<>/test/sort.vcf | /<>/bcftools view | /<>/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /<>/bcftools sort -m 1000 /<>/test/sort.vcf | /<>/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_sort: /<>/bcftools sort -Ob -m 1000 /<>/test/sort.vcf | /<>/bcftools view | /<>/bcftools query -f '%CHROM\t%POS\t%REF,%ALT\n' .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /<>/test/regions.tab /tmp/eP2NabHXBR/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/eP2NabHXBR/regions.vcf.gz | /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /<>/test/regions.tab .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /<>/test/regions.tab /tmp/eP2NabHXBR/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/eP2NabHXBR/regions.tab.gz /tmp/eP2NabHXBR/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/eP2NabHXBR/regions.vcf.gz | /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/eP2NabHXBR/regions.tab.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/eP2NabHXBR/regions.tab.gz /tmp/eP2NabHXBR/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/eP2NabHXBR/regions.bed /tmp/eP2NabHXBR/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/eP2NabHXBR/regions.vcf.gz | /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/eP2NabHXBR/regions.bed .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/eP2NabHXBR/regions.bed /tmp/eP2NabHXBR/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/eP2NabHXBR/regions.bed.gz /tmp/eP2NabHXBR/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/eP2NabHXBR/regions.vcf.gz | /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/eP2NabHXBR/regions.bed.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/eP2NabHXBR/regions.bed.gz /tmp/eP2NabHXBR/regions.vcf.gz .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/eP2NabHXBR/annotate.tab.gz -h /<>/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /<>/test/annotate.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/eP2NabHXBR/annotate.tab.gz -h /<>/test/annotate.hdr -c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL /<>/test/annotate.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/eP2NabHXBR/annotate2.tab.gz -h /<>/test/annotate.hdr -c CHROM,POS,-,T_STR /<>/test/annotate.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/eP2NabHXBR/annotate2.tab.gz -h /<>/test/annotate.hdr -c CHROM,POS,-,T_STR /<>/test/annotate.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/eP2NabHXBR/annotate2.tab.gz -h /<>/test/annotate.hdr -c CHROM,FROM,TO,T_STR /<>/test/annotate.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/eP2NabHXBR/annotate2.tab.gz -h /<>/test/annotate.hdr -c CHROM,FROM,TO,T_STR /<>/test/annotate.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/eP2NabHXBR/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/eP2NabHXBR/annotate.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/eP2NabHXBR/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/eP2NabHXBR/annotate.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/eP2NabHXBR/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/eP2NabHXBR/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/eP2NabHXBR/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/eP2NabHXBR/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/eP2NabHXBR/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/eP2NabHXBR/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/eP2NabHXBR/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/eP2NabHXBR/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/eP2NabHXBR/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/eP2NabHXBR/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/eP2NabHXBR/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/eP2NabHXBR/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/eP2NabHXBR/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/eP2NabHXBR/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/eP2NabHXBR/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/eP2NabHXBR/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/eP2NabHXBR/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/eP2NabHXBR/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/eP2NabHXBR/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/eP2NabHXBR/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /<>/test/annotate3.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -x ID,QUAL,^FILTER/fltA,FILTER/fltB,^INFO/AA,INFO/BB,^FMT/GT,FMT/PL /<>/test/annotate3.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -x FORMAT /<>/test/annotate3.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -x FORMAT /<>/test/annotate3.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/eP2NabHXBR/annots4.vcf.gz -c +INFO /tmp/eP2NabHXBR/annotate4.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/eP2NabHXBR/annots4.vcf.gz -c +INFO /tmp/eP2NabHXBR/annotate4.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/eP2NabHXBR/annots4.tab.gz -h /<>/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /<>/test/annotate4.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/eP2NabHXBR/annots4.tab.gz -h /<>/test/annotate4.hdr -c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR /<>/test/annotate4.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/eP2NabHXBR/annots10.tab.gz -h /<>/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /<>/test/annotate10.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/eP2NabHXBR/annots10.tab.gz -h /<>/test/annotate10.hdr -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR /<>/test/annotate10.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/eP2NabHXBR/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/eP2NabHXBR/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/eP2NabHXBR/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/eP2NabHXBR/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/eP2NabHXBR/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /<>/test/annotate2.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/eP2NabHXBR/annots11.tab.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /<>/test/annotate2.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/eP2NabHXBR/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/eP2NabHXBR/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/eP2NabHXBR/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/eP2NabHXBR/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/eP2NabHXBR/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/eP2NabHXBR/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/eP2NabHXBR/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/eP2NabHXBR/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/eP2NabHXBR/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/eP2NabHXBR/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/eP2NabHXBR/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/eP2NabHXBR/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/eP2NabHXBR/annots11.vcf.gz -c FMT /tmp/eP2NabHXBR/annotate11.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/eP2NabHXBR/annots11.vcf.gz -c FMT /tmp/eP2NabHXBR/annotate11.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/eP2NabHXBR/annots2.vcf.gz -c FMT/newGT:=GT /tmp/eP2NabHXBR/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/eP2NabHXBR/annots2.vcf.gz -c FMT/newGT:=GT /tmp/eP2NabHXBR/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/eP2NabHXBR/annots12.vcf.gz -c FMT/GT:=newGT /tmp/eP2NabHXBR/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/eP2NabHXBR/annots12.vcf.gz -c FMT/GT:=newGT /tmp/eP2NabHXBR/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/eP2NabHXBR/annots13.tab.gz -h /<>/test/annotate13.hdr -c CHROM,BEG,END,ABC /<>/test/annotate13.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/eP2NabHXBR/annots13.tab.gz -h /<>/test/annotate13.hdr -c CHROM,BEG,END,ABC /<>/test/annotate13.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/eP2NabHXBR/annots13.tab.gz -h /<>/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:append /<>/test/annotate13.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/eP2NabHXBR/annots13.tab.gz -h /<>/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:append /<>/test/annotate13.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/eP2NabHXBR/annots13.tab.gz -h /<>/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:unique /<>/test/annotate13.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/eP2NabHXBR/annots13.tab.gz -h /<>/test/annotate13.hdr -c CHROM,BEG,END,ABC -l ABC:unique /<>/test/annotate13.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -x FILTER/XX,INFO/XX --force /<>/test/annotate14.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -x FILTER/XX,INFO/XX --force /<>/test/annotate14.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/eP2NabHXBR/annotate15.tab.gz -h /<>/test/annotate15.hdr -s SAMPLE1 -c CHROM,FROM,TO,FMT/FOO,BAR /<>/test/annotate15.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/eP2NabHXBR/annotate15.tab.gz -h /<>/test/annotate15.hdr -s SAMPLE1 -c CHROM,FROM,TO,FMT/FOO,BAR /<>/test/annotate15.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/eP2NabHXBR/annotate15.tab.gz -h /<>/test/annotate15.hdr -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR /<>/test/annotate15.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/eP2NabHXBR/annotate15.tab.gz -h /<>/test/annotate15.hdr -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR /<>/test/annotate15.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -x FILTER /<>/test/annotate16.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -x FILTER /<>/test/annotate16.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/eP2NabHXBR/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /<>/test/annotate17.1.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/eP2NabHXBR/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /<>/test/annotate17.1.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/eP2NabHXBR/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /<>/test/annotate17.2.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/eP2NabHXBR/annotate17.1.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /<>/test/annotate17.2.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/eP2NabHXBR/annotate17.3.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /<>/test/annotate17.3.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/eP2NabHXBR/annotate17.3.tab.gz -c CHROM,BEG,END,A,B -l A:append,B:append /<>/test/annotate17.3.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/eP2NabHXBR/annotate18.1.tab.gz -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /<>/test/annotate18.1.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/eP2NabHXBR/annotate18.1.tab.gz -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /<>/test/annotate18.1.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/eP2NabHXBR/annotate18.2.tab.gz -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /<>/test/annotate18.2.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/eP2NabHXBR/annotate18.2.tab.gz -c CHROM,BEG,END,A,B,C,D,E -l A:sum,B:avg,C:min,D:max,E:append /<>/test/annotate18.2.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/eP2NabHXBR/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /<>/test/annotate9.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/eP2NabHXBR/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /<>/test/annotate9.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version /tmp/eP2NabHXBR/concat.1.a.vcf.gz /tmp/eP2NabHXBR/concat.1.b.vcf.gz .. ok test_vcf_concat: /<>/bcftools concat -Ob /tmp/eP2NabHXBR/concat.1.a.vcf.gz /tmp/eP2NabHXBR/concat.1.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version /tmp/eP2NabHXBR/concat.1.a.bcf /tmp/eP2NabHXBR/concat.1.b.bcf .. ok test_vcf_concat: /<>/bcftools concat -Ob /tmp/eP2NabHXBR/concat.1.a.bcf /tmp/eP2NabHXBR/concat.1.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -a /tmp/eP2NabHXBR/concat.2.a.vcf.gz /tmp/eP2NabHXBR/concat.2.b.vcf.gz .. ok test_vcf_concat: /<>/bcftools concat -Ob -a /tmp/eP2NabHXBR/concat.2.a.vcf.gz /tmp/eP2NabHXBR/concat.2.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -a /tmp/eP2NabHXBR/concat.2.a.bcf /tmp/eP2NabHXBR/concat.2.b.bcf .. ok test_vcf_concat: /<>/bcftools concat -Ob -a /tmp/eP2NabHXBR/concat.2.a.bcf /tmp/eP2NabHXBR/concat.2.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -aD /tmp/eP2NabHXBR/concat.2.a.vcf.gz /tmp/eP2NabHXBR/concat.2.b.vcf.gz .. ok test_vcf_concat: /<>/bcftools concat -Ob -aD /tmp/eP2NabHXBR/concat.2.a.vcf.gz /tmp/eP2NabHXBR/concat.2.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -aD /tmp/eP2NabHXBR/concat.2.a.bcf /tmp/eP2NabHXBR/concat.2.b.bcf .. ok test_vcf_concat: /<>/bcftools concat -Ob -aD /tmp/eP2NabHXBR/concat.2.a.bcf /tmp/eP2NabHXBR/concat.2.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -l /tmp/eP2NabHXBR/concat.3.a.vcf.gz /tmp/eP2NabHXBR/concat.3.b.vcf.gz /tmp/eP2NabHXBR/concat.3.0.vcf.gz /tmp/eP2NabHXBR/concat.3.c.vcf.gz /tmp/eP2NabHXBR/concat.3.d.vcf.gz /tmp/eP2NabHXBR/concat.3.e.vcf.gz /tmp/eP2NabHXBR/concat.3.f.vcf.gz .. ok test_vcf_concat: /<>/bcftools concat -Ob -l /tmp/eP2NabHXBR/concat.3.a.vcf.gz /tmp/eP2NabHXBR/concat.3.b.vcf.gz /tmp/eP2NabHXBR/concat.3.0.vcf.gz /tmp/eP2NabHXBR/concat.3.c.vcf.gz /tmp/eP2NabHXBR/concat.3.d.vcf.gz /tmp/eP2NabHXBR/concat.3.e.vcf.gz /tmp/eP2NabHXBR/concat.3.f.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -l /tmp/eP2NabHXBR/concat.3.a.bcf /tmp/eP2NabHXBR/concat.3.b.bcf /tmp/eP2NabHXBR/concat.3.0.bcf /tmp/eP2NabHXBR/concat.3.c.bcf /tmp/eP2NabHXBR/concat.3.d.bcf /tmp/eP2NabHXBR/concat.3.e.bcf /tmp/eP2NabHXBR/concat.3.f.bcf .. ok test_vcf_concat: /<>/bcftools concat -Ob -l /tmp/eP2NabHXBR/concat.3.a.bcf /tmp/eP2NabHXBR/concat.3.b.bcf /tmp/eP2NabHXBR/concat.3.0.bcf /tmp/eP2NabHXBR/concat.3.c.bcf /tmp/eP2NabHXBR/concat.3.d.bcf /tmp/eP2NabHXBR/concat.3.e.bcf /tmp/eP2NabHXBR/concat.3.f.bcf | /<>/bcftools view | grep -v ^##bcftools_ Random seed for test_naive_concat: 1915388558 .. ok test_naive_concat: /<>/bcftools concat --naive-force /tmp/eP2NabHXBR/naive_concat.0.bcf /tmp/eP2NabHXBR/naive_concat.1.bcf /tmp/eP2NabHXBR/naive_concat.2.bcf /tmp/eP2NabHXBR/naive_concat.3.bcf /tmp/eP2NabHXBR/naive_concat.4.bcf /tmp/eP2NabHXBR/naive_concat.5.bcf /tmp/eP2NabHXBR/naive_concat.6.bcf /tmp/eP2NabHXBR/naive_concat.7.bcf /tmp/eP2NabHXBR/naive_concat.8.bcf /tmp/eP2NabHXBR/naive_concat.9.bcf | /<>/bcftools view -H .. ok test_naive_concat: /<>/bcftools concat --naive /tmp/eP2NabHXBR/naive_concat.0.vcf.gz /tmp/eP2NabHXBR/naive_concat.1.vcf.gz /tmp/eP2NabHXBR/naive_concat.2.vcf.gz /tmp/eP2NabHXBR/naive_concat.3.vcf.gz /tmp/eP2NabHXBR/naive_concat.4.vcf.gz /tmp/eP2NabHXBR/naive_concat.5.vcf.gz /tmp/eP2NabHXBR/naive_concat.6.vcf.gz /tmp/eP2NabHXBR/naive_concat.7.vcf.gz /tmp/eP2NabHXBR/naive_concat.8.vcf.gz /tmp/eP2NabHXBR/naive_concat.9.vcf.gz | /<>/bcftools view -H .. ok test_vcf_reheader: /<>/bcftools reheader -h /<>/test/reheader.hdr /<>/test/reheader.vcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /<>/test/reheader.vcf | /<>/bcftools reheader -h /<>/test/reheader.hdr | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -h /<>/test/reheader.hdr /tmp/eP2NabHXBR/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/eP2NabHXBR/reheader.bcf | /<>/bcftools reheader -h /<>/test/reheader.hdr | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -h /<>/test/reheader.hdr /tmp/eP2NabHXBR/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/eP2NabHXBR/reheader.vcf.gz | /<>/bcftools reheader -h /<>/test/reheader.hdr | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples /<>/test/reheader.vcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /<>/test/reheader.vcf | /<>/bcftools reheader -s /<>/test/reheader.samples | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples /tmp/eP2NabHXBR/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/eP2NabHXBR/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples /tmp/eP2NabHXBR/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/eP2NabHXBR/reheader.vcf.gz | /<>/bcftools reheader -s /<>/test/reheader.samples | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples2 /<>/test/reheader.vcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /<>/test/reheader.vcf | /<>/bcftools reheader -s /<>/test/reheader.samples2 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples2 /tmp/eP2NabHXBR/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/eP2NabHXBR/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples2 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples2 /tmp/eP2NabHXBR/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/eP2NabHXBR/reheader.vcf.gz | /<>/bcftools reheader -s /<>/test/reheader.samples2 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples3 /<>/test/reheader.vcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /<>/test/reheader.vcf | /<>/bcftools reheader -s /<>/test/reheader.samples3 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples3 /tmp/eP2NabHXBR/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/eP2NabHXBR/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples3 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples3 /tmp/eP2NabHXBR/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/eP2NabHXBR/reheader.vcf.gz | /<>/bcftools reheader -s /<>/test/reheader.samples3 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples4 /<>/test/reheader.vcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /<>/test/reheader.vcf | /<>/bcftools reheader -s /<>/test/reheader.samples4 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples4 /tmp/eP2NabHXBR/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/eP2NabHXBR/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples4 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples4 /tmp/eP2NabHXBR/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/eP2NabHXBR/reheader.vcf.gz | /<>/bcftools reheader -s /<>/test/reheader.samples4 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -h /<>/test/reheader.empty.hdr /<>/test/empty.vcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /<>/test/empty.vcf | /<>/bcftools reheader -h /<>/test/reheader.empty.hdr | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -h /<>/test/reheader.empty.hdr /tmp/eP2NabHXBR/empty.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/eP2NabHXBR/empty.bcf | /<>/bcftools reheader -h /<>/test/reheader.empty.hdr | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -h /<>/test/reheader.empty.hdr /tmp/eP2NabHXBR/empty.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/eP2NabHXBR/empty.vcf.gz | /<>/bcftools reheader -h /<>/test/reheader.empty.hdr | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -f /<>/test/reheader.fai /<>/test/reheader.2.vcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -f /<>/test/reheader.fai /tmp/eP2NabHXBR/reheader.2.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -f /<>/test/reheader.fai /tmp/eP2NabHXBR/reheader.2.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -h /<>/test/reheader.2.hdr -f /<>/test/reheader.fai /<>/test/reheader.2.vcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -h /<>/test/reheader.2.hdr -f /<>/test/reheader.fai /tmp/eP2NabHXBR/reheader.2.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -h /<>/test/reheader.2.hdr -f /<>/test/reheader.fai /tmp/eP2NabHXBR/reheader.2.vcf.gz | /<>/bcftools view --no-version .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/eP2NabHXBR/rename.map -Ov /tmp/eP2NabHXBR/annotate.bcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/eP2NabHXBR/rename.map -Ob /tmp/eP2NabHXBR/annotate.bcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/eP2NabHXBR/rename.map -Ov /<>/test/annotate.vcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/eP2NabHXBR/rename.map -Ob /<>/test/annotate.vcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_vcf_convert: /<>/bcftools convert -g -,. /tmp/eP2NabHXBR/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/eP2NabHXBR/convert.vcf.gz | /<>/bcftools convert -g -,. .. ok test_vcf_convert: /<>/bcftools convert -g .,- /tmp/eP2NabHXBR/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/eP2NabHXBR/convert.vcf.gz | /<>/bcftools convert -g .,- .. ok test_vcf_convert: /<>/bcftools convert -g -,. --tag PL /tmp/eP2NabHXBR/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/eP2NabHXBR/convert.vcf.gz | /<>/bcftools convert -g -,. --tag PL .. ok test_vcf_convert: /<>/bcftools convert -g .,- --tag PL /tmp/eP2NabHXBR/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/eP2NabHXBR/convert.vcf.gz | /<>/bcftools convert -g .,- --tag PL .. ok test_vcf_convert: /<>/bcftools convert -g -,. --vcf-ids /tmp/eP2NabHXBR/check.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/eP2NabHXBR/check.vcf.gz | /<>/bcftools convert -g -,. --vcf-ids .. ok test_vcf_convert: /<>/bcftools convert -g .,- --vcf-ids /tmp/eP2NabHXBR/check.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/eP2NabHXBR/check.vcf.gz | /<>/bcftools convert -g .,- --vcf-ids .. ok test_vcf_convert: /<>/bcftools convert -g -,. --chrom /tmp/eP2NabHXBR/check.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/eP2NabHXBR/check.vcf.gz | /<>/bcftools convert -g -,. --chrom .. ok test_vcf_convert: /<>/bcftools convert -g .,- --chrom /tmp/eP2NabHXBR/check.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/eP2NabHXBR/check.vcf.gz | /<>/bcftools convert -g .,- --chrom .. ok test_vcf_convert: /<>/bcftools convert -g -,. --chrom --vcf-ids /tmp/eP2NabHXBR/check.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/eP2NabHXBR/check.vcf.gz | /<>/bcftools convert -g -,. --chrom --vcf-ids .. ok test_vcf_convert: /<>/bcftools convert -g .,- --chrom --vcf-ids /tmp/eP2NabHXBR/check.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/eP2NabHXBR/check.vcf.gz | /<>/bcftools convert -g .,- --chrom --vcf-ids .. ok test_vcf_convert: /<>/bcftools convert -h -,.,. /tmp/eP2NabHXBR/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/eP2NabHXBR/convert.vcf.gz | /<>/bcftools convert -h -,.,. .. ok test_vcf_convert: /<>/bcftools convert -h .,-,. /tmp/eP2NabHXBR/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/eP2NabHXBR/convert.vcf.gz | /<>/bcftools convert -h .,-,. .. ok test_vcf_convert: /<>/bcftools convert -h .,.,- /tmp/eP2NabHXBR/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/eP2NabHXBR/convert.vcf.gz | /<>/bcftools convert -h .,.,- .. ok test_vcf_convert_hls2vcf: /<>/bcftools convert -H /<>/test/convert.hls.gt.hap,/<>/test/convert.hls.gt.legend,/<>/test/convert.hls.gt.samples | grep -v ^## .. ok test_vcf_convert_hls2vcf: /<>/bcftools convert -H /<>/test/convert.hls.gt.hap,/<>/test/convert.hls.gt.legend,/<>/test/convert.hls.gt.samples -Ou | /<>/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /<>/bcftools convert --hapsample2vcf /<>/test/convert.hs.gt.hap,/<>/test/convert.hs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /<>/bcftools convert --hapsample2vcf /<>/test/convert.hs.gt.hap,/<>/test/convert.hs.gt.samples -Ou | /<>/bcftools view | grep -v ^## .. ok test_vcf_convert: /<>/bcftools convert --hapsample -,. /tmp/eP2NabHXBR/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/eP2NabHXBR/convert.vcf.gz | /<>/bcftools convert --hapsample -,. .. ok test_vcf_convert: /<>/bcftools convert --hapsample .,- /tmp/eP2NabHXBR/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/eP2NabHXBR/convert.vcf.gz | /<>/bcftools convert --hapsample .,- .. ok test_vcf_convert: /<>/bcftools convert --haplegendsample -,.,. /tmp/eP2NabHXBR/convert.hap-missing.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/eP2NabHXBR/convert.hap-missing.vcf.gz | /<>/bcftools convert --haplegendsample -,.,. .. ok test_vcf_convert_gvcf: /<>/bcftools convert --no-version --gvcf2vcf -i'FILTER="PASS"' -f /<>/test/gvcf.fa /tmp/eP2NabHXBR/convert.gvcf.vcf.gz .. ok test_vcf_convert_gvcf: /<>/bcftools view -Ob /tmp/eP2NabHXBR/convert.gvcf.vcf.gz | /<>/bcftools convert --gvcf2vcf -i'FILTER="PASS"' -f /<>/test/gvcf.fa | grep -v ^##bcftools .. ok test_vcf_convert_tsv2vcf: /<>/bcftools convert --no-version -c ID,CHROM,POS,AA -s SAMPLE1 -f /<>/test/23andme.fa --tsv2vcf /<>/test/convert.23andme .. ok test_vcf_convert_tsv2vcf: /<>/bcftools convert -Ou -c ID,CHROM,POS,AA -s SAMPLE1 -f /<>/test/23andme.fa --tsv2vcf /<>/test/convert.23andme | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/eP2NabHXBR/consensus.vcf.gz -f /<>/test/consensus.fa -m /<>/test/consensus.tab .. ok test_vcf_consensus_chain: /<>/bcftools consensus /tmp/eP2NabHXBR/consensus.vcf.gz -f /<>/test/consensus.fa -m /<>/test/consensus.tab -c /tmp/eP2NabHXBR/consensus.1.chain.new >/dev/null; cat /tmp/eP2NabHXBR/consensus.1.chain.new .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/eP2NabHXBR/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 -m /<>/test/consensus.tab .. ok test_vcf_consensus_chain: /<>/bcftools consensus /tmp/eP2NabHXBR/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 -m /<>/test/consensus.tab -c /tmp/eP2NabHXBR/consensus.2.chain.new >/dev/null; cat /tmp/eP2NabHXBR/consensus.2.chain.new .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/eP2NabHXBR/consensus.vcf.gz -f /<>/test/consensus.fa -I -m /<>/test/consensus.tab .. ok test_vcf_consensus_chain: /<>/bcftools consensus /tmp/eP2NabHXBR/consensus.vcf.gz -f /<>/test/consensus.fa -I -m /<>/test/consensus.tab -c /tmp/eP2NabHXBR/consensus.3.chain.new >/dev/null; cat /tmp/eP2NabHXBR/consensus.3.chain.new .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/eP2NabHXBR/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 .. ok test_vcf_consensus_chain: /<>/bcftools consensus /tmp/eP2NabHXBR/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 -c /tmp/eP2NabHXBR/consensus.4.chain.new >/dev/null; cat /tmp/eP2NabHXBR/consensus.4.chain.new .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/eP2NabHXBR/consensus2.vcf.gz -f /<>/test/consensus2.fa -H 1 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/eP2NabHXBR/consensus2.vcf.gz -f /<>/test/consensus2.fa -H 2 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/eP2NabHXBR/empty.vcf.gz -f /<>/test/consensus.fa .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/eP2NabHXBR/consensus3.vcf.gz -f /<>/test/consensus2.fa -H 2 -M "?" .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/eP2NabHXBR/consensus3.vcf.gz -f /<>/test/consensus2.fa -H 2 -M "?" -p xx_ .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/eP2NabHXBR/consensus4.vcf.gz -f /<>/test/consensus2.fa .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/eP2NabHXBR/consensus5.vcf.gz -f /<>/test/consensus5.fa --haplotype LA .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/eP2NabHXBR/consensus6.vcf.gz -f /<>/test/consensus6.fa .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/eP2NabHXBR/consensus7.vcf.gz -f /<>/test/consensus7.fa -H 2 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/eP2NabHXBR/consensus7.vcf.gz -f /<>/test/consensus7.fa -H 2pIu .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/eP2NabHXBR/consensus7.vcf.gz -f /<>/test/consensus7.fa -H 1 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/eP2NabHXBR/consensus7.vcf.gz -f /<>/test/consensus7.fa -H 1pIu .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -f /<>/test/mpileup/mpileup.ref.fa -b /tmp/eP2NabHXBR/mpileup.bam.list --no-version | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -f /<>/test/mpileup/mpileup.ref.fa -Ob -b /tmp/eP2NabHXBR/mpileup.bam.urllist | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -f /<>/test/mpileup/mpileup.ref.fa -b /tmp/eP2NabHXBR/mpileup.cram.list --no-version | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -f /<>/test/mpileup/mpileup.ref.fa -Ob -b /tmp/eP2NabHXBR/mpileup.cram.urllist | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,DV -r17:100-600 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,DV -r17:100-600 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,DV -r17:100-600 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,DV -r17:100-600 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.bam | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -B --ff 0x14 -r17:1050-1060 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.cram | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,DV -r17:100-600 --gvcf 0,2,5 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -s HG00101,HG00102 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -S /<>/test/mplp.samples -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -S /<>/test/mplp.samples -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -S /<>/test/mplp.samples -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -S /<>/test/mplp.samples -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -s ^HG00101,HG00102 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -S ^/<>/test/mplp.samples -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -S ^/<>/test/mplp.samples -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -S ^/<>/test/mplp.samples -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -r17:100-150 -S ^/<>/test/mplp.samples -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -t17:100-150 -S /<>/test/mplp.9.samples -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -t17:100-150 -S /<>/test/mplp.9.samples -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -t17:100-150 -S /<>/test/mplp.9.samples -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -t17:100-150 -S /<>/test/mplp.9.samples -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -t17:100-150 -G /<>/test/mplp.10.samples -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -t17:100-150 -G /<>/test/mplp.10.samples -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.bam /<>/test/mpileup/mpileup.2.bam /<>/test/mpileup/mpileup.3.bam | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -t17:100-150 -G /<>/test/mplp.10.samples -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -t17:100-150 -G /<>/test/mplp.10.samples -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.1.cram /<>/test/mpileup/mpileup.2.cram /<>/test/mpileup/mpileup.3.cram | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.3.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.3.bam | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.3.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.3.cram | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -s HG00102 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.3.bam /<>/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -s HG00102 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.3.bam /<>/test/mpileup/mpileup.4.bam | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -s HG00102 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.3.cram /<>/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -s HG00102 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.3.cram /<>/test/mpileup/mpileup.4.cram | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -s ^HG99999 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.3.bam /<>/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -s ^HG99999 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.3.bam /<>/test/mpileup/mpileup.4.bam | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -s ^HG99999 -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.3.cram /<>/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -s ^HG99999 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.3.cram /<>/test/mpileup/mpileup.4.cram | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -G /<>/test/mplp.11.rgs -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.3.bam /<>/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -G /<>/test/mplp.11.rgs -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.3.bam /<>/test/mpileup/mpileup.4.bam | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -G /<>/test/mplp.11.rgs -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.3.cram /<>/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -G /<>/test/mplp.11.rgs -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.3.cram /<>/test/mpileup/mpileup.4.cram | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -G /<>/test/mplp.11.rgs -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.3.bam /<>/test/mpileup/mpileup.4.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -G /<>/test/mplp.11.rgs -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.3.bam /<>/test/mpileup/mpileup.4.bam | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -G /<>/test/mplp.11.rgs -f /<>/test/mpileup/mpileup.ref.fa /<>/test/mpileup/mpileup.3.cram /<>/test/mpileup/mpileup.4.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -G /<>/test/mplp.11.rgs -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.3.cram /<>/test/mpileup/mpileup.4.cram | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a AD -f /<>/test/mpileup/indel-AD.1.fa /<>/test/mpileup/indel-AD.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a AD -f /<>/test/mpileup/indel-AD.1.fa -Ob /<>/test/mpileup/indel-AD.1.bam | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a AD -f /<>/test/mpileup/indel-AD.1.fa /<>/test/mpileup/indel-AD.1.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a AD -f /<>/test/mpileup/indel-AD.1.fa -Ob /<>/test/mpileup/indel-AD.1.cram | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a INFO/SCR,FMT/SCR -f /<>/test/mpileup/mpileup-SCR.fa /<>/test/mpileup/mpileup-SCR.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a INFO/SCR,FMT/SCR -f /<>/test/mpileup/mpileup-SCR.fa -Ob /<>/test/mpileup/mpileup-SCR.bam | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a INFO/SCR,FMT/SCR -f /<>/test/mpileup/mpileup-SCR.fa /<>/test/mpileup/mpileup-SCR.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a INFO/SCR,FMT/SCR -f /<>/test/mpileup/mpileup-SCR.fa -Ob /<>/test/mpileup/mpileup-SCR.cram | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_csq: /<>/bcftools csq -f /<>/test/csq.fa -g /<>/test/csq.gff3 /<>/test/csq.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000318249.2/ENST00000318249.2.fa -g /<>/test/csq/ENST00000318249.2/ENST00000318249.2.gff /<>/test/csq/ENST00000318249.2/synonymous-start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000382647/ENST00000382647.fa -g /<>/test/csq/ENST00000382647/ENST00000382647.gff /<>/test/csq/ENST00000382647/synon-splice-region-insert.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000520868/ENST00000520868.fa -g /<>/test/csq/ENST00000520868/ENST00000520868.gff /<>/test/csq/ENST00000520868/long-deletion.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000381157/ENST00000381157.fa -g /<>/test/csq/ENST00000381157/ENST00000381157.gff /<>/test/csq/ENST00000381157/haploid-diploid.vcf | /<>/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000357367/ENST00000357367.fa -g /<>/test/csq/ENST00000357367/ENST00000357367.gff /<>/test/csq/ENST00000357367/stop-retained.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000519442/ENST00000519442.fa -g /<>/test/csq/ENST00000519442/ENST00000519442.gff /<>/test/csq/ENST00000519442/synon-splice-region-del.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000368801.2/ENST00000368801.2.fa -g /<>/test/csq/ENST00000368801.2/ENST00000368801.2.gff /<>/test/csq/ENST00000368801.2/start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000520795/ENST00000520795.fa -g /<>/test/csq/ENST00000520795/ENST00000520795.gff /<>/test/csq/ENST00000520795/long-inside-del.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000520795/ENST00000520795.fa -g /<>/test/csq/ENST00000520795/ENST00000520795.gff /<>/test/csq/ENST00000520795/long-inside-del.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/EDUMMY0002/EDUMMY0002.fa -g /<>/test/csq/EDUMMY0002/EDUMMY0002.gff /<>/test/csq/EDUMMY0002/boundaries.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENSG00000173376/ENSG00000173376.fa -g /<>/test/csq/ENSG00000173376/ENSG00000173376.gff /<>/test/csq/ENSG00000173376/synon.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000227471/ENST00000227471.fa -g /<>/test/csq/ENST00000227471/ENST00000227471.gff /<>/test/csq/ENST00000227471/insert-splice-vs-frameshift.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000518414/ENST00000518414.fa -g /<>/test/csq/ENST00000518414/ENST00000518414.gff /<>/test/csq/ENST00000518414/incorrect-inframe-del.vcf | /<>/test/csq/sort-csq | /<>/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 /<>/test/csq/ENSMUST00000133836 && /<>/bcftools csq -f ENSMUST00000133836.fa -g ENSMUST00000133836.gff filter-problem.vcf -i 'FILTER="PASS"' --phase m | ../sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000230048/ENST00000230048.fa -g /<>/test/csq/ENST00000230048/ENST00000230048.gff /<>/test/csq/ENST00000230048/start-del.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000303039/ENST00000303039.fa -g /<>/test/csq/ENST00000303039/ENST00000303039.gff /<>/test/csq/ENST00000303039/not-a-stop.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000303039/ENST00000303039.fa -g /<>/test/csq/ENST00000303039/ENST00000303039.gff /<>/test/csq/ENST00000303039/not-a-stop.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000436063/ENST00000436063.fa -g /<>/test/csq/ENST00000436063/ENST00000436063.gff /<>/test/csq/ENST00000436063/insert-before-utr.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000543077/ENST00000543077.fa -g /<>/test/csq/ENST00000543077/ENST00000543077.gff /<>/test/csq/ENST00000543077/not-a-start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000543077/ENST00000543077.fa -g /<>/test/csq/ENST00000543077/ENST00000543077.gff /<>/test/csq/ENST00000543077/not-a-start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000536784/ENST00000536784.fa -g /<>/test/csq/ENST00000536784/ENST00000536784.gff /<>/test/csq/ENST00000536784/not-a-start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000536784/ENST00000536784.fa -g /<>/test/csq/ENST00000536784/ENST00000536784.gff /<>/test/csq/ENST00000536784/not-a-start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000256452/ENST00000256452.fa -g /<>/test/csq/ENST00000256452/ENST00000256452.gff /<>/test/csq/ENST00000256452/intron.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000624631/ENST00000624631.fa -g /<>/test/csq/ENST00000624631/ENST00000624631.gff /<>/test/csq/ENST00000624631/ambiguous.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000423372/ENST00000423372.fa -g /<>/test/csq/ENST00000423372/ENST00000423372.gff /<>/test/csq/ENST00000423372/insert3.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000423372/ENST00000423372.fa -g /<>/test/csq/ENST00000423372/ENST00000423372.gff /<>/test/csq/ENST00000423372/insert3.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000423372/ENST00000423372.fa -g /<>/test/csq/ENST00000423372/ENST00000423372.gff /<>/test/csq/ENST00000423372/snps.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000423372/ENST00000423372.fa -g /<>/test/csq/ENST00000423372/ENST00000423372.gff /<>/test/csq/ENST00000423372/snps.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000542803/ENST00000542803.fa -g /<>/test/csq/ENST00000542803/ENST00000542803.gff /<>/test/csq/ENST00000542803/splice-region.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000542803/ENST00000542803.fa -g /<>/test/csq/ENST00000542803/ENST00000542803.gff /<>/test/csq/ENST00000542803/splice-region.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000545279/ENST00000545279.fa -g /<>/test/csq/ENST00000545279/ENST00000545279.gff /<>/test/csq/ENST00000545279/splice-region-insert.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000557788/ENST00000557788.fa -g /<>/test/csq/ENST00000557788/ENST00000557788.gff /<>/test/csq/ENST00000557788/long-overlap-del.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/EDUMMY0001/EDUMMY0001.fa -g /<>/test/csq/EDUMMY0001/EDUMMY0001.gff /<>/test/csq/EDUMMY0001/starts-with-1.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/EDUMMY0001/EDUMMY0001.fa -g /<>/test/csq/EDUMMY0001/EDUMMY0001.gff /<>/test/csq/EDUMMY0001/starts-with-1.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000420670/ENST00000420670.fa -g /<>/test/csq/ENST00000420670/ENST00000420670.gff /<>/test/csq/ENST00000420670/start-stop-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000420670/ENST00000420670.fa -g /<>/test/csq/ENST00000420670/ENST00000420670.gff /<>/test/csq/ENST00000420670/segfault.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/EDUMMY0003/EDUMMY0003.fa -g /<>/test/csq/EDUMMY0003/EDUMMY0003.gff /<>/test/csq/EDUMMY0003/long-del.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000218032/ENST00000218032.fa -g /<>/test/csq/ENST00000218032/ENST00000218032.gff /<>/test/csq/ENST00000218032/start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000218032/ENST00000218032.fa -g /<>/test/csq/ENST00000218032/ENST00000218032.gff /<>/test/csq/ENST00000218032/start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000218032/ENST00000218032.fa -g /<>/test/csq/ENST00000218032/ENST00000218032.gff /<>/test/csq/ENST00000218032/start-lost-del.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor4.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor2.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/frame3.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/frame3.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor7.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor9.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/not-a-start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/not-a-start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor5.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/frame2.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/frame2.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor1.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/frame1.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/frame1.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor8.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000479739/ENST00000479739.fa -g /<>/test/csq/ENST00000479739/ENST00000479739.gff /<>/test/csq/ENST00000479739/short-cds-start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000479739/ENST00000479739.fa -g /<>/test/csq/ENST00000479739/ENST00000479739.gff /<>/test/csq/ENST00000479739/short-cds-start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000420190/ENST00000420190.fa -g /<>/test/csq/ENST00000420190/ENST00000420190.gff /<>/test/csq/ENST00000420190/abort-in-csq-push.vcf | /<>/bcftools query -f'[%POS\t%REF\t%ALT\t%TBCSQ\n]\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000318249/ENST00000318249.fa -g /<>/test/csq/ENST00000318249/ENST00000318249.gff /<>/test/csq/ENST00000318249/start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000318249/ENST00000318249.fa -g /<>/test/csq/ENST00000318249/ENST00000318249.gff /<>/test/csq/ENST00000318249/start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000294661/ENST00000294661.fa -g /<>/test/csq/ENST00000294661/ENST00000294661.gff /<>/test/csq/ENST00000294661/non-coding-boundary.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000294661/ENST00000294661.fa -g /<>/test/csq/ENST00000294661/ENST00000294661.gff /<>/test/csq/ENST00000294661/non-coding-boundary.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000271583/ENST00000271583.fa -g /<>/test/csq/ENST00000271583/ENST00000271583.gff /<>/test/csq/ENST00000271583/splice-acceptor.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000390520/ENST00000390520.fa -g /<>/test/csq/ENST00000390520/ENST00000390520.gff /<>/test/csq/ENST00000390520/deletion-overlap.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000375992/ENST00000375992.fa -g /<>/test/csq/ENST00000375992/ENST00000375992.gff /<>/test/csq/ENST00000375992/incorrect-synon-del-not-start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000295641/ENST00000295641.fa -g /<>/test/csq/ENST00000295641/ENST00000295641.gff /<>/test/csq/ENST00000295641/not-a-start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000295641/ENST00000295641.fa -g /<>/test/csq/ENST00000295641/ENST00000295641.gff /<>/test/csq/ENST00000295641/not-a-start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000573314/ENST00000573314.fa -g /<>/test/csq/ENST00000573314/ENST00000573314.gff /<>/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000573314/ENST00000573314.fa -g /<>/test/csq/ENST00000573314/ENST00000573314.gff /<>/test/csq/ENST00000573314/incorrect-insertion-overlap.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000593942/ENST00000593942.fa -g /<>/test/csq/ENST00000593942/ENST00000593942.gff /<>/test/csq/ENST00000593942/last-codon-deletion.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000413103/ENST00000413103.fa -g /<>/test/csq/ENST00000413103/ENST00000413103.gff /<>/test/csq/ENST00000413103/long-deletion.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000378322/ENST00000378322.fa -g /<>/test/csq/ENST00000378322/ENST00000378322.gff /<>/test/csq/ENST00000378322/end-overlap-tscript.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000378322/ENST00000378322.fa -g /<>/test/csq/ENST00000378322/ENST00000378322.gff /<>/test/csq/ENST00000378322/end-overlap-tscript.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000400151/ENST00000400151.fa -g /<>/test/csq/ENST00000400151/ENST00000400151.gff /<>/test/csq/ENST00000400151/long-del.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000528237/ENST00000528237.fa -g /<>/test/csq/ENST00000528237/ENST00000528237.gff /<>/test/csq/ENST00000528237/retained-stop-incomplete-cds.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000329454/ENST00000329454.fa -g /<>/test/csq/ENST00000329454/ENST00000329454.gff /<>/test/csq/ENST00000329454/boundary-deletion.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000329454/ENST00000329454.fa -g /<>/test/csq/ENST00000329454/ENST00000329454.gff /<>/test/csq/ENST00000329454/boundary-deletion.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000373833/ENST00000373833.fa -g /<>/test/csq/ENST00000373833/ENST00000373833.gff /<>/test/csq/ENST00000373833/boundary-insertion.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000373833/ENST00000373833.fa -g /<>/test/csq/ENST00000373833/ENST00000373833.gff /<>/test/csq/ENST00000373833/boundary-insertion.vcf | /<>/test/csq/sort-csq | /<>/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 /<>/test/csq/ENSMUST00000121418 && /<>/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25496' --phase m | ../sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /<>/test/csq/ENSMUST00000121418 && /<>/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25105' --phase m | ../sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: cd /<>/test/csq/ENSMUST00000121418 && /<>/bcftools csq -f ENSMUST00000121418.fa -g ENSMUST00000121418.gff filter-problem.vcf -i 'POS!=25500' --phase m | ../sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000301246/ENST00000301246.fa -g /<>/test/csq/ENST00000301246/ENST00000301246.gff /<>/test/csq/ENST00000301246/15bp-insert.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.fa -g /<>/test/csq/ENST00000518414-ENST00000521270/ENST00000518414-ENST00000521270.gff /<>/test/csq/ENST00000518414-ENST00000521270/valgrind.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000409523/ENST00000409523.fa -g /<>/test/csq/ENST00000409523/ENST00000409523.gff /<>/test/csq/ENST00000409523/long-overlapping-del.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000368801/ENST00000368801.fa -g /<>/test/csq/ENST00000368801/ENST00000368801.gff /<>/test/csq/ENST00000368801/compound-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000448695/ENST00000448695.fa -g /<>/test/csq/ENST00000448695/ENST00000448695.gff /<>/test/csq/ENST00000448695/syn-and-splice-reg.vcf | /<>/test/csq/sort-csq | /<>/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 /<>/test/csq/ENST00000410009 && /<>/bcftools csq -b -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000410009/ENST00000410009.fa -g /<>/test/csq/ENST00000410009/ENST00000410009.gff /<>/test/csq/ENST00000410009/frameshift.vcf | /<>/test/csq/sort-csq | /<>/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 /<>/test/csq/ENST00000410009 && /<>/bcftools csq -lb -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000263103-INS/ENST00000263103-INS.fa -g /<>/test/csq/ENST00000263103-INS/ENST00000263103-INS.gff /<>/test/csq/ENST00000263103-INS/insertions.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok Number of tests: total .. 961 passed .. 961 failed .. 0 make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch dh_testroot -a dh_prep -a dh_auto_install -a make -j4 install DESTDIR=/<>/debian/bcftools AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/<>' mkdir -p -m 755 /<>/debian/bcftools/usr/bin /<>/debian/bcftools/usr/share/man/man1 /<>/debian/bcftools/usr/lib/riscv64-linux-gnu/bcftools install -p bcftools /<>/debian/bcftools/usr/bin install -p misc/color-chrs.pl misc/guess-ploidy.py misc/plot-vcfstats misc/plot-roh.py misc/run-roh.pl misc/vcfutils.pl /<>/debian/bcftools/usr/bin install -p -m 644 doc/bcftools.1 /<>/debian/bcftools/usr/share/man/man1 install -p plugins/*.so /<>/debian/bcftools/usr/lib/riscv64-linux-gnu/bcftools make[1]: Leaving directory '/<>' debian/rules override_dh_install make[1]: Entering directory '/<>' 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 '/<>' dh_installdocs -a dh_installchangelogs -a debian/rules override_dh_installman make[1]: Entering directory '/<>' dh_installman --language=C make[1]: Leaving directory '/<>' dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a INFO: pkgstriptranslations version 144 INFO: pkgstriptranslations version 144 pkgstriptranslations: processing bcftools (in debian/bcftools); do_strip: , oemstrip: pkgstriptranslations: processing bcftools-dbgsym (in debian/.debhelper/bcftools/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/bcftools/DEBIAN/control, package bcftools, directory debian/bcftools pkgstripfiles: Truncating usr/share/doc/bcftools/changelog.Debian.gz to topmost ten records pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: Running PNG optimization (using 4 cpus) for package bcftools ... pkgstripfiles: No PNG files. dpkg-deb: building package 'bcftools' in '../bcftools_1.10.2-2_riscv64.deb'. pkgstripfiles: processing control file: debian/.debhelper/bcftools/dbgsym-root/DEBIAN/control, package bcftools-dbgsym, directory debian/.debhelper/bcftools/dbgsym-root dpkg-deb: building package 'bcftools-dbgsym' in 'debian/.debhelper/scratch-space/build-bcftools/bcftools-dbgsym_1.10.2-2_riscv64.deb'. Renaming bcftools-dbgsym_1.10.2-2_riscv64.deb to bcftools-dbgsym_1.10.2-2_riscv64.ddeb dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../bcftools_1.10.2-2_riscv64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2020-04-06T12:33:18Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ bcftools_1.10.2-2_riscv64.changes: ---------------------------------- Format: 1.8 Date: Thu, 02 Jan 2020 13:58:57 +0100 Source: bcftools Binary: bcftools Architecture: riscv64 Version: 1.10.2-2 Distribution: focal Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Michael R. Crusoe Description: bcftools - genomic variant calling and manipulation of VCF/BCF files Changes: bcftools (1.10.2-2) unstable; urgency=medium . * Fix build on i386 by using SSE2 Checksums-Sha1: e17127de437d4546cde0cb4f4e16e0dcc957a1c9 1575076 bcftools-dbgsym_1.10.2-2_riscv64.ddeb f520fdae98cfc86213438e32130b26d118b3e142 6521 bcftools_1.10.2-2_riscv64.buildinfo 97acf28b86e1fef84969a051dfb0428960a9d77f 569768 bcftools_1.10.2-2_riscv64.deb Checksums-Sha256: 9eaf800ca856220f9cba151c9fb3ca39d0e45afb04df3394d80e2d26ea37f50b 1575076 bcftools-dbgsym_1.10.2-2_riscv64.ddeb 13492f95a5457831d8a37e302c9bda6878fe9fde20530b4ae5f707cf19d3af8a 6521 bcftools_1.10.2-2_riscv64.buildinfo 385910e2441539aece565c03f9bc873b0fc64395b210762047ff1f5526d7250f 569768 bcftools_1.10.2-2_riscv64.deb Files: 0770659df7baae63abe1a4295cb2553f 1575076 debug optional bcftools-dbgsym_1.10.2-2_riscv64.ddeb 5a711ed5f3fe11199cf502b7f7572a4f 6521 science optional bcftools_1.10.2-2_riscv64.buildinfo 922651009b5d2653904b87a09cff942a 569768 science optional bcftools_1.10.2-2_riscv64.deb /<>/bcftools_1.10.2-2_riscv64.changes.new could not be renamed to /<>/bcftools_1.10.2-2_riscv64.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: bcftools Binary: bcftools Architecture: riscv64 Version: 1.10.2-2 Checksums-Md5: 0770659df7baae63abe1a4295cb2553f 1575076 bcftools-dbgsym_1.10.2-2_riscv64.ddeb 922651009b5d2653904b87a09cff942a 569768 bcftools_1.10.2-2_riscv64.deb Checksums-Sha1: e17127de437d4546cde0cb4f4e16e0dcc957a1c9 1575076 bcftools-dbgsym_1.10.2-2_riscv64.ddeb 97acf28b86e1fef84969a051dfb0428960a9d77f 569768 bcftools_1.10.2-2_riscv64.deb Checksums-Sha256: 9eaf800ca856220f9cba151c9fb3ca39d0e45afb04df3394d80e2d26ea37f50b 1575076 bcftools-dbgsym_1.10.2-2_riscv64.ddeb 385910e2441539aece565c03f9bc873b0fc64395b210762047ff1f5526d7250f 569768 bcftools_1.10.2-2_riscv64.deb Build-Origin: Ubuntu Build-Architecture: riscv64 Build-Date: Mon, 06 Apr 2020 12:33:10 +0000 Build-Path: /<> Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: autoconf (= 2.69-11.1), automake (= 1:1.16.1-4ubuntu6), autopoint (= 0.19.8.1-10build1), autotools-dev (= 20180224.1), base-files (= 11ubuntu4), base-passwd (= 3.5.47), bash (= 5.0-6ubuntu1), binutils (= 2.34-5ubuntu1), binutils-common (= 2.34-5ubuntu1), binutils-riscv64-linux-gnu (= 2.34-5ubuntu1), bsdmainutils (= 11.1.2ubuntu3), bsdutils (= 1:2.34-0.1ubuntu8), build-essential (= 12.8ubuntu1), bzip2 (= 1.0.8-2), coreutils (= 8.30-3ubuntu2), cpp (= 4:9.3.0-1ubuntu2), cpp-9 (= 9.3.0-10ubuntu1), dash (= 0.5.10.2-6), debconf (= 1.5.73), debhelper (= 12.10ubuntu1), debianutils (= 4.9.1), dh-autoreconf (= 19), dh-strip-nondeterminism (= 1.6.3-2), diffutils (= 1:3.7-3), dpkg (= 1.19.7ubuntu3), dpkg-dev (= 1.19.7ubuntu3), dwz (= 0.13-5), file (= 1:5.38-4), findutils (= 4.7.0-1ubuntu1), g++ (= 4:9.3.0-1ubuntu2), g++-9 (= 9.3.0-10ubuntu1), gcc (= 4:9.3.0-1ubuntu2), gcc-10-base (= 10-20200324-1ubuntu1), gcc-9 (= 9.3.0-10ubuntu1), gcc-9-base (= 9.3.0-10ubuntu1), gettext (= 0.19.8.1-10build1), gettext-base (= 0.19.8.1-10build1), grep (= 3.4-1), groff-base (= 1.22.4-4build1), gzip (= 1.10-0ubuntu4), hostname (= 3.23), init-system-helpers (= 1.57), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.2.53-6), libarchive-zip-perl (= 1.67-2), libasn1-8-heimdal (= 7.7.0+dfsg-1ubuntu1), libatomic1 (= 10-20200324-1ubuntu1), libattr1 (= 1:2.4.48-5), libaudit-common (= 1:2.8.5-2ubuntu6), libaudit1 (= 1:2.8.5-2ubuntu6), libbinutils (= 2.34-5ubuntu1), libblkid1 (= 2.34-0.1ubuntu8), libbrotli1 (= 1.0.7-6build1), libbsd0 (= 0.10.0-1), libbz2-1.0 (= 1.0.8-2), libbz2-dev (= 1.0.8-2), libc-bin (= 2.31-0ubuntu7), libc-dev-bin (= 2.31-0ubuntu7), libc6 (= 2.31-0ubuntu7), libc6-dev (= 2.31-0ubuntu7), libcap-ng0 (= 0.7.9-2.1build1), libcc1-0 (= 10-20200324-1ubuntu1), libcom-err2 (= 1.45.5-2ubuntu1), libcroco3 (= 0.6.13-1), libcrypt-dev (= 1:4.4.10-10ubuntu4), libcrypt1 (= 1:4.4.10-10ubuntu4), libctf-nobfd0 (= 2.34-5ubuntu1), libctf0 (= 2.34-5ubuntu1), libcurl3-gnutls (= 7.68.0-1ubuntu1), libdb5.3 (= 5.3.28+dfsg1-0.6ubuntu2), libdebconfclient0 (= 0.251ubuntu1), libdebhelper-perl (= 12.10ubuntu1), libdeflate0 (= 1.5-3), libdpkg-perl (= 1.19.7ubuntu3), libelf1 (= 0.176-1.1build1), libffi7 (= 3.3-4), libfile-stripnondeterminism-perl (= 1.6.3-2), libgcc-9-dev (= 9.3.0-10ubuntu1), libgcc-s1 (= 10-20200324-1ubuntu1), libgcrypt20 (= 1.8.5-5ubuntu1), libgdbm-compat4 (= 1.18.1-5), libgdbm6 (= 1.18.1-5), libglib2.0-0 (= 2.64.1-1), libgmp10 (= 2:6.2.0+dfsg-4), libgnutls30 (= 3.6.13-2ubuntu1), libgomp1 (= 10-20200324-1ubuntu1), libgpg-error0 (= 1.37-1), libgsl-dev (= 2.5+dfsg-6build1), libgsl23 (= 2.5+dfsg-6build1), libgslcblas0 (= 2.5+dfsg-6build1), libgssapi-krb5-2 (= 1.17-6ubuntu4), libgssapi3-heimdal (= 7.7.0+dfsg-1ubuntu1), libhcrypto4-heimdal (= 7.7.0+dfsg-1ubuntu1), libheimbase1-heimdal (= 7.7.0+dfsg-1ubuntu1), libheimntlm0-heimdal (= 7.7.0+dfsg-1ubuntu1), libhogweed5 (= 3.5.1+really3.5.1-2), libhts-dev (= 1.10.2-3), libhts3 (= 1.10.2-3), libhx509-5-heimdal (= 7.7.0+dfsg-1ubuntu1), libicu66 (= 66.1-2ubuntu2), libidn2-0 (= 2.2.0-2), libio-pty-perl (= 1:1.12-1), libisl22 (= 0.22.1-1), libk5crypto3 (= 1.17-6ubuntu4), libkeyutils1 (= 1.6-6ubuntu1), libkrb5-26-heimdal (= 7.7.0+dfsg-1ubuntu1), libkrb5-3 (= 1.17-6ubuntu4), libkrb5support0 (= 1.17-6ubuntu4), libldap-2.4-2 (= 2.4.49+dfsg-2ubuntu1), libldap-common (= 2.4.49+dfsg-2ubuntu1), liblz4-1 (= 1.9.2-2), liblzma-dev (= 5.2.4-1), liblzma5 (= 5.2.4-1), libmagic-mgc (= 1:5.38-4), libmagic1 (= 1:5.38-4), libmount1 (= 2.34-0.1ubuntu8), libmpc3 (= 1.1.0-1), libmpfr6 (= 4.0.2-1), libnettle7 (= 3.5.1+really3.5.1-2), libnghttp2-14 (= 1.40.0-1build1), libp11-kit0 (= 0.23.20-1build1), libpam-modules (= 1.3.1-5ubuntu4), libpam-modules-bin (= 1.3.1-5ubuntu4), libpam-runtime (= 1.3.1-5ubuntu4), libpam0g (= 1.3.1-5ubuntu4), libpcre2-8-0 (= 10.34-7), libpcre3 (= 2:8.39-12build1), libperl5.30 (= 5.30.0-9build1), libpipeline1 (= 1.5.2-2build1), libpsl5 (= 0.21.0-1ubuntu1), libroken18-heimdal (= 7.7.0+dfsg-1ubuntu1), librtmp1 (= 2.4+20151223.gitfa8646d.1-2build1), libsasl2-2 (= 2.1.27+dfsg-2), libsasl2-modules-db (= 2.1.27+dfsg-2), libselinux1 (= 3.0-1build2), libsigsegv2 (= 2.12-2), libsmartcols1 (= 2.34-0.1ubuntu8), libsqlite3-0 (= 3.31.1-4), libssh-4 (= 0.9.3-2ubuntu1), libssl1.1 (= 1.1.1d-2ubuntu6), libstdc++-9-dev (= 9.3.0-10ubuntu1), libstdc++6 (= 10-20200324-1ubuntu1), libsub-override-perl (= 0.09-2), libsystemd0 (= 245.2-1ubuntu3), libtasn1-6 (= 4.16.0-2), libtinfo6 (= 6.2-0ubuntu2), libtool (= 2.4.6-13), libuchardet0 (= 0.0.6-3build1), libudev1 (= 245.2-1ubuntu3), libunistring2 (= 0.9.10-2), libuuid1 (= 2.34-0.1ubuntu8), libwind0-heimdal (= 7.7.0+dfsg-1ubuntu1), libxml2 (= 2.9.10+dfsg-4build1), libzstd1 (= 1.4.4+dfsg-3), linux-libc-dev (= 5.4.0-21.25), login (= 1:4.8.1-1ubuntu3), lsb-base (= 11.1.0ubuntu2), m4 (= 1.4.18-4), make (= 4.2.1-1.2), man-db (= 2.9.1-1), mawk (= 1.3.4.20200120-2), ncurses-base (= 6.2-0ubuntu2), ncurses-bin (= 6.2-0ubuntu2), patch (= 2.7.6-6), perl (= 5.30.0-9build1), perl-base (= 5.30.0-9build1), perl-modules-5.30 (= 5.30.0-9build1), po-debconf (= 1.0.21), sed (= 4.7-1), sensible-utils (= 0.0.12+nmu1), sysvinit-utils (= 2.96-2.1ubuntu1), tabix (= 1.10.2-3), tar (= 1.30+dfsg-7), tzdata (= 2019c-3ubuntu1), util-linux (= 2.34-0.1ubuntu8), xz-utils (= 5.2.4-1), zlib1g (= 1:1.2.11.dfsg-2ubuntu1), zlib1g-dev (= 1:1.2.11.dfsg-2ubuntu1) Environment: DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1577969937" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ bcftools_1.10.2-2_riscv64.deb ----------------------------- new Debian package, version 2.0. size 569768 bytes: control archive=2208 bytes. 827 bytes, 17 lines control 3927 bytes, 51 lines md5sums Package: bcftools Version: 1.10.2-2 Architecture: riscv64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 1647 Depends: libc6 (>= 2.27), libhts3 (>= 1.10), zlib1g (>= 1:1.1.4), perl:any Suggests: python, python-numpy, python-matplotlib, texlive-latex-recommended Breaks: samtools (<< 1.0) Replaces: samtools (<< 1.0) Section: science Priority: optional Homepage: http://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. drwxr-xr-x root/root 0 2020-01-02 12:58 ./ drwxr-xr-x root/root 0 2020-01-02 12:58 ./usr/ drwxr-xr-x root/root 0 2020-01-02 12:58 ./usr/bin/ -rwxr-xr-x root/root 767024 2020-01-02 12:58 ./usr/bin/bcftools -rwxr-xr-x root/root 16943 2020-01-02 12:58 ./usr/bin/color-chrs.pl -rwxr-xr-x root/root 4356 2019-12-19 09:57 ./usr/bin/guess-ploidy.py -rwxr-xr-x root/root 15157 2019-12-19 09:57 ./usr/bin/plot-roh.py -rwxr-xr-x root/root 79901 2020-01-02 12:58 ./usr/bin/plot-vcfstats -rwxr-xr-x root/root 13371 2020-01-02 12:58 ./usr/bin/run-roh.pl -rwxr-xr-x root/root 18196 2020-01-02 12:58 ./usr/bin/vcfutils.pl drwxr-xr-x root/root 0 2020-01-02 12:58 ./usr/lib/ drwxr-xr-x root/root 0 2020-01-02 12:58 ./usr/lib/riscv64-linux-gnu/ drwxr-xr-x root/root 0 2020-01-02 12:58 ./usr/lib/riscv64-linux-gnu/bcftools/ -rw-r--r-- root/root 14456 2020-01-02 12:58 ./usr/lib/riscv64-linux-gnu/bcftools/GTisec.so -rw-r--r-- root/root 10264 2020-01-02 12:58 ./usr/lib/riscv64-linux-gnu/bcftools/GTsubset.so -rw-r--r-- root/root 63896 2020-01-02 12:58 ./usr/lib/riscv64-linux-gnu/bcftools/ad-bias.so -rw-r--r-- root/root 10136 2020-01-02 12:58 ./usr/lib/riscv64-linux-gnu/bcftools/add-variantkey.so -rw-r--r-- root/root 14472 2020-01-02 12:58 ./usr/lib/riscv64-linux-gnu/bcftools/af-dist.so -rw-r--r-- root/root 6000 2020-01-02 12:58 ./usr/lib/riscv64-linux-gnu/bcftools/allele-length.so -rw-r--r-- root/root 10120 2020-01-02 12:58 ./usr/lib/riscv64-linux-gnu/bcftools/check-ploidy.so -rw-r--r-- root/root 14632 2020-01-02 12:58 ./usr/lib/riscv64-linux-gnu/bcftools/check-sparsity.so -rw-r--r-- root/root 18560 2020-01-02 12:58 ./usr/lib/riscv64-linux-gnu/bcftools/color-chrs.so -rw-r--r-- root/root 19112 2020-01-02 12:58 ./usr/lib/riscv64-linux-gnu/bcftools/contrast.so -rw-r--r-- root/root 6040 2020-01-02 12:58 ./usr/lib/riscv64-linux-gnu/bcftools/counts.so -rw-r--r-- root/root 14488 2020-01-02 12:58 ./usr/lib/riscv64-linux-gnu/bcftools/dosage.so -rw-r--r-- root/root 10152 2020-01-02 12:58 ./usr/lib/riscv64-linux-gnu/bcftools/fill-AN-AC.so -rw-r--r-- root/root 68160 2020-01-02 12:58 ./usr/lib/riscv64-linux-gnu/bcftools/fill-from-fasta.so -rw-r--r-- root/root 26864 2020-01-02 12:58 ./usr/lib/riscv64-linux-gnu/bcftools/fill-tags.so -rw-r--r-- root/root 26888 2020-01-02 12:58 ./usr/lib/riscv64-linux-gnu/bcftools/fixploidy.so -rw-r--r-- root/root 18792 2020-01-02 12:58 ./usr/lib/riscv64-linux-gnu/bcftools/fixref.so -rw-r--r-- root/root 10264 2020-01-02 12:58 ./usr/lib/riscv64-linux-gnu/bcftools/frameshifts.so -rw-r--r-- root/root 18960 2020-01-02 12:58 ./usr/lib/riscv64-linux-gnu/bcftools/guess-ploidy.so -rw-r--r-- root/root 14752 2020-01-02 12:58 ./usr/lib/riscv64-linux-gnu/bcftools/gvcfz.so -rw-r--r-- root/root 10208 2020-01-02 12:58 ./usr/lib/riscv64-linux-gnu/bcftools/impute-info.so -rw-r--r-- root/root 23136 2020-01-02 12:58 ./usr/lib/riscv64-linux-gnu/bcftools/indel-stats.so -rw-r--r-- root/root 14592 2020-01-02 12:58 ./usr/lib/riscv64-linux-gnu/bcftools/isecGT.so -rw-r--r-- root/root 18992 2020-01-02 12:58 ./usr/lib/riscv64-linux-gnu/bcftools/mendelian.so -rw-r--r-- root/root 10304 2020-01-02 12:58 ./usr/lib/riscv64-linux-gnu/bcftools/missing2ref.so -rw-r--r-- root/root 14696 2020-01-02 12:58 ./usr/lib/riscv64-linux-gnu/bcftools/parental-origin.so -rw-r--r-- root/root 14920 2020-01-02 12:58 ./usr/lib/riscv64-linux-gnu/bcftools/prune.so -rw-r--r-- root/root 14728 2020-01-02 12:58 ./usr/lib/riscv64-linux-gnu/bcftools/remove-overlaps.so -rw-r--r-- root/root 14496 2020-01-02 12:58 ./usr/lib/riscv64-linux-gnu/bcftools/setGT.so -rw-r--r-- root/root 18800 2020-01-02 12:58 ./usr/lib/riscv64-linux-gnu/bcftools/smpl-stats.so -rw-r--r-- root/root 35752 2020-01-02 12:58 ./usr/lib/riscv64-linux-gnu/bcftools/split-vep.so -rw-r--r-- root/root 18904 2020-01-02 12:58 ./usr/lib/riscv64-linux-gnu/bcftools/split.so -rw-r--r-- root/root 10416 2020-01-02 12:58 ./usr/lib/riscv64-linux-gnu/bcftools/tag2tag.so -rw-r--r-- root/root 18984 2020-01-02 12:58 ./usr/lib/riscv64-linux-gnu/bcftools/trio-dnm.so -rw-r--r-- root/root 23096 2020-01-02 12:58 ./usr/lib/riscv64-linux-gnu/bcftools/trio-stats.so -rw-r--r-- root/root 14400 2020-01-02 12:58 ./usr/lib/riscv64-linux-gnu/bcftools/trio-switch-rate.so -rw-r--r-- root/root 14320 2020-01-02 12:58 ./usr/lib/riscv64-linux-gnu/bcftools/variantkey-hex.so drwxr-xr-x root/root 0 2020-01-02 12:58 ./usr/share/ drwxr-xr-x root/root 0 2020-01-02 12:58 ./usr/share/doc/ drwxr-xr-x root/root 0 2020-01-02 12:58 ./usr/share/doc/bcftools/ -rw-r--r-- root/root 246 2019-12-19 09:57 ./usr/share/doc/bcftools/README -rw-r--r-- root/root 842 2020-01-02 12:58 ./usr/share/doc/bcftools/changelog.Debian.gz -rw-r--r-- root/root 2541 2019-08-06 16:45 ./usr/share/doc/bcftools/copyright drwxr-xr-x root/root 0 2020-01-02 12:58 ./usr/share/man/ drwxr-xr-x root/root 0 2020-01-02 12:58 ./usr/share/man/man1/ -rw-r--r-- root/root 36625 2020-01-02 12:58 ./usr/share/man/man1/bcftools.1.gz -rw-r--r-- root/root 253 2020-01-02 12:58 ./usr/share/man/man1/color-chrs.pl.1.gz -rw-r--r-- root/root 271 2020-01-02 12:58 ./usr/share/man/man1/plot-vcfstats.1.gz -rw-r--r-- root/root 208 2020-01-02 12:58 ./usr/share/man/man1/vcfutils.pl.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: riscv64 Build Type: any Build-Space: 60544 Build-Time: 1417 Distribution: focal Host Architecture: riscv64 Install-Time: 129 Job: bcftools_1.10.2-2.dsc Machine Architecture: riscv64 Package: bcftools Package-Time: 1574 Source-Version: 1.10.2-2 Space: 60544 Status: successful Version: 1.10.2-2 -------------------------------------------------------------------------------- Finished at 2020-04-06T12:33:18Z Build needed 00:26:14, 60544k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=focal --arch=riscv64 PACKAGEBUILD-19100310 Scanning for processes to kill in build PACKAGEBUILD-19100310 RUN: /usr/share/launchpad-buildd/bin/in-target umount-chroot --backend=chroot --series=focal --arch=riscv64 PACKAGEBUILD-19100310 Stopping target for build PACKAGEBUILD-19100310 RUN: /usr/share/launchpad-buildd/bin/in-target remove-build --backend=chroot --series=focal --arch=riscv64 PACKAGEBUILD-19100310 Removing build PACKAGEBUILD-19100310