https://launchpad.net/ubuntu/+source/bcftools/1.13-1/+build/22292590 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-arm64-049 4.15.0-159-generic #167-Ubuntu SMP Mon Sep 20 23:06:52 UTC 2021 aarch64 Buildd toolchain package versions: launchpad-buildd_203~505~ubuntu18.04.1 python3-lpbuildd_203~505~ubuntu18.04.1 sbuild_0.75.0-1ubuntu1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu16.04.1 bzr_2.7.0+bzr6622-10 git-build-recipe_0.3.6~git201906051340.ff11471~ubuntu18.04.1 git_1:2.17.1-1ubuntu0.9 dpkg-dev_1.19.0.5ubuntu2.3 python-debian_0.1.32 python3-debian_0.1.32. Syncing the system clock with the buildd NTP service... 18 Oct 21:33:12 ntpdate[1702]: adjust time server 10.211.37.1 offset 0.000530 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=jammy --arch=arm64 PACKAGEBUILD-22292590 --image-type chroot /home/buildd/filecache-default/6b7e80eac91fd42d8bfd6a97b8740e65a0846fd4 Creating target for build PACKAGEBUILD-22292590 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=jammy --arch=arm64 PACKAGEBUILD-22292590 Starting target for build PACKAGEBUILD-22292590 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=jammy --arch=arm64 PACKAGEBUILD-22292590 'deb http://ftpmaster.internal/ubuntu jammy main universe' 'deb http://ftpmaster.internal/ubuntu jammy-security main universe' 'deb http://ftpmaster.internal/ubuntu jammy-updates main universe' 'deb http://ftpmaster.internal/ubuntu jammy-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-22292590 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=jammy --arch=arm64 PACKAGEBUILD-22292590 Updating target for build PACKAGEBUILD-22292590 Get:1 http://ftpmaster.internal/ubuntu jammy InRelease [224 kB] Get:2 http://ftpmaster.internal/ubuntu jammy-security InRelease [74.9 kB] Get:3 http://ftpmaster.internal/ubuntu jammy-updates InRelease [74.9 kB] Get:4 http://ftpmaster.internal/ubuntu jammy-proposed InRelease [74.9 kB] Get:5 http://ftpmaster.internal/ubuntu jammy/main arm64 Packages [1371 kB] Get:6 http://ftpmaster.internal/ubuntu jammy/main Translation-en [512 kB] Get:7 http://ftpmaster.internal/ubuntu jammy/universe arm64 Packages [12.9 MB] Get:8 http://ftpmaster.internal/ubuntu jammy/universe Translation-en [5463 kB] Get:9 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 Packages [120 kB] Get:10 http://ftpmaster.internal/ubuntu jammy-proposed/main Translation-en [55.0 kB] Get:11 http://ftpmaster.internal/ubuntu jammy-proposed/universe arm64 Packages [203 kB] Get:12 http://ftpmaster.internal/ubuntu jammy-proposed/universe Translation-en [89.0 kB] Fetched 21.2 MB in 8s (2734 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: base-files base-passwd bsdutils bzip2 coreutils debianutils fakeroot gzip libapparmor1 libargon2-1 libattr1 libaudit-common libaudit1 libblkid1 libbz2-1.0 libcap-ng0 libcap2 libcrypt-dev libcrypt1 libdb5.3 libdebconfclient0 libfakeroot libgdbm-compat4 libgdbm6 libgmp10 libgpg-error0 libgssapi-krb5-2 libhogweed6 libidn2-0 libip4tc2 libisl23 libjson-c5 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblz4-1 liblzma5 libmount1 libmpc3 libmpfr6 libncurses6 libncursesw6 libnettle8 libnpth0 libpcre3 libreadline8 libseccomp2 libselinux1 libsemanage-common libsemanage1 libsmartcols1 libtasn1-6 libtinfo6 libuuid1 libzstd1 lockfile-progs make mawk mount ncurses-base ncurses-bin patch pinentry-curses readline-common sed sysvinit-utils tar util-linux xz-utils 70 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 9584 kB of archives. After this operation, 1454 kB disk space will be freed. Get:1 http://ftpmaster.internal/ubuntu jammy/main arm64 libcrypt-dev arm64 1:4.4.18-4ubuntu2 [119 kB] Get:2 http://ftpmaster.internal/ubuntu jammy/main arm64 libcrypt1 arm64 1:4.4.18-4ubuntu2 [87.1 kB] Get:3 http://ftpmaster.internal/ubuntu jammy/main arm64 base-files arm64 12ubuntu1 [63.2 kB] Get:4 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 bsdutils arm64 1:2.36.1-8ubuntu2 [81.0 kB] Get:5 http://ftpmaster.internal/ubuntu jammy/main arm64 coreutils arm64 8.32-4ubuntu3 [1398 kB] Get:6 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 debianutils arm64 5.5-1 [77.5 kB] Get:7 http://ftpmaster.internal/ubuntu jammy/main arm64 gzip arm64 1.10-4ubuntu2 [94.4 kB] Get:8 http://ftpmaster.internal/ubuntu jammy/main arm64 ncurses-bin arm64 6.2+20201114-2build2 [179 kB] Get:9 http://ftpmaster.internal/ubuntu jammy/main arm64 sed arm64 4.7-1ubuntu2 [186 kB] Get:10 http://ftpmaster.internal/ubuntu jammy/main arm64 tar arm64 1.34+dfsg-1build2 [287 kB] Get:11 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 util-linux arm64 2.36.1-8ubuntu2 [1004 kB] Get:12 http://ftpmaster.internal/ubuntu jammy/main arm64 libdebconfclient0 arm64 0.256ubuntu4 [6262 B] Get:13 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 base-passwd arm64 3.5.52 [48.9 kB] Get:14 http://ftpmaster.internal/ubuntu jammy/main arm64 ncurses-base all 6.2+20201114-2build2 [19.5 kB] Get:15 http://ftpmaster.internal/ubuntu jammy/main arm64 sysvinit-utils arm64 2.96-7ubuntu2 [20.6 kB] Get:16 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 mount arm64 2.36.1-8ubuntu2 [109 kB] Get:17 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libattr1 arm64 1:2.5.1-1 [13.3 kB] Get:18 http://ftpmaster.internal/ubuntu jammy/main arm64 libaudit-common all 1:3.0-2ubuntu3 [4688 B] Get:19 http://ftpmaster.internal/ubuntu jammy/main arm64 libcap-ng0 arm64 0.7.9-2.2build2 [11.2 kB] Get:20 http://ftpmaster.internal/ubuntu jammy/main arm64 libaudit1 arm64 1:3.0-2ubuntu3 [45.8 kB] Get:21 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libblkid1 arm64 2.36.1-8ubuntu2 [97.8 kB] Get:22 http://ftpmaster.internal/ubuntu jammy/main arm64 bzip2 arm64 1.0.8-4ubuntu4 [34.5 kB] Get:23 http://ftpmaster.internal/ubuntu jammy/main arm64 libbz2-1.0 arm64 1.0.8-4ubuntu4 [35.7 kB] Get:24 http://ftpmaster.internal/ubuntu jammy/main arm64 libcap2 arm64 1:2.44-1build2 [17.9 kB] Get:25 http://ftpmaster.internal/ubuntu jammy/main arm64 libdb5.3 arm64 5.3.28+dfsg1-0.8ubuntu2 [714 kB] Get:26 http://ftpmaster.internal/ubuntu jammy/main arm64 libgmp10 arm64 2:6.2.1+dfsg-1ubuntu3 [243 kB] Get:27 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libgpg-error0 arm64 1.42-3 [67.7 kB] Get:28 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libk5crypto3 arm64 1.18.3-7 [91.5 kB] Get:29 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libkrb5support0 arm64 1.18.3-7 [32.3 kB] Get:30 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libkrb5-3 arm64 1.18.3-7 [357 kB] Get:31 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libgssapi-krb5-2 arm64 1.18.3-7 [141 kB] Get:32 http://ftpmaster.internal/ubuntu jammy/main arm64 libkeyutils1 arm64 1.6.1-2ubuntu2 [10.1 kB] Get:33 http://ftpmaster.internal/ubuntu jammy/main arm64 liblz4-1 arm64 1.9.3-2build1 [57.7 kB] Get:34 http://ftpmaster.internal/ubuntu jammy/main arm64 liblzma5 arm64 5.2.5-2build1 [98.5 kB] Get:35 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libselinux1 arm64 3.1-3build3 [74.1 kB] Get:36 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libmount1 arm64 2.36.1-8ubuntu2 [115 kB] Get:37 http://ftpmaster.internal/ubuntu jammy/main arm64 libpcre3 arm64 2:8.39-13build4 [231 kB] Get:38 http://ftpmaster.internal/ubuntu jammy/main arm64 libsemanage-common all 3.1-1ubuntu3 [9606 B] Get:39 http://ftpmaster.internal/ubuntu jammy/main arm64 libsemanage1 arm64 3.1-1ubuntu3 [94.5 kB] Get:40 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libsmartcols1 arm64 2.36.1-8ubuntu2 [48.5 kB] Get:41 http://ftpmaster.internal/ubuntu jammy/main arm64 libncurses6 arm64 6.2+20201114-2build2 [106 kB] Get:42 http://ftpmaster.internal/ubuntu jammy/main arm64 libncursesw6 arm64 6.2+20201114-2build2 [141 kB] Get:43 http://ftpmaster.internal/ubuntu jammy/main arm64 libtinfo6 arm64 6.2+20201114-2build2 [102 kB] Get:44 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libuuid1 arm64 2.36.1-8ubuntu2 [23.2 kB] Get:45 http://ftpmaster.internal/ubuntu jammy/main arm64 libzstd1 arm64 1.4.8+dfsg-2.1build1 [311 kB] Get:46 http://ftpmaster.internal/ubuntu jammy/main arm64 libnettle8 arm64 3.7.3-1build1 [170 kB] Get:47 http://ftpmaster.internal/ubuntu jammy/main arm64 libhogweed6 arm64 3.7.3-1build1 [197 kB] Get:48 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libidn2-0 arm64 2.3.2-2 [67.1 kB] Get:49 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libseccomp2 arm64 2.5.1-1ubuntu2 [47.8 kB] Get:50 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libtasn1-6 arm64 4.17.0-2 [42.8 kB] Get:51 http://ftpmaster.internal/ubuntu jammy/main arm64 mawk arm64 1.3.4.20200120-2build1 [101 kB] Get:52 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libapparmor1 arm64 3.0.3-0ubuntu2 [37.4 kB] Get:53 http://ftpmaster.internal/ubuntu jammy/main arm64 libargon2-1 arm64 0~20171227-0.2build22 [18.6 kB] Get:54 http://ftpmaster.internal/ubuntu jammy/main arm64 libip4tc2 arm64 1.8.7-1ubuntu3 [19.8 kB] Get:55 http://ftpmaster.internal/ubuntu jammy/main arm64 libjson-c5 arm64 0.15-2build3 [32.6 kB] Get:56 http://ftpmaster.internal/ubuntu jammy/main arm64 readline-common all 8.1-2build1 [53.6 kB] Get:57 http://ftpmaster.internal/ubuntu jammy/main arm64 libreadline8 arm64 8.1-2build1 [153 kB] Get:58 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libgdbm6 arm64 1.21-1 [35.1 kB] Get:59 http://ftpmaster.internal/ubuntu jammy/main arm64 xz-utils arm64 5.2.5-2build1 [84.2 kB] Get:60 http://ftpmaster.internal/ubuntu jammy/main arm64 libfakeroot arm64 1.25.3-1.1ubuntu3 [32.1 kB] Get:61 http://ftpmaster.internal/ubuntu jammy/main arm64 fakeroot arm64 1.25.3-1.1ubuntu3 [60.5 kB] Get:62 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libgdbm-compat4 arm64 1.21-1 [6418 B] Get:63 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libisl23 arm64 0.24-2 [690 kB] Get:64 http://ftpmaster.internal/ubuntu jammy/main arm64 libmpfr6 arm64 4.1.0-3build2 [245 kB] Get:65 http://ftpmaster.internal/ubuntu jammy/main arm64 libnpth0 arm64 1.6-3build1 [8176 B] Get:66 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 lockfile-progs arm64 0.1.19 [9778 B] Get:67 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 make arm64 4.3-4ubuntu2 [176 kB] Get:68 http://ftpmaster.internal/ubuntu jammy/main arm64 patch arm64 2.7.6-7build1 [105 kB] Get:69 http://ftpmaster.internal/ubuntu jammy/main arm64 pinentry-curses arm64 1.1.1-1build1 [33.5 kB] Get:70 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libmpc3 arm64 1.2.1-1 [48.1 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 9584 kB in 1s (16.7 MB/s) (Reading database ... 13240 files and directories currently installed.) 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Setting up libncursesw6:arm64 (6.2+20201114-2build2) ... Setting up mount (2.36.1-8ubuntu2) ... Setting up libcrypt-dev:arm64 (1:4.4.18-4ubuntu2) ... Setting up mawk (1.3.4.20200120-2build1) ... Setting up libisl23:arm64 (0.24-2) ... Setting up libjson-c5:arm64 (0.15-2build3) ... Setting up readline-common (8.1-2build1) ... Setting up libgdbm6:arm64 (1.21-1) ... Setting up pinentry-curses (1.1.1-1build1) ... Setting up libreadline8:arm64 (8.1-2build1) ... Setting up libgdbm-compat4:arm64 (1.21-1) ... Processing triggers for libc-bin (2.34-0ubuntu3) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-22292590 arm64 jammy-proposed -c chroot:build-PACKAGEBUILD-22292590 --arch=arm64 --dist=jammy-proposed --nolog bcftools_1.13-1.dsc Initiating build PACKAGEBUILD-22292590 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.15.0-159-generic #167-Ubuntu SMP Mon Sep 20 23:06:52 UTC 2021 aarch64 sbuild (Debian sbuild) 0.75.0 (21 Mar 2018) on bos02-arm64-049.buildd +==============================================================================+ | bcftools 1.13-1 (arm64) Mon, 18 Oct 2021 21:34:01 +0000 | +==============================================================================+ Package: bcftools Version: 1.13-1 Source Version: 1.13-1 Distribution: jammy-proposed Machine Architecture: arm64 Host Architecture: arm64 Build Architecture: arm64 Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-22292590/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- bcftools_1.13-1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/bcftools-SZs89l/bcftools-1.13' with '<>' I: NOTICE: Log filtering will replace 'build/bcftools-SZs89l' with '<>' +------------------------------------------------------------------------------+ | Install build-essential | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-p0lQxQ/apt_archive/sbuild-build-depends-core-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy dpkg-scanpackages: info: Wrote 1 entries to output Packages file. Ign:1 copy:/<>/resolver-p0lQxQ/apt_archive ./ InRelease Get:2 copy:/<>/resolver-p0lQxQ/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-p0lQxQ/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-p0lQxQ/apt_archive ./ Sources [349 B] Get:5 copy:/<>/resolver-p0lQxQ/apt_archive ./ Packages [430 B] Fetched 1736 B in 0s (46.0 kB/s) Reading package lists... Reading package lists... Install core build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 654 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-p0lQxQ/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [654 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 654 B in 0s (48.4 kB/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 13235 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_arm64.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (arm64 included in any) +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), zlib1g-dev, libbz2-dev, liblzma-dev, libhts-dev (>= 1.12), libgsl-dev, tabix, libio-pty-perl Filtered Build-Depends: debhelper-compat (= 13), zlib1g-dev, libbz2-dev, liblzma-dev, libhts-dev (>= 1.12), libgsl-dev, tabix, libio-pty-perl dpkg-deb: building package 'sbuild-build-depends-bcftools-dummy' in '/<>/resolver-p0lQxQ/apt_archive/sbuild-build-depends-bcftools-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-bcftools-dummy sbuild-build-depends-core-dummy dpkg-scanpackages: info: Wrote 2 entries to output Packages file. Ign:1 copy:/<>/resolver-p0lQxQ/apt_archive ./ InRelease Get:2 copy:/<>/resolver-p0lQxQ/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-p0lQxQ/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-p0lQxQ/apt_archive ./ Sources [553 B] Get:5 copy:/<>/resolver-p0lQxQ/apt_archive ./ Packages [621 B] Fetched 2137 B in 0s (64.7 kB/s) Reading package lists... Reading package lists... Install bcftools build dependencies (apt-based resolver) -------------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbrotli1 libbz2-dev libcurl3-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libdw1 libelf1 libfile-stripnondeterminism-perl libgsl-dev libgsl25 libgslcblas0 libhts-dev libhts3 libhtscodecs2 libicu67 libio-pty-perl libldap-2.5-0 liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db po-debconf tabix zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libcurl4-doc libgnutls28-dev libidn11-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev pkg-config gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html 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 libldap-common publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbrotli1 libbz2-dev libcurl3-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libdw1 libelf1 libfile-stripnondeterminism-perl libgsl-dev libgsl25 libgslcblas0 libhts-dev libhts3 libhtscodecs2 libicu67 libio-pty-perl libldap-2.5-0 liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db po-debconf sbuild-build-depends-bcftools-dummy tabix zlib1g-dev 0 upgraded, 56 newly installed, 0 to remove and 0 not upgraded. Need to get 28.0 MB of archives. After this operation, 92.7 MB of additional disk space will be used. Get:1 copy:/<>/resolver-p0lQxQ/apt_archive ./ sbuild-build-depends-bcftools-dummy 0.invalid.0 [716 B] Get:2 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 bsdextrautils arm64 2.36.1-8ubuntu2 [73.6 kB] Get:3 http://ftpmaster.internal/ubuntu jammy/main arm64 libuchardet0 arm64 0.0.7-1build1 [76.8 kB] Get:4 http://ftpmaster.internal/ubuntu jammy/main arm64 groff-base arm64 1.22.4-7 [918 kB] Get:5 http://ftpmaster.internal/ubuntu jammy/main arm64 libpipeline1 arm64 1.5.3-1build1 [22.9 kB] Get:6 http://ftpmaster.internal/ubuntu jammy/main arm64 man-db arm64 2.9.4-2build1 [1175 kB] Get:7 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libelf1 arm64 0.185-2 [51.1 kB] Get:8 http://ftpmaster.internal/ubuntu jammy/main arm64 libicu67 arm64 67.1-7ubuntu1 [10.0 MB] Get:9 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libxml2 arm64 2.9.12+dfsg-5 [725 kB] Get:10 http://ftpmaster.internal/ubuntu jammy/main arm64 libmagic-mgc arm64 1:5.39-3build1 [236 kB] Get:11 http://ftpmaster.internal/ubuntu jammy/main arm64 libmagic1 arm64 1:5.39-3build1 [87.8 kB] Get:12 http://ftpmaster.internal/ubuntu jammy/main arm64 file arm64 1:5.39-3build1 [24.7 kB] Get:13 http://ftpmaster.internal/ubuntu jammy/main arm64 gettext-base arm64 0.21-4ubuntu3 [35.2 kB] Get:14 http://ftpmaster.internal/ubuntu jammy/main arm64 libpsl5 arm64 0.21.0-1.2build1 [57.5 kB] Get:15 http://ftpmaster.internal/ubuntu jammy/main arm64 libsigsegv2 arm64 2.13-1ubuntu2 [14.5 kB] Get:16 http://ftpmaster.internal/ubuntu jammy/main arm64 m4 arm64 1.4.18-5ubuntu1 [196 kB] Get:17 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 autoconf all 2.71-2 [338 kB] Get:18 http://ftpmaster.internal/ubuntu jammy/main arm64 autotools-dev all 20180224.1+nmu1 [39.4 kB] Get:19 http://ftpmaster.internal/ubuntu jammy/main arm64 automake all 1:1.16.4-2 [557 kB] Get:20 http://ftpmaster.internal/ubuntu jammy/main arm64 autopoint all 0.21-4ubuntu3 [422 kB] Get:21 http://ftpmaster.internal/ubuntu jammy/main arm64 libdebhelper-perl all 13.3.4ubuntu2 [62.5 kB] Get:22 http://ftpmaster.internal/ubuntu jammy/main arm64 libtool all 2.4.6-15build1 [164 kB] Get:23 http://ftpmaster.internal/ubuntu jammy/main arm64 dh-autoreconf all 20 [16.1 kB] Get:24 http://ftpmaster.internal/ubuntu jammy/main arm64 libarchive-zip-perl all 1.68-1 [90.2 kB] Get:25 http://ftpmaster.internal/ubuntu jammy/main arm64 libsub-override-perl all 0.09-2 [9532 B] Get:26 http://ftpmaster.internal/ubuntu jammy/main arm64 libfile-stripnondeterminism-perl all 1.12.0-1 [17.5 kB] Get:27 http://ftpmaster.internal/ubuntu jammy/main arm64 dh-strip-nondeterminism all 1.12.0-1 [5228 B] Get:28 http://ftpmaster.internal/ubuntu jammy-proposed/main arm64 libdw1 arm64 0.185-2 [244 kB] Get:29 http://ftpmaster.internal/ubuntu jammy/main arm64 debugedit arm64 1:5.0-0ubuntu2 [47.0 kB] Get:30 http://ftpmaster.internal/ubuntu jammy/main arm64 dwz arm64 0.14-1build1 [102 kB] Get:31 http://ftpmaster.internal/ubuntu jammy/main arm64 gettext arm64 0.21-4ubuntu3 [775 kB] Get:32 http://ftpmaster.internal/ubuntu jammy/main arm64 intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:33 http://ftpmaster.internal/ubuntu jammy/main arm64 po-debconf all 1.0.21+nmu1 [233 kB] Get:34 http://ftpmaster.internal/ubuntu jammy/main arm64 debhelper all 13.3.4ubuntu2 [921 kB] Get:35 http://ftpmaster.internal/ubuntu jammy/main arm64 libbrotli1 arm64 1.0.9-2build4 [314 kB] Get:36 http://ftpmaster.internal/ubuntu jammy/main arm64 libbz2-dev arm64 1.0.8-4ubuntu4 [34.5 kB] Get:37 http://ftpmaster.internal/ubuntu jammy/main arm64 libsasl2-modules-db arm64 2.1.27+dfsg-2.1build1 [14.8 kB] Get:38 http://ftpmaster.internal/ubuntu jammy/main arm64 libsasl2-2 arm64 2.1.27+dfsg-2.1build1 [45.1 kB] Get:39 http://ftpmaster.internal/ubuntu jammy/main arm64 libldap-2.5-0 arm64 2.5.6+dfsg-1~exp1ubuntu1 [184 kB] Get:40 http://ftpmaster.internal/ubuntu jammy/main arm64 libnghttp2-14 arm64 1.43.0-1build1 [75.3 kB] Get:41 http://ftpmaster.internal/ubuntu jammy/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2build3 [59.3 kB] Get:42 http://ftpmaster.internal/ubuntu jammy/main arm64 libssh-4 arm64 0.9.6-1 [184 kB] Get:43 http://ftpmaster.internal/ubuntu jammy/main arm64 libcurl3-gnutls arm64 7.74.0-1.3ubuntu2 [264 kB] Get:44 http://ftpmaster.internal/ubuntu jammy/main arm64 libcurl4-gnutls-dev arm64 7.74.0-1.3ubuntu2 [366 kB] Get:45 http://ftpmaster.internal/ubuntu jammy/main arm64 libdeflate0 arm64 1.7-2ubuntu2 [53.1 kB] Get:46 http://ftpmaster.internal/ubuntu jammy/main arm64 libdeflate-dev arm64 1.7-2ubuntu2 [47.2 kB] Get:47 http://ftpmaster.internal/ubuntu jammy/universe arm64 libgslcblas0 arm64 2.6+dfsg-2 [56.2 kB] Get:48 http://ftpmaster.internal/ubuntu jammy/universe arm64 libgsl25 arm64 2.6+dfsg-2 [787 kB] Get:49 http://ftpmaster.internal/ubuntu jammy/universe arm64 libgsl-dev arm64 2.6+dfsg-2 [1007 kB] Get:50 http://ftpmaster.internal/ubuntu jammy/universe arm64 libhtscodecs2 arm64 1.1.1-2 [55.7 kB] Get:51 http://ftpmaster.internal/ubuntu jammy/universe arm64 libhts3 arm64 1.13+ds-2 [378 kB] Get:52 http://ftpmaster.internal/ubuntu jammy/main arm64 liblzma-dev arm64 5.2.5-2build1 [159 kB] Get:53 http://ftpmaster.internal/ubuntu jammy/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-2ubuntu7 [163 kB] Get:54 http://ftpmaster.internal/ubuntu jammy/universe arm64 libhts-dev arm64 1.13+ds-2 [5555 kB] Get:55 http://ftpmaster.internal/ubuntu jammy/main arm64 libio-pty-perl arm64 1:1.15-2build1 [34.7 kB] Get:56 http://ftpmaster.internal/ubuntu jammy/universe arm64 tabix arm64 1.13+ds-2 [344 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 28.0 MB in 2s (16.9 MB/s) Selecting previously unselected package bsdextrautils. 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Setting up zlib1g-dev:arm64 (1:1.2.11.dfsg-2ubuntu7) ... Setting up libuchardet0:arm64 (0.0.7-1build1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libdeflate-dev:arm64 (1.7-2ubuntu2) ... Setting up tabix (1.13+ds-2) ... Setting up libelf1:arm64 (0.185-2) ... Setting up libxml2:arm64 (2.9.12+dfsg-5) ... Setting up libbz2-dev:arm64 (1.0.8-4ubuntu4) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up libdw1:arm64 (0.185-2) ... Setting up gettext (0.21-4ubuntu3) ... Setting up libgsl-dev (2.6+dfsg-2) ... Setting up libtool (2.4.6-15build1) ... Setting up m4 (1.4.18-5ubuntu1) ... Setting up libldap-2.5-0:arm64 (2.5.6+dfsg-1~exp1ubuntu1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up autoconf (2.71-2) ... Setting up dh-strip-nondeterminism (1.12.0-1) ... Setting up dwz (0.14-1build1) ... Setting up groff-base (1.22.4-7) ... Setting up debugedit (1:5.0-0ubuntu2) ... Setting up automake (1:1.16.4-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3-gnutls:arm64 (7.74.0-1.3ubuntu2) ... Setting up libcurl4-gnutls-dev:arm64 (7.74.0-1.3ubuntu2) ... Setting up man-db (2.9.4-2build1) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up dh-autoreconf (20) ... Setting up libhts3:arm64 (1.13+ds-2) ... Setting up libhts-dev:arm64 (1.13+ds-2) ... Setting up debhelper (13.3.4ubuntu2) ... Setting up sbuild-build-depends-bcftools-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.34-0ubuntu3) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.15.0-159-generic arm64 (aarch64) Toolchain package versions: binutils_2.37-7ubuntu1 dpkg-dev_1.20.9ubuntu2 g++-11_11.2.0-7ubuntu2 gcc-11_11.2.0-7ubuntu2 libc6-dev_2.34-0ubuntu3 libstdc++-11-dev_11.2.0-7ubuntu2 libstdc++6_11.2.0-7ubuntu2 linux-libc-dev_5.13.0-19.19 Package versions: adduser_3.118ubuntu5 advancecomp_2.1-2.1ubuntu1 apt_2.3.9 autoconf_2.71-2 automake_1:1.16.4-2 autopoint_0.21-4ubuntu3 autotools-dev_20180224.1+nmu1 base-files_12ubuntu1 base-passwd_3.5.52 bash_5.1-3ubuntu2 binutils_2.37-7ubuntu1 binutils-aarch64-linux-gnu_2.37-7ubuntu1 binutils-common_2.37-7ubuntu1 bsdextrautils_2.36.1-8ubuntu2 bsdutils_1:2.36.1-8ubuntu2 build-essential_12.9ubuntu2 bzip2_1.0.8-4ubuntu4 ca-certificates_20210119ubuntu1 coreutils_8.32-4ubuntu3 cpp_4:11.2.0-1ubuntu1 cpp-11_11.2.0-7ubuntu2 dash_0.5.11+git20210120+802ebd4-1build1 debconf_1.5.77 debhelper_13.3.4ubuntu2 debianutils_5.5-1 debugedit_1:5.0-0ubuntu2 dh-autoreconf_20 dh-strip-nondeterminism_1.12.0-1 diffutils_1:3.8-0ubuntu1 dpkg_1.20.9ubuntu2 dpkg-dev_1.20.9ubuntu2 dwz_0.14-1build1 e2fsprogs_1.46.3-1ubuntu3 fakeroot_1.25.3-1.1ubuntu3 file_1:5.39-3build1 findutils_4.8.0-1ubuntu2 g++_4:11.2.0-1ubuntu1 g++-11_11.2.0-7ubuntu2 gcc_4:11.2.0-1ubuntu1 gcc-11_11.2.0-7ubuntu2 gcc-11-base_11.2.0-7ubuntu2 gettext_0.21-4ubuntu3 gettext-base_0.21-4ubuntu3 gpg_2.2.20-1ubuntu4 gpg-agent_2.2.20-1ubuntu4 gpgconf_2.2.20-1ubuntu4 gpgv_2.2.20-1ubuntu4 grep_3.7-0ubuntu1 groff-base_1.22.4-7 gzip_1.10-4ubuntu2 hostname_3.23ubuntu1 init_1.60build1 init-system-helpers_1.60build1 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-10ubuntu2 libapparmor1_3.0.3-0ubuntu2 libapt-pkg6.0_2.3.9 libarchive-zip-perl_1.68-1 libargon2-1_0~20171227-0.2build22 libasan6_11.2.0-7ubuntu2 libassuan0_2.5.5-1 libatomic1_11.2.0-7ubuntu2 libattr1_1:2.5.1-1 libaudit-common_1:3.0-2ubuntu3 libaudit1_1:3.0-2ubuntu3 libbinutils_2.37-7ubuntu1 libblkid1_2.36.1-8ubuntu2 libbrotli1_1.0.9-2build4 libbz2-1.0_1.0.8-4ubuntu4 libbz2-dev_1.0.8-4ubuntu4 libc-bin_2.34-0ubuntu3 libc-dev-bin_2.34-0ubuntu3 libc6_2.34-0ubuntu3 libc6-dev_2.34-0ubuntu3 libcap-ng0_0.7.9-2.2build2 libcap2_1:2.44-1build2 libcc1-0_11.2.0-7ubuntu2 libcom-err2_1.46.3-1ubuntu3 libcrypt-dev_1:4.4.18-4ubuntu2 libcrypt1_1:4.4.18-4ubuntu2 libcryptsetup12_2:2.3.6-0ubuntu1 libctf-nobfd0_2.37-7ubuntu1 libctf0_2.37-7ubuntu1 libcurl3-gnutls_7.74.0-1.3ubuntu2 libcurl4-gnutls-dev_7.74.0-1.3ubuntu2 libdb5.3_5.3.28+dfsg1-0.8ubuntu2 libdebconfclient0_0.256ubuntu4 libdebhelper-perl_13.3.4ubuntu2 libdeflate-dev_1.7-2ubuntu2 libdeflate0_1.7-2ubuntu2 libdevmapper1.02.1_2:1.02.175-2.1ubuntu3 libdpkg-perl_1.20.9ubuntu2 libdw1_0.185-2 libelf1_0.185-2 libext2fs2_1.46.3-1ubuntu3 libfakeroot_1.25.3-1.1ubuntu3 libffi8_3.4.2-1ubuntu5 libfile-stripnondeterminism-perl_1.12.0-1 libgcc-11-dev_11.2.0-7ubuntu2 libgcc-s1_11.2.0-7ubuntu2 libgcrypt20_1.8.7-5ubuntu2 libgdbm-compat4_1.21-1 libgdbm6_1.21-1 libgmp10_2:6.2.1+dfsg-1ubuntu3 libgnutls30_3.7.1-5ubuntu1 libgomp1_11.2.0-7ubuntu2 libgpg-error0_1.42-3 libgsl-dev_2.6+dfsg-2 libgsl25_2.6+dfsg-2 libgslcblas0_2.6+dfsg-2 libgssapi-krb5-2_1.18.3-7 libhogweed6_3.7.3-1build1 libhts-dev_1.13+ds-2 libhts3_1.13+ds-2 libhtscodecs2_1.1.1-2 libhwasan0_11.2.0-7ubuntu2 libicu67_67.1-7ubuntu1 libidn2-0_2.3.2-2 libio-pty-perl_1:1.15-2build1 libip4tc2_1.8.7-1ubuntu3 libisl23_0.24-2 libitm1_11.2.0-7ubuntu2 libjson-c5_0.15-2build3 libk5crypto3_1.18.3-7 libkeyutils1_1.6.1-2ubuntu2 libkmod2_28-1ubuntu4 libkrb5-3_1.18.3-7 libkrb5support0_1.18.3-7 libldap-2.5-0_2.5.6+dfsg-1~exp1ubuntu1 liblockfile-bin_1.17-1build1 liblockfile1_1.17-1build1 liblsan0_11.2.0-7ubuntu2 liblz4-1_1.9.3-2build1 liblzma-dev_5.2.5-2build1 liblzma5_5.2.5-2build1 libmagic-mgc_1:5.39-3build1 libmagic1_1:5.39-3build1 libmount1_2.36.1-8ubuntu2 libmpc3_1.2.1-1 libmpfr6_4.1.0-3build2 libncurses6_6.2+20201114-2build2 libncursesw6_6.2+20201114-2build2 libnettle8_3.7.3-1build1 libnghttp2-14_1.43.0-1build1 libnpth0_1.6-3build1 libnsl-dev_1.3.0-2build1 libnsl2_1.3.0-2build1 libp11-kit0_0.23.22-1build1 libpam-modules_1.3.1-5ubuntu11 libpam-modules-bin_1.3.1-5ubuntu11 libpam-runtime_1.3.1-5ubuntu11 libpam0g_1.3.1-5ubuntu11 libpcre2-8-0_10.37-0ubuntu2 libpcre3_2:8.39-13build4 libperl5.32_5.32.1-3ubuntu3 libpipeline1_1.5.3-1build1 libpng16-16_1.6.37-3build4 libprocps8_2:3.3.17-5ubuntu3 libpsl5_0.21.0-1.2build1 libreadline8_8.1-2build1 librtmp1_2.4+20151223.gitfa8646d.1-2build3 libsasl2-2_2.1.27+dfsg-2.1build1 libsasl2-modules-db_2.1.27+dfsg-2.1build1 libseccomp2_2.5.1-1ubuntu2 libselinux1_3.1-3build3 libsemanage-common_3.1-1ubuntu3 libsemanage1_3.1-1ubuntu3 libsepol1_3.1-1ubuntu2 libsigsegv2_2.13-1ubuntu2 libsmartcols1_2.36.1-8ubuntu2 libsqlite3-0_3.35.5-1 libss2_1.46.3-1ubuntu3 libssh-4_0.9.6-1 libssl1.1_1.1.1l-1ubuntu1 libstdc++-11-dev_11.2.0-7ubuntu2 libstdc++6_11.2.0-7ubuntu2 libsub-override-perl_0.09-2 libsystemd0_248.3-1ubuntu8 libtasn1-6_4.17.0-2 libtinfo6_6.2+20201114-2build2 libtirpc-common_1.3.2-2 libtirpc-dev_1.3.2-2 libtirpc3_1.3.2-2 libtool_2.4.6-15build1 libtsan0_11.2.0-7ubuntu2 libubsan1_11.2.0-7ubuntu2 libuchardet0_0.0.7-1build1 libudev1_248.3-1ubuntu8 libunistring2_0.9.10-6 libuuid1_2.36.1-8ubuntu2 libxml2_2.9.12+dfsg-5 libxxhash0_0.8.0-2build1 libzstd1_1.4.8+dfsg-2.1build1 linux-libc-dev_5.13.0-19.19 lockfile-progs_0.1.19 login_1:4.8.1-1ubuntu9 logsave_1.46.3-1ubuntu3 lsb-base_11.1.0ubuntu3 lto-disabled-list_16 m4_1.4.18-5ubuntu1 make_4.3-4ubuntu2 man-db_2.9.4-2build1 mawk_1.3.4.20200120-2build1 mount_2.36.1-8ubuntu2 ncurses-base_6.2+20201114-2build2 ncurses-bin_6.2+20201114-2build2 openssl_1.1.1l-1ubuntu1 optipng_0.7.7-1build1 passwd_1:4.8.1-1ubuntu9 patch_2.7.6-7build1 perl_5.32.1-3ubuntu3 perl-base_5.32.1-3ubuntu3 perl-modules-5.32_5.32.1-3ubuntu3 pinentry-curses_1.1.1-1build1 pkgbinarymangler_148 po-debconf_1.0.21+nmu1 policyrcd-script-zg2_0.1-3 procps_2:3.3.17-5ubuntu3 readline-common_8.1-2build1 rpcsvc-proto_1.4.2-0ubuntu5 sbuild-build-depends-bcftools-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.7-1ubuntu2 sensible-utils_0.0.14 systemd_248.3-1ubuntu8 systemd-sysv_248.3-1ubuntu8 systemd-timesyncd_248.3-1ubuntu8 sysvinit-utils_2.96-7ubuntu2 tabix_1.13+ds-2 tar_1.34+dfsg-1build2 tzdata_2021a-2ubuntu1 ubuntu-keyring_2021.03.26 usrmerge_25ubuntu1 util-linux_2.36.1-8ubuntu2 xz-utils_5.2.5-2build1 zlib1g_1:1.2.11.dfsg-2ubuntu7 zlib1g-dev_1:1.2.11.dfsg-2ubuntu7 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Fri Aug 27 14:55:28 2021 UTC gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./bcftools_1.13-1.dsc dpkg-source: info: extracting bcftools in /<> dpkg-source: info: unpacking bcftools_1.13.orig.tar.gz dpkg-source: info: unpacking bcftools_1.13-1.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 dpkg-source: info: applying 2to3.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-22292590 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-22292590 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-22292590 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package bcftools dpkg-buildpackage: info: source version 1.13-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean rm -f config.mk && touch config.mk dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' dh_auto_clean make -j4 distclean make[2]: Entering directory '/<>' rm -f test/*.o test/*.fa.fai test/*~ test/test-rbuf test/test-regidx rm -f plugins/*.so plugins/*.P rm -rf plugins/*.dSYM rm -f test/*.unsorted.hex test/*.unsorted.tsv rm -f gmon.out *.o *.a *~ bcftools version.h rm -rf *.dSYM test/*.dSYM rm -f config.cache config.h config.log config.mk config.status rm -rf autom4te.cache rm -f TAGS make[2]: Leaving directory '/<>' rm -f test/mpileup/indel-AD.1.out.new test/view-t.1.out.new test/view-t.2.out.new make[1]: Leaving directory '/<>' dh_clean debian/rules binary-arch dh binary-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.m4:1096: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:94: the top level make[1]: Leaving directory '/<>' 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/aarch64-linux-gnu/bcftools ./configure --build=aarch64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/aarch64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system --enable-gsl --with-cblas=gslcblas --with-bcf-plugin-dir=/usr/lib/aarch64-linux-gnu/bcftools checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking for 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... none required checking if the compiler accepts -rdynamic... yes checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing regcomp... none required configure: creating ./config.status config.status: creating config.mk config.status: creating config.h make[1]: Leaving directory '/<>' dh_auto_build -a make -j4 make[1]: Entering directory '/<>' echo '#define BCFTOOLS_VERSION "1.13"' > version.h gcc -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfindex.o vcfindex.c gcc -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tabix.o tabix.c gcc -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfstats.o vcfstats.c gcc -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfisec.o vcfisec.c gcc -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfmerge.o vcfmerge.c gcc -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfquery.o vcfquery.c gcc -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcffilter.o vcffilter.c gcc -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o filter.o filter.c gcc -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfsom.o vcfsom.c gcc -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfnorm.o vcfnorm.c gcc -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfgtcheck.o vcfgtcheck.c gcc -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfview.o vcfview.c gcc -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfannotate.o vcfannotate.c gcc -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfroh.o vcfroh.c gcc -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfconcat.o vcfconcat.c gcc -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcall.o vcfcall.c gcc -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mcall.o mcall.c gcc -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcmp.o vcmp.c gcc -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gvcf.o gvcf.c gcc -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o reheader.o reheader.c gcc -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o convert.o convert.c gcc -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfconvert.o vcfconvert.c gcc -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tsv2vcf.o tsv2vcf.c gcc -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcnv.o vcfcnv.c gcc -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o HMM.o HMM.c gcc -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o consensus.o consensus.c gcc -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ploidy.o ploidy.c gcc -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bin.o bin.c gcc -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hclust.o hclust.c gcc -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o version.o version.c gcc -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o regidx.o regidx.c gcc -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o csq.o csq.c gcc -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfbuf.o vcfbuf.c gcc -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mpileup.o mpileup.c gcc -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c gcc -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfsort.o vcfsort.c gcc -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cols.o cols.c gcc -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o extsort.o extsort.c gcc -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dist.o dist.c gcc -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o abuf.o abuf.c gcc -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ccall.o ccall.c gcc -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o em.o em.c gcc -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o prob1.o prob1.c gcc -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kmin.o kmin.c gcc -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o str_finder.o str_finder.c gcc -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DPLUGINPATH='"/usr/lib/aarch64-linux-gnu/bcftools"' -c -o vcfplugin.o vcfplugin.c gcc -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -o plugins/GTisec.so version.c plugins/GTisec.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -o plugins/GTsubset.so version.c plugins/GTsubset.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -o plugins/ad-bias.so convert.c version.c plugins/ad-bias.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -o plugins/add-variantkey.so version.c plugins/add-variantkey.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -o plugins/af-dist.so bin.c version.c plugins/af-dist.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -o plugins/allele-length.so version.c plugins/allele-length.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -o plugins/check-ploidy.so version.c plugins/check-ploidy.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -o plugins/check-sparsity.so version.c plugins/check-sparsity.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -o plugins/color-chrs.so HMM.c version.c plugins/color-chrs.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -o plugins/contrast.so version.c plugins/contrast.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -o plugins/counts.so version.c plugins/counts.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -o plugins/dosage.so version.c plugins/dosage.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -o plugins/fill-AN-AC.so version.c plugins/fill-AN-AC.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -o plugins/fill-from-fasta.so filter.c version.c plugins/fill-from-fasta.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -o plugins/fill-tags.so version.c plugins/fill-tags.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -o plugins/fixploidy.so ploidy.c regidx.c version.c plugins/fixploidy.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -o plugins/fixref.so version.c plugins/fixref.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -o plugins/frameshifts.so version.c plugins/frameshifts.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -o plugins/guess-ploidy.so version.c plugins/guess-ploidy.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -o plugins/gvcfz.so version.c plugins/gvcfz.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -o plugins/impute-info.so version.c plugins/impute-info.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -o plugins/indel-stats.so version.c plugins/indel-stats.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -o plugins/isecGT.so smpl_ilist.c version.c plugins/isecGT.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -o plugins/mendelian.so version.c plugins/mendelian.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -o plugins/missing2ref.so version.c plugins/missing2ref.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -o plugins/parental-origin.so version.c plugins/parental-origin.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -o plugins/prune.so version.c plugins/prune.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -o plugins/remove-overlaps.so version.c plugins/remove-overlaps.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -o plugins/scatter.so version.c plugins/scatter.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -o plugins/setGT.so version.c plugins/setGT.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -o plugins/smpl-stats.so version.c plugins/smpl-stats.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -o plugins/split-vep.so version.c plugins/split-vep.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -o plugins/split.so version.c plugins/split.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -o plugins/tag2tag.so version.c plugins/tag2tag.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -o plugins/trio-dnm2.so version.c plugins/trio-dnm2.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -o plugins/trio-stats.so version.c plugins/trio-stats.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -o plugins/trio-switch-rate.so version.c plugins/trio-switch-rate.c gcc -fPIC -shared -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -o plugins/variantkey-hex.so version.c plugins/variantkey-hex.c gcc -Wall -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o main.o main.c gcc -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -o test/test-rbuf test/test-rbuf.o -lz gcc -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -o test/test-regidx test/test-regidx.o regidx.o -lhts -lpthread -lz gcc -rdynamic -Wl,-Bsymbolic-functions -flto=auto -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 extsort.o dist.o abuf.o ccall.o em.o prob1.o kmin.o str_finder.o vcfplugin.o -lhts -lm -lz -lpthread vcfcnv.c:1132:5: warning: type of ‘read_AF’ does not match original declaration [-Wlto-type-mismatch] 1132 | int read_AF(bcf_sr_regions_t *tgt, bcf1_t *line, double *alt_freq); | ^ vcfroh.c:661:5: note: type mismatch in parameter 4 661 | int read_AF(args_t *args, bcf_sr_regions_t *tgt, bcf1_t *line, double *alt_freq) | ^ vcfroh.c:661:5: note: ‘read_AF’ was previously declared here 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/tiM8I5IySO/merge.a.vcf.gz 2:3199812-3199812 .. ok test_tabix: /<>/bcftools view -H /tmp/tiM8I5IySO/merge.a.bcf 2:3199812-3199812 .. ok test_tabix: tabix /tmp/tiM8I5IySO/merge.a.vcf.gz 1:3000151-3000151 .. ok test_tabix: /<>/bcftools view -H /tmp/tiM8I5IySO/merge.a.bcf 1:3000151-3000151 .. ok test_index: /<>/bcftools view -H /tmp/tiM8I5IySO/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/tiM8I5IySO/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/tiM8I5IySO/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/tiM8I5IySO/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/tiM8I5IySO/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/tiM8I5IySO/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /<>/bcftools view -H /tmp/tiM8I5IySO/large_chrom_csi_limit.bcf chr20 .. ok test_index: /<>/bcftools view -H /tmp/tiM8I5IySO/large_chrom_csi_limit.bcf chr20 .. ok test_index: /<>/bcftools view -H /tmp/tiM8I5IySO/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /<>/bcftools view -H /tmp/tiM8I5IySO/large_chrom_csi_limit.bcf chr20 .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/tiM8I5IySO/idx.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/tiM8I5IySO/idx.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/tiM8I5IySO/idx.bcf .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/tiM8I5IySO/idx.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/tiM8I5IySO/idx.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/tiM8I5IySO/idx.vcf.gz.csi .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/tiM8I5IySO/idx.bcf .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/tiM8I5IySO/idx.bcf.csi .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/tiM8I5IySO/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/tiM8I5IySO/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/tiM8I5IySO/empty.bcf .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/tiM8I5IySO/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/tiM8I5IySO/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/tiM8I5IySO/empty.vcf.gz.csi .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/tiM8I5IySO/empty.bcf .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/tiM8I5IySO/empty.bcf.csi .. ok test_vcf_check: /<>/bcftools stats -s - /tmp/tiM8I5IySO/check.vcf.gz | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/check.1.chk /tmp/tiM8I5IySO/check.2.chk /tmp/tiM8I5IySO/check.3.chk /tmp/tiM8I5IySO/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/tiM8I5IySO/stats.a.vcf.gz /tmp/tiM8I5IySO/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /<>/bcftools stats -s B /tmp/tiM8I5IySO/stats.a.vcf.gz /tmp/tiM8I5IySO/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /<>/bcftools stats -s - /tmp/tiM8I5IySO/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_isec: /<>/bcftools isec -n =2 /tmp/tiM8I5IySO/isec.a.vcf.gz /tmp/tiM8I5IySO/isec.b.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 /tmp/tiM8I5IySO/isec.a.vcf.gz /tmp/tiM8I5IySO/isec.b.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/tiM8I5IySO/isec.a.vcf.gz /tmp/tiM8I5IySO/isec.b.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 -i"STRLEN(REF)==2" /tmp/tiM8I5IySO/isec.a.vcf.gz /tmp/tiM8I5IySO/isec.b.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -n =2 -c both /tmp/tiM8I5IySO/isec.a.vcf.gz /tmp/tiM8I5IySO/isec.b.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 -c both /tmp/tiM8I5IySO/isec.a.vcf.gz /tmp/tiM8I5IySO/isec.b.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -n =2 -c any /tmp/tiM8I5IySO/isec.a.vcf.gz /tmp/tiM8I5IySO/isec.b.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 -c any /tmp/tiM8I5IySO/isec.a.vcf.gz /tmp/tiM8I5IySO/isec.b.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -C -c any /tmp/tiM8I5IySO/isec.a.vcf.gz /tmp/tiM8I5IySO/isec.b.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -Ob -C -c any /tmp/tiM8I5IySO/isec.a.vcf.gz /tmp/tiM8I5IySO/isec.b.vcf.gz .. ok test_vcf_isec2: /<>/bcftools isec --no-version -T /tmp/tiM8I5IySO/isec.tab.gz /tmp/tiM8I5IySO/isec.a.vcf.gz .. ok test_vcf_isec2: /<>/bcftools isec -Ob -T /tmp/tiM8I5IySO/isec.tab.gz /tmp/tiM8I5IySO/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/tiM8I5IySO/isec-miss.1.1.vcf.gz /tmp/tiM8I5IySO/isec-miss.1.2.vcf.gz /tmp/tiM8I5IySO/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/tiM8I5IySO/isec-miss.1.1.vcf.gz /tmp/tiM8I5IySO/isec-miss.1.2.vcf.gz /tmp/tiM8I5IySO/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -R /<>/test/isec-miss.1.regs.txt -n +1 /tmp/tiM8I5IySO/isec-miss.1.1.vcf.gz /tmp/tiM8I5IySO/isec-miss.1.2.vcf.gz /tmp/tiM8I5IySO/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -Ob -R /<>/test/isec-miss.1.regs.txt -n +1 /tmp/tiM8I5IySO/isec-miss.1.1.vcf.gz /tmp/tiM8I5IySO/isec-miss.1.2.vcf.gz /tmp/tiM8I5IySO/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/tiM8I5IySO/isec-miss.2.1.vcf.gz /tmp/tiM8I5IySO/isec-miss.2.2.vcf.gz /tmp/tiM8I5IySO/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/tiM8I5IySO/isec-miss.2.1.vcf.gz /tmp/tiM8I5IySO/isec-miss.2.2.vcf.gz /tmp/tiM8I5IySO/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -R /<>/test/isec-miss.1.regs.txt -n +1 /tmp/tiM8I5IySO/isec-miss.2.1.vcf.gz /tmp/tiM8I5IySO/isec-miss.2.2.vcf.gz /tmp/tiM8I5IySO/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -Ob -R /<>/test/isec-miss.1.regs.txt -n +1 /tmp/tiM8I5IySO/isec-miss.2.1.vcf.gz /tmp/tiM8I5IySO/isec-miss.2.2.vcf.gz /tmp/tiM8I5IySO/isec-miss.2.3.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -i AF:join /tmp/tiM8I5IySO/merge.join.a.vcf.gz /tmp/tiM8I5IySO/merge.join.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob -i AF:join /tmp/tiM8I5IySO/merge.join.a.vcf.gz /tmp/tiM8I5IySO/merge.join.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version -i AF:join /tmp/tiM8I5IySO/merge.join.a.bcf /tmp/tiM8I5IySO/merge.join.b.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob -i AF:join /tmp/tiM8I5IySO/merge.join.a.bcf /tmp/tiM8I5IySO/merge.join.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples /tmp/tiM8I5IySO/merge.LPL.a.vcf.gz /tmp/tiM8I5IySO/merge.LPL.b.vcf.gz /tmp/tiM8I5IySO/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples /tmp/tiM8I5IySO/merge.LPL.a.vcf.gz /tmp/tiM8I5IySO/merge.LPL.b.vcf.gz /tmp/tiM8I5IySO/merge.LPL.c.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples /tmp/tiM8I5IySO/merge.LPL.a.bcf /tmp/tiM8I5IySO/merge.LPL.b.bcf /tmp/tiM8I5IySO/merge.LPL.c.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples /tmp/tiM8I5IySO/merge.LPL.a.bcf /tmp/tiM8I5IySO/merge.LPL.b.bcf /tmp/tiM8I5IySO/merge.LPL.c.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -L 1 /tmp/tiM8I5IySO/merge.LPL.a.vcf.gz /tmp/tiM8I5IySO/merge.LPL.b.vcf.gz /tmp/tiM8I5IySO/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -L 1 /tmp/tiM8I5IySO/merge.LPL.a.vcf.gz /tmp/tiM8I5IySO/merge.LPL.b.vcf.gz /tmp/tiM8I5IySO/merge.LPL.c.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -L 1 /tmp/tiM8I5IySO/merge.LPL.a.bcf /tmp/tiM8I5IySO/merge.LPL.b.bcf /tmp/tiM8I5IySO/merge.LPL.c.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -L 1 /tmp/tiM8I5IySO/merge.LPL.a.bcf /tmp/tiM8I5IySO/merge.LPL.b.bcf /tmp/tiM8I5IySO/merge.LPL.c.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -L 2 /tmp/tiM8I5IySO/merge.LPL.a.vcf.gz /tmp/tiM8I5IySO/merge.LPL.b.vcf.gz /tmp/tiM8I5IySO/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -L 2 /tmp/tiM8I5IySO/merge.LPL.a.vcf.gz /tmp/tiM8I5IySO/merge.LPL.b.vcf.gz /tmp/tiM8I5IySO/merge.LPL.c.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -L 2 /tmp/tiM8I5IySO/merge.LPL.a.bcf /tmp/tiM8I5IySO/merge.LPL.b.bcf /tmp/tiM8I5IySO/merge.LPL.c.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -L 2 /tmp/tiM8I5IySO/merge.LPL.a.bcf /tmp/tiM8I5IySO/merge.LPL.b.bcf /tmp/tiM8I5IySO/merge.LPL.c.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -L 3 /tmp/tiM8I5IySO/merge.LPL.a.vcf.gz /tmp/tiM8I5IySO/merge.LPL.b.vcf.gz /tmp/tiM8I5IySO/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -L 3 /tmp/tiM8I5IySO/merge.LPL.a.vcf.gz /tmp/tiM8I5IySO/merge.LPL.b.vcf.gz /tmp/tiM8I5IySO/merge.LPL.c.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -L 3 /tmp/tiM8I5IySO/merge.LPL.a.bcf /tmp/tiM8I5IySO/merge.LPL.b.bcf /tmp/tiM8I5IySO/merge.LPL.c.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -L 3 /tmp/tiM8I5IySO/merge.LPL.a.bcf /tmp/tiM8I5IySO/merge.LPL.b.bcf /tmp/tiM8I5IySO/merge.LPL.c.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -L 4 /tmp/tiM8I5IySO/merge.LPL.a.vcf.gz /tmp/tiM8I5IySO/merge.LPL.b.vcf.gz /tmp/tiM8I5IySO/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -L 4 /tmp/tiM8I5IySO/merge.LPL.a.vcf.gz /tmp/tiM8I5IySO/merge.LPL.b.vcf.gz /tmp/tiM8I5IySO/merge.LPL.c.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -L 4 /tmp/tiM8I5IySO/merge.LPL.a.bcf /tmp/tiM8I5IySO/merge.LPL.b.bcf /tmp/tiM8I5IySO/merge.LPL.c.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -L 4 /tmp/tiM8I5IySO/merge.LPL.a.bcf /tmp/tiM8I5IySO/merge.LPL.b.bcf /tmp/tiM8I5IySO/merge.LPL.c.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -L 5 /tmp/tiM8I5IySO/merge.LPL.a.vcf.gz /tmp/tiM8I5IySO/merge.LPL.b.vcf.gz /tmp/tiM8I5IySO/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -L 5 /tmp/tiM8I5IySO/merge.LPL.a.vcf.gz /tmp/tiM8I5IySO/merge.LPL.b.vcf.gz /tmp/tiM8I5IySO/merge.LPL.c.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -L 5 /tmp/tiM8I5IySO/merge.LPL.a.bcf /tmp/tiM8I5IySO/merge.LPL.b.bcf /tmp/tiM8I5IySO/merge.LPL.c.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -L 5 /tmp/tiM8I5IySO/merge.LPL.a.bcf /tmp/tiM8I5IySO/merge.LPL.b.bcf /tmp/tiM8I5IySO/merge.LPL.c.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples /tmp/tiM8I5IySO/merge.a.vcf.gz /tmp/tiM8I5IySO/merge.b.vcf.gz /tmp/tiM8I5IySO/merge.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples /tmp/tiM8I5IySO/merge.a.vcf.gz /tmp/tiM8I5IySO/merge.b.vcf.gz /tmp/tiM8I5IySO/merge.c.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples /tmp/tiM8I5IySO/merge.a.bcf /tmp/tiM8I5IySO/merge.b.bcf /tmp/tiM8I5IySO/merge.c.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples /tmp/tiM8I5IySO/merge.a.bcf /tmp/tiM8I5IySO/merge.b.bcf /tmp/tiM8I5IySO/merge.c.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -Fx /tmp/tiM8I5IySO/merge.a.vcf.gz /tmp/tiM8I5IySO/merge.b.vcf.gz /tmp/tiM8I5IySO/merge.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -Fx /tmp/tiM8I5IySO/merge.a.vcf.gz /tmp/tiM8I5IySO/merge.b.vcf.gz /tmp/tiM8I5IySO/merge.c.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -Fx /tmp/tiM8I5IySO/merge.a.bcf /tmp/tiM8I5IySO/merge.b.bcf /tmp/tiM8I5IySO/merge.c.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -Fx /tmp/tiM8I5IySO/merge.a.bcf /tmp/tiM8I5IySO/merge.b.bcf /tmp/tiM8I5IySO/merge.c.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -0 /tmp/tiM8I5IySO/merge.a.vcf.gz /tmp/tiM8I5IySO/merge.b.vcf.gz /tmp/tiM8I5IySO/merge.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -0 /tmp/tiM8I5IySO/merge.a.vcf.gz /tmp/tiM8I5IySO/merge.b.vcf.gz /tmp/tiM8I5IySO/merge.c.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -0 /tmp/tiM8I5IySO/merge.a.bcf /tmp/tiM8I5IySO/merge.b.bcf /tmp/tiM8I5IySO/merge.c.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -0 /tmp/tiM8I5IySO/merge.a.bcf /tmp/tiM8I5IySO/merge.b.bcf /tmp/tiM8I5IySO/merge.c.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -m none /tmp/tiM8I5IySO/merge.2.a.vcf.gz /tmp/tiM8I5IySO/merge.2.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -m none /tmp/tiM8I5IySO/merge.2.a.vcf.gz /tmp/tiM8I5IySO/merge.2.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -m none /tmp/tiM8I5IySO/merge.2.a.bcf /tmp/tiM8I5IySO/merge.2.b.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -m none /tmp/tiM8I5IySO/merge.2.a.bcf /tmp/tiM8I5IySO/merge.2.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -m both /tmp/tiM8I5IySO/merge.2.a.vcf.gz /tmp/tiM8I5IySO/merge.2.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -m both /tmp/tiM8I5IySO/merge.2.a.vcf.gz /tmp/tiM8I5IySO/merge.2.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -m both /tmp/tiM8I5IySO/merge.2.a.bcf /tmp/tiM8I5IySO/merge.2.b.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -m both /tmp/tiM8I5IySO/merge.2.a.bcf /tmp/tiM8I5IySO/merge.2.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -m all /tmp/tiM8I5IySO/merge.2.a.vcf.gz /tmp/tiM8I5IySO/merge.2.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -m all /tmp/tiM8I5IySO/merge.2.a.vcf.gz /tmp/tiM8I5IySO/merge.2.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -m all /tmp/tiM8I5IySO/merge.2.a.bcf /tmp/tiM8I5IySO/merge.2.b.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -m all /tmp/tiM8I5IySO/merge.2.a.bcf /tmp/tiM8I5IySO/merge.2.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/tiM8I5IySO/merge.3.a.vcf.gz /tmp/tiM8I5IySO/merge.3.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/tiM8I5IySO/merge.3.a.vcf.gz /tmp/tiM8I5IySO/merge.3.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/tiM8I5IySO/merge.3.a.bcf /tmp/tiM8I5IySO/merge.3.b.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/tiM8I5IySO/merge.3.a.bcf /tmp/tiM8I5IySO/merge.3.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -m id /tmp/tiM8I5IySO/merge.4.a.vcf.gz /tmp/tiM8I5IySO/merge.4.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -m id /tmp/tiM8I5IySO/merge.4.a.vcf.gz /tmp/tiM8I5IySO/merge.4.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -m id /tmp/tiM8I5IySO/merge.4.a.bcf /tmp/tiM8I5IySO/merge.4.b.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples -m id /tmp/tiM8I5IySO/merge.4.a.bcf /tmp/tiM8I5IySO/merge.4.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/tiM8I5IySO/gvcf.merge.1.vcf.gz /tmp/tiM8I5IySO/gvcf.merge.2.vcf.gz /tmp/tiM8I5IySO/gvcf.merge.3.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --gvcf - /tmp/tiM8I5IySO/gvcf.merge.1.vcf.gz /tmp/tiM8I5IySO/gvcf.merge.2.vcf.gz /tmp/tiM8I5IySO/gvcf.merge.3.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/tiM8I5IySO/gvcf.merge.1.bcf /tmp/tiM8I5IySO/gvcf.merge.2.bcf /tmp/tiM8I5IySO/gvcf.merge.3.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob --gvcf - /tmp/tiM8I5IySO/gvcf.merge.1.bcf /tmp/tiM8I5IySO/gvcf.merge.2.bcf /tmp/tiM8I5IySO/gvcf.merge.3.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/tiM8I5IySO/merge.gvcf.2.a.vcf.gz /tmp/tiM8I5IySO/merge.gvcf.2.b.vcf.gz /tmp/tiM8I5IySO/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --gvcf - /tmp/tiM8I5IySO/merge.gvcf.2.a.vcf.gz /tmp/tiM8I5IySO/merge.gvcf.2.b.vcf.gz /tmp/tiM8I5IySO/merge.gvcf.2.c.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - -i SRC:join /tmp/tiM8I5IySO/merge.gvcf.3.a.vcf.gz /tmp/tiM8I5IySO/merge.gvcf.3.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --gvcf - -i SRC:join /tmp/tiM8I5IySO/merge.gvcf.3.a.vcf.gz /tmp/tiM8I5IySO/merge.gvcf.3.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/tiM8I5IySO/merge.gvcf.4.a.vcf.gz /tmp/tiM8I5IySO/merge.gvcf.4.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --gvcf - /tmp/tiM8I5IySO/merge.gvcf.4.a.vcf.gz /tmp/tiM8I5IySO/merge.gvcf.4.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/tiM8I5IySO/merge.gvcf.4.a.bcf /tmp/tiM8I5IySO/merge.gvcf.4.b.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob --gvcf - /tmp/tiM8I5IySO/merge.gvcf.4.a.bcf /tmp/tiM8I5IySO/merge.gvcf.4.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version /tmp/tiM8I5IySO/merge.5.a.vcf.gz /tmp/tiM8I5IySO/merge.5.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob /tmp/tiM8I5IySO/merge.5.a.vcf.gz /tmp/tiM8I5IySO/merge.5.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version /tmp/tiM8I5IySO/merge.5.a.bcf /tmp/tiM8I5IySO/merge.5.b.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob /tmp/tiM8I5IySO/merge.5.a.bcf /tmp/tiM8I5IySO/merge.5.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version /tmp/tiM8I5IySO/merge.6.a.vcf.gz /tmp/tiM8I5IySO/merge.6.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob /tmp/tiM8I5IySO/merge.6.a.vcf.gz /tmp/tiM8I5IySO/merge.6.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version /tmp/tiM8I5IySO/merge.6.a.bcf /tmp/tiM8I5IySO/merge.6.b.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob /tmp/tiM8I5IySO/merge.6.a.bcf /tmp/tiM8I5IySO/merge.6.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/tiM8I5IySO/merge.gvcf.7.a.vcf.gz /tmp/tiM8I5IySO/merge.gvcf.7.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --gvcf - /tmp/tiM8I5IySO/merge.gvcf.7.a.vcf.gz /tmp/tiM8I5IySO/merge.gvcf.7.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/tiM8I5IySO/merge.gvcf.7.a.bcf /tmp/tiM8I5IySO/merge.gvcf.7.b.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob --gvcf - /tmp/tiM8I5IySO/merge.gvcf.7.a.bcf /tmp/tiM8I5IySO/merge.gvcf.7.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/tiM8I5IySO/merge.gvcf.8.a.vcf.gz /tmp/tiM8I5IySO/merge.gvcf.8.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --gvcf - /tmp/tiM8I5IySO/merge.gvcf.8.a.vcf.gz /tmp/tiM8I5IySO/merge.gvcf.8.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/tiM8I5IySO/merge.gvcf.8.a.bcf /tmp/tiM8I5IySO/merge.gvcf.8.b.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob --gvcf - /tmp/tiM8I5IySO/merge.gvcf.8.a.bcf /tmp/tiM8I5IySO/merge.gvcf.8.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples /tmp/tiM8I5IySO/merge.7.a.vcf.gz /tmp/tiM8I5IySO/merge.7.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples /tmp/tiM8I5IySO/merge.7.a.vcf.gz /tmp/tiM8I5IySO/merge.7.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples /tmp/tiM8I5IySO/merge.7.a.bcf /tmp/tiM8I5IySO/merge.7.b.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob --force-samples /tmp/tiM8I5IySO/merge.7.a.bcf /tmp/tiM8I5IySO/merge.7.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf /<>/test/gvcf.fa /tmp/tiM8I5IySO/merge.gvcf.9a.vcf.gz /tmp/tiM8I5IySO/merge.gvcf.9b.vcf.gz /tmp/tiM8I5IySO/merge.gvcf.9c.vcf.gz /tmp/tiM8I5IySO/merge.gvcf.9d.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --gvcf /<>/test/gvcf.fa /tmp/tiM8I5IySO/merge.gvcf.9a.vcf.gz /tmp/tiM8I5IySO/merge.gvcf.9b.vcf.gz /tmp/tiM8I5IySO/merge.gvcf.9c.vcf.gz /tmp/tiM8I5IySO/merge.gvcf.9d.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf /<>/test/gvcf.fa /tmp/tiM8I5IySO/merge.gvcf.9a.bcf /tmp/tiM8I5IySO/merge.gvcf.9b.bcf /tmp/tiM8I5IySO/merge.gvcf.9c.bcf /tmp/tiM8I5IySO/merge.gvcf.9d.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob --gvcf /<>/test/gvcf.fa /tmp/tiM8I5IySO/merge.gvcf.9a.bcf /tmp/tiM8I5IySO/merge.gvcf.9b.bcf /tmp/tiM8I5IySO/merge.gvcf.9c.bcf /tmp/tiM8I5IySO/merge.gvcf.9d.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf /<>/test/gvcf.fa -r 22:21-23 /tmp/tiM8I5IySO/merge.gvcf.9a.vcf.gz /tmp/tiM8I5IySO/merge.gvcf.9b.vcf.gz /tmp/tiM8I5IySO/merge.gvcf.9c.vcf.gz /tmp/tiM8I5IySO/merge.gvcf.9d.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --gvcf /<>/test/gvcf.fa -r 22:21-23 /tmp/tiM8I5IySO/merge.gvcf.9a.vcf.gz /tmp/tiM8I5IySO/merge.gvcf.9b.vcf.gz /tmp/tiM8I5IySO/merge.gvcf.9c.vcf.gz /tmp/tiM8I5IySO/merge.gvcf.9d.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf /<>/test/gvcf.fa -r 22:21-23 /tmp/tiM8I5IySO/merge.gvcf.9a.bcf /tmp/tiM8I5IySO/merge.gvcf.9b.bcf /tmp/tiM8I5IySO/merge.gvcf.9c.bcf /tmp/tiM8I5IySO/merge.gvcf.9d.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob --gvcf /<>/test/gvcf.fa -r 22:21-23 /tmp/tiM8I5IySO/merge.gvcf.9a.bcf /tmp/tiM8I5IySO/merge.gvcf.9b.bcf /tmp/tiM8I5IySO/merge.gvcf.9c.bcf /tmp/tiM8I5IySO/merge.gvcf.9d.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf /<>/test/gvcf.fa /tmp/tiM8I5IySO/merge.gvcf.9a.vcf.gz /tmp/tiM8I5IySO/merge.gvcf.9b.vcf.gz /tmp/tiM8I5IySO/merge.gvcf.9c.vcf.gz /tmp/tiM8I5IySO/merge.gvcf.9d.vcf.gz /tmp/tiM8I5IySO/merge.gvcf.9e.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --gvcf /<>/test/gvcf.fa /tmp/tiM8I5IySO/merge.gvcf.9a.vcf.gz /tmp/tiM8I5IySO/merge.gvcf.9b.vcf.gz /tmp/tiM8I5IySO/merge.gvcf.9c.vcf.gz /tmp/tiM8I5IySO/merge.gvcf.9d.vcf.gz /tmp/tiM8I5IySO/merge.gvcf.9e.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf /<>/test/gvcf.fa /tmp/tiM8I5IySO/merge.gvcf.9a.bcf /tmp/tiM8I5IySO/merge.gvcf.9b.bcf /tmp/tiM8I5IySO/merge.gvcf.9c.bcf /tmp/tiM8I5IySO/merge.gvcf.9d.bcf /tmp/tiM8I5IySO/merge.gvcf.9e.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob --gvcf /<>/test/gvcf.fa /tmp/tiM8I5IySO/merge.gvcf.9a.bcf /tmp/tiM8I5IySO/merge.gvcf.9b.bcf /tmp/tiM8I5IySO/merge.gvcf.9c.bcf /tmp/tiM8I5IySO/merge.gvcf.9d.bcf /tmp/tiM8I5IySO/merge.gvcf.9e.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf /<>/test/gvcf.fa -r 22:21-23 /tmp/tiM8I5IySO/merge.gvcf.9a.vcf.gz /tmp/tiM8I5IySO/merge.gvcf.9b.vcf.gz /tmp/tiM8I5IySO/merge.gvcf.9c.vcf.gz /tmp/tiM8I5IySO/merge.gvcf.9d.vcf.gz /tmp/tiM8I5IySO/merge.gvcf.9e.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob --gvcf /<>/test/gvcf.fa -r 22:21-23 /tmp/tiM8I5IySO/merge.gvcf.9a.vcf.gz /tmp/tiM8I5IySO/merge.gvcf.9b.vcf.gz /tmp/tiM8I5IySO/merge.gvcf.9c.vcf.gz /tmp/tiM8I5IySO/merge.gvcf.9d.vcf.gz /tmp/tiM8I5IySO/merge.gvcf.9e.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf /<>/test/gvcf.fa -r 22:21-23 /tmp/tiM8I5IySO/merge.gvcf.9a.bcf /tmp/tiM8I5IySO/merge.gvcf.9b.bcf /tmp/tiM8I5IySO/merge.gvcf.9c.bcf /tmp/tiM8I5IySO/merge.gvcf.9d.bcf /tmp/tiM8I5IySO/merge.gvcf.9e.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob --gvcf /<>/test/gvcf.fa -r 22:21-23 /tmp/tiM8I5IySO/merge.gvcf.9a.bcf /tmp/tiM8I5IySO/merge.gvcf.9b.bcf /tmp/tiM8I5IySO/merge.gvcf.9c.bcf /tmp/tiM8I5IySO/merge.gvcf.9d.bcf /tmp/tiM8I5IySO/merge.gvcf.9e.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version /tmp/tiM8I5IySO/merge.gvcf.10.a.vcf.gz /tmp/tiM8I5IySO/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob /tmp/tiM8I5IySO/merge.gvcf.10.a.vcf.gz /tmp/tiM8I5IySO/merge.gvcf.10.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version /tmp/tiM8I5IySO/merge.gvcf.10.a.bcf /tmp/tiM8I5IySO/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob /tmp/tiM8I5IySO/merge.gvcf.10.a.bcf /tmp/tiM8I5IySO/merge.gvcf.10.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version -m none /tmp/tiM8I5IySO/merge.gvcf.10.a.vcf.gz /tmp/tiM8I5IySO/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob -m none /tmp/tiM8I5IySO/merge.gvcf.10.a.vcf.gz /tmp/tiM8I5IySO/merge.gvcf.10.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version -m none /tmp/tiM8I5IySO/merge.gvcf.10.a.bcf /tmp/tiM8I5IySO/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob -m none /tmp/tiM8I5IySO/merge.gvcf.10.a.bcf /tmp/tiM8I5IySO/merge.gvcf.10.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version -g /<>/test/merge.gvcf.10.fa /tmp/tiM8I5IySO/merge.gvcf.10.a.vcf.gz /tmp/tiM8I5IySO/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob -g /<>/test/merge.gvcf.10.fa /tmp/tiM8I5IySO/merge.gvcf.10.a.vcf.gz /tmp/tiM8I5IySO/merge.gvcf.10.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version -g /<>/test/merge.gvcf.10.fa /tmp/tiM8I5IySO/merge.gvcf.10.a.bcf /tmp/tiM8I5IySO/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob -g /<>/test/merge.gvcf.10.fa /tmp/tiM8I5IySO/merge.gvcf.10.a.bcf /tmp/tiM8I5IySO/merge.gvcf.10.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version -g /<>/test/merge.gvcf.10.fa -m none /tmp/tiM8I5IySO/merge.gvcf.10.a.vcf.gz /tmp/tiM8I5IySO/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob -g /<>/test/merge.gvcf.10.fa -m none /tmp/tiM8I5IySO/merge.gvcf.10.a.vcf.gz /tmp/tiM8I5IySO/merge.gvcf.10.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version -g /<>/test/merge.gvcf.10.fa -m none /tmp/tiM8I5IySO/merge.gvcf.10.a.bcf /tmp/tiM8I5IySO/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob -g /<>/test/merge.gvcf.10.fa -m none /tmp/tiM8I5IySO/merge.gvcf.10.a.bcf /tmp/tiM8I5IySO/merge.gvcf.10.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version -g /<>/test/merge.gvcf.10.fa /tmp/tiM8I5IySO/merge.gvcf.10.b.vcf.gz /tmp/tiM8I5IySO/merge.gvcf.10.a.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob -g /<>/test/merge.gvcf.10.fa /tmp/tiM8I5IySO/merge.gvcf.10.b.vcf.gz /tmp/tiM8I5IySO/merge.gvcf.10.a.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version -g /<>/test/merge.gvcf.10.fa /tmp/tiM8I5IySO/merge.gvcf.10.b.bcf /tmp/tiM8I5IySO/merge.gvcf.10.a.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob -g /<>/test/merge.gvcf.10.fa /tmp/tiM8I5IySO/merge.gvcf.10.b.bcf /tmp/tiM8I5IySO/merge.gvcf.10.a.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version -g /<>/test/merge.gvcf.10.fa -m none /tmp/tiM8I5IySO/merge.gvcf.10.b.vcf.gz /tmp/tiM8I5IySO/merge.gvcf.10.a.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob -g /<>/test/merge.gvcf.10.fa -m none /tmp/tiM8I5IySO/merge.gvcf.10.b.vcf.gz /tmp/tiM8I5IySO/merge.gvcf.10.a.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version -g /<>/test/merge.gvcf.10.fa -m none /tmp/tiM8I5IySO/merge.gvcf.10.b.bcf /tmp/tiM8I5IySO/merge.gvcf.10.a.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob -g /<>/test/merge.gvcf.10.fa -m none /tmp/tiM8I5IySO/merge.gvcf.10.b.bcf /tmp/tiM8I5IySO/merge.gvcf.10.a.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version /tmp/tiM8I5IySO/merge.noidx.a.vcf.gz /tmp/tiM8I5IySO/merge.noidx.b.vcf.gz /tmp/tiM8I5IySO/merge.noidx.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge -Ob /tmp/tiM8I5IySO/merge.noidx.a.vcf.gz /tmp/tiM8I5IySO/merge.noidx.b.vcf.gz /tmp/tiM8I5IySO/merge.noidx.c.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version /tmp/tiM8I5IySO/merge.noidx.a.bcf /tmp/tiM8I5IySO/merge.noidx.b.bcf /tmp/tiM8I5IySO/merge.noidx.c.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob /tmp/tiM8I5IySO/merge.noidx.a.bcf /tmp/tiM8I5IySO/merge.noidx.b.bcf /tmp/tiM8I5IySO/merge.noidx.c.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --no-index /<>/test/merge.noidx.a.vcf /<>/test/merge.noidx.b.vcf /<>/test/merge.noidx.c.vcf .. ok test_vcf_merge: /<>/bcftools merge -Ob --no-index /<>/test/merge.noidx.a.vcf /<>/test/merge.noidx.b.vcf /<>/test/merge.noidx.c.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --no-index /tmp/tiM8I5IySO/merge.noidx.a.bcf /tmp/tiM8I5IySO/merge.noidx.b.bcf /tmp/tiM8I5IySO/merge.noidx.c.bcf .. ok test_vcf_merge: /<>/bcftools merge -Ob --no-index /tmp/tiM8I5IySO/merge.noidx.a.bcf /tmp/tiM8I5IySO/merge.noidx.b.bcf /tmp/tiM8I5IySO/merge.noidx.c.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_query: /<>/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided,_conflicting_interpretations"' /tmp/tiM8I5IySO/query.string.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/query.string.vcf.gz | /<>/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided,_conflicting_interpretations"' .. ok test_vcf_query: /<>/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" || CLNREVSTAT="_conflicting_interpretations"' /tmp/tiM8I5IySO/query.string.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/query.string.vcf.gz | /<>/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" || CLNREVSTAT="_conflicting_interpretations"' .. ok test_vcf_query: /<>/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" && CLNREVSTAT="_conflicting_interpretations"' /tmp/tiM8I5IySO/query.string.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/query.string.vcf.gz | /<>/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided" && CLNREVSTAT="_conflicting_interpretations"' .. ok test_vcf_query: /<>/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' /tmp/tiM8I5IySO/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/query.variantkey.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/query.variantkey.vcf.gz | /<>/bcftools query -f '%RSX\t%VKX\n' .. ok test_vcf_query: /<>/bcftools query -f'%XRI\n' -i'XRI[*]>1111' /tmp/tiM8I5IySO/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/view.vectors.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/query.2.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/missing.vcf.gz | /<>/bcftools query -i'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /<>/bcftools query -i'IINT!="."' -f'%POS %IINT\n' /tmp/tiM8I5IySO/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/missing.vcf.gz | /<>/bcftools query -i'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /<>/bcftools query -e'IINT!="."' -f'%POS %IINT\n' /tmp/tiM8I5IySO/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/missing.vcf.gz | /<>/bcftools query -e'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /<>/bcftools query -e'IINT="."' -f'%POS %IINT\n' /tmp/tiM8I5IySO/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/missing.vcf.gz | /<>/bcftools query -e'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /<>/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' /tmp/tiM8I5IySO/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/missing.vcf.gz | /<>/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /<>/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' /tmp/tiM8I5IySO/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/missing.vcf.gz | /<>/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /<>/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' /tmp/tiM8I5IySO/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/missing.vcf.gz | /<>/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /<>/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' /tmp/tiM8I5IySO/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/missing.vcf.gz | /<>/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /<>/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' /tmp/tiM8I5IySO/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/missing.vcf.gz | /<>/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /<>/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' /tmp/tiM8I5IySO/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/missing.vcf.gz | /<>/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /<>/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' /tmp/tiM8I5IySO/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/missing.vcf.gz | /<>/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /<>/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' /tmp/tiM8I5IySO/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/missing.vcf.gz | /<>/bcftools query -i'FILTER="q11"' -f'%POS %ISTR\n' .. ok test_vcf_query: /<>/bcftools query -i'FILTER="A"' -f'%POS %FILTER\n' /tmp/tiM8I5IySO/filter.11.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/filter.11.vcf.gz | /<>/bcftools query -i'FILTER="A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /<>/bcftools query -i'FILTER!="A"' -f'%POS %FILTER\n' /tmp/tiM8I5IySO/filter.11.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/filter.11.vcf.gz | /<>/bcftools query -i'FILTER!="A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /<>/bcftools query -i'FILTER~"A"' -f'%POS %FILTER\n' /tmp/tiM8I5IySO/filter.11.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/filter.11.vcf.gz | /<>/bcftools query -i'FILTER~"A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /<>/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n' /tmp/tiM8I5IySO/filter.11.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/filter.11.vcf.gz | /<>/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /<>/bcftools query -f'%LINE' /tmp/tiM8I5IySO/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/query.vcf.gz | /<>/bcftools query -f'%LINE' .. ok test_vcf_query: /<>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' /tmp/tiM8I5IySO/query.filter-type.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/query.filter-type.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/query.filter-type.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/query.filter-type.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/query.filter-type.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/filter-missing-floats.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/filter-missing-floats.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/query.filter.2.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/filter.5.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/filter.5.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/query.filter.3.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/query.filter.3.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/query.filter.3.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/filter.5.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/query.filter.4.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/view.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/query.filter.5.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/query.filter.5.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/query.filter.5.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/query.negative.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/query.negative.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/query.negative.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/query.negative.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")==1' /tmp/tiM8I5IySO/query.filter.11.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/query.filter.11.vcf.gz | /<>/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")==1' .. ok test_vcf_query: /<>/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")!=1' /tmp/tiM8I5IySO/query.filter.11.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/query.filter.11.vcf.gz | /<>/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -i'N_PASS(GT="alt")!=1' .. ok test_vcf_query: /<>/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")==1' /tmp/tiM8I5IySO/query.filter.11.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/query.filter.11.vcf.gz | /<>/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")==1' .. ok test_vcf_query: /<>/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")!=1' /tmp/tiM8I5IySO/query.filter.11.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/query.filter.11.vcf.gz | /<>/bcftools query -f'[%POS\t%SAMPLE\t%GT\n]' -e'N_PASS(GT="alt")!=1' .. ok test_vcf_query: /<>/bcftools query -f'%CHROM\t%POS\t%INFO\t%FORMAT\n' -s D,C /tmp/tiM8I5IySO/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/query.filter.6.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/query.filter.7.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/query.filter.7.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/query.filter.7.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/query.filter.7.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/query.filter.7.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/query.filter.7.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/query.filter.7.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/query.filter.7.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/query.filter.8.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/query.filter.8.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/query.filter.9.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/query.filter.9.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/query.filter.10.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/query.filter.10.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/query.filter.10.vcf.gz | /<>/bcftools query -f'%POS %STR_TAG\n' -i'COUNT(INFO/STR_TAG)=2' .. ok test_vcf_query: /<>/bcftools query -f '%CHROM:%POS\t%N_PASS(GT="alt" & GQ>110)\t[\t%GT]\t[\t%GQ]\n' /tmp/tiM8I5IySO/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/query.vcf.gz | /<>/bcftools query -f '%CHROM:%POS\t%N_PASS(GT="alt" & GQ>110)\t[\t%GT]\t[\t%GQ]\n' .. ok test_vcf_query: /<>/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 1,3,0 /tmp/tiM8I5IySO/query.filter.12.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/query.filter.12.vcf.gz | /<>/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 1,3,0 .. ok test_vcf_query: /<>/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 0,1,3 /tmp/tiM8I5IySO/query.filter.12.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/tiM8I5IySO/query.filter.12.vcf.gz | /<>/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 0,1,3 .. ok test_vcf_norm: /<>/bcftools norm --no-version -cx -f /<>/test/norm.fa /tmp/tiM8I5IySO/norm.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -cx -f /<>/test/norm.fa /tmp/tiM8I5IySO/norm.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- /tmp/tiM8I5IySO/norm.split.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -m- /tmp/tiM8I5IySO/norm.split.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- /tmp/tiM8I5IySO/norm.split.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -m- /tmp/tiM8I5IySO/norm.split.2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- --force /tmp/tiM8I5IySO/norm.split.3.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -m- --force /tmp/tiM8I5IySO/norm.split.3.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- /tmp/tiM8I5IySO/norm.split.4.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -m- /tmp/tiM8I5IySO/norm.split.4.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- --keep-sum AD /tmp/tiM8I5IySO/norm.split.4.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -m- --keep-sum AD /tmp/tiM8I5IySO/norm.split.4.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- -f /<>/test/norm.fa /tmp/tiM8I5IySO/norm.split.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -m- -f /<>/test/norm.fa /tmp/tiM8I5IySO/norm.split.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m+ /tmp/tiM8I5IySO/norm.merge.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -m+ /tmp/tiM8I5IySO/norm.merge.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m+ /tmp/tiM8I5IySO/norm.merge.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -m+ /tmp/tiM8I5IySO/norm.merge.2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m+ /tmp/tiM8I5IySO/norm.merge.3.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -m+ /tmp/tiM8I5IySO/norm.merge.3.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m+ -s /tmp/tiM8I5IySO/norm.merge.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -m+ -s /tmp/tiM8I5IySO/norm.merge.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -Nc s -f /<>/test/norm.fa /tmp/tiM8I5IySO/norm.setref.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -Nc s -f /<>/test/norm.fa /tmp/tiM8I5IySO/norm.setref.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -f /<>/test/norm.fa /tmp/tiM8I5IySO/norm.telomere.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -f /<>/test/norm.fa /tmp/tiM8I5IySO/norm.telomere.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d snps /tmp/tiM8I5IySO/norm.rmdup.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -d snps /tmp/tiM8I5IySO/norm.rmdup.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d indels /tmp/tiM8I5IySO/norm.rmdup.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -d indels /tmp/tiM8I5IySO/norm.rmdup.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d both /tmp/tiM8I5IySO/norm.rmdup.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -d both /tmp/tiM8I5IySO/norm.rmdup.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d all /tmp/tiM8I5IySO/norm.rmdup.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -d all /tmp/tiM8I5IySO/norm.rmdup.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d none /tmp/tiM8I5IySO/norm.rmdup.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -d none /tmp/tiM8I5IySO/norm.rmdup.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d exact /tmp/tiM8I5IySO/norm.rmdup.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -d exact /tmp/tiM8I5IySO/norm.rmdup.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d none /tmp/tiM8I5IySO/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -d none /tmp/tiM8I5IySO/norm.rmdup.2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d exact /tmp/tiM8I5IySO/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -d exact /tmp/tiM8I5IySO/norm.rmdup.2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d indels /tmp/tiM8I5IySO/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -d indels /tmp/tiM8I5IySO/norm.rmdup.2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d any /tmp/tiM8I5IySO/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -d any /tmp/tiM8I5IySO/norm.rmdup.2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d both /tmp/tiM8I5IySO/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -d both /tmp/tiM8I5IySO/norm.rmdup.2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d snps /tmp/tiM8I5IySO/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -d snps /tmp/tiM8I5IySO/norm.rmdup.2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -f /<>/test/norm.2.fa /tmp/tiM8I5IySO/norm.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -f /<>/test/norm.2.fa /tmp/tiM8I5IySO/norm.2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -c s -f /<>/test/norm.iupac.fa /tmp/tiM8I5IySO/norm.iupac.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -c s -f /<>/test/norm.iupac.fa /tmp/tiM8I5IySO/norm.iupac.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -c s -f /<>/test/norm.3.fa /tmp/tiM8I5IySO/norm.3.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob -c s -f /<>/test/norm.3.fa /tmp/tiM8I5IySO/norm.3.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/tiM8I5IySO/atomize.split.1.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob --atomize --old-rec-tag OLD_REC /tmp/tiM8I5IySO/atomize.split.1.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/tiM8I5IySO/atomize.split.1.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/tiM8I5IySO/atomize.split.1.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/tiM8I5IySO/atomize.split.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob --atomize --old-rec-tag OLD_REC /tmp/tiM8I5IySO/atomize.split.2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/tiM8I5IySO/atomize.split.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm -Ob --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/tiM8I5IySO/atomize.split.2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -aUc1 -C1 -s NA00002 -v snps /tmp/tiM8I5IySO/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/tiM8I5IySO/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -f PASS -Xks NA00003 /tmp/tiM8I5IySO/view.vcf.gz -r20,Y .. ok test_vcf_view: /<>/bcftools view -Ob -f PASS -Xks NA00003 /tmp/tiM8I5IySO/view.vcf.gz -r20,Y | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -xs NA00003 /tmp/tiM8I5IySO/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -xs NA00003 /tmp/tiM8I5IySO/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/tiM8I5IySO/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/tiM8I5IySO/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -p /tmp/tiM8I5IySO/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -p /tmp/tiM8I5IySO/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -P /tmp/tiM8I5IySO/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -P /tmp/tiM8I5IySO/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -hm2 -M2 -q0.3 -Q0.7 /tmp/tiM8I5IySO/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/tiM8I5IySO/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -Hu /tmp/tiM8I5IySO/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -GVsnps /tmp/tiM8I5IySO/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -GVsnps /tmp/tiM8I5IySO/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -ne 'INDEL=1 || PV4[0]<0.006' /tmp/tiM8I5IySO/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/tiM8I5IySO/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -s ^NA00003 /tmp/tiM8I5IySO/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -s ^NA00003 /tmp/tiM8I5IySO/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version /tmp/tiM8I5IySO/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob /tmp/tiM8I5IySO/view.omitgenotypes.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -G /tmp/tiM8I5IySO/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -G /tmp/tiM8I5IySO/view.omitgenotypes.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -HG /tmp/tiM8I5IySO/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -a /tmp/tiM8I5IySO/many.alleles.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -a /tmp/tiM8I5IySO/many.alleles.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -asA /tmp/tiM8I5IySO/view.vectors.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -asA /tmp/tiM8I5IySO/view.vectors.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -asB /tmp/tiM8I5IySO/view.vectors.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -asB /tmp/tiM8I5IySO/view.vectors.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -asA /tmp/tiM8I5IySO/view.vectors.2.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -asA /tmp/tiM8I5IySO/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/tiM8I5IySO/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'FMT/FGS[*:2]="C"' /tmp/tiM8I5IySO/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'FMT/FGS[*:4]="EE"' /tmp/tiM8I5IySO/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'FMT/FRS[*:1]="BB"' /tmp/tiM8I5IySO/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'TXT0="text"' /tmp/tiM8I5IySO/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -T /<>/test/view.chrs.tab /tmp/tiM8I5IySO/view.chrs.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -T /<>/test/view.chrs.tab /tmp/tiM8I5IySO/view.chrs.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -i 'POS>=3062917' /tmp/tiM8I5IySO/filter.2.vcf.gz 1:3062917-3157410 .. ok test_vcf_view: /<>/bcftools view -Ob -i 'POS>=3062917' /tmp/tiM8I5IySO/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/tiM8I5IySO/idx.1.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -r 1:1172777-1172804,1:1172806-1172808 /tmp/tiM8I5IySO/idx.2.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -R /<>/test/idx.2.bed /tmp/tiM8I5IySO/idx.2.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -R /<>/test/idx.3.bed /tmp/tiM8I5IySO/idx.3.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -R /<>/test/idx.4.bed /tmp/tiM8I5IySO/idx.4.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -Ht 2 /tmp/tiM8I5IySO/view-t.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -Ht 3 /tmp/tiM8I5IySO/view-t.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_view: /<>/bcftools view --no-version -H -C5:nonmajor /tmp/tiM8I5IySO/view.minmaxac.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -c6:nonmajor /tmp/tiM8I5IySO/view.minmaxac.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -q0.3:major /tmp/tiM8I5IySO/view.minmaxac.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/tiM8I5IySO/view.filter.annovar.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i 'Gene.refGene~"NOD"' /tmp/tiM8I5IySO/view.filter.annovar.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i 'LJB2_MutationTaster=="0.291000"' /tmp/tiM8I5IySO/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 - --group-samples-tag AD /<>/test/mpileup.NA19213.NA19129.vcf .. ok test_vcf_call: /<>/bcftools call -Ob -mv -G - --group-samples-tag AD /<>/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 - --group-samples-tag AD /<>/test/mpileup.hwe.vcf .. ok test_vcf_call: /<>/bcftools call -Ob -mv -G - --group-samples-tag AD /<>/test/mpileup.hwe.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /<>/bcftools call --no-version -mv -G /<>/test/mpileup.hwe.samples --group-samples-tag AD /<>/test/mpileup.hwe.vcf .. ok test_vcf_call: /<>/bcftools call -Ob -mv -G /<>/test/mpileup.hwe.samples --group-samples-tag AD /<>/test/mpileup.hwe.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call_cAls: /<>/bcftools call --no-version -mA -C alleles -T /tmp/tiM8I5IySO/mpileup.tab.gz /<>/test/mpileup.vcf .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/tiM8I5IySO/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/tiM8I5IySO/mpileup.2.tab.gz /<>/test/mpileup.2.vcf .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/tiM8I5IySO/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/tiM8I5IySO/mpileup.3.tab.gz -i /<>/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/tiM8I5IySO/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/tiM8I5IySO/mpileup.4.tab.gz -i /<>/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/tiM8I5IySO/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/tiM8I5IySO/mpileup.5.tab.gz -i /<>/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/tiM8I5IySO/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/tiM8I5IySO/mpileup.6.tab.gz -i /<>/test/mpileup.4.vcf .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/tiM8I5IySO/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/tiM8I5IySO/mpileup.7.tab.gz -i /<>/test/mpileup.5.vcf .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/tiM8I5IySO/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/tiM8I5IySO/mpileup.cals.1.tab.gz /<>/test/mpileup.cals.1.vcf .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/tiM8I5IySO/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/tiM8I5IySO/mpileup.cals.2.tab.gz /<>/test/mpileup.cals.2.vcf .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/tiM8I5IySO/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_call: /<>/bcftools call --no-version -mv /<>/test/call-G.vcf .. ok test_vcf_call: /<>/bcftools call -Ob -mv /<>/test/call-G.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /<>/bcftools call --no-version -mv -G - --group-samples-tag AD /<>/test/call-G.vcf .. ok test_vcf_call: /<>/bcftools call -Ob -mv -G - --group-samples-tag AD /<>/test/call-G.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /<>/bcftools call --no-version -mv -F AN_POP,AC_POP /<>/test/call-G.2.vcf .. ok test_vcf_call: /<>/bcftools call -Ob -mv -F AN_POP,AC_POP /<>/test/call-G.2.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /<>/bcftools call --no-version -m /<>/test/call.af-fixation.vcf .. ok test_vcf_call: /<>/bcftools call -Ob -m /<>/test/call.af-fixation.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /<>/bcftools call --no-version -m -G /<>/test/call.af-fixation.txt /<>/test/call.af-fixation.vcf .. ok test_vcf_call: /<>/bcftools call -Ob -m -G /<>/test/call.af-fixation.txt /<>/test/call.af-fixation.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_call: /<>/bcftools call --no-version -m -G /<>/test/call.af-fixation.txt -a GP,GQ /<>/test/call.af-fixation.vcf .. ok test_vcf_call: /<>/bcftools call -Ob -m -G /<>/test/call.af-fixation.txt -a GP,GQ /<>/test/call.af-fixation.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. 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_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_filter: /<>/bcftools filter -mx -s + -g2:mnp,indel,other /<>/test/filter.7.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -mx -s + -g2:mnp,indel,other /<>/test/filter.7.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S . -e 'FORMAT/AO==4' /<>/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S . -e 'FORMAT/AO==4' /<>/test/filter.8.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S . -e 'MAX(FORMAT/AO[0:])==4' /<>/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S . -e 'MAX(FORMAT/AO[0:])==4' /<>/test/filter.8.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S . -e 'MAX(FORMAT/AO)==4' /<>/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S . -e 'MAX(FORMAT/AO)==4' /<>/test/filter.8.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S . -e 'MIN(FORMAT/AO[0:])==3' /<>/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO[0:])==3' /<>/test/filter.8.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S . -e 'MIN(FORMAT/AO)==2' /<>/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO)==2' /<>/test/filter.8.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S . -e 'MIN(FORMAT/AO[0:])==3' /<>/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S . -e 'MIN(FORMAT/AO[0:])==3' /<>/test/filter.8.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S . -e 'AVG(FORMAT/AO[2:])==4' /<>/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S . -e 'AVG(FORMAT/AO[2:])==4' /<>/test/filter.8.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S . -e 'MEDIAN(FORMAT/AO[2:])==4' /<>/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S . -e 'MEDIAN(FORMAT/AO[2:])==4' /<>/test/filter.8.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S . -e 'STDEV(FORMAT/AO[0:])=0.5' /<>/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S . -e 'STDEV(FORMAT/AO[0:])=0.5' /<>/test/filter.8.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S . -e 'SUM(FORMAT/AO[0:])=7' /<>/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S . -e 'SUM(FORMAT/AO[0:])=7' /<>/test/filter.8.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S . -e 'SMPL_MAX(FORMAT/AO)==4' /<>/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S . -e 'SMPL_MAX(FORMAT/AO)==4' /<>/test/filter.8.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S . -e 'sMIN(FORMAT/AO)==2' /<>/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S . -e 'sMIN(FORMAT/AO)==2' /<>/test/filter.8.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S . -e 'ABS(sAVG(FORMAT/AO)-3.66666)<1e-5' /<>/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S . -e 'ABS(sAVG(FORMAT/AO)-3.66666)<1e-5' /<>/test/filter.8.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S . -e 'sMEDIAN(FORMAT/AO)==4' /<>/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S . -e 'sMEDIAN(FORMAT/AO)==4' /<>/test/filter.8.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S . -e 'ABS(sSTDEV(FORMAT/AO)-1.2472191)<1e-5' /<>/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S . -e 'ABS(sSTDEV(FORMAT/AO)-1.2472191)<1e-5' /<>/test/filter.8.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S . -e 'sSUM(FORMAT/AO)==11' /<>/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S . -e 'sSUM(FORMAT/AO)==11' /<>/test/filter.8.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -i 'QUAL/FMT/AD==55' /<>/test/filter.9.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -i 'QUAL/FMT/AD==55' /<>/test/filter.9.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -i 'QUAL/INFO/AD==10' /<>/test/filter.9.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -i 'QUAL/INFO/AD==10' /<>/test/filter.9.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S . -e 'ABS(SMPL_MAX(FORMAT/AO))=5' /<>/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S . -e 'ABS(SMPL_MAX(FORMAT/AO))=5' /<>/test/filter.8.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S . -e 'PHRED(AO[1:])>-4' /<>/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S . -e 'PHRED(AO[1:])>-4' /<>/test/filter.8.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -S . -e 'ABS(AO[1:])==2' /<>/test/filter.8.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -S . -e 'ABS(AO[1:])==2' /<>/test/filter.8.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -i 'sum(AD[*]) > FORMAT/DP' /<>/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -i 'sum(AD[*]) > FORMAT/DP' /<>/test/filter.10.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -i 'FORMAT/DP < sum(AD[*])' /<>/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -i 'FORMAT/DP < sum(AD[*])' /<>/test/filter.10.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -i 'sum(AD[*]) < FORMAT/DP' /<>/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -i 'sum(AD[*]) < FORMAT/DP' /<>/test/filter.10.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -i 'FORMAT/DP > sum(AD[*])' /<>/test/filter.10.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob -i 'FORMAT/DP > sum(AD[*])' /<>/test/filter.10.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. 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/tiM8I5IySO/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/tiM8I5IySO/regions.tab.gz /tmp/tiM8I5IySO/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/tiM8I5IySO/regions.vcf.gz | /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/tiM8I5IySO/regions.tab.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/tiM8I5IySO/regions.tab.gz /tmp/tiM8I5IySO/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/tiM8I5IySO/regions.bed /tmp/tiM8I5IySO/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/tiM8I5IySO/regions.vcf.gz | /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/tiM8I5IySO/regions.bed .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/tiM8I5IySO/regions.bed /tmp/tiM8I5IySO/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/tiM8I5IySO/regions.bed.gz /tmp/tiM8I5IySO/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/tiM8I5IySO/regions.vcf.gz | /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/tiM8I5IySO/regions.bed.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/tiM8I5IySO/regions.bed.gz /tmp/tiM8I5IySO/regions.vcf.gz .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/tiM8I5IySO/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/tiM8I5IySO/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/tiM8I5IySO/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/tiM8I5IySO/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/tiM8I5IySO/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/tiM8I5IySO/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/tiM8I5IySO/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/tiM8I5IySO/annotate.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/tiM8I5IySO/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/tiM8I5IySO/annotate.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/tiM8I5IySO/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/tiM8I5IySO/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/tiM8I5IySO/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/tiM8I5IySO/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/tiM8I5IySO/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/tiM8I5IySO/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/tiM8I5IySO/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/tiM8I5IySO/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/tiM8I5IySO/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/tiM8I5IySO/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/tiM8I5IySO/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/tiM8I5IySO/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/tiM8I5IySO/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/tiM8I5IySO/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/tiM8I5IySO/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/tiM8I5IySO/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/tiM8I5IySO/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/tiM8I5IySO/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/tiM8I5IySO/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/tiM8I5IySO/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/tiM8I5IySO/annots4.vcf.gz -c +INFO /tmp/tiM8I5IySO/annotate4.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/tiM8I5IySO/annots4.vcf.gz -c +INFO /tmp/tiM8I5IySO/annotate4.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/tiM8I5IySO/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/tiM8I5IySO/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/tiM8I5IySO/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/tiM8I5IySO/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/tiM8I5IySO/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/tiM8I5IySO/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/tiM8I5IySO/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/tiM8I5IySO/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/tiM8I5IySO/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/tiM8I5IySO/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/tiM8I5IySO/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/tiM8I5IySO/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/tiM8I5IySO/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/tiM8I5IySO/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/tiM8I5IySO/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/tiM8I5IySO/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/tiM8I5IySO/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/tiM8I5IySO/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/tiM8I5IySO/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/tiM8I5IySO/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/tiM8I5IySO/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/tiM8I5IySO/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/tiM8I5IySO/annots11.vcf.gz -c FMT /tmp/tiM8I5IySO/annotate11.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/tiM8I5IySO/annots11.vcf.gz -c FMT /tmp/tiM8I5IySO/annotate11.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/tiM8I5IySO/annots2.vcf.gz -c FMT/newGT:=GT /tmp/tiM8I5IySO/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/tiM8I5IySO/annots2.vcf.gz -c FMT/newGT:=GT /tmp/tiM8I5IySO/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/tiM8I5IySO/annots12.vcf.gz -c FMT/GT:=newGT /tmp/tiM8I5IySO/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/tiM8I5IySO/annots12.vcf.gz -c FMT/GT:=newGT /tmp/tiM8I5IySO/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/tiM8I5IySO/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/tiM8I5IySO/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/tiM8I5IySO/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/tiM8I5IySO/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/tiM8I5IySO/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/tiM8I5IySO/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/tiM8I5IySO/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/tiM8I5IySO/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/tiM8I5IySO/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/tiM8I5IySO/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/tiM8I5IySO/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/tiM8I5IySO/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/tiM8I5IySO/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/tiM8I5IySO/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/tiM8I5IySO/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/tiM8I5IySO/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/tiM8I5IySO/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/tiM8I5IySO/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/tiM8I5IySO/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/tiM8I5IySO/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/tiM8I5IySO/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/tiM8I5IySO/annotate19.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/tiM8I5IySO/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/tiM8I5IySO/annotate19.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/tiM8I5IySO/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/tiM8I5IySO/annotate19.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/tiM8I5IySO/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/tiM8I5IySO/annotate19.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/tiM8I5IySO/annotate20.src.vcf.gz -c FMT/GT /tmp/tiM8I5IySO/annotate20.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/tiM8I5IySO/annotate20.src.vcf.gz -c FMT/GT /tmp/tiM8I5IySO/annotate20.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/tiM8I5IySO/annotate20.src.vcf.gz -c +FMT/GT /tmp/tiM8I5IySO/annotate20.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/tiM8I5IySO/annotate20.src.vcf.gz -c +FMT/GT /tmp/tiM8I5IySO/annotate20.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/tiM8I5IySO/annotate20.src.vcf.gz -c -FMT/GT /tmp/tiM8I5IySO/annotate20.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/tiM8I5IySO/annotate20.src.vcf.gz -c -FMT/GT /tmp/tiM8I5IySO/annotate20.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/tiM8I5IySO/annotate.multi.tab.gz -c CHROM,POS,REF,ALT,ANN -l ANN:append /<>/test/annotate.multi.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/tiM8I5IySO/annotate.multi.tab.gz -c CHROM,POS,REF,ALT,ANN -l ANN:append /<>/test/annotate.multi.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/tiM8I5IySO/annotate.missing-append.tab.gz -c CHROM,POS,REF,ALT,STR,INT,FLT -l STR:append-missing,INT:append-missing,FLT:append-missing /<>/test/annotate.missing-append.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/tiM8I5IySO/annotate.missing-append.tab.gz -c CHROM,POS,REF,ALT,STR,INT,FLT -l STR:append-missing,INT:append-missing,FLT:append-missing /<>/test/annotate.missing-append.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/tiM8I5IySO/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/tiM8I5IySO/annots9.tab.gz -c CHROM,POS,REF,ALT,+ID /<>/test/annotate9.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate --rename-annots /<>/test/annotate21.txt /<>/test/annotate21.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob --rename-annots /<>/test/annotate21.txt /<>/test/annotate21.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/tiM8I5IySO/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/tiM8I5IySO/annotate22.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/tiM8I5IySO/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/tiM8I5IySO/annotate22.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/tiM8I5IySO/annotate23.tab.gz -c CHROM,POS,~ID,REF,ALT,INFO/END /<>/test/annotate23.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/tiM8I5IySO/annotate23.tab.gz -c CHROM,POS,~ID,REF,ALT,INFO/END /<>/test/annotate23.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version /tmp/tiM8I5IySO/concat.1.a.vcf.gz /tmp/tiM8I5IySO/concat.1.b.vcf.gz .. ok test_vcf_concat: /<>/bcftools concat -Ob /tmp/tiM8I5IySO/concat.1.a.vcf.gz /tmp/tiM8I5IySO/concat.1.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version /tmp/tiM8I5IySO/concat.1.a.bcf /tmp/tiM8I5IySO/concat.1.b.bcf .. ok test_vcf_concat: /<>/bcftools concat -Ob /tmp/tiM8I5IySO/concat.1.a.bcf /tmp/tiM8I5IySO/concat.1.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -a /tmp/tiM8I5IySO/concat.2.a.vcf.gz /tmp/tiM8I5IySO/concat.2.b.vcf.gz .. ok test_vcf_concat: /<>/bcftools concat -Ob -a /tmp/tiM8I5IySO/concat.2.a.vcf.gz /tmp/tiM8I5IySO/concat.2.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -a /tmp/tiM8I5IySO/concat.2.a.bcf /tmp/tiM8I5IySO/concat.2.b.bcf .. ok test_vcf_concat: /<>/bcftools concat -Ob -a /tmp/tiM8I5IySO/concat.2.a.bcf /tmp/tiM8I5IySO/concat.2.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -aD /tmp/tiM8I5IySO/concat.2.a.vcf.gz /tmp/tiM8I5IySO/concat.2.b.vcf.gz .. ok test_vcf_concat: /<>/bcftools concat -Ob -aD /tmp/tiM8I5IySO/concat.2.a.vcf.gz /tmp/tiM8I5IySO/concat.2.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -aD /tmp/tiM8I5IySO/concat.2.a.bcf /tmp/tiM8I5IySO/concat.2.b.bcf .. ok test_vcf_concat: /<>/bcftools concat -Ob -aD /tmp/tiM8I5IySO/concat.2.a.bcf /tmp/tiM8I5IySO/concat.2.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -l /tmp/tiM8I5IySO/concat.3.a.vcf.gz /tmp/tiM8I5IySO/concat.3.b.vcf.gz /tmp/tiM8I5IySO/concat.3.0.vcf.gz /tmp/tiM8I5IySO/concat.3.c.vcf.gz /tmp/tiM8I5IySO/concat.3.d.vcf.gz /tmp/tiM8I5IySO/concat.3.e.vcf.gz /tmp/tiM8I5IySO/concat.3.f.vcf.gz .. ok test_vcf_concat: /<>/bcftools concat -Ob -l /tmp/tiM8I5IySO/concat.3.a.vcf.gz /tmp/tiM8I5IySO/concat.3.b.vcf.gz /tmp/tiM8I5IySO/concat.3.0.vcf.gz /tmp/tiM8I5IySO/concat.3.c.vcf.gz /tmp/tiM8I5IySO/concat.3.d.vcf.gz /tmp/tiM8I5IySO/concat.3.e.vcf.gz /tmp/tiM8I5IySO/concat.3.f.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -l /tmp/tiM8I5IySO/concat.3.a.bcf /tmp/tiM8I5IySO/concat.3.b.bcf /tmp/tiM8I5IySO/concat.3.0.bcf /tmp/tiM8I5IySO/concat.3.c.bcf /tmp/tiM8I5IySO/concat.3.d.bcf /tmp/tiM8I5IySO/concat.3.e.bcf /tmp/tiM8I5IySO/concat.3.f.bcf .. ok test_vcf_concat: /<>/bcftools concat -Ob -l /tmp/tiM8I5IySO/concat.3.a.bcf /tmp/tiM8I5IySO/concat.3.b.bcf /tmp/tiM8I5IySO/concat.3.0.bcf /tmp/tiM8I5IySO/concat.3.c.bcf /tmp/tiM8I5IySO/concat.3.d.bcf /tmp/tiM8I5IySO/concat.3.e.bcf /tmp/tiM8I5IySO/concat.3.f.bcf | /<>/bcftools view | grep -v ^##bcftools_ Random seed for test_naive_concat: 267751242 .. ok test_naive_concat: /<>/bcftools concat --naive-force /tmp/tiM8I5IySO/naive_concat.0.bcf /tmp/tiM8I5IySO/naive_concat.1.bcf /tmp/tiM8I5IySO/naive_concat.2.bcf /tmp/tiM8I5IySO/naive_concat.3.bcf /tmp/tiM8I5IySO/naive_concat.4.bcf /tmp/tiM8I5IySO/naive_concat.5.bcf /tmp/tiM8I5IySO/naive_concat.6.bcf /tmp/tiM8I5IySO/naive_concat.7.bcf /tmp/tiM8I5IySO/naive_concat.8.bcf /tmp/tiM8I5IySO/naive_concat.9.bcf | /<>/bcftools view -H .. ok test_naive_concat: /<>/bcftools concat --naive /tmp/tiM8I5IySO/naive_concat.0.vcf.gz /tmp/tiM8I5IySO/naive_concat.1.vcf.gz /tmp/tiM8I5IySO/naive_concat.2.vcf.gz /tmp/tiM8I5IySO/naive_concat.3.vcf.gz /tmp/tiM8I5IySO/naive_concat.4.vcf.gz /tmp/tiM8I5IySO/naive_concat.5.vcf.gz /tmp/tiM8I5IySO/naive_concat.6.vcf.gz /tmp/tiM8I5IySO/naive_concat.7.vcf.gz /tmp/tiM8I5IySO/naive_concat.8.vcf.gz /tmp/tiM8I5IySO/naive_concat.9.vcf.gz | /<>/bcftools view -H .. ok test_vcf_concat: /<>/bcftools concat --no-version -l /tmp/tiM8I5IySO/concat.4.a.vcf.gz /tmp/tiM8I5IySO/concat.4.b.vcf.gz .. ok test_vcf_concat: /<>/bcftools concat -Ob -l /tmp/tiM8I5IySO/concat.4.a.vcf.gz /tmp/tiM8I5IySO/concat.4.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -l /tmp/tiM8I5IySO/concat.4.a.bcf /tmp/tiM8I5IySO/concat.4.b.bcf .. ok test_vcf_concat: /<>/bcftools concat -Ob -l /tmp/tiM8I5IySO/concat.4.a.bcf /tmp/tiM8I5IySO/concat.4.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. 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/tiM8I5IySO/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/tiM8I5IySO/reheader.bcf | /<>/bcftools reheader -h /<>/test/reheader.hdr | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -h /<>/test/reheader.hdr /tmp/tiM8I5IySO/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/tiM8I5IySO/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/tiM8I5IySO/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/tiM8I5IySO/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples /tmp/tiM8I5IySO/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/tiM8I5IySO/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/tiM8I5IySO/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/tiM8I5IySO/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples2 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples2 /tmp/tiM8I5IySO/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/tiM8I5IySO/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/tiM8I5IySO/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/tiM8I5IySO/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples3 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples3 /tmp/tiM8I5IySO/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/tiM8I5IySO/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/tiM8I5IySO/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/tiM8I5IySO/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples4 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples4 /tmp/tiM8I5IySO/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/tiM8I5IySO/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/tiM8I5IySO/empty.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/tiM8I5IySO/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/tiM8I5IySO/empty.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/tiM8I5IySO/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/tiM8I5IySO/reheader.2.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -f /<>/test/reheader.fai /tmp/tiM8I5IySO/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/tiM8I5IySO/reheader.2.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -h /<>/test/reheader.2.hdr -f /<>/test/reheader.fai /tmp/tiM8I5IySO/reheader.2.vcf.gz | /<>/bcftools view --no-version .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/tiM8I5IySO/rename.map -Ov /tmp/tiM8I5IySO/annotate.bcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/tiM8I5IySO/rename.map -Ob /tmp/tiM8I5IySO/annotate.bcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/tiM8I5IySO/rename.map -Ov /<>/test/annotate.vcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/tiM8I5IySO/rename.map -Ob /<>/test/annotate.vcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_vcf_convert: /<>/bcftools convert -g -,. /tmp/tiM8I5IySO/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/tiM8I5IySO/convert.vcf.gz | /<>/bcftools convert -g -,. .. ok test_vcf_convert: /<>/bcftools convert -g .,- /tmp/tiM8I5IySO/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/tiM8I5IySO/convert.vcf.gz | /<>/bcftools convert -g .,- .. ok test_vcf_convert: /<>/bcftools convert -g -,. --tag PL /tmp/tiM8I5IySO/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/tiM8I5IySO/convert.vcf.gz | /<>/bcftools convert -g -,. --tag PL .. ok test_vcf_convert: /<>/bcftools convert -g .,- --tag PL /tmp/tiM8I5IySO/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/tiM8I5IySO/convert.vcf.gz | /<>/bcftools convert -g .,- --tag PL .. ok test_vcf_convert: /<>/bcftools convert -g -,. --vcf-ids /tmp/tiM8I5IySO/check.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/tiM8I5IySO/check.vcf.gz | /<>/bcftools convert -g -,. --vcf-ids .. ok test_vcf_convert: /<>/bcftools convert -g .,- --vcf-ids /tmp/tiM8I5IySO/check.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/tiM8I5IySO/check.vcf.gz | /<>/bcftools convert -g .,- --vcf-ids .. ok test_vcf_convert: /<>/bcftools convert -g -,. --chrom /tmp/tiM8I5IySO/check.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/tiM8I5IySO/check.vcf.gz | /<>/bcftools convert -g -,. --chrom .. ok test_vcf_convert: /<>/bcftools convert -g .,- --chrom /tmp/tiM8I5IySO/check.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/tiM8I5IySO/check.vcf.gz | /<>/bcftools convert -g .,- --chrom .. ok test_vcf_convert: /<>/bcftools convert -g -,. --chrom --vcf-ids /tmp/tiM8I5IySO/check.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/tiM8I5IySO/check.vcf.gz | /<>/bcftools convert -g -,. --chrom --vcf-ids .. ok test_vcf_convert: /<>/bcftools convert -g .,- --chrom --vcf-ids /tmp/tiM8I5IySO/check.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/tiM8I5IySO/check.vcf.gz | /<>/bcftools convert -g .,- --chrom --vcf-ids .. ok test_vcf_convert: /<>/bcftools convert -h -,.,. /tmp/tiM8I5IySO/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/tiM8I5IySO/convert.vcf.gz | /<>/bcftools convert -h -,.,. .. ok test_vcf_convert: /<>/bcftools convert -h .,-,. /tmp/tiM8I5IySO/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/tiM8I5IySO/convert.vcf.gz | /<>/bcftools convert -h .,-,. .. ok test_vcf_convert: /<>/bcftools convert -h .,.,- /tmp/tiM8I5IySO/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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_hls2vcf: /<>/bcftools convert --vcf-ids -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 --vcf-ids -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_hs2vcf: /<>/bcftools convert --vcf-ids --hapsample2vcf /<>/test/convert.hs.gt.hap,/<>/test/convert.hs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /<>/bcftools convert --vcf-ids --hapsample2vcf /<>/test/convert.hs.gt.hap,/<>/test/convert.hs.gt.samples -Ou | /<>/bcftools view | grep -v ^## .. ok test_vcf_convert: /<>/bcftools convert --hapsample -,. /tmp/tiM8I5IySO/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/tiM8I5IySO/convert.vcf.gz | /<>/bcftools convert --hapsample -,. .. ok test_vcf_convert: /<>/bcftools convert --hapsample .,- /tmp/tiM8I5IySO/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/tiM8I5IySO/convert.vcf.gz | /<>/bcftools convert --hapsample .,- .. ok test_vcf_convert: /<>/bcftools convert --haplegendsample -,.,. /tmp/tiM8I5IySO/convert.hap-missing.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/convert.gvcf.vcf.gz .. ok test_vcf_convert_gvcf: /<>/bcftools view -Ob /tmp/tiM8I5IySO/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/tiM8I5IySO/consensus.vcf.gz -f /<>/test/consensus.fa -m /<>/test/consensus.tab .. ok test_vcf_consensus_chain: /<>/bcftools consensus /tmp/tiM8I5IySO/consensus.vcf.gz -f /<>/test/consensus.fa -m /<>/test/consensus.tab -c /tmp/tiM8I5IySO/consensus.1.chain.new >/dev/null; cat /tmp/tiM8I5IySO/consensus.1.chain.new .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/tiM8I5IySO/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 -m /<>/test/consensus.tab .. ok test_vcf_consensus_chain: /<>/bcftools consensus /tmp/tiM8I5IySO/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 -m /<>/test/consensus.tab -c /tmp/tiM8I5IySO/consensus.2.chain.new >/dev/null; cat /tmp/tiM8I5IySO/consensus.2.chain.new .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/tiM8I5IySO/consensus.vcf.gz -f /<>/test/consensus.fa -I -m /<>/test/consensus.tab .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/tiM8I5IySO/consensus.vcf.gz -f /<>/test/consensus.fa -I -m /<>/test/consensus.tab --mask-with X -m /<>/test/consensus.tab --mask-with lc .. ok test_vcf_consensus_chain: /<>/bcftools consensus /tmp/tiM8I5IySO/consensus.vcf.gz -f /<>/test/consensus.fa -I -m /<>/test/consensus.tab -c /tmp/tiM8I5IySO/consensus.3.chain.new >/dev/null; cat /tmp/tiM8I5IySO/consensus.3.chain.new .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/tiM8I5IySO/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 .. ok test_vcf_consensus_chain: /<>/bcftools consensus /tmp/tiM8I5IySO/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 -c /tmp/tiM8I5IySO/consensus.4.chain.new >/dev/null; cat /tmp/tiM8I5IySO/consensus.4.chain.new .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/tiM8I5IySO/consensus2.vcf.gz -f /<>/test/consensus2.fa -H 1 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/tiM8I5IySO/consensus2.vcf.gz -f /<>/test/consensus2.fa -H 2 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/tiM8I5IySO/empty.vcf.gz -f /<>/test/consensus.fa .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/tiM8I5IySO/consensus3.vcf.gz -f /<>/test/consensus2.fa -H 2 -M "?" .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/tiM8I5IySO/consensus3.vcf.gz -f /<>/test/consensus2.fa -H 2 -M "?" -p xx_ .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/tiM8I5IySO/consensus4.vcf.gz -f /<>/test/consensus2.fa .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/tiM8I5IySO/consensus5.vcf.gz -f /<>/test/consensus5.fa --haplotype LA .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/tiM8I5IySO/consensus6.vcf.gz -f /<>/test/consensus6.fa .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/tiM8I5IySO/consensus7.vcf.gz -f /<>/test/consensus7.fa -H 2 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/tiM8I5IySO/consensus7.vcf.gz -f /<>/test/consensus7.fa -H 2pIu .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/tiM8I5IySO/consensus7.vcf.gz -f /<>/test/consensus7.fa -H 1 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/tiM8I5IySO/consensus7.vcf.gz -f /<>/test/consensus7.fa -H 1pIu .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/tiM8I5IySO/consensus8.vcf.gz -f /<>/test/consensus.fa .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/tiM8I5IySO/consensus8.vcf.gz -f /<>/test/consensus.fa -a . .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/tiM8I5IySO/consensus8.vcf.gz -f /<>/test/consensus.fa -a . -i 'type="snp" || type="ref"' .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/tiM8I5IySO/consensus8.vcf.gz -f /<>/test/consensus.fa -a . -i 'ALT!=""' .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/tiM8I5IySO/consensus8.vcf.gz -f /<>/test/consensus.fa -a . -e 'MinDP>15' .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/tiM8I5IySO/consensus8.vcf.gz -f /<>/test/consensus.fa -a . -e 'MinDP<15' .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/tiM8I5IySO/consensus.9.vcf.gz -f /<>/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/tiM8I5IySO/consensus.9.vcf.gz -f /<>/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/tiM8I5IySO/consensus.10.vcf.gz -f /<>/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/tiM8I5IySO/consensus.10.vcf.gz -f /<>/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/tiM8I5IySO/consensus.11.vcf.gz -f /<>/test/consensus.11.fa -s smpl .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/tiM8I5IySO/consensus.11.vcf.gz -f /<>/test/consensus.11.fa -s smpl -a N .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/tiM8I5IySO/consensus.12.vcf.gz -f /<>/test/consensus.12.fa .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/tiM8I5IySO/consensus.13.vcf.gz -f /<>/test/consensus.13.fa .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/tiM8I5IySO/consensus.14.vcf.gz -f /<>/test/consensus.14.fa .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/tiM8I5IySO/consensus.12.vcf.gz -f /<>/test/consensus.12.fa --mark-del - --mark-ins uc --mark-snv uc .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/tiM8I5IySO/consensus.15.vcf.gz -f /<>/test/consensus.15.fa -H I --mark-ins lc --mark-snv lc .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/tiM8I5IySO/consensus.16.vcf.gz -f /<>/test/consensus.fa -I .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/tiM8I5IySO/consensus.16.vcf.gz -f /<>/test/consensus.fa -H I .. 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/tiM8I5IySO/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/tiM8I5IySO/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/tiM8I5IySO/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/tiM8I5IySO/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 AD -r 11:75 -f /<>/test/mpileup/indel-AD.2.fa /<>/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a AD -r 11:75 -f /<>/test/mpileup/indel-AD.2.fa -Ob /<>/test/mpileup/indel-AD.2.bam | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a AD -r 11:75 -f /<>/test/mpileup/indel-AD.2.fa /<>/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a AD -r 11:75 -f /<>/test/mpileup/indel-AD.2.fa -Ob /<>/test/mpileup/indel-AD.2.cram | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /<>/test/mpileup/indel-AD.2.fa /<>/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /<>/test/mpileup/indel-AD.2.fa -Ob /<>/test/mpileup/indel-AD.2.bam | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /<>/test/mpileup/indel-AD.2.fa /<>/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD -f /<>/test/mpileup/indel-AD.2.fa -Ob /<>/test/mpileup/indel-AD.2.cram | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /<>/test/mpileup/indel-AD.2.fa /<>/test/mpileup/indel-AD.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /<>/test/mpileup/indel-AD.2.fa -Ob /<>/test/mpileup/indel-AD.2.bam | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /<>/test/mpileup/indel-AD.2.fa /<>/test/mpileup/indel-AD.2.cram | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a AD -r 11:75 --ambig-reads incAD0 -f /<>/test/mpileup/indel-AD.2.fa -Ob /<>/test/mpileup/indel-AD.2.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: /<>/bcftools csq -f /<>/test/csq.fa -g /<>/test/csq.chr.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: /<>/bcftools csq -f /<>/test/csq.fa -g /<>/test/csq.2.gff /<>/test/csq.2.vcf | /<>/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /<>/bcftools csq -f /<>/test/csq.fa -g /<>/test/csq.2.gff --ncsq 64 /<>/test/csq.2.vcf | /<>/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. 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/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/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/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/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/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-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/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/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/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/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/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: 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: 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: /<>/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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: /<>/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/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/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: /<>/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/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-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/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-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/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/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/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-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-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/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/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-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/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/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: cd /<>/test/csq/ENST00000410009 && /<>/bcftools csq -B 5 -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: 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/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 -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/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/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/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/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/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/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/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/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: cd /<>/test/csq/EMN908947 && /<>/bcftools csq -f EMN908947.fa -g ribosomal-slippage.gff ribosomal-slippage.vcf --force | ../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/EMN908947 && /<>/bcftools csq -f EMN908947.fa -g simple.gff simple.vcf | ../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/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/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/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 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/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_roh: /<>/bcftools roh /<>/test/roh.1.vcf.gz -Or -G30 --AF-dflt 0.4| grep -v ^# .. ok test_roh: /<>/bcftools roh /<>/test/roh.1.vcf.gz -Or -G30 --AF-file /<>/test/roh.1.tab.gz| grep -v ^# .. ok test_roh: /<>/bcftools roh /<>/test/roh.1.vcf.gz -Or -G30 --AF-file /<>/test/roh.1.tab.gz --ignore-homref| grep -v ^# .. ok test_roh: /<>/bcftools roh /<>/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245| grep -v ^# .. ok test_roh: /<>/bcftools roh /<>/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --ignore-homref| grep -v ^# .. ok test_roh: /<>/bcftools roh /<>/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --ignore-homref --include-noalt| grep -v ^# .. ok test_roh: /<>/bcftools roh /<>/test/roh.1.vcf.gz -G30 --AF-dflt 0.4 -r 1:100174876-100318245 --include-noalt| grep -v ^# .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 /tmp/tiM8I5IySO/gtcheck.1.vcf.gz -g /tmp/tiM8I5IySO/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -u GT,GT /tmp/tiM8I5IySO/gtcheck.1.vcf.gz -g /tmp/tiM8I5IySO/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -u GT,PL /tmp/tiM8I5IySO/gtcheck.1.vcf.gz -g /tmp/tiM8I5IySO/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -u PL,GT /tmp/tiM8I5IySO/gtcheck.1.vcf.gz -g /tmp/tiM8I5IySO/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -u PL,PL /tmp/tiM8I5IySO/gtcheck.1.vcf.gz -g /tmp/tiM8I5IySO/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -p s1,s1 /tmp/tiM8I5IySO/gtcheck.1.vcf.gz -g /tmp/tiM8I5IySO/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 /tmp/tiM8I5IySO/gtcheck.2.vcf.gz -g /tmp/tiM8I5IySO/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 /tmp/tiM8I5IySO/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -p B,A,C,A,C,B,D,A,D,B,D,C,E,A,E,B,E,C,E,D /tmp/tiM8I5IySO/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -P /<>/test/gtcheck.3.pairs /tmp/tiM8I5IySO/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -u PL /tmp/tiM8I5IySO/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 --n-matches 4 /tmp/tiM8I5IySO/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO | sort .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -s qry:E,D,C /tmp/tiM8I5IySO/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -s qry:E,D,C -u PL /tmp/tiM8I5IySO/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -s qry:B -s gt:D /tmp/tiM8I5IySO/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -s qry:B -s gt:D -u PL /tmp/tiM8I5IySO/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -s qry:B -s gt:D,C /tmp/tiM8I5IySO/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -p B,C,B,D /tmp/tiM8I5IySO/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -u GT,GT -H /tmp/tiM8I5IySO/gtcheck.1.vcf.gz -g /tmp/tiM8I5IySO/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -u GT,PL -H /tmp/tiM8I5IySO/gtcheck.1.vcf.gz -g /tmp/tiM8I5IySO/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -u PL,GT -H /tmp/tiM8I5IySO/gtcheck.1.vcf.gz -g /tmp/tiM8I5IySO/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -u PL,PL -H /tmp/tiM8I5IySO/gtcheck.1.vcf.gz -g /tmp/tiM8I5IySO/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -P /<>/test/gtcheck.4.pairs --distinctive-sites 3 /tmp/tiM8I5IySO/gtcheck.4.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -P /<>/test/gtcheck.4.pairs --distinctive-sites 3,1 /tmp/tiM8I5IySO/gtcheck.4.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -u GT -e 30 /tmp/tiM8I5IySO/gtcheck.1.vcf.gz -g /tmp/tiM8I5IySO/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -u GT -e 30 -p s1,s1 /tmp/tiM8I5IySO/gtcheck.1.vcf.gz -g /tmp/tiM8I5IySO/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -u GT -e 300 /tmp/tiM8I5IySO/gtcheck.1.vcf.gz -g /tmp/tiM8I5IySO/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -u PL -e 30 /tmp/tiM8I5IySO/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck /tmp/tiM8I5IySO/gtcheck.ntop.vcf.gz -g /tmp/tiM8I5IySO/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck --n-matches 2 /tmp/tiM8I5IySO/gtcheck.ntop.vcf.gz -g /tmp/tiM8I5IySO/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck /tmp/tiM8I5IySO/gtcheck.5.vcf.gz -g /tmp/tiM8I5IySO/gtcheck.5.gts.vcf.gz | grep -v ^# | grep -v Time .. ok Number of tests: total .. 1285 passed .. 1285 failed .. 0 make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp 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/aarch64-linux-gnu/bcftools install -p bcftools /<>/debian/bcftools/usr/bin install -p misc/color-chrs.pl misc/gff2gff.py misc/guess-ploidy.py misc/plot-vcfstats misc/plot-roh.py misc/run-roh.pl misc/vcfutils.pl /<>/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/aarch64-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 -a dh_strip -a -a debugedit: debian/bcftools/usr/lib/aarch64-linux-gnu/bcftools/variantkey-hex.so: Unknown DWARF DW_FORM_0x1f20 3299c9dd5d8b4447f9d63d8f290768423b80aed2 debugedit: debian/bcftools/usr/lib/aarch64-linux-gnu/bcftools/setGT.so: Unknown DWARF DW_FORM_0x1f21 bdde690d2efc4ea46771ed70e5721ebaf6b3d903 debugedit: debian/bcftools/usr/lib/aarch64-linux-gnu/bcftools/scatter.so: Unknown DWARF DW_FORM_0x1f20 f8cc5685762dcc4021223de548b5325e5fb077d7 debugedit: debian/bcftools/usr/lib/aarch64-linux-gnu/bcftools/parental-origin.so: Unknown DWARF DW_FORM_0x1f20 f733ed540d9135cf7d7b823b0bae07736c29bbca debugedit: debian/bcftools/usr/lib/aarch64-linux-gnu/bcftools/smpl-stats.so: Unknown DWARF DW_FORM_0x1f21 e15ced4d7bc72f232dbf98f39f41de02080fd527 debugedit: debian/bcftools/usr/lib/aarch64-linux-gnu/bcftools/GTisec.so: Unknown DWARF DW_FORM_0x1f21 8b8861570868721cf5b01460556ba7ce8d79d66b debugedit: debian/bcftools/usr/lib/aarch64-linux-gnu/bcftools/fill-tags.so: Unknown DWARF DW_FORM_0x1f21 2a518989b8409d89d34fe4ed476232a64b323d03 debugedit: debian/bcftools/usr/lib/aarch64-linux-gnu/bcftools/fill-from-fasta.so: Unknown DWARF DW_FORM_0x1f20 c1aec67534968c7358e832094ca3512fae3b2ee5 debugedit: debian/bcftools/usr/lib/aarch64-linux-gnu/bcftools/missing2ref.so: Unknown DWARF DW_FORM_0x1f20 80115b2151e00e4f9114006daa77a4e677ff7aa9 debugedit: debian/bcftools/usr/lib/aarch64-linux-gnu/bcftools/prune.so: Unknown DWARF DW_FORM_0x1f20 049ad59c8b56e0675721cea33441d493b0801953 debugedit: debian/bcftools/usr/lib/aarch64-linux-gnu/bcftools/check-ploidy.so: Unknown DWARF DW_FORM_0x1f20 eb08ce92b4d8bb84ad6a47a1a781732a30a93c11 debugedit: debian/bcftools/usr/lib/aarch64-linux-gnu/bcftools/fixref.so: Unknown DWARF DW_FORM_0x1f20 fc03c9b49fcee000bb4d9696c3e6c42926725d8d debugedit: debian/bcftools/usr/lib/aarch64-linux-gnu/bcftools/check-sparsity.so: Unknown DWARF DW_FORM_0x1f21 cd7680b4765a27aa711a8218134bf013975400ed debugedit: debian/bcftools/usr/lib/aarch64-linux-gnu/bcftools/split-vep.so: Unknown DWARF DW_FORM_0x1f21 7ece77e4760b29789927f63c89653bdc6fca4931 debugedit: debian/bcftools/usr/lib/aarch64-linux-gnu/bcftools/frameshifts.so: Unknown DWARF DW_FORM_0x1f21 2aab61a58e8b9ee78eb86c74e5f82356d4c174dd debugedit: debian/bcftools/usr/lib/aarch64-linux-gnu/bcftools/remove-overlaps.so: Unknown DWARF DW_FORM_0x1f20 ccba2705ddc9c962f4e695cae1b33d59e40b9443 debugedit: debian/bcftools/usr/lib/aarch64-linux-gnu/bcftools/GTsubset.so: Unknown DWARF DW_FORM_0x1f20 fb0026013c47b8bede5ebf8123fb91447248ade0 debugedit: debian/bcftools/usr/lib/aarch64-linux-gnu/bcftools/indel-stats.so: Unknown DWARF DW_FORM_0x1f21 e4246a839aedd49c7e825c5d17bf82e7dd75969d debugedit: debian/bcftools/usr/lib/aarch64-linux-gnu/bcftools/ad-bias.so: Unknown DWARF DW_FORM_0x1f20 6507bf527bb892aa48bdaa1ae68b2c67ebf58300 debugedit: debian/bcftools/usr/lib/aarch64-linux-gnu/bcftools/trio-stats.so: Unknown DWARF DW_FORM_0x1f21 b65e36101c5f977f10bacc321ed83255494a4195 debugedit: debian/bcftools/usr/lib/aarch64-linux-gnu/bcftools/gvcfz.so: Unknown DWARF DW_FORM_0x1f20 bd9d194165e9666a304a62b664b02e0edf68215c debugedit: debian/bcftools/usr/lib/aarch64-linux-gnu/bcftools/contrast.so: Unknown DWARF DW_FORM_0x1f21 f110b4bc89d4edb382f298d1d433ec1f98df1ab8 debugedit: debian/bcftools/usr/lib/aarch64-linux-gnu/bcftools/guess-ploidy.so: Unknown DWARF DW_FORM_0x1f20 dc8f4d63f25ba8a8fa9ef00f8e7ecaa03ed96f09 debugedit: debian/bcftools/usr/lib/aarch64-linux-gnu/bcftools/split.so: Unknown DWARF DW_FORM_0x1f20 65c7e3906d4cf9025c9440dbb620f7fa21fcc6c3 debugedit: debian/bcftools/usr/lib/aarch64-linux-gnu/bcftools/trio-dnm2.so: Unknown DWARF DW_FORM_0x1f20 76bda9f50fc64e94eeb29ae93b72fea4a75868f2 debugedit: debian/bcftools/usr/lib/aarch64-linux-gnu/bcftools/mendelian.so: Unknown DWARF DW_FORM_0x1f21 88fbf9a5426d16cdb47f2df7f0971077591e1e59 debugedit: debian/bcftools/usr/lib/aarch64-linux-gnu/bcftools/trio-switch-rate.so: Unknown DWARF DW_FORM_0x1f20 3c77d97816f4b5be9c3f0774373b807d79e9f118 debugedit: debian/bcftools/usr/lib/aarch64-linux-gnu/bcftools/tag2tag.so: Unknown DWARF DW_FORM_0x1f20 e3d58d3fa83ce97ec5fe2ad0ebd92172313f62aa debugedit: debian/bcftools/usr/lib/aarch64-linux-gnu/bcftools/impute-info.so: Unknown DWARF DW_FORM_0x1f20 9587ace496f46b46dd3292e87fcac096fe8259c5 debugedit: debian/bcftools/usr/lib/aarch64-linux-gnu/bcftools/fill-AN-AC.so: Unknown DWARF DW_FORM_0x1f20 f9b2c6074dfbdfb00fea95fad2f54d3758fb6a2c debugedit: debian/bcftools/usr/lib/aarch64-linux-gnu/bcftools/color-chrs.so: Unknown DWARF DW_FORM_0x1f21 1573f145a9a4bcd97d41598cc9c40f2060668f65 debugedit: debian/bcftools/usr/lib/aarch64-linux-gnu/bcftools/fixploidy.so: Unknown DWARF DW_FORM_0x1f21 e4bb0edb083511af7730e6345d6b6ae69decd95e debugedit: debian/bcftools/usr/lib/aarch64-linux-gnu/bcftools/counts.so: Unknown DWARF DW_FORM_0x1f20 0fea7013040ee1c13295b10247712a6be568c52d debugedit: debian/bcftools/usr/lib/aarch64-linux-gnu/bcftools/af-dist.so: Unknown DWARF DW_FORM_0x1f20 4bcf454b4aa97f316100d8bf2d58ee7890066a23 debugedit: debian/bcftools/usr/lib/aarch64-linux-gnu/bcftools/dosage.so: Unknown DWARF DW_FORM_0x1f20 6b1aff98214ff24c2b9179ee18adc42f769579cd debugedit: debian/bcftools/usr/lib/aarch64-linux-gnu/bcftools/add-variantkey.so: Unknown DWARF DW_FORM_0x1f20 eec1dacdc784a4bf63a74f5bf829656d5d621d58 debugedit: debian/bcftools/usr/lib/aarch64-linux-gnu/bcftools/allele-length.so: Unknown DWARF DW_FORM_0x1f20 20343cac500ebaedaef30d00bcf095b3fad00bf1 debugedit: debian/bcftools/usr/lib/aarch64-linux-gnu/bcftools/isecGT.so: Unknown DWARF DW_FORM_0x1f20 2123f7f253f671e8de961f3bbaa995c146dbf996 debugedit: debian/bcftools/usr/bin/bcftools: Unknown DWARF DW_FORM_0x1f20 978a72863c56383106d0633738cf6eae732cab7a dh_makeshlibs -a -a dh_shlibdeps -a -a dh_installdeb -a dh_gencontrol -a dpkg-gencontrol: warning: package bcftools: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package bcftools: substitution variable ${perl:Depends} unused, but is defined dh_md5sums -a dh_builddeb -a /usr/bin/which: this version of `which' is deprecated; use `command -v' in scripts instead. /usr/bin/which: this version of `which' is deprecated; use `command -v' in scripts instead. /usr/bin/which: this version of `which' is deprecated; use `command -v' in scripts instead. /usr/bin/which: this version of `which' is deprecated; use `command -v' in scripts instead. INFO: pkgstriptranslations version 148 INFO: pkgstriptranslations version 148 pkgstriptranslations: processing bcftools (in debian/bcftools); do_strip: , oemstrip: pkgstriptranslations: processing bcftools-dbgsym (in debian/.debhelper/bcftools/dbgsym-root); do_strip: , oemstrip: /usr/bin/which: this version of `which' is deprecated; use `command -v' in scripts instead. /usr/bin/which: this version of `which' is deprecated; use `command -v' in scripts instead. pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " /usr/bin/which: this version of `which' is deprecated; use `command -v' in scripts instead. pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " /usr/bin/which: this version of `which' is deprecated; use `command -v' in scripts instead. pkgstripfiles: processing control file: debian/bcftools/DEBIAN/control, package bcftools, directory debian/bcftools 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_1.13-1_arm64.deb'. pkgstripfiles: Truncating usr/share/doc/bcftools/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package bcftools ... pkgstripfiles: No PNG files. dpkg-deb: building package 'bcftools' in '../bcftools_1.13-1_arm64.deb'. Renaming bcftools-dbgsym_1.13-1_arm64.deb to bcftools-dbgsym_1.13-1_arm64.ddeb dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../bcftools_1.13-1_arm64.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 2021-10-18T21:38:10Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ bcftools_1.13-1_arm64.changes: ------------------------------ Format: 1.8 Date: Fri, 27 Aug 2021 16:36:54 +0200 Source: bcftools Binary: bcftools Built-For-Profiles: noudeb Architecture: arm64 Version: 1.13-1 Distribution: jammy-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Étienne Mollier Description: bcftools - genomic variant calling and manipulation of VCF/BCF files Changes: bcftools (1.13-1) unstable; urgency=medium . [ Steffen Moeller ] * New upstream version * Standards-Version: 4.5.1 (routine-update) * No tab in license text (routine-update) * watch file standard 4 (routine-update) . [ Étienne Mollier ] * Standards-Version: 4.6.0 (routine-update) * Use secure URI in Homepage field. * d/control: add myself to uploaders Checksums-Sha1: f18241ddee9d2f5f383d0eef977232aae47d99d5 1786626 bcftools-dbgsym_1.13-1_arm64.ddeb e5636669d172c28e11a5b8b6958296d2c8d9e2ae 6726 bcftools_1.13-1_arm64.buildinfo a860e78ca18f6f36f862ac455acdf56b30370998 684972 bcftools_1.13-1_arm64.deb Checksums-Sha256: 6a33d01282d37bc760403794574d362b1182bd3acf759f975ede663970c9a5b3 1786626 bcftools-dbgsym_1.13-1_arm64.ddeb 90a7b0635ad86369b34d5455407ac146a7c6f04089061d62a79f2c1e62877d85 6726 bcftools_1.13-1_arm64.buildinfo ef0d3026e060a3ddfd63d701e7ce71e9501d1a7fa98a9062fe129645fd5e1d59 684972 bcftools_1.13-1_arm64.deb Files: 1014840a2a7fe608898c233bd42bad01 1786626 debug optional bcftools-dbgsym_1.13-1_arm64.ddeb ae15b1792b24074a28ce8faf4f672ade 6726 science optional bcftools_1.13-1_arm64.buildinfo 6c0f1b2469ccc36230f065b78defe105 684972 science optional bcftools_1.13-1_arm64.deb +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: bcftools Binary: bcftools bcftools-dbgsym Architecture: arm64 Version: 1.13-1 Checksums-Md5: 1014840a2a7fe608898c233bd42bad01 1786626 bcftools-dbgsym_1.13-1_arm64.ddeb 6c0f1b2469ccc36230f065b78defe105 684972 bcftools_1.13-1_arm64.deb Checksums-Sha1: f18241ddee9d2f5f383d0eef977232aae47d99d5 1786626 bcftools-dbgsym_1.13-1_arm64.ddeb a860e78ca18f6f36f862ac455acdf56b30370998 684972 bcftools_1.13-1_arm64.deb Checksums-Sha256: 6a33d01282d37bc760403794574d362b1182bd3acf759f975ede663970c9a5b3 1786626 bcftools-dbgsym_1.13-1_arm64.ddeb ef0d3026e060a3ddfd63d701e7ce71e9501d1a7fa98a9062fe129645fd5e1d59 684972 bcftools_1.13-1_arm64.deb Build-Origin: Ubuntu Build-Architecture: arm64 Build-Date: Mon, 18 Oct 2021 21:38:09 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: autoconf (= 2.71-2), automake (= 1:1.16.4-2), autopoint (= 0.21-4ubuntu3), autotools-dev (= 20180224.1+nmu1), base-files (= 12ubuntu1), base-passwd (= 3.5.52), bash (= 5.1-3ubuntu2), binutils (= 2.37-7ubuntu1), binutils-aarch64-linux-gnu (= 2.37-7ubuntu1), binutils-common (= 2.37-7ubuntu1), bsdextrautils (= 2.36.1-8ubuntu2), bsdutils (= 1:2.36.1-8ubuntu2), build-essential (= 12.9ubuntu2), bzip2 (= 1.0.8-4ubuntu4), coreutils (= 8.32-4ubuntu3), cpp (= 4:11.2.0-1ubuntu1), cpp-11 (= 11.2.0-7ubuntu2), dash (= 0.5.11+git20210120+802ebd4-1build1), debconf (= 1.5.77), debhelper (= 13.3.4ubuntu2), debianutils (= 5.5-1), debugedit (= 1:5.0-0ubuntu2), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.12.0-1), diffutils (= 1:3.8-0ubuntu1), dpkg (= 1.20.9ubuntu2), dpkg-dev (= 1.20.9ubuntu2), dwz (= 0.14-1build1), file (= 1:5.39-3build1), findutils (= 4.8.0-1ubuntu2), g++ (= 4:11.2.0-1ubuntu1), g++-11 (= 11.2.0-7ubuntu2), gcc (= 4:11.2.0-1ubuntu1), gcc-11 (= 11.2.0-7ubuntu2), gcc-11-base (= 11.2.0-7ubuntu2), gettext (= 0.21-4ubuntu3), gettext-base (= 0.21-4ubuntu3), grep (= 3.7-0ubuntu1), groff-base (= 1.22.4-7), gzip (= 1.10-4ubuntu2), hostname (= 3.23ubuntu1), init-system-helpers (= 1.60build1), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.2.53-10ubuntu2), libarchive-zip-perl (= 1.68-1), libasan6 (= 11.2.0-7ubuntu2), libatomic1 (= 11.2.0-7ubuntu2), libattr1 (= 1:2.5.1-1), libaudit-common (= 1:3.0-2ubuntu3), libaudit1 (= 1:3.0-2ubuntu3), libbinutils (= 2.37-7ubuntu1), libblkid1 (= 2.36.1-8ubuntu2), libbrotli1 (= 1.0.9-2build4), libbz2-1.0 (= 1.0.8-4ubuntu4), libbz2-dev (= 1.0.8-4ubuntu4), libc-bin (= 2.34-0ubuntu3), libc-dev-bin (= 2.34-0ubuntu3), libc6 (= 2.34-0ubuntu3), libc6-dev (= 2.34-0ubuntu3), libcap-ng0 (= 0.7.9-2.2build2), libcap2 (= 1:2.44-1build2), libcc1-0 (= 11.2.0-7ubuntu2), libcom-err2 (= 1.46.3-1ubuntu3), libcrypt-dev (= 1:4.4.18-4ubuntu2), libcrypt1 (= 1:4.4.18-4ubuntu2), libctf-nobfd0 (= 2.37-7ubuntu1), libctf0 (= 2.37-7ubuntu1), libcurl3-gnutls (= 7.74.0-1.3ubuntu2), libcurl4-gnutls-dev (= 7.74.0-1.3ubuntu2), libdb5.3 (= 5.3.28+dfsg1-0.8ubuntu2), libdebconfclient0 (= 0.256ubuntu4), libdebhelper-perl (= 13.3.4ubuntu2), libdeflate-dev (= 1.7-2ubuntu2), libdeflate0 (= 1.7-2ubuntu2), libdpkg-perl (= 1.20.9ubuntu2), libdw1 (= 0.185-2), libelf1 (= 0.185-2), libffi8 (= 3.4.2-1ubuntu5), libfile-stripnondeterminism-perl (= 1.12.0-1), libgcc-11-dev (= 11.2.0-7ubuntu2), libgcc-s1 (= 11.2.0-7ubuntu2), libgcrypt20 (= 1.8.7-5ubuntu2), libgdbm-compat4 (= 1.21-1), libgdbm6 (= 1.21-1), libgmp10 (= 2:6.2.1+dfsg-1ubuntu3), libgnutls30 (= 3.7.1-5ubuntu1), libgomp1 (= 11.2.0-7ubuntu2), libgpg-error0 (= 1.42-3), libgsl-dev (= 2.6+dfsg-2), libgsl25 (= 2.6+dfsg-2), libgslcblas0 (= 2.6+dfsg-2), libgssapi-krb5-2 (= 1.18.3-7), libhogweed6 (= 3.7.3-1build1), libhts-dev (= 1.13+ds-2), libhts3 (= 1.13+ds-2), libhtscodecs2 (= 1.1.1-2), libhwasan0 (= 11.2.0-7ubuntu2), libicu67 (= 67.1-7ubuntu1), libidn2-0 (= 2.3.2-2), libio-pty-perl (= 1:1.15-2build1), libisl23 (= 0.24-2), libitm1 (= 11.2.0-7ubuntu2), libk5crypto3 (= 1.18.3-7), libkeyutils1 (= 1.6.1-2ubuntu2), libkrb5-3 (= 1.18.3-7), libkrb5support0 (= 1.18.3-7), libldap-2.5-0 (= 2.5.6+dfsg-1~exp1ubuntu1), liblsan0 (= 11.2.0-7ubuntu2), liblz4-1 (= 1.9.3-2build1), liblzma-dev (= 5.2.5-2build1), liblzma5 (= 5.2.5-2build1), libmagic-mgc (= 1:5.39-3build1), libmagic1 (= 1:5.39-3build1), libmount1 (= 2.36.1-8ubuntu2), libmpc3 (= 1.2.1-1), libmpfr6 (= 4.1.0-3build2), libnettle8 (= 3.7.3-1build1), libnghttp2-14 (= 1.43.0-1build1), libnsl-dev (= 1.3.0-2build1), libnsl2 (= 1.3.0-2build1), libp11-kit0 (= 0.23.22-1build1), libpam-modules (= 1.3.1-5ubuntu11), libpam-modules-bin (= 1.3.1-5ubuntu11), libpam-runtime (= 1.3.1-5ubuntu11), libpam0g (= 1.3.1-5ubuntu11), libpcre2-8-0 (= 10.37-0ubuntu2), libpcre3 (= 2:8.39-13build4), libperl5.32 (= 5.32.1-3ubuntu3), libpipeline1 (= 1.5.3-1build1), libpsl5 (= 0.21.0-1.2build1), librtmp1 (= 2.4+20151223.gitfa8646d.1-2build3), libsasl2-2 (= 2.1.27+dfsg-2.1build1), libsasl2-modules-db (= 2.1.27+dfsg-2.1build1), libseccomp2 (= 2.5.1-1ubuntu2), libselinux1 (= 3.1-3build3), libsigsegv2 (= 2.13-1ubuntu2), libsmartcols1 (= 2.36.1-8ubuntu2), libssh-4 (= 0.9.6-1), libssl1.1 (= 1.1.1l-1ubuntu1), libstdc++-11-dev (= 11.2.0-7ubuntu2), libstdc++6 (= 11.2.0-7ubuntu2), libsub-override-perl (= 0.09-2), libsystemd0 (= 248.3-1ubuntu8), libtasn1-6 (= 4.17.0-2), libtinfo6 (= 6.2+20201114-2build2), libtirpc-common (= 1.3.2-2), libtirpc-dev (= 1.3.2-2), libtirpc3 (= 1.3.2-2), libtool (= 2.4.6-15build1), libtsan0 (= 11.2.0-7ubuntu2), libubsan1 (= 11.2.0-7ubuntu2), libuchardet0 (= 0.0.7-1build1), libudev1 (= 248.3-1ubuntu8), libunistring2 (= 0.9.10-6), libuuid1 (= 2.36.1-8ubuntu2), libxml2 (= 2.9.12+dfsg-5), libzstd1 (= 1.4.8+dfsg-2.1build1), linux-libc-dev (= 5.13.0-19.19), login (= 1:4.8.1-1ubuntu9), lsb-base (= 11.1.0ubuntu3), lto-disabled-list (= 16), m4 (= 1.4.18-5ubuntu1), make (= 4.3-4ubuntu2), man-db (= 2.9.4-2build1), mawk (= 1.3.4.20200120-2build1), ncurses-base (= 6.2+20201114-2build2), ncurses-bin (= 6.2+20201114-2build2), patch (= 2.7.6-7build1), perl (= 5.32.1-3ubuntu3), perl-base (= 5.32.1-3ubuntu3), perl-modules-5.32 (= 5.32.1-3ubuntu3), po-debconf (= 1.0.21+nmu1), rpcsvc-proto (= 1.4.2-0ubuntu5), sed (= 4.7-1ubuntu2), sensible-utils (= 0.0.14), sysvinit-utils (= 2.96-7ubuntu2), tabix (= 1.13+ds-2), tar (= 1.34+dfsg-1build2), util-linux (= 2.36.1-8ubuntu2), xz-utils (= 5.2.5-2build1), zlib1g (= 1:1.2.11.dfsg-2ubuntu7), zlib1g-dev (= 1:1.2.11.dfsg-2ubuntu7) Environment: DEB_BUILD_OPTIONS="parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1630075014" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ bcftools_1.13-1_arm64.deb ------------------------- new Debian package, version 2.0. size 684972 bytes: control archive=2179 bytes. 834 bytes, 18 lines control 4061 bytes, 53 lines md5sums Package: bcftools Version: 1.13-1 Architecture: arm64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 2026 Depends: libc6 (>= 2.34), libhts3 (>= 1.13), zlib1g (>= 1:1.1.4) Recommends: perl Suggests: python3, python3-numpy, python3-matplotlib, texlive-latex-recommended Breaks: samtools (<< 1.0) Replaces: samtools (<< 1.0) Section: science Priority: optional Homepage: https://samtools.github.io/bcftools/ Description: genomic variant calling and manipulation of VCF/BCF files BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. drwxr-xr-x root/root 0 2021-08-27 14:36 ./ drwxr-xr-x root/root 0 2021-08-27 14:36 ./usr/ drwxr-xr-x root/root 0 2021-08-27 14:36 ./usr/bin/ -rwxr-xr-x root/root 950712 2021-08-27 14:36 ./usr/bin/bcftools -rwxr-xr-x root/root 16949 2021-08-27 14:36 ./usr/bin/color-chrs.pl -rwxr-xr-x root/root 7404 2021-07-07 17:18 ./usr/bin/gff2gff.py -rwxr-xr-x root/root 4325 2021-08-27 14:36 ./usr/bin/guess-ploidy.py -rwxr-xr-x root/root 15164 2021-07-07 17:18 ./usr/bin/plot-roh.py -rwxr-xr-x root/root 84568 2021-08-27 14:36 ./usr/bin/plot-vcfstats -rwxr-xr-x root/root 13914 2021-08-27 14:36 ./usr/bin/run-roh.pl -rwxr-xr-x root/root 18202 2021-08-27 14:36 ./usr/bin/vcfutils.pl drwxr-xr-x root/root 0 2021-08-27 14:36 ./usr/lib/ drwxr-xr-x root/root 0 2021-08-27 14:36 ./usr/lib/aarch64-linux-gnu/ drwxr-xr-x root/root 0 2021-08-27 14:36 ./usr/lib/aarch64-linux-gnu/bcftools/ -rw-r--r-- root/root 18792 2021-08-27 14:36 ./usr/lib/aarch64-linux-gnu/bcftools/GTisec.so -rw-r--r-- root/root 10504 2021-08-27 14:36 ./usr/lib/aarch64-linux-gnu/bcftools/GTsubset.so -rw-r--r-- root/root 60080 2021-08-27 14:36 ./usr/lib/aarch64-linux-gnu/bcftools/ad-bias.so -rw-r--r-- root/root 14464 2021-08-27 14:36 ./usr/lib/aarch64-linux-gnu/bcftools/add-variantkey.so -rw-r--r-- root/root 14712 2021-08-27 14:36 ./usr/lib/aarch64-linux-gnu/bcftools/af-dist.so -rw-r--r-- root/root 10352 2021-08-27 14:36 ./usr/lib/aarch64-linux-gnu/bcftools/allele-length.so -rw-r--r-- root/root 10376 2021-08-27 14:36 ./usr/lib/aarch64-linux-gnu/bcftools/check-ploidy.so -rw-r--r-- root/root 14832 2021-08-27 14:36 ./usr/lib/aarch64-linux-gnu/bcftools/check-sparsity.so -rw-r--r-- root/root 22880 2021-08-27 14:36 ./usr/lib/aarch64-linux-gnu/bcftools/color-chrs.so -rw-r--r-- root/root 23416 2021-08-27 14:36 ./usr/lib/aarch64-linux-gnu/bcftools/contrast.so -rw-r--r-- root/root 10344 2021-08-27 14:36 ./usr/lib/aarch64-linux-gnu/bcftools/counts.so -rw-r--r-- root/root 18688 2021-08-27 14:36 ./usr/lib/aarch64-linux-gnu/bcftools/dosage.so -rw-r--r-- root/root 10376 2021-08-27 14:36 ./usr/lib/aarch64-linux-gnu/bcftools/fill-AN-AC.so -rw-r--r-- root/root 92880 2021-08-27 14:36 ./usr/lib/aarch64-linux-gnu/bcftools/fill-from-fasta.so -rw-r--r-- root/root 39448 2021-08-27 14:36 ./usr/lib/aarch64-linux-gnu/bcftools/fill-tags.so -rw-r--r-- root/root 31184 2021-08-27 14:36 ./usr/lib/aarch64-linux-gnu/bcftools/fixploidy.so -rw-r--r-- root/root 23104 2021-08-27 14:36 ./usr/lib/aarch64-linux-gnu/bcftools/fixref.so -rw-r--r-- root/root 10472 2021-08-27 14:36 ./usr/lib/aarch64-linux-gnu/bcftools/frameshifts.so -rw-r--r-- root/root 19168 2021-08-27 14:36 ./usr/lib/aarch64-linux-gnu/bcftools/guess-ploidy.so -rw-r--r-- root/root 19072 2021-08-27 14:36 ./usr/lib/aarch64-linux-gnu/bcftools/gvcfz.so -rw-r--r-- root/root 10384 2021-08-27 14:36 ./usr/lib/aarch64-linux-gnu/bcftools/impute-info.so -rw-r--r-- root/root 27448 2021-08-27 14:36 ./usr/lib/aarch64-linux-gnu/bcftools/indel-stats.so -rw-r--r-- root/root 14840 2021-08-27 14:36 ./usr/lib/aarch64-linux-gnu/bcftools/isecGT.so -rw-r--r-- root/root 27488 2021-08-27 14:36 ./usr/lib/aarch64-linux-gnu/bcftools/mendelian.so -rw-r--r-- root/root 10488 2021-08-27 14:36 ./usr/lib/aarch64-linux-gnu/bcftools/missing2ref.so -rw-r--r-- root/root 19016 2021-08-27 14:36 ./usr/lib/aarch64-linux-gnu/bcftools/parental-origin.so -rw-r--r-- root/root 23472 2021-08-27 14:36 ./usr/lib/aarch64-linux-gnu/bcftools/prune.so -rw-r--r-- root/root 14960 2021-08-27 14:36 ./usr/lib/aarch64-linux-gnu/bcftools/remove-overlaps.so -rw-r--r-- root/root 23496 2021-08-27 14:36 ./usr/lib/aarch64-linux-gnu/bcftools/scatter.so -rw-r--r-- root/root 18856 2021-08-27 14:36 ./usr/lib/aarch64-linux-gnu/bcftools/setGT.so -rw-r--r-- root/root 19016 2021-08-27 14:36 ./usr/lib/aarch64-linux-gnu/bcftools/smpl-stats.so -rw-r--r-- root/root 40192 2021-08-27 14:36 ./usr/lib/aarch64-linux-gnu/bcftools/split-vep.so -rw-r--r-- root/root 31520 2021-08-27 14:36 ./usr/lib/aarch64-linux-gnu/bcftools/split.so -rw-r--r-- root/root 14936 2021-08-27 14:36 ./usr/lib/aarch64-linux-gnu/bcftools/tag2tag.so -rw-r--r-- root/root 44288 2021-08-27 14:36 ./usr/lib/aarch64-linux-gnu/bcftools/trio-dnm2.so -rw-r--r-- root/root 27408 2021-08-27 14:36 ./usr/lib/aarch64-linux-gnu/bcftools/trio-stats.so -rw-r--r-- root/root 14640 2021-08-27 14:36 ./usr/lib/aarch64-linux-gnu/bcftools/trio-switch-rate.so -rw-r--r-- root/root 14512 2021-08-27 14:36 ./usr/lib/aarch64-linux-gnu/bcftools/variantkey-hex.so drwxr-xr-x root/root 0 2021-08-27 14:36 ./usr/share/ drwxr-xr-x root/root 0 2021-08-27 14:36 ./usr/share/doc/ drwxr-xr-x root/root 0 2021-08-27 14:36 ./usr/share/doc/bcftools/ -rw-r--r-- root/root 2192 2021-07-07 17:18 ./usr/share/doc/bcftools/README -rw-r--r-- root/root 1041 2021-08-27 14:36 ./usr/share/doc/bcftools/changelog.Debian.gz -rw-r--r-- root/root 2613 2021-08-27 14:36 ./usr/share/doc/bcftools/copyright drwxr-xr-x root/root 0 2021-08-27 14:36 ./usr/share/man/ drwxr-xr-x root/root 0 2021-08-27 14:36 ./usr/share/man/man1/ -rw-r--r-- root/root 41591 2021-08-27 14:36 ./usr/share/man/man1/bcftools.1.gz -rw-r--r-- root/root 253 2021-08-27 14:36 ./usr/share/man/man1/color-chrs.pl.1.gz -rw-r--r-- root/root 271 2021-08-27 14:36 ./usr/share/man/man1/plot-vcfstats.1.gz -rw-r--r-- root/root 208 2021-08-27 14:36 ./usr/share/man/man1/vcfutils.pl.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: arm64 Build Type: any Build-Space: n/a Build-Time: 222 Distribution: jammy-proposed Host Architecture: arm64 Install-Time: 23 Job: bcftools_1.13-1.dsc Machine Architecture: arm64 Package: bcftools Package-Time: 249 Source-Version: 1.13-1 Space: n/a Status: successful Version: 1.13-1 -------------------------------------------------------------------------------- Finished at 2021-10-18T21:38:10Z Build needed 00:04:09, no disk space Adding user buildd to group lxd RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=jammy --arch=arm64 PACKAGEBUILD-22292590 Scanning for processes to kill in build PACKAGEBUILD-22292590