sbuild (Debian sbuild) 0.85.9 (29 May 2024) on carme.larted.org.uk +==============================================================================+ | bcftools 1.20-1 (amd64) Sun, 02 Jun 2024 23:50:45 +0000 | +==============================================================================+ Package: bcftools Version: 1.20-1 Source Version: 1.20-1 Distribution: perl-5.40-throwaway Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: full I: NOTICE: Log filtering will replace 'var/run/schroot/mount/perl-5.40-amd64-debomatic-70a0a797-9ad2-4d4d-9b64-548e81a91d77' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup bcftools_1.20-1 perl-5.40-throwaway amd64 ---------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup bcftools_1.20-1 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: NOTICE: Log filtering will replace 'build/bcftools-UXBhLH/resolver-VPoIPz' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.40 InRelease [3039 B] Hit:2 http://localhost:3142/debian unstable InRelease Get:1 file:/srv/reprepro perl-5.40 InRelease [3039 B] Hit:3 http://localhost:3142/debian sid InRelease Get:4 file:/srv/reprepro perl-5.40/main amd64 Packages [598 kB] Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/bcftools_1.20-1.dsc exists in /srv/debomatic/incoming; copying to chroot I: NOTICE: Log filtering will replace 'build/bcftools-UXBhLH/bcftools-1.20' with '<>' I: NOTICE: Log filtering will replace 'build/bcftools-UXBhLH' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), zlib1g-dev, libbz2-dev, liblzma-dev, libhts-dev (>= 1.14), libgsl-dev, tabix, libio-pty-perl, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), zlib1g-dev, libbz2-dev, liblzma-dev, libhts-dev (>= 1.14), libgsl-dev, tabix, libio-pty-perl, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [609 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [733 B] Get:5 copy:/<>/apt_archive ./ Packages [743 B] Fetched 2085 B in 0s (0 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper dh-autoreconf dh-strip-nondeterminism dwz fakeroot file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbrotli1 libbz2-dev libcom-err2 libcurl3t64-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libelf1t64 libfakeroot libfile-stripnondeterminism-perl libgsl-dev libgsl27 libgslcblas0 libgssapi-krb5-2 libhts-dev libhts3t64 libhtscodecs2 libicu72 libio-pty-perl libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblzma-dev libmagic-mgc libmagic1t64 libnghttp2-14 libpipeline1 libpsl5t64 librtmp1 libssh2-1t64 libtool libuchardet0 libxml2 m4 man-db po-debconf sensible-utils tabix zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libcurl4-doc libgnutls28-dev libidn-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev pkgconf gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html krb5-doc krb5-user liblzma-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx bzip2-doc ca-certificates libarchive-cpio-perl krb5-locales publicsuffix libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper dh-autoreconf dh-strip-nondeterminism dwz fakeroot file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbrotli1 libbz2-dev libcom-err2 libcurl3t64-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libelf1t64 libfakeroot libfile-stripnondeterminism-perl libgsl-dev libgsl27 libgslcblas0 libgssapi-krb5-2 libhts-dev libhts3t64 libhtscodecs2 libicu72 libio-pty-perl libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblzma-dev libmagic-mgc libmagic1t64 libnghttp2-14 libpipeline1 libpsl5t64 librtmp1 libssh2-1t64 libtool libuchardet0 libxml2 m4 man-db po-debconf sbuild-build-depends-main-dummy sensible-utils tabix zlib1g-dev 0 upgraded, 58 newly installed, 0 to remove and 0 not upgraded. Need to get 27.7 MB/27.7 MB of archives. After this operation, 105 MB of additional disk space will be used. Get:1 file:/srv/reprepro perl-5.40/main amd64 libio-pty-perl amd64 1:1.20-1+b2 [34.3 kB] Get:2 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [936 B] Get:3 http://localhost:3142/debian unstable/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get:4 http://localhost:3142/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get:5 http://localhost:3142/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get:6 http://localhost:3142/debian unstable/main amd64 file amd64 1:5.45-3 [42.9 kB] Get:7 http://localhost:3142/debian unstable/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get:8 http://localhost:3142/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get:9 http://localhost:3142/debian unstable/main amd64 groff-base amd64 1.23.0-4 [1180 kB] Get:10 http://localhost:3142/debian unstable/main amd64 bsdextrautils amd64 2.40.1-7 [95.9 kB] Get:11 http://localhost:3142/debian unstable/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get:12 http://localhost:3142/debian unstable/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get:13 http://localhost:3142/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get:14 http://localhost:3142/debian unstable/main amd64 autoconf all 2.71-3 [332 kB] Get:15 http://localhost:3142/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get:16 http://localhost:3142/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get:17 http://localhost:3142/debian unstable/main amd64 autopoint all 0.21-14 [496 kB] Get:18 http://localhost:3142/debian unstable/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get:19 http://localhost:3142/debian unstable/main amd64 libtool all 2.4.7-7 [517 kB] Get:20 http://localhost:3142/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get:21 http://localhost:3142/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:22 http://localhost:3142/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get:23 http://localhost:3142/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get:24 http://localhost:3142/debian unstable/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get:25 http://localhost:3142/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get:26 http://localhost:3142/debian unstable/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get:27 http://localhost:3142/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg-2 [670 kB] Get:28 http://localhost:3142/debian unstable/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get:29 http://localhost:3142/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:30 http://localhost:3142/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:31 http://localhost:3142/debian unstable/main amd64 debhelper all 13.15.3 [901 kB] Get:32 http://localhost:3142/debian unstable/main amd64 libfakeroot amd64 1.34-1 [28.9 kB] Get:33 http://localhost:3142/debian unstable/main amd64 fakeroot amd64 1.34-1 [74.0 kB] Get:34 http://localhost:3142/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get:35 http://localhost:3142/debian unstable/main amd64 libbz2-dev amd64 1.0.8-5.1 [31.3 kB] Get:36 http://localhost:3142/debian unstable/main amd64 libcom-err2 amd64 1.47.1-1 [22.9 kB] Get:37 http://localhost:3142/debian unstable/main amd64 libkrb5support0 amd64 1.20.1-6+b1 [33.3 kB] Get:38 http://localhost:3142/debian unstable/main amd64 libk5crypto3 amd64 1.20.1-6+b1 [79.8 kB] Get:39 http://localhost:3142/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get:40 http://localhost:3142/debian unstable/main amd64 libkrb5-3 amd64 1.20.1-6+b1 [333 kB] Get:41 http://localhost:3142/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.20.1-6+b1 [135 kB] Get:42 http://localhost:3142/debian unstable/main amd64 libnghttp2-14 amd64 1.61.0-1+b1 [75.6 kB] Get:43 http://localhost:3142/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get:44 http://localhost:3142/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get:45 http://localhost:3142/debian unstable/main amd64 libssh2-1t64 amd64 1.11.0-5 [215 kB] Get:46 http://localhost:3142/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.8.0-1 [434 kB] Get:47 http://localhost:3142/debian unstable/main amd64 libcurl4-gnutls-dev amd64 8.8.0-1 [540 kB] Get:48 http://localhost:3142/debian unstable/main amd64 libdeflate0 amd64 1.20-1 [46.0 kB] Get:49 http://localhost:3142/debian unstable/main amd64 libdeflate-dev amd64 1.20-1 [54.5 kB] Get:50 http://localhost:3142/debian unstable/main amd64 libgslcblas0 amd64 2.7.1+dfsg-6+b1 [107 kB] Get:51 http://localhost:3142/debian unstable/main amd64 libgsl27 amd64 2.7.1+dfsg-6+b1 [934 kB] Get:52 http://localhost:3142/debian unstable/main amd64 libgsl-dev amd64 2.7.1+dfsg-6+b1 [1146 kB] Get:53 http://localhost:3142/debian unstable/main amd64 libhtscodecs2 amd64 1.6.0-1+b1 [93.0 kB] Get:54 http://localhost:3142/debian unstable/main amd64 libhts3t64 amd64 1.20+ds-1 [452 kB] Get:55 http://localhost:3142/debian unstable/main amd64 liblzma-dev amd64 5.6.1+really5.4.5-1 [293 kB] Get:56 http://localhost:3142/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1 [919 kB] Get:57 http://localhost:3142/debian unstable/main amd64 libhts-dev amd64 1.20+ds-1 [1684 kB] Get:58 http://localhost:3142/debian unstable/main amd64 tabix amd64 1.20+ds-1 [483 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 27.7 MB in 0s (68.2 MB/s) Selecting previously unselected package sensible-utils. (Reading database ... 21779 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3_amd64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-14+b1_amd64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b1) ... 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Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1) ... Selecting previously unselected package libhts-dev:amd64. Preparing to unpack .../54-libhts-dev_1.20+ds-1_amd64.deb ... Unpacking libhts-dev:amd64 (1.20+ds-1) ... Selecting previously unselected package libio-pty-perl. Preparing to unpack .../55-libio-pty-perl_1.20-1+b2_amd64.deb ... Unpacking libio-pty-perl (1:1.20-1+b2) ... Selecting previously unselected package tabix. Preparing to unpack .../56-tabix_1.20+ds-1_amd64.deb ... Unpacking tabix (1.20+ds-1) ... Selecting previously unselected package sbuild-build-depends-main-dummy. Preparing to unpack .../57-sbuild-build-depends-main-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up libhtscodecs2:amd64 (1.6.0-1+b1) ... Setting up libpipeline1:amd64 (1.5.7-2) ... Setting up libkeyutils1:amd64 (1.6.3-3) ... Setting up libicu72:amd64 (72.1-4+b1) ... Setting up bsdextrautils (2.40.1-7) ... Setting up libgslcblas0:amd64 (2.7.1+dfsg-6+b1) ... Setting up libio-pty-perl (1:1.20-1+b2) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libbrotli1:amd64 (1.1.0-2+b3) ... Setting up libmagic1t64:amd64 (1:5.45-3) ... Setting up libpsl5t64:amd64 (0.21.2-1.1) ... Setting up libnghttp2-14:amd64 (1.61.0-1+b1) ... Setting up libdeflate0:amd64 (1.20-1) ... Setting up gettext-base (0.21-14+b1) ... Setting up libgsl27:amd64 (2.7.1+dfsg-6+b1) ... Setting up m4 (1.4.19-4) ... Setting up libcom-err2:amd64 (1.47.1-1) ... Setting up file (1:5.45-3) ... Setting up libfakeroot:amd64 (1.34-1) ... Setting up libelf1t64:amd64 (0.191-1+b1) ... Setting up libkrb5support0:amd64 (1.20.1-6+b1) ... Setting up fakeroot (1.34-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Setting up autotools-dev (20220109.1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up autopoint (0.21-14) ... Setting up libk5crypto3:amd64 (1.20.1-6+b1) ... Setting up autoconf (2.71-3) ... Setting up liblzma-dev:amd64 (5.6.1+really5.4.5-1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up libkrb5-3:amd64 (1.20.1-6+b1) ... Setting up libssh2-1t64:amd64 (1.11.0-5) ... Setting up libdeflate-dev:amd64 (1.20-1) ... Setting up tabix (1.20+ds-1) ... Setting up libxml2:amd64 (2.12.7+dfsg-2) ... Setting up libbz2-dev:amd64 (1.0.8-5.1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up gettext (0.21-14+b1) ... Setting up libgsl-dev (2.7.1+dfsg-6+b1) ... Setting up libtool (2.4.7-7) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-6+b1) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3t64-gnutls:amd64 (8.8.0-1) ... Setting up libcurl4-gnutls-dev:amd64 (8.8.0-1) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libhts3t64:amd64 (1.20+ds-1) ... Setting up libhts-dev:amd64 (1.20+ds-1) ... Setting up debhelper (13.15.3) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.38-12) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) amd64 (x86_64) Toolchain package versions: binutils_2.42-4 dpkg-dev_1.22.6 g++-13_13.2.0-25 gcc-13_13.2.0-25 libc6-dev_2.38-12 libstdc++-13-dev_13.2.0-25 libstdc++6_14.1.0-1 linux-libc-dev_6.8.12-1 Package versions: adduser_3.137 apt_2.9.4 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-14 autotools-dev_20220109.1 base-files_13.2 base-passwd_3.6.3 bash_5.2.21-2+b1 binutils_2.42-4 binutils-common_2.42-4 binutils-x86-64-linux-gnu_2.42-4 bsdextrautils_2.40.1-7 bsdutils_1:2.40.1-7 build-essential_12.10 bzip2_1.0.8-5.1 coreutils_9.4-3.1 cpp_4:13.2.0-7 cpp-13_13.2.0-25 cpp-13-x86-64-linux-gnu_13.2.0-25 cpp-x86-64-linux-gnu_4:13.2.0-7 dash_0.5.12-8 debconf_1.5.86 debhelper_13.15.3 debian-archive-keyring_2023.4 debianutils_5.17 dh-autoreconf_20 dh-strip-nondeterminism_1.14.0-1 diffutils_1:3.10-1 dirmngr_2.2.43-7 dpkg_1.22.6 dpkg-dev_1.22.6 dwz_0.15-1+b1 eatmydata_131-2 fakeroot_1.34-1 file_1:5.45-3 findutils_4.9.0-6 g++_4:13.2.0-7 g++-13_13.2.0-25 g++-13-x86-64-linux-gnu_13.2.0-25 g++-x86-64-linux-gnu_4:13.2.0-7 gcc_4:13.2.0-7 gcc-13_13.2.0-25 gcc-13-base_13.2.0-25 gcc-13-x86-64-linux-gnu_13.2.0-25 gcc-14-base_14.1.0-1 gcc-x86-64-linux-gnu_4:13.2.0-7 gettext_0.21-14+b1 gettext-base_0.21-14+b1 gnupg_2.2.43-7 gnupg-l10n_2.2.43-7 gnupg-utils_2.2.43-7 gpg_2.2.43-7 gpg-agent_2.2.43-7 gpg-wks-client_2.2.43-7 gpgconf_2.2.43-7 gpgsm_2.2.43-7 gpgv_2.2.43-7 grep_3.11-4 groff-base_1.23.0-4 gzip_1.12-1.1 hostname_3.23+nmu2 init-system-helpers_1.66 intltool-debian_0.35.0+20060710.6 libacl1_2.3.2-2 libapt-pkg6.0t64_2.9.4 libarchive-zip-perl_1.68-1 libasan8_14.1.0-1 libassuan0_2.5.6-1+b1 libatomic1_14.1.0-1 libattr1_1:2.5.2-1 libaudit-common_1:3.1.2-2.1 libaudit1_1:3.1.2-2.1 libbinutils_2.42-4 libblkid1_2.40.1-7 libbrotli1_1.1.0-2+b3 libbz2-1.0_1.0.8-5.1 libbz2-dev_1.0.8-5.1 libc-bin_2.38-12 libc-dev-bin_2.38-12 libc-l10n_2.38-12 libc6_2.38-12 libc6-dev_2.38-12 libcap-ng0_0.8.5-1 libcap2_1:2.66-5 libcc1-0_14.1.0-1 libcom-err2_1.47.1-1 libcrypt-dev_1:4.4.36-4 libcrypt1_1:4.4.36-4 libctf-nobfd0_2.42-4 libctf0_2.42-4 libcurl3t64-gnutls_8.8.0-1 libcurl4-gnutls-dev_8.8.0-1 libdb5.3t64_5.3.28+dfsg2-7 libdebconfclient0_0.272 libdebhelper-perl_13.15.3 libdeflate-dev_1.20-1 libdeflate0_1.20-1 libdpkg-perl_1.22.6 libeatmydata1_131-2 libelf1t64_0.191-1+b1 libfakeroot_1.34-1 libffi8_3.4.6-1 libfile-stripnondeterminism-perl_1.14.0-1 libgcc-13-dev_13.2.0-25 libgcc-s1_14.1.0-1 libgcrypt20_1.10.3-3 libgdbm-compat4t64_1.23-5.1+b1 libgdbm6t64_1.23-5.1+b1 libgmp10_2:6.3.0+dfsg-2+b1 libgnutls30t64_3.8.5-4 libgomp1_14.1.0-1 libgpg-error0_1.49-2 libgprofng0_2.42-4 libgsl-dev_2.7.1+dfsg-6+b1 libgsl27_2.7.1+dfsg-6+b1 libgslcblas0_2.7.1+dfsg-6+b1 libgssapi-krb5-2_1.20.1-6+b1 libhogweed6t64_3.9.1-2.2 libhts-dev_1.20+ds-1 libhts3t64_1.20+ds-1 libhtscodecs2_1.6.0-1+b1 libhwasan0_14.1.0-1 libicu72_72.1-4+b1 libidn2-0_2.3.7-2 libio-pty-perl_1:1.20-1+b2 libisl23_0.26-3+b2 libitm1_14.1.0-1 libjansson4_2.14-2+b2 libk5crypto3_1.20.1-6+b1 libkeyutils1_1.6.3-3 libkrb5-3_1.20.1-6+b1 libkrb5support0_1.20.1-6+b1 libksba8_1.6.6-1 libldap-2.5-0_2.5.17+dfsg-1+b1 liblsan0_14.1.0-1 liblz4-1_1.9.4-2 liblzma-dev_5.6.1+really5.4.5-1 liblzma5_5.6.1+really5.4.5-1 libmagic-mgc_1:5.45-3 libmagic1t64_1:5.45-3 libmd0_1.1.0-2 libmount1_2.40.1-7 libmpc3_1.3.1-1+b2 libmpfr6_4.2.1-1+b1 libncursesw6_6.5-2 libnettle8t64_3.9.1-2.2 libnghttp2-14_1.61.0-1+b1 libnpth0t64_1.6-3.1 libp11-kit0_0.25.3-5 libpam-modules_1.5.3-7 libpam-modules-bin_1.5.3-7 libpam-runtime_1.5.3-7 libpam0g_1.5.3-7 libpcre2-8-0_10.42-4+b1 libperl5.38t64_5.38.2-5 libperl5.40_5.40.0~rc1-1 libpipeline1_1.5.7-2 libpsl5t64_0.21.2-1.1 libquadmath0_14.1.0-1 libreadline8t64_8.2-4 librtmp1_2.4+20151223.gitfa8646d.1-2+b4 libsasl2-2_2.1.28+dfsg1-6 libsasl2-modules-db_2.1.28+dfsg1-6 libseccomp2_2.5.5-1 libselinux1_3.5-2+b2 libsemanage-common_3.5-1 libsemanage2_3.5-1+b3 libsepol2_3.5-2+b1 libsframe1_2.42-4 libsmartcols1_2.40.1-7 libsqlite3-0_3.46.0-1 libssh2-1t64_1.11.0-5 libssl3t64_3.2.1-3 libstdc++-13-dev_13.2.0-25 libstdc++6_14.1.0-1 libsystemd0_256~rc3-7 libtasn1-6_4.19.0-3+b2 libtinfo6_6.5-2 libtool_2.4.7-7 libtsan2_14.1.0-1 libubsan1_14.1.0-1 libuchardet0_0.0.8-1+b1 libudev1_256~rc3-7 libunistring5_1.2-1 libuuid1_2.40.1-7 libxml2_2.12.7+dfsg-2 libxxhash0_0.8.2-2+b1 libzstd1_1.5.5+dfsg2-2 linux-libc-dev_6.8.12-1 locales-all_2.38-12 login_1:4.13+dfsg1-4 m4_1.4.19-4 make_4.3-4.1 man-db_2.12.1-1 mawk_1.3.4.20240123-1 ncurses-base_6.5-2 ncurses-bin_6.5-2 passwd_1:4.13+dfsg1-4 patch_2.7.6-7 perl_5.40.0~rc1-1 perl-base_5.40.0~rc1-1 perl-modules-5.38_5.38.2-5 perl-modules-5.40_5.40.0~rc1-1 pinentry-curses_1.2.1-3+b2 po-debconf_1.0.21+nmu1 readline-common_8.2-4 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.22 sysvinit-utils_3.09-1 tabix_1.20+ds-1 tar_1.35+dfsg-3 usr-is-merged_39 util-linux_2.40.1-7 xz-utils_5.6.1+really5.4.5-1 zlib1g_1:1.3.dfsg+really1.3.1-1 zlib1g-dev_1:1.3.dfsg+really1.3.1-1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: bcftools Binary: bcftools Architecture: any Version: 1.20-1 Maintainer: Debian Med Packaging Team Uploaders: Michael R. Crusoe , Étienne Mollier Homepage: https://samtools.github.io/bcftools/ Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/bcftools Vcs-Git: https://salsa.debian.org/med-team/bcftools.git Testsuite: autopkgtest Testsuite-Triggers: perl, tabix Build-Depends: debhelper-compat (= 13), zlib1g-dev, libbz2-dev, liblzma-dev, libhts-dev (>= 1.14), libgsl-dev, tabix , libio-pty-perl Package-List: bcftools deb science optional arch=any Checksums-Sha1: a3505e61b1e5d646a0e221abe2698b8c42e71993 3621678 bcftools_1.20.orig.tar.gz 57185d0f9f03b467c1aed4d25e2b266bfa38f6bc 7796 bcftools_1.20-1.debian.tar.xz Checksums-Sha256: 7f34abf9bc0ded947e1a1409b65eda4a00eb17e33b71ba92b883902709840fbc 3621678 bcftools_1.20.orig.tar.gz 22aa10ee052576b64dfd4cca6dde6a50fea352d222bb1518b453430448690274 7796 bcftools_1.20-1.debian.tar.xz Files: c4b63687a028a08467f64f2a209c7dbd 3621678 bcftools_1.20.orig.tar.gz 1beeb07d6acfb6e408c0d2633e68ee34 7796 bcftools_1.20-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmYhS7gRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtEcshAAhLnC16iB7XfYQO/uE5MkE2qysdE96f/j VBTMYvpnb/v98GlHkADUS8/WVrjkXQvXwBbPxY7lkNMXJPqQeQJebmUnICR1ZZei NncsZiY+OsFNlHBBqFCPvROanl8rpgr8AOY+r/WHVddGPJAvXpWBcKnUMbDJbP0f Pk4bfpEIxZxuEnNBblPKaeyFLpBSILsJB1ZCncCHbIYC+U8q0891Qr083NrEhqxH PPyMZcyEBlEx22jhXPbzCLK91M3ufdHoZjAS2Ljg/jS5ltB4mGNgtlApbwk7elHG q/lrLwmIjZi6WOhKUyU+BUv2vGbtyUlRW2a569qjsuDvm/tHgH3fIX5VrFvtUdoO YFSVy+LALdP5HLcvM8ikPoRcwnoZ3KSWZUIMYp4u2PqtOKDRrG+7d1Y6bCDJnDAj zP1ZWxncs9KJHZJmHkzrSUu3eNABZUgIwnEaB6t00v2SfVSUoGGel+89HFkslsTU zkHeYmw7MJNGWSR88242RHw5hK/OR9kFbUjuMwGOTFxxNZXPYF8yhRQxiovd1ieX xT6zideAdKltuBYJR5y3Z9iehxMAqKuNL8fZ6KkAcm+AYAY5sR2Ssw9VL4SS0EQV 3XTwxAQSfTA5tbmlyJDcKQeV0wLBuCHeA+t2xidlgc0KuYK/x6V82/126oo06VjL nuhuEvh7QMY= =YmBq -----END PGP SIGNATURE----- gpgv: Signature made Thu Apr 18 16:35:04 2024 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./bcftools_1.20-1.dsc: no acceptable signature found dpkg-source: info: extracting bcftools in /<> dpkg-source: info: unpacking bcftools_1.20.orig.tar.gz dpkg-source: info: unpacking bcftools_1.20-1.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 +------------------------------------------------------------------------------+ | Starting Timed Build Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network bcftools_1.20-1 perl-5.40-throwaway amd64 ---------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network bcftools_1.20-1 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANG=en_GB.UTF-8 LANGUAGE=en_GB:en LC_ALL=C.UTF-8 LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so LOGNAME=debomatic PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games PWD=/<> SCHROOT_ALIAS_NAME=perl-5.40-throwaway-amd64-debomatic SCHROOT_CHROOT_NAME=perl-5.40-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=110 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=perl-5.40-amd64-debomatic-70a0a797-9ad2-4d4d-9b64-548e81a91d77 SCHROOT_UID=1002 SCHROOT_USER=debomatic SHELL=/bin/sh USER=debomatic dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -rfakeroot -Zxz dpkg-buildpackage: info: source package bcftools dpkg-buildpackage: info: source version 1.20-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source -Zxz --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean rm -f config.mk && touch config.mk dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' dh_auto_clean make -j2 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 -f test/*.unsorted.hex test/*.unsorted.tsv rm -rf plugins/*.dSYM rm -f gmon.out *.o *.a *~ bcftools version.h rm -rf *.dSYM test/*.dSYM rm -f config.cache config.h config.log config.mk config.status rm -rf autom4te.cache rm -f TAGS make[2]: Leaving directory '/<>' 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 dpkg-source -Zxz -b . dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building bcftools using existing ./bcftools_1.20.orig.tar.gz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: building bcftools in bcftools_1.20-1.debian.tar.xz dpkg-source: info: building bcftools in bcftools_1.20-1.dsc debian/rules binary dh binary dh_update_autotools_config 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/x86_64-linux-gnu/bcftools ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system --enable-gsl --with-cblas=gslcblas --with-bcf-plugin-dir=/usr/lib/x86_64-linux-gnu/bcftools checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking for 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 make -j2 make[1]: Entering directory '/<>' echo '#define BCFTOOLS_VERSION "1.20"' > version.h gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfindex.o vcfindex.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tabix.o tabix.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfstats.o vcfstats.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfisec.o vcfisec.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfmerge.o vcfmerge.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfquery.o vcfquery.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcffilter.o vcffilter.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o filter.o filter.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfsom.o vcfsom.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfnorm.o vcfnorm.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfgtcheck.o vcfgtcheck.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfview.o vcfview.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfannotate.o vcfannotate.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfroh.o vcfroh.c gcc -Wall -g -O2 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tsv2vcf.o tsv2vcf.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfcnv.o vcfcnv.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfhead.o vcfhead.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o HMM.o HMM.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o consensus.o consensus.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ploidy.o ploidy.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bin.o bin.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hclust.o hclust.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o version.o version.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o regidx.o regidx.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o smpl_ilist.o smpl_ilist.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o csq.o csq.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfbuf.o vcfbuf.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mpileup.o mpileup.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_iaux.o bam2bcf_iaux.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_edlib.o bam2bcf_edlib.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o read_consensus.o read_consensus.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sample.o bam_sample.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcfsort.o vcfsort.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cols.o cols.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o extsort.o extsort.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dist.o dist.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o abuf.o abuf.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ccall.o ccall.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o em.o em.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o prob1.o prob1.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kmin.o kmin.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o str_finder.o str_finder.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gff.o gff.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o edlib.o edlib.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DPLUGINPATH='"/usr/lib/x86_64-linux-gnu/bcftools"' -c -o vcfplugin.o vcfplugin.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-rbuf.o test/test-rbuf.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test-regidx.o test/test-regidx.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/GTisec.so version.c plugins/GTisec.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/GTsubset.so version.c plugins/GTsubset.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/ad-bias.so convert.c version.c plugins/ad-bias.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/add-variantkey.so version.c plugins/add-variantkey.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/af-dist.so bin.c version.c plugins/af-dist.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/allele-length.so version.c plugins/allele-length.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/check-ploidy.so version.c plugins/check-ploidy.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/check-sparsity.so version.c plugins/check-sparsity.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/color-chrs.so HMM.c version.c plugins/color-chrs.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/contrast.so version.c plugins/contrast.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/counts.so version.c plugins/counts.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/dosage.so version.c plugins/dosage.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fill-AN-AC.so version.c plugins/fill-AN-AC.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fill-from-fasta.so filter.c version.c plugins/fill-from-fasta.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fill-tags.so version.c plugins/fill-tags.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fixploidy.so ploidy.c regidx.c version.c plugins/fixploidy.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/fixref.so version.c plugins/fixref.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/frameshifts.so version.c plugins/frameshifts.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/guess-ploidy.so version.c plugins/guess-ploidy.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/gvcfz.so version.c plugins/gvcfz.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/impute-info.so version.c plugins/impute-info.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/indel-stats.so version.c plugins/indel-stats.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/isecGT.so smpl_ilist.c version.c plugins/isecGT.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/mendelian2.so version.c plugins/mendelian2.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/missing2ref.so version.c plugins/missing2ref.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/parental-origin.so version.c plugins/parental-origin.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/prune.so version.c plugins/prune.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/remove-overlaps.so version.c plugins/remove-overlaps.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/scatter.so version.c plugins/scatter.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/setGT.so version.c plugins/setGT.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/smpl-stats.so version.c plugins/smpl-stats.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/split-vep.so version.c plugins/split-vep.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/split.so version.c plugins/split.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/tag2tag.so version.c plugins/tag2tag.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/trio-dnm2.so version.c plugins/trio-dnm2.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/trio-stats.so version.c plugins/trio-stats.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/trio-switch-rate.so version.c plugins/trio-switch-rate.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/variant-distance.so version.c plugins/variant-distance.c gcc -fPIC -shared -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -o plugins/variantkey-hex.so version.c plugins/variantkey-hex.c gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o main.o main.c gcc -Wl,-z,relro -o test/test-rbuf test/test-rbuf.o -lz gcc -Wl,-z,relro -o test/test-regidx test/test-regidx.o regidx.o -lhts -lpthread -lz gcc -rdynamic -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 vcfhead.o HMM.o consensus.o ploidy.o bin.o hclust.o version.o regidx.o smpl_ilist.o csq.o vcfbuf.o mpileup.o bam2bcf.o bam2bcf_indel.o bam2bcf_iaux.o bam2bcf_edlib.o read_consensus.o bam_sample.o vcfsort.o cols.o extsort.o dist.o abuf.o ccall.o em.o prob1.o kmin.o str_finder.o gff.o edlib.o vcfplugin.o -lhts -lm -lz -lpthread make[1]: Leaving directory '/<>' 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 head .. ok test_usage_subcommand: bcftools isec .. ok test_usage_subcommand: bcftools merge .. ok test_usage_subcommand: bcftools norm .. ok test_usage_subcommand: bcftools plugin .. ok test_usage_subcommand: bcftools query .. ok test_usage_subcommand: bcftools reheader .. ok test_usage_subcommand: bcftools sort .. ok test_usage_subcommand: bcftools view .. ok test_usage_subcommand: bcftools call .. ok test_usage_subcommand: bcftools consensus .. ok test_usage_subcommand: bcftools cnv .. ok test_usage_subcommand: bcftools csq .. ok test_usage_subcommand: bcftools filter .. ok test_usage_subcommand: bcftools gtcheck .. ok test_usage_subcommand: bcftools mpileup .. ok test_usage_subcommand: bcftools roh .. ok test_usage_subcommand: bcftools stats .. ok test_tabix: tabix /tmp/zey1Mm0xMJ/merge.a.vcf.gz 2:3199812-3199812 .. ok test_tabix: /<>/bcftools view -H /tmp/zey1Mm0xMJ/merge.a.bcf 2:3199812-3199812 .. ok test_tabix: tabix /tmp/zey1Mm0xMJ/merge.a.vcf.gz 1:3000151-3000151 .. ok test_tabix: /<>/bcftools view -H /tmp/zey1Mm0xMJ/merge.a.bcf 1:3000151-3000151 .. ok test_index: /<>/bcftools view -H /tmp/zey1Mm0xMJ/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/zey1Mm0xMJ/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/zey1Mm0xMJ/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/zey1Mm0xMJ/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/zey1Mm0xMJ/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/zey1Mm0xMJ/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /<>/bcftools view -H /tmp/zey1Mm0xMJ/large_chrom_csi_limit.bcf chr20 .. ok test_index: /<>/bcftools view -H /tmp/zey1Mm0xMJ/large_chrom_csi_limit.bcf chr20 .. ok test_index: /<>/bcftools view -H /tmp/zey1Mm0xMJ/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /<>/bcftools view -H /tmp/zey1Mm0xMJ/large_chrom_csi_limit.bcf chr20 .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/zey1Mm0xMJ/idx.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/zey1Mm0xMJ/idx.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/zey1Mm0xMJ/idx.bcf .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/zey1Mm0xMJ/idx.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/zey1Mm0xMJ/idx.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/zey1Mm0xMJ/idx.vcf.gz.csi .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/zey1Mm0xMJ/idx.bcf .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/zey1Mm0xMJ/idx.bcf.csi .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/zey1Mm0xMJ/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/zey1Mm0xMJ/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/zey1Mm0xMJ/empty.bcf .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/zey1Mm0xMJ/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/zey1Mm0xMJ/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/zey1Mm0xMJ/empty.vcf.gz.csi .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/zey1Mm0xMJ/empty.bcf .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/zey1Mm0xMJ/empty.bcf.csi .. ok test_vcf_check: /<>/bcftools stats -s - /tmp/zey1Mm0xMJ/check.vcf.gz | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/check.1.chk /tmp/zey1Mm0xMJ/check.2.chk /tmp/zey1Mm0xMJ/check.3.chk /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/stats.a.vcf.gz /tmp/zey1Mm0xMJ/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /<>/bcftools stats -s B /tmp/zey1Mm0xMJ/stats.a.vcf.gz /tmp/zey1Mm0xMJ/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /<>/bcftools stats -s - /tmp/zey1Mm0xMJ/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /<>/bcftools stats -s - -i 'type="snp"' /tmp/zey1Mm0xMJ/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /<>/bcftools stats -s - /tmp/zey1Mm0xMJ/stats.vaf.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_isec: /<>/bcftools isec -n =2 /tmp/zey1Mm0xMJ/isec.a.vcf.gz /tmp/zey1Mm0xMJ/isec.b.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 /tmp/zey1Mm0xMJ/isec.a.vcf.gz /tmp/zey1Mm0xMJ/isec.b.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/zey1Mm0xMJ/isec.a.vcf.gz /tmp/zey1Mm0xMJ/isec.b.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 -i"STRLEN(REF)==2" /tmp/zey1Mm0xMJ/isec.a.vcf.gz /tmp/zey1Mm0xMJ/isec.b.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -n =2 -c both /tmp/zey1Mm0xMJ/isec.a.vcf.gz /tmp/zey1Mm0xMJ/isec.b.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 -c both /tmp/zey1Mm0xMJ/isec.a.vcf.gz /tmp/zey1Mm0xMJ/isec.b.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -n =2 -c any /tmp/zey1Mm0xMJ/isec.a.vcf.gz /tmp/zey1Mm0xMJ/isec.b.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 -c any /tmp/zey1Mm0xMJ/isec.a.vcf.gz /tmp/zey1Mm0xMJ/isec.b.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -C -c any /tmp/zey1Mm0xMJ/isec.a.vcf.gz /tmp/zey1Mm0xMJ/isec.b.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -Ob -C -c any /tmp/zey1Mm0xMJ/isec.a.vcf.gz /tmp/zey1Mm0xMJ/isec.b.vcf.gz .. ok test_vcf_isec2: /<>/bcftools isec --no-version -T /tmp/zey1Mm0xMJ/isec.tab.gz /tmp/zey1Mm0xMJ/isec.a.vcf.gz .. ok test_vcf_isec2: /<>/bcftools isec -Ob -T /tmp/zey1Mm0xMJ/isec.tab.gz /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/isec-miss.1.1.vcf.gz /tmp/zey1Mm0xMJ/isec-miss.1.2.vcf.gz /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/isec-miss.1.1.vcf.gz /tmp/zey1Mm0xMJ/isec-miss.1.2.vcf.gz /tmp/zey1Mm0xMJ/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -R /<>/test/isec-miss.1.regs.txt -n +1 /tmp/zey1Mm0xMJ/isec-miss.1.1.vcf.gz /tmp/zey1Mm0xMJ/isec-miss.1.2.vcf.gz /tmp/zey1Mm0xMJ/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -Ob -R /<>/test/isec-miss.1.regs.txt -n +1 /tmp/zey1Mm0xMJ/isec-miss.1.1.vcf.gz /tmp/zey1Mm0xMJ/isec-miss.1.2.vcf.gz /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/isec-miss.2.1.vcf.gz /tmp/zey1Mm0xMJ/isec-miss.2.2.vcf.gz /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/isec-miss.2.1.vcf.gz /tmp/zey1Mm0xMJ/isec-miss.2.2.vcf.gz /tmp/zey1Mm0xMJ/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -R /<>/test/isec-miss.1.regs.txt -n +1 /tmp/zey1Mm0xMJ/isec-miss.2.1.vcf.gz /tmp/zey1Mm0xMJ/isec-miss.2.2.vcf.gz /tmp/zey1Mm0xMJ/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -Ob -R /<>/test/isec-miss.1.regs.txt -n +1 /tmp/zey1Mm0xMJ/isec-miss.2.1.vcf.gz /tmp/zey1Mm0xMJ/isec-miss.2.2.vcf.gz /tmp/zey1Mm0xMJ/isec-miss.2.3.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -i AF:join /tmp/zey1Mm0xMJ/merge.join.a.vcf.gz /tmp/zey1Mm0xMJ/merge.join.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob -i AF:join /tmp/zey1Mm0xMJ/merge.join.a.vcf.gz /tmp/zey1Mm0xMJ/merge.join.b.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version -i AF:join /tmp/zey1Mm0xMJ/merge.join.a.bcf /tmp/zey1Mm0xMJ/merge.join.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob -i AF:join /tmp/zey1Mm0xMJ/merge.join.a.bcf /tmp/zey1Mm0xMJ/merge.join.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-single /tmp/zey1Mm0xMJ/merge.LPL.a.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-single /tmp/zey1Mm0xMJ/merge.LPL.a.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-single /tmp/zey1Mm0xMJ/merge.LPL.a.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-single /tmp/zey1Mm0xMJ/merge.LPL.a.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples /tmp/zey1Mm0xMJ/merge.LPL.a.vcf.gz /tmp/zey1Mm0xMJ/merge.LPL.b.vcf.gz /tmp/zey1Mm0xMJ/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples /tmp/zey1Mm0xMJ/merge.LPL.a.vcf.gz /tmp/zey1Mm0xMJ/merge.LPL.b.vcf.gz /tmp/zey1Mm0xMJ/merge.LPL.c.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples /tmp/zey1Mm0xMJ/merge.LPL.a.bcf /tmp/zey1Mm0xMJ/merge.LPL.b.bcf /tmp/zey1Mm0xMJ/merge.LPL.c.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples /tmp/zey1Mm0xMJ/merge.LPL.a.bcf /tmp/zey1Mm0xMJ/merge.LPL.b.bcf /tmp/zey1Mm0xMJ/merge.LPL.c.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -L 1 /tmp/zey1Mm0xMJ/merge.LPL.a.vcf.gz /tmp/zey1Mm0xMJ/merge.LPL.b.vcf.gz /tmp/zey1Mm0xMJ/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -L 1 /tmp/zey1Mm0xMJ/merge.LPL.a.vcf.gz /tmp/zey1Mm0xMJ/merge.LPL.b.vcf.gz /tmp/zey1Mm0xMJ/merge.LPL.c.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -L 1 /tmp/zey1Mm0xMJ/merge.LPL.a.bcf /tmp/zey1Mm0xMJ/merge.LPL.b.bcf /tmp/zey1Mm0xMJ/merge.LPL.c.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -L 1 /tmp/zey1Mm0xMJ/merge.LPL.a.bcf /tmp/zey1Mm0xMJ/merge.LPL.b.bcf /tmp/zey1Mm0xMJ/merge.LPL.c.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -L 2 /tmp/zey1Mm0xMJ/merge.LPL.a.vcf.gz /tmp/zey1Mm0xMJ/merge.LPL.b.vcf.gz /tmp/zey1Mm0xMJ/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -L 2 /tmp/zey1Mm0xMJ/merge.LPL.a.vcf.gz /tmp/zey1Mm0xMJ/merge.LPL.b.vcf.gz /tmp/zey1Mm0xMJ/merge.LPL.c.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -L 2 /tmp/zey1Mm0xMJ/merge.LPL.a.bcf /tmp/zey1Mm0xMJ/merge.LPL.b.bcf /tmp/zey1Mm0xMJ/merge.LPL.c.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -L 2 /tmp/zey1Mm0xMJ/merge.LPL.a.bcf /tmp/zey1Mm0xMJ/merge.LPL.b.bcf /tmp/zey1Mm0xMJ/merge.LPL.c.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -L 3 /tmp/zey1Mm0xMJ/merge.LPL.a.vcf.gz /tmp/zey1Mm0xMJ/merge.LPL.b.vcf.gz /tmp/zey1Mm0xMJ/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -L 3 /tmp/zey1Mm0xMJ/merge.LPL.a.vcf.gz /tmp/zey1Mm0xMJ/merge.LPL.b.vcf.gz /tmp/zey1Mm0xMJ/merge.LPL.c.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -L 3 /tmp/zey1Mm0xMJ/merge.LPL.a.bcf /tmp/zey1Mm0xMJ/merge.LPL.b.bcf /tmp/zey1Mm0xMJ/merge.LPL.c.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -L 3 /tmp/zey1Mm0xMJ/merge.LPL.a.bcf /tmp/zey1Mm0xMJ/merge.LPL.b.bcf /tmp/zey1Mm0xMJ/merge.LPL.c.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -L 4 /tmp/zey1Mm0xMJ/merge.LPL.a.vcf.gz /tmp/zey1Mm0xMJ/merge.LPL.b.vcf.gz /tmp/zey1Mm0xMJ/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -L 4 /tmp/zey1Mm0xMJ/merge.LPL.a.vcf.gz /tmp/zey1Mm0xMJ/merge.LPL.b.vcf.gz /tmp/zey1Mm0xMJ/merge.LPL.c.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -L 4 /tmp/zey1Mm0xMJ/merge.LPL.a.bcf /tmp/zey1Mm0xMJ/merge.LPL.b.bcf /tmp/zey1Mm0xMJ/merge.LPL.c.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -L 4 /tmp/zey1Mm0xMJ/merge.LPL.a.bcf /tmp/zey1Mm0xMJ/merge.LPL.b.bcf /tmp/zey1Mm0xMJ/merge.LPL.c.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -L 5 /tmp/zey1Mm0xMJ/merge.LPL.a.vcf.gz /tmp/zey1Mm0xMJ/merge.LPL.b.vcf.gz /tmp/zey1Mm0xMJ/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -L 5 /tmp/zey1Mm0xMJ/merge.LPL.a.vcf.gz /tmp/zey1Mm0xMJ/merge.LPL.b.vcf.gz /tmp/zey1Mm0xMJ/merge.LPL.c.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -L 5 /tmp/zey1Mm0xMJ/merge.LPL.a.bcf /tmp/zey1Mm0xMJ/merge.LPL.b.bcf /tmp/zey1Mm0xMJ/merge.LPL.c.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -L 5 /tmp/zey1Mm0xMJ/merge.LPL.a.bcf /tmp/zey1Mm0xMJ/merge.LPL.b.bcf /tmp/zey1Mm0xMJ/merge.LPL.c.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples /tmp/zey1Mm0xMJ/merge.a.vcf.gz /tmp/zey1Mm0xMJ/merge.b.vcf.gz /tmp/zey1Mm0xMJ/merge.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples /tmp/zey1Mm0xMJ/merge.a.vcf.gz /tmp/zey1Mm0xMJ/merge.b.vcf.gz /tmp/zey1Mm0xMJ/merge.c.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples /tmp/zey1Mm0xMJ/merge.a.bcf /tmp/zey1Mm0xMJ/merge.b.bcf /tmp/zey1Mm0xMJ/merge.c.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples /tmp/zey1Mm0xMJ/merge.a.bcf /tmp/zey1Mm0xMJ/merge.b.bcf /tmp/zey1Mm0xMJ/merge.c.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -Fx /tmp/zey1Mm0xMJ/merge.a.vcf.gz /tmp/zey1Mm0xMJ/merge.b.vcf.gz /tmp/zey1Mm0xMJ/merge.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -Fx /tmp/zey1Mm0xMJ/merge.a.vcf.gz /tmp/zey1Mm0xMJ/merge.b.vcf.gz /tmp/zey1Mm0xMJ/merge.c.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -Fx /tmp/zey1Mm0xMJ/merge.a.bcf /tmp/zey1Mm0xMJ/merge.b.bcf /tmp/zey1Mm0xMJ/merge.c.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -Fx /tmp/zey1Mm0xMJ/merge.a.bcf /tmp/zey1Mm0xMJ/merge.b.bcf /tmp/zey1Mm0xMJ/merge.c.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -0 /tmp/zey1Mm0xMJ/merge.a.vcf.gz /tmp/zey1Mm0xMJ/merge.b.vcf.gz /tmp/zey1Mm0xMJ/merge.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -0 /tmp/zey1Mm0xMJ/merge.a.vcf.gz /tmp/zey1Mm0xMJ/merge.b.vcf.gz /tmp/zey1Mm0xMJ/merge.c.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -0 /tmp/zey1Mm0xMJ/merge.a.bcf /tmp/zey1Mm0xMJ/merge.b.bcf /tmp/zey1Mm0xMJ/merge.c.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -0 /tmp/zey1Mm0xMJ/merge.a.bcf /tmp/zey1Mm0xMJ/merge.b.bcf /tmp/zey1Mm0xMJ/merge.c.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -m none /tmp/zey1Mm0xMJ/merge.2.a.vcf.gz /tmp/zey1Mm0xMJ/merge.2.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -m none /tmp/zey1Mm0xMJ/merge.2.a.vcf.gz /tmp/zey1Mm0xMJ/merge.2.b.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -m none /tmp/zey1Mm0xMJ/merge.2.a.bcf /tmp/zey1Mm0xMJ/merge.2.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -m none /tmp/zey1Mm0xMJ/merge.2.a.bcf /tmp/zey1Mm0xMJ/merge.2.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -m both /tmp/zey1Mm0xMJ/merge.2.a.vcf.gz /tmp/zey1Mm0xMJ/merge.2.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -m both /tmp/zey1Mm0xMJ/merge.2.a.vcf.gz /tmp/zey1Mm0xMJ/merge.2.b.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -m both /tmp/zey1Mm0xMJ/merge.2.a.bcf /tmp/zey1Mm0xMJ/merge.2.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -m both /tmp/zey1Mm0xMJ/merge.2.a.bcf /tmp/zey1Mm0xMJ/merge.2.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -m all /tmp/zey1Mm0xMJ/merge.2.a.vcf.gz /tmp/zey1Mm0xMJ/merge.2.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -m all /tmp/zey1Mm0xMJ/merge.2.a.vcf.gz /tmp/zey1Mm0xMJ/merge.2.b.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -m all /tmp/zey1Mm0xMJ/merge.2.a.bcf /tmp/zey1Mm0xMJ/merge.2.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -m all /tmp/zey1Mm0xMJ/merge.2.a.bcf /tmp/zey1Mm0xMJ/merge.2.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/zey1Mm0xMJ/merge.3.a.vcf.gz /tmp/zey1Mm0xMJ/merge.3.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/zey1Mm0xMJ/merge.3.a.vcf.gz /tmp/zey1Mm0xMJ/merge.3.b.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -i TR:sum,TA:sum,TG:sum /tmp/zey1Mm0xMJ/merge.3.a.bcf /tmp/zey1Mm0xMJ/merge.3.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/zey1Mm0xMJ/merge.3.a.bcf /tmp/zey1Mm0xMJ/merge.3.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -m id /tmp/zey1Mm0xMJ/merge.4.a.vcf.gz /tmp/zey1Mm0xMJ/merge.4.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -m id /tmp/zey1Mm0xMJ/merge.4.a.vcf.gz /tmp/zey1Mm0xMJ/merge.4.b.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -m id /tmp/zey1Mm0xMJ/merge.4.a.bcf /tmp/zey1Mm0xMJ/merge.4.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -m id /tmp/zey1Mm0xMJ/merge.4.a.bcf /tmp/zey1Mm0xMJ/merge.4.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/zey1Mm0xMJ/gvcf.merge.1.vcf.gz /tmp/zey1Mm0xMJ/gvcf.merge.2.vcf.gz /tmp/zey1Mm0xMJ/gvcf.merge.3.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - /tmp/zey1Mm0xMJ/gvcf.merge.1.vcf.gz /tmp/zey1Mm0xMJ/gvcf.merge.2.vcf.gz /tmp/zey1Mm0xMJ/gvcf.merge.3.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/zey1Mm0xMJ/gvcf.merge.1.bcf /tmp/zey1Mm0xMJ/gvcf.merge.2.bcf /tmp/zey1Mm0xMJ/gvcf.merge.3.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - /tmp/zey1Mm0xMJ/gvcf.merge.1.bcf /tmp/zey1Mm0xMJ/gvcf.merge.2.bcf /tmp/zey1Mm0xMJ/gvcf.merge.3.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/zey1Mm0xMJ/merge.gvcf.2.a.vcf.gz /tmp/zey1Mm0xMJ/merge.gvcf.2.b.vcf.gz /tmp/zey1Mm0xMJ/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - /tmp/zey1Mm0xMJ/merge.gvcf.2.a.vcf.gz /tmp/zey1Mm0xMJ/merge.gvcf.2.b.vcf.gz /tmp/zey1Mm0xMJ/merge.gvcf.2.c.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - -m both,* /tmp/zey1Mm0xMJ/merge.gvcf.2.a.vcf.gz /tmp/zey1Mm0xMJ/merge.gvcf.2.b.vcf.gz /tmp/zey1Mm0xMJ/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - -m both,* /tmp/zey1Mm0xMJ/merge.gvcf.2.a.vcf.gz /tmp/zey1Mm0xMJ/merge.gvcf.2.b.vcf.gz /tmp/zey1Mm0xMJ/merge.gvcf.2.c.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - -m both,** /tmp/zey1Mm0xMJ/merge.gvcf.2.a.vcf.gz /tmp/zey1Mm0xMJ/merge.gvcf.2.b.vcf.gz /tmp/zey1Mm0xMJ/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - -m both,** /tmp/zey1Mm0xMJ/merge.gvcf.2.a.vcf.gz /tmp/zey1Mm0xMJ/merge.gvcf.2.b.vcf.gz /tmp/zey1Mm0xMJ/merge.gvcf.2.c.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - -i SRC:join /tmp/zey1Mm0xMJ/merge.gvcf.3.a.vcf.gz /tmp/zey1Mm0xMJ/merge.gvcf.3.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - -i SRC:join /tmp/zey1Mm0xMJ/merge.gvcf.3.a.vcf.gz /tmp/zey1Mm0xMJ/merge.gvcf.3.b.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/zey1Mm0xMJ/merge.gvcf.4.a.vcf.gz /tmp/zey1Mm0xMJ/merge.gvcf.4.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - /tmp/zey1Mm0xMJ/merge.gvcf.4.a.vcf.gz /tmp/zey1Mm0xMJ/merge.gvcf.4.b.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/zey1Mm0xMJ/merge.gvcf.4.a.bcf /tmp/zey1Mm0xMJ/merge.gvcf.4.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - /tmp/zey1Mm0xMJ/merge.gvcf.4.a.bcf /tmp/zey1Mm0xMJ/merge.gvcf.4.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version /tmp/zey1Mm0xMJ/merge.5.a.vcf.gz /tmp/zey1Mm0xMJ/merge.5.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob /tmp/zey1Mm0xMJ/merge.5.a.vcf.gz /tmp/zey1Mm0xMJ/merge.5.b.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version /tmp/zey1Mm0xMJ/merge.5.a.bcf /tmp/zey1Mm0xMJ/merge.5.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob /tmp/zey1Mm0xMJ/merge.5.a.bcf /tmp/zey1Mm0xMJ/merge.5.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version /tmp/zey1Mm0xMJ/merge.6.a.vcf.gz /tmp/zey1Mm0xMJ/merge.6.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob /tmp/zey1Mm0xMJ/merge.6.a.vcf.gz /tmp/zey1Mm0xMJ/merge.6.b.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version /tmp/zey1Mm0xMJ/merge.6.a.bcf /tmp/zey1Mm0xMJ/merge.6.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob /tmp/zey1Mm0xMJ/merge.6.a.bcf /tmp/zey1Mm0xMJ/merge.6.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/zey1Mm0xMJ/merge.gvcf.7.a.vcf.gz /tmp/zey1Mm0xMJ/merge.gvcf.7.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - /tmp/zey1Mm0xMJ/merge.gvcf.7.a.vcf.gz /tmp/zey1Mm0xMJ/merge.gvcf.7.b.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/zey1Mm0xMJ/merge.gvcf.7.a.bcf /tmp/zey1Mm0xMJ/merge.gvcf.7.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - /tmp/zey1Mm0xMJ/merge.gvcf.7.a.bcf /tmp/zey1Mm0xMJ/merge.gvcf.7.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/zey1Mm0xMJ/merge.gvcf.8.a.vcf.gz /tmp/zey1Mm0xMJ/merge.gvcf.8.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - /tmp/zey1Mm0xMJ/merge.gvcf.8.a.vcf.gz /tmp/zey1Mm0xMJ/merge.gvcf.8.b.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/zey1Mm0xMJ/merge.gvcf.8.a.bcf /tmp/zey1Mm0xMJ/merge.gvcf.8.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - /tmp/zey1Mm0xMJ/merge.gvcf.8.a.bcf /tmp/zey1Mm0xMJ/merge.gvcf.8.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples /tmp/zey1Mm0xMJ/merge.7.a.vcf.gz /tmp/zey1Mm0xMJ/merge.7.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples /tmp/zey1Mm0xMJ/merge.7.a.vcf.gz /tmp/zey1Mm0xMJ/merge.7.b.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples /tmp/zey1Mm0xMJ/merge.7.a.bcf /tmp/zey1Mm0xMJ/merge.7.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples /tmp/zey1Mm0xMJ/merge.7.a.bcf /tmp/zey1Mm0xMJ/merge.7.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf /<>/test/gvcf.fa /tmp/zey1Mm0xMJ/merge.gvcf.9a.vcf.gz /tmp/zey1Mm0xMJ/merge.gvcf.9b.vcf.gz /tmp/zey1Mm0xMJ/merge.gvcf.9c.vcf.gz /tmp/zey1Mm0xMJ/merge.gvcf.9d.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf /<>/test/gvcf.fa /tmp/zey1Mm0xMJ/merge.gvcf.9a.vcf.gz /tmp/zey1Mm0xMJ/merge.gvcf.9b.vcf.gz /tmp/zey1Mm0xMJ/merge.gvcf.9c.vcf.gz /tmp/zey1Mm0xMJ/merge.gvcf.9d.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf /<>/test/gvcf.fa /tmp/zey1Mm0xMJ/merge.gvcf.9a.bcf /tmp/zey1Mm0xMJ/merge.gvcf.9b.bcf /tmp/zey1Mm0xMJ/merge.gvcf.9c.bcf /tmp/zey1Mm0xMJ/merge.gvcf.9d.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf /<>/test/gvcf.fa /tmp/zey1Mm0xMJ/merge.gvcf.9a.bcf /tmp/zey1Mm0xMJ/merge.gvcf.9b.bcf /tmp/zey1Mm0xMJ/merge.gvcf.9c.bcf /tmp/zey1Mm0xMJ/merge.gvcf.9d.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf /<>/test/gvcf.fa -r 22:21-23 /tmp/zey1Mm0xMJ/merge.gvcf.9a.vcf.gz /tmp/zey1Mm0xMJ/merge.gvcf.9b.vcf.gz /tmp/zey1Mm0xMJ/merge.gvcf.9c.vcf.gz /tmp/zey1Mm0xMJ/merge.gvcf.9d.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf /<>/test/gvcf.fa -r 22:21-23 /tmp/zey1Mm0xMJ/merge.gvcf.9a.vcf.gz /tmp/zey1Mm0xMJ/merge.gvcf.9b.vcf.gz /tmp/zey1Mm0xMJ/merge.gvcf.9c.vcf.gz /tmp/zey1Mm0xMJ/merge.gvcf.9d.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf /<>/test/gvcf.fa -r 22:21-23 /tmp/zey1Mm0xMJ/merge.gvcf.9a.bcf /tmp/zey1Mm0xMJ/merge.gvcf.9b.bcf /tmp/zey1Mm0xMJ/merge.gvcf.9c.bcf /tmp/zey1Mm0xMJ/merge.gvcf.9d.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf /<>/test/gvcf.fa -r 22:21-23 /tmp/zey1Mm0xMJ/merge.gvcf.9a.bcf /tmp/zey1Mm0xMJ/merge.gvcf.9b.bcf /tmp/zey1Mm0xMJ/merge.gvcf.9c.bcf /tmp/zey1Mm0xMJ/merge.gvcf.9d.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf /<>/test/gvcf.fa /tmp/zey1Mm0xMJ/merge.gvcf.9a.vcf.gz /tmp/zey1Mm0xMJ/merge.gvcf.9b.vcf.gz /tmp/zey1Mm0xMJ/merge.gvcf.9c.vcf.gz /tmp/zey1Mm0xMJ/merge.gvcf.9d.vcf.gz /tmp/zey1Mm0xMJ/merge.gvcf.9e.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf /<>/test/gvcf.fa /tmp/zey1Mm0xMJ/merge.gvcf.9a.vcf.gz /tmp/zey1Mm0xMJ/merge.gvcf.9b.vcf.gz /tmp/zey1Mm0xMJ/merge.gvcf.9c.vcf.gz /tmp/zey1Mm0xMJ/merge.gvcf.9d.vcf.gz /tmp/zey1Mm0xMJ/merge.gvcf.9e.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf /<>/test/gvcf.fa /tmp/zey1Mm0xMJ/merge.gvcf.9a.bcf /tmp/zey1Mm0xMJ/merge.gvcf.9b.bcf /tmp/zey1Mm0xMJ/merge.gvcf.9c.bcf /tmp/zey1Mm0xMJ/merge.gvcf.9d.bcf /tmp/zey1Mm0xMJ/merge.gvcf.9e.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf /<>/test/gvcf.fa /tmp/zey1Mm0xMJ/merge.gvcf.9a.bcf /tmp/zey1Mm0xMJ/merge.gvcf.9b.bcf /tmp/zey1Mm0xMJ/merge.gvcf.9c.bcf /tmp/zey1Mm0xMJ/merge.gvcf.9d.bcf /tmp/zey1Mm0xMJ/merge.gvcf.9e.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf /<>/test/gvcf.fa -r 22:21-23 /tmp/zey1Mm0xMJ/merge.gvcf.9a.vcf.gz /tmp/zey1Mm0xMJ/merge.gvcf.9b.vcf.gz /tmp/zey1Mm0xMJ/merge.gvcf.9c.vcf.gz /tmp/zey1Mm0xMJ/merge.gvcf.9d.vcf.gz /tmp/zey1Mm0xMJ/merge.gvcf.9e.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf /<>/test/gvcf.fa -r 22:21-23 /tmp/zey1Mm0xMJ/merge.gvcf.9a.vcf.gz /tmp/zey1Mm0xMJ/merge.gvcf.9b.vcf.gz /tmp/zey1Mm0xMJ/merge.gvcf.9c.vcf.gz /tmp/zey1Mm0xMJ/merge.gvcf.9d.vcf.gz /tmp/zey1Mm0xMJ/merge.gvcf.9e.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf /<>/test/gvcf.fa -r 22:21-23 /tmp/zey1Mm0xMJ/merge.gvcf.9a.bcf /tmp/zey1Mm0xMJ/merge.gvcf.9b.bcf /tmp/zey1Mm0xMJ/merge.gvcf.9c.bcf /tmp/zey1Mm0xMJ/merge.gvcf.9d.bcf /tmp/zey1Mm0xMJ/merge.gvcf.9e.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf /<>/test/gvcf.fa -r 22:21-23 /tmp/zey1Mm0xMJ/merge.gvcf.9a.bcf /tmp/zey1Mm0xMJ/merge.gvcf.9b.bcf /tmp/zey1Mm0xMJ/merge.gvcf.9c.bcf /tmp/zey1Mm0xMJ/merge.gvcf.9d.bcf /tmp/zey1Mm0xMJ/merge.gvcf.9e.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version /tmp/zey1Mm0xMJ/merge.gvcf.10.a.vcf.gz /tmp/zey1Mm0xMJ/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob /tmp/zey1Mm0xMJ/merge.gvcf.10.a.vcf.gz /tmp/zey1Mm0xMJ/merge.gvcf.10.b.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version /tmp/zey1Mm0xMJ/merge.gvcf.10.a.bcf /tmp/zey1Mm0xMJ/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob /tmp/zey1Mm0xMJ/merge.gvcf.10.a.bcf /tmp/zey1Mm0xMJ/merge.gvcf.10.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version -m none /tmp/zey1Mm0xMJ/merge.gvcf.10.a.vcf.gz /tmp/zey1Mm0xMJ/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob -m none /tmp/zey1Mm0xMJ/merge.gvcf.10.a.vcf.gz /tmp/zey1Mm0xMJ/merge.gvcf.10.b.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version -m none /tmp/zey1Mm0xMJ/merge.gvcf.10.a.bcf /tmp/zey1Mm0xMJ/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob -m none /tmp/zey1Mm0xMJ/merge.gvcf.10.a.bcf /tmp/zey1Mm0xMJ/merge.gvcf.10.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version -g /<>/test/merge.gvcf.10.fa /tmp/zey1Mm0xMJ/merge.gvcf.10.a.vcf.gz /tmp/zey1Mm0xMJ/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob -g /<>/test/merge.gvcf.10.fa /tmp/zey1Mm0xMJ/merge.gvcf.10.a.vcf.gz /tmp/zey1Mm0xMJ/merge.gvcf.10.b.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version -g /<>/test/merge.gvcf.10.fa /tmp/zey1Mm0xMJ/merge.gvcf.10.a.bcf /tmp/zey1Mm0xMJ/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob -g /<>/test/merge.gvcf.10.fa /tmp/zey1Mm0xMJ/merge.gvcf.10.a.bcf /tmp/zey1Mm0xMJ/merge.gvcf.10.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version -g /<>/test/merge.gvcf.10.fa -m none /tmp/zey1Mm0xMJ/merge.gvcf.10.a.vcf.gz /tmp/zey1Mm0xMJ/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob -g /<>/test/merge.gvcf.10.fa -m none /tmp/zey1Mm0xMJ/merge.gvcf.10.a.vcf.gz /tmp/zey1Mm0xMJ/merge.gvcf.10.b.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version -g /<>/test/merge.gvcf.10.fa -m none /tmp/zey1Mm0xMJ/merge.gvcf.10.a.bcf /tmp/zey1Mm0xMJ/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob -g /<>/test/merge.gvcf.10.fa -m none /tmp/zey1Mm0xMJ/merge.gvcf.10.a.bcf /tmp/zey1Mm0xMJ/merge.gvcf.10.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version /tmp/zey1Mm0xMJ/merge.noidx.a.vcf.gz /tmp/zey1Mm0xMJ/merge.noidx.b.vcf.gz /tmp/zey1Mm0xMJ/merge.noidx.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob /tmp/zey1Mm0xMJ/merge.noidx.a.vcf.gz /tmp/zey1Mm0xMJ/merge.noidx.b.vcf.gz /tmp/zey1Mm0xMJ/merge.noidx.c.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version /tmp/zey1Mm0xMJ/merge.noidx.a.bcf /tmp/zey1Mm0xMJ/merge.noidx.b.bcf /tmp/zey1Mm0xMJ/merge.noidx.c.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob /tmp/zey1Mm0xMJ/merge.noidx.a.bcf /tmp/zey1Mm0xMJ/merge.noidx.b.bcf /tmp/zey1Mm0xMJ/merge.noidx.c.bcf | /<>/bcftools view --no-version | 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 --no-version -Ob --no-index /<>/test/merge.noidx.a.vcf /<>/test/merge.noidx.b.vcf /<>/test/merge.noidx.c.vcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --no-index /tmp/zey1Mm0xMJ/merge.noidx.a.bcf /tmp/zey1Mm0xMJ/merge.noidx.b.bcf /tmp/zey1Mm0xMJ/merge.noidx.c.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --no-index /tmp/zey1Mm0xMJ/merge.noidx.a.bcf /tmp/zey1Mm0xMJ/merge.noidx.b.bcf /tmp/zey1Mm0xMJ/merge.noidx.c.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version /tmp/zey1Mm0xMJ/merge.8.a.vcf.gz /tmp/zey1Mm0xMJ/merge.8.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob /tmp/zey1Mm0xMJ/merge.8.a.vcf.gz /tmp/zey1Mm0xMJ/merge.8.b.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version /tmp/zey1Mm0xMJ/merge.8.a.bcf /tmp/zey1Mm0xMJ/merge.8.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob /tmp/zey1Mm0xMJ/merge.8.a.bcf /tmp/zey1Mm0xMJ/merge.8.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version -i AN:sum,AC:sum /tmp/zey1Mm0xMJ/merge.8.a.vcf.gz /tmp/zey1Mm0xMJ/merge.8.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/zey1Mm0xMJ/merge.8.a.vcf.gz /tmp/zey1Mm0xMJ/merge.8.b.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version -i AN:sum,AC:sum /tmp/zey1Mm0xMJ/merge.8.a.bcf /tmp/zey1Mm0xMJ/merge.8.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/zey1Mm0xMJ/merge.8.a.bcf /tmp/zey1Mm0xMJ/merge.8.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version /tmp/zey1Mm0xMJ/merge.9.a.vcf.gz /tmp/zey1Mm0xMJ/merge.9.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob /tmp/zey1Mm0xMJ/merge.9.a.vcf.gz /tmp/zey1Mm0xMJ/merge.9.b.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version /tmp/zey1Mm0xMJ/merge.9.a.bcf /tmp/zey1Mm0xMJ/merge.9.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob /tmp/zey1Mm0xMJ/merge.9.a.bcf /tmp/zey1Mm0xMJ/merge.9.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version -i AN:sum,AC:sum /tmp/zey1Mm0xMJ/merge.9.a.vcf.gz /tmp/zey1Mm0xMJ/merge.9.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/zey1Mm0xMJ/merge.9.a.vcf.gz /tmp/zey1Mm0xMJ/merge.9.b.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version -i AN:sum,AC:sum /tmp/zey1Mm0xMJ/merge.9.a.bcf /tmp/zey1Mm0xMJ/merge.9.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/zey1Mm0xMJ/merge.9.a.bcf /tmp/zey1Mm0xMJ/merge.9.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version -m none /tmp/zey1Mm0xMJ/merge.10.a.vcf.gz /tmp/zey1Mm0xMJ/merge.10.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob -m none /tmp/zey1Mm0xMJ/merge.10.a.vcf.gz /tmp/zey1Mm0xMJ/merge.10.b.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version -m none /tmp/zey1Mm0xMJ/merge.10.a.bcf /tmp/zey1Mm0xMJ/merge.10.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob -m none /tmp/zey1Mm0xMJ/merge.10.a.bcf /tmp/zey1Mm0xMJ/merge.10.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version -m both /tmp/zey1Mm0xMJ/merge.10.a.vcf.gz /tmp/zey1Mm0xMJ/merge.10.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob -m both /tmp/zey1Mm0xMJ/merge.10.a.vcf.gz /tmp/zey1Mm0xMJ/merge.10.b.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version -m both /tmp/zey1Mm0xMJ/merge.10.a.bcf /tmp/zey1Mm0xMJ/merge.10.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob -m both /tmp/zey1Mm0xMJ/merge.10.a.bcf /tmp/zey1Mm0xMJ/merge.10.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version -m snp-ins-del /tmp/zey1Mm0xMJ/merge.10.a.vcf.gz /tmp/zey1Mm0xMJ/merge.10.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob -m snp-ins-del /tmp/zey1Mm0xMJ/merge.10.a.vcf.gz /tmp/zey1Mm0xMJ/merge.10.b.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version -m snp-ins-del /tmp/zey1Mm0xMJ/merge.10.a.bcf /tmp/zey1Mm0xMJ/merge.10.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob -m snp-ins-del /tmp/zey1Mm0xMJ/merge.10.a.bcf /tmp/zey1Mm0xMJ/merge.10.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/zey1Mm0xMJ/merge.mrules.1.a.vcf.gz /tmp/zey1Mm0xMJ/merge.mrules.1.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - /tmp/zey1Mm0xMJ/merge.mrules.1.a.vcf.gz /tmp/zey1Mm0xMJ/merge.mrules.1.b.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/zey1Mm0xMJ/merge.mrules.1.a.bcf /tmp/zey1Mm0xMJ/merge.mrules.1.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - /tmp/zey1Mm0xMJ/merge.mrules.1.a.bcf /tmp/zey1Mm0xMJ/merge.mrules.1.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - -M AD:.,PL:. /tmp/zey1Mm0xMJ/merge.mrules.1.a.vcf.gz /tmp/zey1Mm0xMJ/merge.mrules.1.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - -M AD:.,PL:. /tmp/zey1Mm0xMJ/merge.mrules.1.a.vcf.gz /tmp/zey1Mm0xMJ/merge.mrules.1.b.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - -M AD:.,PL:. /tmp/zey1Mm0xMJ/merge.mrules.1.a.bcf /tmp/zey1Mm0xMJ/merge.mrules.1.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - -M AD:.,PL:. /tmp/zey1Mm0xMJ/merge.mrules.1.a.bcf /tmp/zey1Mm0xMJ/merge.mrules.1.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/zey1Mm0xMJ/merge.gvcf.5.a.vcf.gz /tmp/zey1Mm0xMJ/merge.gvcf.5.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - /tmp/zey1Mm0xMJ/merge.gvcf.5.a.vcf.gz /tmp/zey1Mm0xMJ/merge.gvcf.5.b.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/zey1Mm0xMJ/merge.gvcf.5.a.bcf /tmp/zey1Mm0xMJ/merge.gvcf.5.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - /tmp/zey1Mm0xMJ/merge.gvcf.5.a.bcf /tmp/zey1Mm0xMJ/merge.gvcf.5.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - --merge none /tmp/zey1Mm0xMJ/merge.gvcf.5.a.vcf.gz /tmp/zey1Mm0xMJ/merge.gvcf.5.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - --merge none /tmp/zey1Mm0xMJ/merge.gvcf.5.a.vcf.gz /tmp/zey1Mm0xMJ/merge.gvcf.5.b.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - --merge none /tmp/zey1Mm0xMJ/merge.gvcf.5.a.bcf /tmp/zey1Mm0xMJ/merge.gvcf.5.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - --merge none /tmp/zey1Mm0xMJ/merge.gvcf.5.a.bcf /tmp/zey1Mm0xMJ/merge.gvcf.5.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/zey1Mm0xMJ/merge.gvcf.11.a.vcf.gz /tmp/zey1Mm0xMJ/merge.gvcf.11.b.vcf.gz /tmp/zey1Mm0xMJ/merge.gvcf.11.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - /tmp/zey1Mm0xMJ/merge.gvcf.11.a.vcf.gz /tmp/zey1Mm0xMJ/merge.gvcf.11.b.vcf.gz /tmp/zey1Mm0xMJ/merge.gvcf.11.c.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/zey1Mm0xMJ/merge.gvcf.11.a.bcf /tmp/zey1Mm0xMJ/merge.gvcf.11.b.bcf /tmp/zey1Mm0xMJ/merge.gvcf.11.c.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - /tmp/zey1Mm0xMJ/merge.gvcf.11.a.bcf /tmp/zey1Mm0xMJ/merge.gvcf.11.b.bcf /tmp/zey1Mm0xMJ/merge.gvcf.11.c.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_query: /<>/bcftools query -f '%CHROM\t%POS\t%CLNREVSTAT\n' -i'CLNREVSTAT="criteria_provided,_conflicting_interpretations"' /tmp/zey1Mm0xMJ/query.string.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/query.string.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/query.string.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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%INFO/STR\n' -i'INFO/STR=@/<>/test/query.string.2.1.txt' /tmp/zey1Mm0xMJ/query.string.2.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/query.string.2.vcf.gz | /<>/bcftools query -f '%CHROM\t%POS\t%INFO/STR\n' -i'INFO/STR=@/<>/test/query.string.2.1.txt' .. ok test_vcf_query: /<>/bcftools query -f '%CHROM\t%POS[\t%STR]\n' -i'FMT/STR=@/<>/test/query.string.2.2.txt' /tmp/zey1Mm0xMJ/query.string.2.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/query.string.2.vcf.gz | /<>/bcftools query -f '%CHROM\t%POS[\t%STR]\n' -i'FMT/STR=@/<>/test/query.string.2.2.txt' .. ok test_vcf_query: /<>/bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n' /tmp/zey1Mm0xMJ/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/query.variantkey.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/query.variantkey.vcf.gz | /<>/bcftools query -f '%RSX\t%VKX\n' .. ok test_vcf_query: /<>/bcftools query -f'%XRI\n' -i'XRI[*]>1111' /tmp/zey1Mm0xMJ/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/view.vectors.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/query.2.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/missing.vcf.gz | /<>/bcftools query -i'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /<>/bcftools query -i'IINT!="."' -f'%POS %IINT\n' /tmp/zey1Mm0xMJ/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/missing.vcf.gz | /<>/bcftools query -i'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /<>/bcftools query -e'IINT!="."' -f'%POS %IINT\n' /tmp/zey1Mm0xMJ/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/missing.vcf.gz | /<>/bcftools query -e'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /<>/bcftools query -e'IINT="."' -f'%POS %IINT\n' /tmp/zey1Mm0xMJ/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/missing.vcf.gz | /<>/bcftools query -e'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /<>/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' /tmp/zey1Mm0xMJ/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/missing.vcf.gz | /<>/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /<>/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' /tmp/zey1Mm0xMJ/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/missing.vcf.gz | /<>/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /<>/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' /tmp/zey1Mm0xMJ/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/missing.vcf.gz | /<>/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /<>/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' /tmp/zey1Mm0xMJ/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/missing.vcf.gz | /<>/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /<>/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' /tmp/zey1Mm0xMJ/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/missing.vcf.gz | /<>/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /<>/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' /tmp/zey1Mm0xMJ/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/missing.vcf.gz | /<>/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /<>/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' /tmp/zey1Mm0xMJ/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/missing.vcf.gz | /<>/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /<>/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' /tmp/zey1Mm0xMJ/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/filter.11.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/filter.11.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/filter.11.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/filter.11.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/filter.11.vcf.gz | /<>/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /<>/bcftools query -f'%LINE' /tmp/zey1Mm0xMJ/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/query.vcf.gz | /<>/bcftools query -f'%LINE' .. ok test_vcf_query: /<>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' /tmp/zey1Mm0xMJ/query.filter-type.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/query.filter-type.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/query.filter-type.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/query.filter-type.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/query.filter-type.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/filter-missing-floats.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/filter-missing-floats.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/query.filter.2.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/filter.5.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/filter.5.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/query.filter.3.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/query.filter.3.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/query.filter.3.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/filter.5.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/query.filter.4.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/view.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/query.filter.5.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/query.filter.5.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/query.filter.5.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[GT]==10' /tmp/zey1Mm0xMJ/query.filter.5.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/query.filter.5.vcf.gz | /<>/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[GT]==10' .. ok test_vcf_query: /<>/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'sSUM(FMT/AD[GT])==210' /tmp/zey1Mm0xMJ/query.filter.5.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/query.filter.5.vcf.gz | /<>/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'sSUM(FMT/AD[GT])==210' .. ok test_vcf_query: /<>/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[0:GT]==30' /tmp/zey1Mm0xMJ/query.filter.5.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/query.filter.5.vcf.gz | /<>/bcftools query -f'[%POS\t%GT\t%SAMPLE\t%AD\n]' -i'FMT/AD[0:GT]==30' .. ok test_vcf_query: /<>/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TF[:GT]==1 && FMT/TF[:GT]==2' /tmp/zey1Mm0xMJ/query.gtidx.1.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/query.gtidx.1.vcf.gz | /<>/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TF[:GT]==1 && FMT/TF[:GT]==2' .. ok test_vcf_query: /<>/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TI[:GT]==1 && FMT/TF[:GT]==2' /tmp/zey1Mm0xMJ/query.gtidx.1.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/query.gtidx.1.vcf.gz | /<>/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TI[:GT]==1 && FMT/TF[:GT]==2' .. ok test_vcf_query: /<>/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TS[:GT]=="BB" && FMT/TS[:GT]=="CC"' /tmp/zey1Mm0xMJ/query.gtidx.1.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/query.gtidx.1.vcf.gz | /<>/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TS[:GT]=="BB" && FMT/TS[:GT]=="CC"' .. ok test_vcf_query: /<>/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TC[:GT]=="B" && FMT/TC[:GT]=="C"' /tmp/zey1Mm0xMJ/query.gtidx.1.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/query.gtidx.1.vcf.gz | /<>/bcftools query -f'[%GT %TC %TS %TI %TF\n]' -i'FMT/TC[:GT]=="B" && FMT/TC[:GT]=="C"' .. ok test_vcf_query: /<>/bcftools query -f'[%GT %TI\n]' -i'FMT/TI[:GT]=="."' /tmp/zey1Mm0xMJ/query.gtidx.1.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/query.gtidx.1.vcf.gz | /<>/bcftools query -f'[%GT %TI\n]' -i'FMT/TI[:GT]=="."' .. ok test_vcf_query: /<>/bcftools query -f'%CHROM %POS\n' -i'CHROM="4"' /tmp/zey1Mm0xMJ/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/query.negative.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/query.negative.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/query.negative.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/query.negative.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/query.filter.11.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/query.filter.11.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/query.filter.11.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/query.filter.11.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/query.filter.6.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/query.filter.7.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/query.filter.7.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/query.filter.7.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/query.filter.7.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/query.filter.7.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/query.filter.7.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/query.filter.7.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/query.filter.7.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/query.filter.8.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/query.filter.8.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/query.filter.9.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/query.filter.9.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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'[ %AD\n]' -i'AD[:1] / sum(AD[*]) > 0.5' /tmp/zey1Mm0xMJ/query.filter.13.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/query.filter.13.vcf.gz | /<>/bcftools query -f'[ %AD\n]' -i'AD[:1] / sum(AD[*]) > 0.5' .. ok test_vcf_query: /<>/bcftools query -f'%POS %NUM_TAG\n' -i'COUNT(INFO/NUM_TAG)=2' /tmp/zey1Mm0xMJ/query.filter.10.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/query.filter.10.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/query.filter.12.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/query.filter.12.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/query.filter.12.vcf.gz | /<>/bcftools query -f '%CHROM:%POS[\t%SAMPLE=%GT]\n' -e 'GT="mis"' -s 0,1,3 .. ok test_vcf_query: /<>/bcftools query -f "[%SAMPLE %GT\n]" -S /<>/test/query.smpl.11.txt /tmp/zey1Mm0xMJ/query.smpl.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/query.smpl.vcf.gz | /<>/bcftools query -f "[%SAMPLE %GT\n]" -S /<>/test/query.smpl.11.txt .. ok test_vcf_query: /<>/bcftools query -l -S /<>/test/query.smpl.11.txt /tmp/zey1Mm0xMJ/query.smpl.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/query.smpl.vcf.gz | /<>/bcftools query -l -S /<>/test/query.smpl.11.txt .. ok test_vcf_query: /<>/bcftools query -f "[%SAMPLE %GT\n]" -S ^/<>/test/query.smpl.11.txt /tmp/zey1Mm0xMJ/query.smpl.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/query.smpl.vcf.gz | /<>/bcftools query -f "[%SAMPLE %GT\n]" -S ^/<>/test/query.smpl.11.txt .. ok test_vcf_query: /<>/bcftools query -l -S ^/<>/test/query.smpl.11.txt /tmp/zey1Mm0xMJ/query.smpl.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/query.smpl.vcf.gz | /<>/bcftools query -l -S ^/<>/test/query.smpl.11.txt .. ok test_vcf_query: /<>/bcftools query -f "[%SAMPLE %GT\n]" -S /<>/test/query.smpl.txt /tmp/zey1Mm0xMJ/query.smpl.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/query.smpl.vcf.gz | /<>/bcftools query -f "[%SAMPLE %GT\n]" -S /<>/test/query.smpl.txt .. ok test_vcf_query: /<>/bcftools query -l -S /<>/test/query.smpl.txt /tmp/zey1Mm0xMJ/query.smpl.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/query.smpl.vcf.gz | /<>/bcftools query -l -S /<>/test/query.smpl.txt .. ok test_vcf_query: /<>/bcftools query -f'%ID\n' -i'ID~"s12"' /tmp/zey1Mm0xMJ/query.filter.id.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/query.filter.id.vcf.gz | /<>/bcftools query -f'%ID\n' -i'ID~"s12"' .. ok test_vcf_query: /<>/bcftools query -f'%ID\n' -i'ID="rs123"' /tmp/zey1Mm0xMJ/query.filter.id.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/query.filter.id.vcf.gz | /<>/bcftools query -f'%ID\n' -i'ID="rs123"' .. ok test_vcf_query: /<>/bcftools query -i'FILTER="A"' -f'%FILTER\n' /tmp/zey1Mm0xMJ/filter.12.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/filter.12.vcf.gz | /<>/bcftools query -i'FILTER="A"' -f'%FILTER\n' .. ok test_vcf_query: /<>/bcftools query -i'FILTER~"A"' -f'%FILTER\n' /tmp/zey1Mm0xMJ/filter.12.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/filter.12.vcf.gz | /<>/bcftools query -i'FILTER~"A"' -f'%FILTER\n' .. ok test_vcf_query: /<>/bcftools query -i'FILTER="A;B"' -f'%FILTER\n' /tmp/zey1Mm0xMJ/filter.12.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/filter.12.vcf.gz | /<>/bcftools query -i'FILTER="A;B"' -f'%FILTER\n' .. ok test_vcf_query: /<>/bcftools query -i'FILTER!="A;B"' -f'%FILTER\n' /tmp/zey1Mm0xMJ/filter.12.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/filter.12.vcf.gz | /<>/bcftools query -i'FILTER!="A;B"' -f'%FILTER\n' .. ok test_vcf_query: /<>/bcftools query -i'FILTER~"A;B"' -f'%FILTER\n' /tmp/zey1Mm0xMJ/filter.12.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/filter.12.vcf.gz | /<>/bcftools query -i'FILTER~"A;B"' -f'%FILTER\n' .. ok test_vcf_query: /<>/bcftools query -i'FILTER!~"A;B"' -f'%FILTER\n' /tmp/zey1Mm0xMJ/filter.12.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/filter.12.vcf.gz | /<>/bcftools query -i'FILTER!~"A;B"' -f'%FILTER\n' .. ok test_vcf_query: /<>/bcftools query -i'DP%10==2' -f'[ %DP]\n' /tmp/zey1Mm0xMJ/filter.10.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/filter.10.vcf.gz | /<>/bcftools query -i'DP%10==2' -f'[ %DP]\n' .. ok test_vcf_query: /<>/bcftools query -i'REF="N"' -f'%CHROM %POS %REF %ALT %QUAL\n' /tmp/zey1Mm0xMJ/filter.13.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/filter.13.vcf.gz | /<>/bcftools query -i'REF="N"' -f'%CHROM %POS %REF %ALT %QUAL\n' .. ok test_vcf_query: /<>/bcftools query -H -f'[%CHROM %POS %SAMPLE %DP %GT\n]' /tmp/zey1Mm0xMJ/query.header.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/query.header.vcf.gz | /<>/bcftools query -H -f'[%CHROM %POS %SAMPLE %DP %GT\n]' .. ok test_vcf_query: /<>/bcftools query -H -f'[%CHROM %POS %SAMPLE %DP %GT\t]\n' /tmp/zey1Mm0xMJ/query.header.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/query.header.vcf.gz | /<>/bcftools query -H -f'[%CHROM %POS %SAMPLE %DP %GT\t]\n' .. ok test_vcf_query: /<>/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]\n' /tmp/zey1Mm0xMJ/query.header.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/query.header.vcf.gz | /<>/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]\n' .. ok test_vcf_query: /<>/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]' /tmp/zey1Mm0xMJ/query.header.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/query.header.vcf.gz | /<>/bcftools query -H -f'%CHROM %POS[ %SAMPLE %DP %GT]' .. ok test_vcf_query: /<>/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]\n' /tmp/zey1Mm0xMJ/query.header.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/query.header.vcf.gz | /<>/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]\n' .. ok test_vcf_query: /<>/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]' /tmp/zey1Mm0xMJ/query.header.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/query.header.vcf.gz | /<>/bcftools query -H -f'%CHROM %POS[ %SAMPLE][ %DP][ %GT]' .. ok test_vcf_query: /<>/bcftools query -f'[%SAMPLE %DP\n]' -i'DP=1 || DP=2' /tmp/zey1Mm0xMJ/query.filter-or.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/query.filter-or.vcf.gz | /<>/bcftools query -f'[%SAMPLE %DP\n]' -i'DP=1 || DP=2' .. ok test_vcf_query: /<>/bcftools query -f'[%SAMPLE %DP\n]' -i'DP=1 | DP=2' /tmp/zey1Mm0xMJ/query.filter-or.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/query.filter-or.vcf.gz | /<>/bcftools query -f'[%SAMPLE %DP\n]' -i'DP=1 | DP=2' .. ok test_vcf_norm: /<>/bcftools norm --no-version -cx /tmp/zey1Mm0xMJ/norm.vcf.gz -f /<>/test/norm.fa .. ok test_vcf_norm: /<>/bcftools norm --no-version -cx /tmp/zey1Mm0xMJ/norm.vcf.gz -f /<>/test/norm.fa -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- /tmp/zey1Mm0xMJ/norm.split.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- /tmp/zey1Mm0xMJ/norm.split.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- /tmp/zey1Mm0xMJ/norm.split.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- /tmp/zey1Mm0xMJ/norm.split.2.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- --force /tmp/zey1Mm0xMJ/norm.split.3.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- --force /tmp/zey1Mm0xMJ/norm.split.3.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- /tmp/zey1Mm0xMJ/norm.split.4.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- /tmp/zey1Mm0xMJ/norm.split.4.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- --keep-sum AD /tmp/zey1Mm0xMJ/norm.split.4.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- --keep-sum AD /tmp/zey1Mm0xMJ/norm.split.4.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- /tmp/zey1Mm0xMJ/norm.split.vcf.gz -f /<>/test/norm.fa .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- /tmp/zey1Mm0xMJ/norm.split.vcf.gz -f /<>/test/norm.fa -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m+ /tmp/zey1Mm0xMJ/norm.merge.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -m+ /tmp/zey1Mm0xMJ/norm.merge.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m+ /tmp/zey1Mm0xMJ/norm.merge.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -m+ /tmp/zey1Mm0xMJ/norm.merge.2.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m+ /tmp/zey1Mm0xMJ/norm.merge.3.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -m+ /tmp/zey1Mm0xMJ/norm.merge.3.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m+ -s /tmp/zey1Mm0xMJ/norm.merge.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -m+ -s /tmp/zey1Mm0xMJ/norm.merge.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -Nc s /tmp/zey1Mm0xMJ/norm.setref.vcf.gz -f /<>/test/norm.fa .. ok test_vcf_norm: /<>/bcftools norm --no-version -Nc s /tmp/zey1Mm0xMJ/norm.setref.vcf.gz -f /<>/test/norm.fa -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version /tmp/zey1Mm0xMJ/norm.telomere.vcf.gz -f /<>/test/norm.fa .. ok test_vcf_norm: /<>/bcftools norm --no-version /tmp/zey1Mm0xMJ/norm.telomere.vcf.gz -f /<>/test/norm.fa -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d snps /tmp/zey1Mm0xMJ/norm.rmdup.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -d snps /tmp/zey1Mm0xMJ/norm.rmdup.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d indels /tmp/zey1Mm0xMJ/norm.rmdup.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -d indels /tmp/zey1Mm0xMJ/norm.rmdup.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d both /tmp/zey1Mm0xMJ/norm.rmdup.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -d both /tmp/zey1Mm0xMJ/norm.rmdup.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d all /tmp/zey1Mm0xMJ/norm.rmdup.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -d all /tmp/zey1Mm0xMJ/norm.rmdup.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d none /tmp/zey1Mm0xMJ/norm.rmdup.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -d none /tmp/zey1Mm0xMJ/norm.rmdup.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d exact /tmp/zey1Mm0xMJ/norm.rmdup.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -d exact /tmp/zey1Mm0xMJ/norm.rmdup.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d none /tmp/zey1Mm0xMJ/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -d none /tmp/zey1Mm0xMJ/norm.rmdup.2.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d exact /tmp/zey1Mm0xMJ/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -d exact /tmp/zey1Mm0xMJ/norm.rmdup.2.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d indels /tmp/zey1Mm0xMJ/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -d indels /tmp/zey1Mm0xMJ/norm.rmdup.2.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d any /tmp/zey1Mm0xMJ/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -d any /tmp/zey1Mm0xMJ/norm.rmdup.2.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d both /tmp/zey1Mm0xMJ/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -d both /tmp/zey1Mm0xMJ/norm.rmdup.2.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d snps /tmp/zey1Mm0xMJ/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -d snps /tmp/zey1Mm0xMJ/norm.rmdup.2.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -c s -a /tmp/zey1Mm0xMJ/norm.2.vcf.gz -f /<>/test/norm.2.fa .. ok test_vcf_norm: /<>/bcftools norm --no-version -c s -a /tmp/zey1Mm0xMJ/norm.2.vcf.gz -f /<>/test/norm.2.fa -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -c s /tmp/zey1Mm0xMJ/norm.iupac.vcf.gz -f /<>/test/norm.iupac.fa .. ok test_vcf_norm: /<>/bcftools norm --no-version -c s /tmp/zey1Mm0xMJ/norm.iupac.vcf.gz -f /<>/test/norm.iupac.fa -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -c s /tmp/zey1Mm0xMJ/norm.3.vcf.gz -f /<>/test/norm.3.fa .. ok test_vcf_norm: /<>/bcftools norm --no-version -c s /tmp/zey1Mm0xMJ/norm.3.vcf.gz -f /<>/test/norm.3.fa -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -a --old-rec-tag OLD_REC /tmp/zey1Mm0xMJ/atomize.split.1.vcf.gz | /<>/bcftools norm --no-version -m -any --force .. ok test_vcf_norm: /<>/bcftools norm --no-version -a --old-rec-tag OLD_REC /tmp/zey1Mm0xMJ/atomize.split.1.vcf.gz | /<>/bcftools norm --no-version -m -any --force -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m -any --old-rec-tag OLD_REC --force /tmp/zey1Mm0xMJ/atomize.split.1.vcf.gz | /<>/bcftools norm --no-version -a .. ok test_vcf_norm: /<>/bcftools norm --no-version -m -any --old-rec-tag OLD_REC --force /tmp/zey1Mm0xMJ/atomize.split.1.vcf.gz | /<>/bcftools norm --no-version -a -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m -any --old-rec-tag OLD_REC --force -a /tmp/zey1Mm0xMJ/atomize.split.1.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -m -any --old-rec-tag OLD_REC --force -a /tmp/zey1Mm0xMJ/atomize.split.1.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/zey1Mm0xMJ/atomize.split.1.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/zey1Mm0xMJ/atomize.split.1.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/zey1Mm0xMJ/atomize.split.1.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/zey1Mm0xMJ/atomize.split.1.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/zey1Mm0xMJ/atomize.split.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/zey1Mm0xMJ/atomize.split.2.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/zey1Mm0xMJ/atomize.split.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/zey1Mm0xMJ/atomize.split.2.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version --atomize --atom-overlaps . /tmp/zey1Mm0xMJ/atomize.split.3.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version --atomize --atom-overlaps . /tmp/zey1Mm0xMJ/atomize.split.3.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/zey1Mm0xMJ/atomize.split.4.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/zey1Mm0xMJ/atomize.split.4.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m +both /tmp/zey1Mm0xMJ/norm.4.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -m +both /tmp/zey1Mm0xMJ/norm.4.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m +any /tmp/zey1Mm0xMJ/norm.4.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -m +any /tmp/zey1Mm0xMJ/norm.4.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m - --multi-overlaps 0 /tmp/zey1Mm0xMJ/norm.5.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -m - --multi-overlaps 0 /tmp/zey1Mm0xMJ/norm.5.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m - --multi-overlaps . /tmp/zey1Mm0xMJ/norm.5.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -m - --multi-overlaps . /tmp/zey1Mm0xMJ/norm.5.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m -any /tmp/zey1Mm0xMJ/norm.m-any.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -m -any /tmp/zey1Mm0xMJ/norm.m-any.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m -any /tmp/zey1Mm0xMJ/norm.phased-split.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -m -any /tmp/zey1Mm0xMJ/norm.phased-split.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m +any /tmp/zey1Mm0xMJ/norm.phased-join.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -m +any /tmp/zey1Mm0xMJ/norm.phased-join.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version --old-rec-tag ORI /tmp/zey1Mm0xMJ/norm.symbolic.vcf.gz -f /<>/test/norm.symbolic.fa .. ok test_vcf_norm: /<>/bcftools norm --no-version --old-rec-tag ORI /tmp/zey1Mm0xMJ/norm.symbolic.vcf.gz -f /<>/test/norm.symbolic.fa -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version --old-rec-tag ORI /tmp/zey1Mm0xMJ/norm.symbolic.2.vcf.gz -f /<>/test/norm.symbolic.fa .. ok test_vcf_norm: /<>/bcftools norm --no-version --old-rec-tag ORI /tmp/zey1Mm0xMJ/norm.symbolic.2.vcf.gz -f /<>/test/norm.symbolic.fa -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version --old-rec-tag ORI /tmp/zey1Mm0xMJ/norm.right-align.vcf.gz -f /<>/test/norm.right-align.fa .. ok test_vcf_norm: /<>/bcftools norm --no-version --old-rec-tag ORI /tmp/zey1Mm0xMJ/norm.right-align.vcf.gz -f /<>/test/norm.right-align.fa -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version --old-rec-tag ORI -g /<>/test/norm.right-align.gff /tmp/zey1Mm0xMJ/norm.right-align.vcf.gz -f /<>/test/norm.right-align.fa .. ok test_vcf_norm: /<>/bcftools norm --no-version --old-rec-tag ORI -g /<>/test/norm.right-align.gff /tmp/zey1Mm0xMJ/norm.right-align.vcf.gz -f /<>/test/norm.right-align.fa -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version --old-rec-tag ORI -a -m -any /tmp/zey1Mm0xMJ/norm.atom-split-norm.vcf.gz -f /<>/test/norm.atom-split-norm.fa .. ok test_vcf_norm: /<>/bcftools norm --no-version --old-rec-tag ORI -a -m -any /tmp/zey1Mm0xMJ/norm.atom-split-norm.vcf.gz -f /<>/test/norm.atom-split-norm.fa -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m -any /tmp/zey1Mm0xMJ/norm.string-tags.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -m -any /tmp/zey1Mm0xMJ/norm.string-tags.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m - /tmp/zey1Mm0xMJ/norm.split.merge.vcf.gz | /<>/bcftools norm --no-version -m +both .. ok test_vcf_norm: /<>/bcftools norm --no-version -m - /tmp/zey1Mm0xMJ/norm.split.merge.vcf.gz | /<>/bcftools norm --no-version -m +both -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m - /tmp/zey1Mm0xMJ/norm.split.merge.vcf.gz | /<>/bcftools norm --no-version -m +indels .. ok test_vcf_norm: /<>/bcftools norm --no-version -m - /tmp/zey1Mm0xMJ/norm.split.merge.vcf.gz | /<>/bcftools norm --no-version -m +indels -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m - /tmp/zey1Mm0xMJ/norm.split.merge.vcf.gz | /<>/bcftools norm --no-version -m +snps .. ok test_vcf_norm: /<>/bcftools norm --no-version -m - /tmp/zey1Mm0xMJ/norm.split.merge.vcf.gz | /<>/bcftools norm --no-version -m +snps -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m - /tmp/zey1Mm0xMJ/norm.split.merge.vcf.gz | /<>/bcftools norm --no-version -m +any .. ok test_vcf_norm: /<>/bcftools norm --no-version -m - /tmp/zey1Mm0xMJ/norm.split.merge.vcf.gz | /<>/bcftools norm --no-version -m +any -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m +any /tmp/zey1Mm0xMJ/norm.merge.4.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -m +any /tmp/zey1Mm0xMJ/norm.merge.4.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m +both /tmp/zey1Mm0xMJ/norm.merge.4.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -m +both /tmp/zey1Mm0xMJ/norm.merge.4.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -i 'INFO/TAG=@/<>/test/filter.string.1.txt' /tmp/zey1Mm0xMJ/filter.string.1.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -i 'INFO/TAG=@/<>/test/filter.string.1.txt' /tmp/zey1Mm0xMJ/filter.string.1.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -i 'FMT/TAG=@/<>/test/filter.string.1.txt' /tmp/zey1Mm0xMJ/filter.string.1.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -i 'FMT/TAG=@/<>/test/filter.string.1.txt' /tmp/zey1Mm0xMJ/filter.string.1.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -HA /tmp/zey1Mm0xMJ/merge.gvcf.2.a.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -HAA /tmp/zey1Mm0xMJ/merge.gvcf.2.a.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version /tmp/zey1Mm0xMJ/weird-chr-names.vcf.gz -r 1 .. ok test_vcf_view: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/weird-chr-names.vcf.gz -r 1 | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version /tmp/zey1Mm0xMJ/weird-chr-names.vcf.gz -r 1:1-2 .. ok test_vcf_view: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/weird-chr-names.vcf.gz -r 1:1-2 | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version /tmp/zey1Mm0xMJ/weird-chr-names.vcf.gz -r 1:1,1:2 .. ok test_vcf_view: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/weird-chr-names.vcf.gz -r 1:1,1:2 | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version /tmp/zey1Mm0xMJ/weird-chr-names.vcf.gz -r 1:1-1 .. ok test_vcf_view: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/weird-chr-names.vcf.gz -r 1:1-1 | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version /tmp/zey1Mm0xMJ/weird-chr-names.vcf.gz -r {1:1} .. ok test_vcf_view: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/weird-chr-names.vcf.gz -r {1:1} | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version /tmp/zey1Mm0xMJ/weird-chr-names.vcf.gz -r {1:1}:1-2 .. ok test_vcf_view: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/weird-chr-names.vcf.gz -r {1:1}:1-2 | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version /tmp/zey1Mm0xMJ/weird-chr-names.vcf.gz -r {1:1}:1,{1:1}:2 .. ok test_vcf_view: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/weird-chr-names.vcf.gz -r {1:1}:1,{1:1}:2 | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version /tmp/zey1Mm0xMJ/weird-chr-names.vcf.gz -r {1:1}:1-1 .. ok test_vcf_view: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/weird-chr-names.vcf.gz -r {1:1}:1-1 | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version /tmp/zey1Mm0xMJ/weird-chr-names.vcf.gz -r {1:1-1} .. ok test_vcf_view: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/weird-chr-names.vcf.gz -r {1:1-1} | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version /tmp/zey1Mm0xMJ/weird-chr-names.vcf.gz -r {1:1-1}:1-2 .. ok test_vcf_view: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/weird-chr-names.vcf.gz -r {1:1-1}:1-2 | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version /tmp/zey1Mm0xMJ/weird-chr-names.vcf.gz -r {1:1-1}:1,{1:1-1}:2 .. ok test_vcf_view: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/weird-chr-names.vcf.gz -r {1:1-1}:1,{1:1-1}:2 | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version /tmp/zey1Mm0xMJ/weird-chr-names.vcf.gz -r {1:1-1}:1-1 .. ok test_vcf_view: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/weird-chr-names.vcf.gz -r {1:1-1}:1-1 | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version /tmp/zey1Mm0xMJ/weird-chr-names.vcf.gz -r {1:1-1}-2 .. ok, expected non-zero status test_vcf_view: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/weird-chr-names.vcf.gz -r {1:1-1}-2 | /<>/bcftools view | grep -v ^##bcftools_ .. ok, expected non-zero status test_vcf_view: /<>/bcftools view --no-version -aUc1 -C1 -s NA00002 -v snps /tmp/zey1Mm0xMJ/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/zey1Mm0xMJ/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -f PASS -Xks NA00003 /tmp/zey1Mm0xMJ/view.vcf.gz -r20,Y .. ok test_vcf_view: /<>/bcftools view -Ob -f PASS -Xks NA00003 /tmp/zey1Mm0xMJ/view.vcf.gz -r20,Y | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -xs NA00003 /tmp/zey1Mm0xMJ/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -xs NA00003 /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/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/zey1Mm0xMJ/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -p /tmp/zey1Mm0xMJ/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -p /tmp/zey1Mm0xMJ/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -P /tmp/zey1Mm0xMJ/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -P /tmp/zey1Mm0xMJ/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -hm2 -M2 -q0.3 -Q0.7 /tmp/zey1Mm0xMJ/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/zey1Mm0xMJ/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -Hu /tmp/zey1Mm0xMJ/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -GVsnps /tmp/zey1Mm0xMJ/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -GVsnps /tmp/zey1Mm0xMJ/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -ne 'INDEL=1 || PV4[0]<0.006' /tmp/zey1Mm0xMJ/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/zey1Mm0xMJ/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -s ^NA00003 /tmp/zey1Mm0xMJ/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -s ^NA00003 /tmp/zey1Mm0xMJ/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version /tmp/zey1Mm0xMJ/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/view.omitgenotypes.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -G /tmp/zey1Mm0xMJ/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -G /tmp/zey1Mm0xMJ/view.omitgenotypes.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -HG /tmp/zey1Mm0xMJ/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -a /tmp/zey1Mm0xMJ/many.alleles.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -a /tmp/zey1Mm0xMJ/many.alleles.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -asA /tmp/zey1Mm0xMJ/view.vectors.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -asA /tmp/zey1Mm0xMJ/view.vectors.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -asB /tmp/zey1Mm0xMJ/view.vectors.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -asB /tmp/zey1Mm0xMJ/view.vectors.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -asA /tmp/zey1Mm0xMJ/view.vectors.2.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -asA /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'FMT/FGS[*:2]="C"' /tmp/zey1Mm0xMJ/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'FMT/FGS[*:4]="EE"' /tmp/zey1Mm0xMJ/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'FMT/FRS[*:1]="BB"' /tmp/zey1Mm0xMJ/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'TXT0="text"' /tmp/zey1Mm0xMJ/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -T /<>/test/view.chrs.tab /tmp/zey1Mm0xMJ/view.chrs.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -T /<>/test/view.chrs.tab /tmp/zey1Mm0xMJ/view.chrs.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -i 'POS>=3062917' /tmp/zey1Mm0xMJ/filter.2.vcf.gz 1:3062917-3157410 .. ok test_vcf_view: /<>/bcftools view -Ob -i 'POS>=3062917' /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/idx.1.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -r 1:1172777-1172804,1:1172806-1172808 /tmp/zey1Mm0xMJ/idx.2.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -R /<>/test/idx.2.bed /tmp/zey1Mm0xMJ/idx.2.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -R /<>/test/idx.3.bed /tmp/zey1Mm0xMJ/idx.3.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -R /<>/test/idx.4.bed /tmp/zey1Mm0xMJ/idx.4.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -Ht 2 /tmp/zey1Mm0xMJ/view-t.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -Ht 3 /tmp/zey1Mm0xMJ/view-t.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 0 /tmp/zey1Mm0xMJ/overlap.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 1 /tmp/zey1Mm0xMJ/overlap.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 2 /tmp/zey1Mm0xMJ/overlap.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 0 /tmp/zey1Mm0xMJ/overlap.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 1 /tmp/zey1Mm0xMJ/overlap.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 2 /tmp/zey1Mm0xMJ/overlap.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 0 /tmp/zey1Mm0xMJ/overlap.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 1 /tmp/zey1Mm0xMJ/overlap.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 2 /tmp/zey1Mm0xMJ/overlap.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/zey1Mm0xMJ/view.minmaxac.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -c6:nonmajor /tmp/zey1Mm0xMJ/view.minmaxac.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -q0.3:major /tmp/zey1Mm0xMJ/view.minmaxac.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/zey1Mm0xMJ/view.filter.annovar.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i 'Gene.refGene~"NOD"' /tmp/zey1Mm0xMJ/view.filter.annovar.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i 'LJB2_MutationTaster=="0.291000"' /tmp/zey1Mm0xMJ/view.filter.annovar.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -a /tmp/zey1Mm0xMJ/view-a.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -T /<>/test/view.sites.txt /tmp/zey1Mm0xMJ/view.sites.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -T /<>/test/view.sites.txt /tmp/zey1Mm0xMJ/view.sites.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -T /<>/test/view.sites.txt.gz /tmp/zey1Mm0xMJ/view.sites.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -T /<>/test/view.sites.txt.gz /tmp/zey1Mm0xMJ/view.sites.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_head: /<>/bcftools head /<>/test/mpileup.2.vcf .. ok test_vcf_head: /<>/bcftools head -h 0 /<>/test/mpileup.2.vcf .. ok test_vcf_head: /<>/bcftools head -h 1 /<>/test/mpileup.2.vcf .. ok test_vcf_head: /<>/bcftools head -h 5 /<>/test/mpileup.2.vcf .. ok test_vcf_head: /<>/bcftools head -h 22 /<>/test/mpileup.2.vcf .. ok test_vcf_head: /<>/bcftools head -h 23 /<>/test/mpileup.2.vcf .. ok test_vcf_head: /<>/bcftools head -n 0 /<>/test/mpileup.2.vcf .. ok test_vcf_head: /<>/bcftools head -n 1 /<>/test/mpileup.2.vcf .. ok test_vcf_head: /<>/bcftools head -n 5 /<>/test/mpileup.2.vcf .. ok test_vcf_head: /<>/bcftools head -h 5 -n 5 < /<>/test/mpileup.2.vcf .. ok test_vcf_head2: /<>/bcftools head -s0 /tmp/zey1Mm0xMJ/mpileup.2.vcf.gz .. ok test_vcf_head2: /<>/bcftools view --no-version -Ob /tmp/zey1Mm0xMJ/mpileup.2.vcf.gz | /<>/bcftools head -s0 .. ok test_vcf_head2: /<>/bcftools head -s1 /tmp/zey1Mm0xMJ/mpileup.2.vcf.gz .. ok test_vcf_head2: /<>/bcftools view --no-version -Ob /tmp/zey1Mm0xMJ/mpileup.2.vcf.gz | /<>/bcftools head -s1 .. ok test_vcf_head2: /<>/bcftools head -s2 -h2 /tmp/zey1Mm0xMJ/mpileup.2.vcf.gz .. ok test_vcf_head2: /<>/bcftools view --no-version -Ob /tmp/zey1Mm0xMJ/mpileup.2.vcf.gz | /<>/bcftools head -s2 -h2 .. 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/zey1Mm0xMJ/mpileup.tab.gz /<>/test/mpileup.vcf .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/mpileup.2.tab.gz /<>/test/mpileup.2.vcf .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/mpileup.3.tab.gz -i /<>/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/mpileup.4.tab.gz -i /<>/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/mpileup.5.tab.gz -i /<>/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/mpileup.6.tab.gz -i /<>/test/mpileup.4.vcf .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/mpileup.7.tab.gz -i /<>/test/mpileup.5.vcf .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/mpileup.cals.1.tab.gz /<>/test/mpileup.cals.1.vcf .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/mpileup.cals.2.tab.gz /<>/test/mpileup.cals.2.vcf .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/zey1Mm0xMJ/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_filter: /<>/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 0 /<>/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 0 /<>/test/filter.1.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 1 /<>/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 1 /<>/test/filter.1.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter --soft-filter xxx --mask 2:1005-1008 --mask-overlap 2 /<>/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob --soft-filter xxx --mask 2:1005-1008 --mask-overlap 2 /<>/test/filter.1.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter --soft-filter xxx --mask ^2:1005-1008 /<>/test/filter.1.vcf | grep -v ^##bcftools_ .. ok test_vcf_filter: /<>/bcftools filter -Ob --soft-filter xxx --mask ^2:1005-1008 /<>/test/filter.1.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/zey1Mm0xMJ/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/zey1Mm0xMJ/regions.tab.gz /tmp/zey1Mm0xMJ/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/regions.vcf.gz | /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/zey1Mm0xMJ/regions.tab.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/zey1Mm0xMJ/regions.tab.gz /tmp/zey1Mm0xMJ/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/zey1Mm0xMJ/regions.bed /tmp/zey1Mm0xMJ/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/regions.vcf.gz | /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/zey1Mm0xMJ/regions.bed .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/zey1Mm0xMJ/regions.bed /tmp/zey1Mm0xMJ/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/zey1Mm0xMJ/regions.bed.gz /tmp/zey1Mm0xMJ/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/regions.vcf.gz | /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/zey1Mm0xMJ/regions.bed.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/zey1Mm0xMJ/regions.bed.gz /tmp/zey1Mm0xMJ/regions.vcf.gz .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/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/zey1Mm0xMJ/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/zey1Mm0xMJ/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/zey1Mm0xMJ/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/zey1Mm0xMJ/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/zey1Mm0xMJ/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/zey1Mm0xMJ/annotate.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/zey1Mm0xMJ/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/zey1Mm0xMJ/annotate.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/zey1Mm0xMJ/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/zey1Mm0xMJ/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/zey1Mm0xMJ/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/zey1Mm0xMJ/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/zey1Mm0xMJ/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/zey1Mm0xMJ/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/zey1Mm0xMJ/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/zey1Mm0xMJ/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/zey1Mm0xMJ/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/zey1Mm0xMJ/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/zey1Mm0xMJ/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/zey1Mm0xMJ/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/zey1Mm0xMJ/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/zey1Mm0xMJ/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/zey1Mm0xMJ/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/zey1Mm0xMJ/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/zey1Mm0xMJ/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/zey1Mm0xMJ/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/zey1Mm0xMJ/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/annots4.vcf.gz -c +INFO /tmp/zey1Mm0xMJ/annotate4.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/zey1Mm0xMJ/annots4.vcf.gz -c +INFO /tmp/zey1Mm0xMJ/annotate4.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/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/zey1Mm0xMJ/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/zey1Mm0xMJ/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/zey1Mm0xMJ/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/zey1Mm0xMJ/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/zey1Mm0xMJ/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/zey1Mm0xMJ/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/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/zey1Mm0xMJ/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/zey1Mm0xMJ/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/zey1Mm0xMJ/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/zey1Mm0xMJ/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/zey1Mm0xMJ/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/zey1Mm0xMJ/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/zey1Mm0xMJ/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/zey1Mm0xMJ/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/zey1Mm0xMJ/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/zey1Mm0xMJ/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/zey1Mm0xMJ/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/zey1Mm0xMJ/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/zey1Mm0xMJ/annots11.vcf.gz -c FMT /tmp/zey1Mm0xMJ/annotate11.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/zey1Mm0xMJ/annots11.vcf.gz -c FMT /tmp/zey1Mm0xMJ/annotate11.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/zey1Mm0xMJ/annots2.vcf.gz -c FMT/newGT:=GT /tmp/zey1Mm0xMJ/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/zey1Mm0xMJ/annots2.vcf.gz -c FMT/newGT:=GT /tmp/zey1Mm0xMJ/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/zey1Mm0xMJ/annots12.vcf.gz -c FMT/GT:=newGT /tmp/zey1Mm0xMJ/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/zey1Mm0xMJ/annots12.vcf.gz -c FMT/GT:=newGT /tmp/zey1Mm0xMJ/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/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/zey1Mm0xMJ/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/zey1Mm0xMJ/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/zey1Mm0xMJ/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/zey1Mm0xMJ/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/zey1Mm0xMJ/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/zey1Mm0xMJ/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/zey1Mm0xMJ/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/zey1Mm0xMJ/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 -a /tmp/zey1Mm0xMJ/annotate15.tab.gz -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR -H '##FORMAT=' -H '##INFO=' /<>/test/annotate15.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/zey1Mm0xMJ/annotate15.tab.gz -s SAMPLE2 -c CHROM,FROM,TO,FMT/FOO,BAR -H '##FORMAT=' -H '##INFO=' /<>/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/zey1Mm0xMJ/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/zey1Mm0xMJ/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/zey1Mm0xMJ/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/zey1Mm0xMJ/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/zey1Mm0xMJ/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/zey1Mm0xMJ/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/zey1Mm0xMJ/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/zey1Mm0xMJ/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/zey1Mm0xMJ/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/zey1Mm0xMJ/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/zey1Mm0xMJ/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/zey1Mm0xMJ/annotate19.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/zey1Mm0xMJ/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/zey1Mm0xMJ/annotate19.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/zey1Mm0xMJ/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/zey1Mm0xMJ/annotate19.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/zey1Mm0xMJ/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/zey1Mm0xMJ/annotate19.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/zey1Mm0xMJ/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/zey1Mm0xMJ/annotate19.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/zey1Mm0xMJ/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/zey1Mm0xMJ/annotate19.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -c INFO/FILTER:=FILTER /<>/test/annotate19.dst.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -c INFO/FILTER:=FILTER /<>/test/annotate19.dst.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/zey1Mm0xMJ/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER /tmp/zey1Mm0xMJ/annotate19.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/zey1Mm0xMJ/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER /tmp/zey1Mm0xMJ/annotate19.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/zey1Mm0xMJ/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER /tmp/zey1Mm0xMJ/annotate19.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/zey1Mm0xMJ/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER /tmp/zey1Mm0xMJ/annotate19.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/zey1Mm0xMJ/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER,FILTER /tmp/zey1Mm0xMJ/annotate19.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/zey1Mm0xMJ/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER,FILTER /tmp/zey1Mm0xMJ/annotate19.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/zey1Mm0xMJ/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=./FILTER /tmp/zey1Mm0xMJ/annotate19.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/zey1Mm0xMJ/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=./FILTER /tmp/zey1Mm0xMJ/annotate19.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/zey1Mm0xMJ/annotate20.src.vcf.gz -c FMT/GT /tmp/zey1Mm0xMJ/annotate20.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/zey1Mm0xMJ/annotate20.src.vcf.gz -c FMT/GT /tmp/zey1Mm0xMJ/annotate20.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/zey1Mm0xMJ/annotate20.src.vcf.gz -c +FMT/GT /tmp/zey1Mm0xMJ/annotate20.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/zey1Mm0xMJ/annotate20.src.vcf.gz -c +FMT/GT /tmp/zey1Mm0xMJ/annotate20.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/zey1Mm0xMJ/annotate20.src.vcf.gz -c -FMT/GT /tmp/zey1Mm0xMJ/annotate20.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/zey1Mm0xMJ/annotate20.src.vcf.gz -c -FMT/GT /tmp/zey1Mm0xMJ/annotate20.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/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/zey1Mm0xMJ/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/zey1Mm0xMJ/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/zey1Mm0xMJ/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/zey1Mm0xMJ/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 -c XX:=FORMAT/X-X,YY:=FORMAT/Y-Y,AA:=FORMAT/A-A,AA:=INFO/A-A,BB:=INFO/B-B,XX:=INFO/X-X,YY:=INFO/Y-Y,fltA:=FILTER/flt-A,fltB:=FILTER/flt-B,fltX:=FILTER/flt-X,fltY:=FILTER/flt-Y /<>/test/annotate21.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -c XX:=FORMAT/X-X,YY:=FORMAT/Y-Y,AA:=FORMAT/A-A,AA:=INFO/A-A,BB:=INFO/B-B,XX:=INFO/X-X,YY:=INFO/Y-Y,fltA:=FILTER/flt-A,fltB:=FILTER/flt-B,fltX:=FILTER/flt-X,fltY:=FILTER/flt-Y /<>/test/annotate21.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/zey1Mm0xMJ/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/zey1Mm0xMJ/annotate22.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/zey1Mm0xMJ/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/zey1Mm0xMJ/annotate22.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/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 -a /tmp/zey1Mm0xMJ/annotate24.src.vcf.gz -c XX /tmp/zey1Mm0xMJ/annotate24.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/zey1Mm0xMJ/annotate24.src.vcf.gz -c XX /tmp/zey1Mm0xMJ/annotate24.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/zey1Mm0xMJ/annotate25.tab.gz -c CHROM,POS,ID,REF,ALT,~INFO/END /<>/test/annotate25.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/zey1Mm0xMJ/annotate25.tab.gz -c CHROM,POS,ID,REF,ALT,~INFO/END /<>/test/annotate25.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/zey1Mm0xMJ/annotate26.tab.gz -c CHROM,POS,~POS /<>/test/annotate26.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/zey1Mm0xMJ/annotate26.tab.gz -c CHROM,POS,~POS /<>/test/annotate26.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/zey1Mm0xMJ/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,TSTR,TFLT,TINT /<>/test/annotate.missing.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/zey1Mm0xMJ/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,TSTR,TFLT,TINT /<>/test/annotate.missing.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/zey1Mm0xMJ/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.TSTR,.TFLT,.TINT /<>/test/annotate.missing.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/zey1Mm0xMJ/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.TSTR,.TFLT,.TINT /<>/test/annotate.missing.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/zey1Mm0xMJ/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.+TSTR,.+TFLT,.+TINT /<>/test/annotate.missing.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/zey1Mm0xMJ/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.+TSTR,.+TFLT,.+TINT /<>/test/annotate.missing.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/zey1Mm0xMJ/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,+TSTR,+TFLT,+TINT /<>/test/annotate.missing.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/zey1Mm0xMJ/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,+TSTR,+TFLT,+TINT /<>/test/annotate.missing.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/zey1Mm0xMJ/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.=TSTR,.=TFLT,.=TINT /<>/test/annotate.missing.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/zey1Mm0xMJ/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,.=TSTR,.=TFLT,.=TINT /<>/test/annotate.missing.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/zey1Mm0xMJ/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,=TSTR,=TFLT,=TINT /<>/test/annotate.missing.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/zey1Mm0xMJ/annotate.missing.tab.gz -c CHROM,POS,REF,ALT,=TSTR,=TFLT,=TINT /<>/test/annotate.missing.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/zey1Mm0xMJ/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique /<>/test/annotate.olap.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/zey1Mm0xMJ/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique /<>/test/annotate.olap.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/zey1Mm0xMJ/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique --min-overlap 0.4:0.5 -m XXX /<>/test/annotate.olap.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/zey1Mm0xMJ/annots.olap.tab.gz -c CHROM,BEG,END,DB -l DB:unique --min-overlap 0.4:0.5 -m XXX /<>/test/annotate.olap.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/zey1Mm0xMJ/annots.id.vcf.gz -c ALT /tmp/zey1Mm0xMJ/annotate.id.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/zey1Mm0xMJ/annots.id.vcf.gz -c ALT /tmp/zey1Mm0xMJ/annotate.id.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/zey1Mm0xMJ/annots.id.vcf.gz -c +ALT /tmp/zey1Mm0xMJ/annotate.id.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/zey1Mm0xMJ/annots.id.vcf.gz -c +ALT /tmp/zey1Mm0xMJ/annotate.id.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/zey1Mm0xMJ/annots.id.2.vcf.gz --pair-logic some -c +ID /tmp/zey1Mm0xMJ/annotate.id.2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/zey1Mm0xMJ/annots.id.2.vcf.gz --pair-logic some -c +ID /tmp/zey1Mm0xMJ/annotate.id.2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/zey1Mm0xMJ/annots.id.2.vcf.gz --pair-logic any -c +ID /tmp/zey1Mm0xMJ/annotate.id.2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/zey1Mm0xMJ/annots.id.2.vcf.gz --pair-logic any -c +ID /tmp/zey1Mm0xMJ/annotate.id.2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/zey1Mm0xMJ/annotate27.tab.gz -c CHROM,POS,REF,ALT,EVIDENCE /<>/test/annotate27.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/zey1Mm0xMJ/annotate27.tab.gz -c CHROM,POS,REF,ALT,EVIDENCE /<>/test/annotate27.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/zey1Mm0xMJ/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1,smpl2 /<>/test/annotate28.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/zey1Mm0xMJ/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1,smpl2 /<>/test/annotate28.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/zey1Mm0xMJ/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2,smpl1 /<>/test/annotate28.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/zey1Mm0xMJ/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2,smpl1 /<>/test/annotate28.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/zey1Mm0xMJ/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1 /<>/test/annotate28.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/zey1Mm0xMJ/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl1 /<>/test/annotate28.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/zey1Mm0xMJ/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2 /<>/test/annotate28.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/zey1Mm0xMJ/annots28.tab.gz -c CHROM,POS,REF,ALT,FMT/TEST -s smpl2 /<>/test/annotate28.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -m XXX /<>/test/annotate.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -m XXX /<>/test/annotate.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/zey1Mm0xMJ/annots34.tab.gz -c CHROM,FROM,TO,INFO/END -H '##INFO=' /<>/test/annotate34.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/zey1Mm0xMJ/annots34.tab.gz -c CHROM,FROM,TO,INFO/END -H '##INFO=' /<>/test/annotate34.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/zey1Mm0xMJ/annots-mark.bed.gz -c CHROM,FROM,TO -m TAG /<>/test/annots-mark.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/zey1Mm0xMJ/annots-mark.bed.gz -c CHROM,FROM,TO -m TAG /<>/test/annots-mark.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version /tmp/zey1Mm0xMJ/concat.1.a.vcf.gz /tmp/zey1Mm0xMJ/concat.1.b.vcf.gz .. ok test_vcf_concat: /<>/bcftools concat -Ob /tmp/zey1Mm0xMJ/concat.1.a.vcf.gz /tmp/zey1Mm0xMJ/concat.1.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version /tmp/zey1Mm0xMJ/concat.1.a.bcf /tmp/zey1Mm0xMJ/concat.1.b.bcf .. ok test_vcf_concat: /<>/bcftools concat -Ob /tmp/zey1Mm0xMJ/concat.1.a.bcf /tmp/zey1Mm0xMJ/concat.1.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -a /tmp/zey1Mm0xMJ/concat.2.a.vcf.gz /tmp/zey1Mm0xMJ/concat.2.b.vcf.gz .. ok test_vcf_concat: /<>/bcftools concat -Ob -a /tmp/zey1Mm0xMJ/concat.2.a.vcf.gz /tmp/zey1Mm0xMJ/concat.2.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -a /tmp/zey1Mm0xMJ/concat.2.a.bcf /tmp/zey1Mm0xMJ/concat.2.b.bcf .. ok test_vcf_concat: /<>/bcftools concat -Ob -a /tmp/zey1Mm0xMJ/concat.2.a.bcf /tmp/zey1Mm0xMJ/concat.2.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -aD /tmp/zey1Mm0xMJ/concat.2.a.vcf.gz /tmp/zey1Mm0xMJ/concat.2.b.vcf.gz .. ok test_vcf_concat: /<>/bcftools concat -Ob -aD /tmp/zey1Mm0xMJ/concat.2.a.vcf.gz /tmp/zey1Mm0xMJ/concat.2.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -aD /tmp/zey1Mm0xMJ/concat.2.a.bcf /tmp/zey1Mm0xMJ/concat.2.b.bcf .. ok test_vcf_concat: /<>/bcftools concat -Ob -aD /tmp/zey1Mm0xMJ/concat.2.a.bcf /tmp/zey1Mm0xMJ/concat.2.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -l --ligate-warn /tmp/zey1Mm0xMJ/concat.3.a.vcf.gz /tmp/zey1Mm0xMJ/concat.3.b.vcf.gz /tmp/zey1Mm0xMJ/concat.3.0.vcf.gz /tmp/zey1Mm0xMJ/concat.3.c.vcf.gz /tmp/zey1Mm0xMJ/concat.3.d.vcf.gz /tmp/zey1Mm0xMJ/concat.3.e.vcf.gz /tmp/zey1Mm0xMJ/concat.3.f.vcf.gz .. ok test_vcf_concat: /<>/bcftools concat -Ob -l --ligate-warn /tmp/zey1Mm0xMJ/concat.3.a.vcf.gz /tmp/zey1Mm0xMJ/concat.3.b.vcf.gz /tmp/zey1Mm0xMJ/concat.3.0.vcf.gz /tmp/zey1Mm0xMJ/concat.3.c.vcf.gz /tmp/zey1Mm0xMJ/concat.3.d.vcf.gz /tmp/zey1Mm0xMJ/concat.3.e.vcf.gz /tmp/zey1Mm0xMJ/concat.3.f.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -l --ligate-warn /tmp/zey1Mm0xMJ/concat.3.a.bcf /tmp/zey1Mm0xMJ/concat.3.b.bcf /tmp/zey1Mm0xMJ/concat.3.0.bcf /tmp/zey1Mm0xMJ/concat.3.c.bcf /tmp/zey1Mm0xMJ/concat.3.d.bcf /tmp/zey1Mm0xMJ/concat.3.e.bcf /tmp/zey1Mm0xMJ/concat.3.f.bcf .. ok test_vcf_concat: /<>/bcftools concat -Ob -l --ligate-warn /tmp/zey1Mm0xMJ/concat.3.a.bcf /tmp/zey1Mm0xMJ/concat.3.b.bcf /tmp/zey1Mm0xMJ/concat.3.0.bcf /tmp/zey1Mm0xMJ/concat.3.c.bcf /tmp/zey1Mm0xMJ/concat.3.d.bcf /tmp/zey1Mm0xMJ/concat.3.e.bcf /tmp/zey1Mm0xMJ/concat.3.f.bcf | /<>/bcftools view | grep -v ^##bcftools_ Random seed for test_naive_concat: 654918540 .. ok test_naive_concat: /<>/bcftools concat --naive-force /tmp/zey1Mm0xMJ/naive_concat.0.bcf /tmp/zey1Mm0xMJ/naive_concat.1.bcf /tmp/zey1Mm0xMJ/naive_concat.2.bcf /tmp/zey1Mm0xMJ/naive_concat.3.bcf /tmp/zey1Mm0xMJ/naive_concat.4.bcf /tmp/zey1Mm0xMJ/naive_concat.5.bcf /tmp/zey1Mm0xMJ/naive_concat.6.bcf /tmp/zey1Mm0xMJ/naive_concat.7.bcf /tmp/zey1Mm0xMJ/naive_concat.8.bcf /tmp/zey1Mm0xMJ/naive_concat.9.bcf | /<>/bcftools view -H .. ok test_naive_concat: /<>/bcftools concat --naive /tmp/zey1Mm0xMJ/naive_concat.0.vcf.gz /tmp/zey1Mm0xMJ/naive_concat.1.vcf.gz /tmp/zey1Mm0xMJ/naive_concat.2.vcf.gz /tmp/zey1Mm0xMJ/naive_concat.3.vcf.gz /tmp/zey1Mm0xMJ/naive_concat.4.vcf.gz /tmp/zey1Mm0xMJ/naive_concat.5.vcf.gz /tmp/zey1Mm0xMJ/naive_concat.6.vcf.gz /tmp/zey1Mm0xMJ/naive_concat.7.vcf.gz /tmp/zey1Mm0xMJ/naive_concat.8.vcf.gz /tmp/zey1Mm0xMJ/naive_concat.9.vcf.gz | /<>/bcftools view -H .. ok test_vcf_concat: /<>/bcftools concat --no-version -l /tmp/zey1Mm0xMJ/concat.4.a.vcf.gz /tmp/zey1Mm0xMJ/concat.4.b.vcf.gz .. ok test_vcf_concat: /<>/bcftools concat -Ob -l /tmp/zey1Mm0xMJ/concat.4.a.vcf.gz /tmp/zey1Mm0xMJ/concat.4.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -l /tmp/zey1Mm0xMJ/concat.4.a.bcf /tmp/zey1Mm0xMJ/concat.4.b.bcf .. ok test_vcf_concat: /<>/bcftools concat -Ob -l /tmp/zey1Mm0xMJ/concat.4.a.bcf /tmp/zey1Mm0xMJ/concat.4.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -l --ligate-warn /tmp/zey1Mm0xMJ/concat.5.a.vcf.gz /tmp/zey1Mm0xMJ/concat.5.b.vcf.gz /tmp/zey1Mm0xMJ/concat.5.c.vcf.gz .. ok test_vcf_concat: /<>/bcftools concat -Ob -l --ligate-warn /tmp/zey1Mm0xMJ/concat.5.a.vcf.gz /tmp/zey1Mm0xMJ/concat.5.b.vcf.gz /tmp/zey1Mm0xMJ/concat.5.c.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -l --ligate-warn /tmp/zey1Mm0xMJ/concat.5.a.bcf /tmp/zey1Mm0xMJ/concat.5.b.bcf /tmp/zey1Mm0xMJ/concat.5.c.bcf .. ok test_vcf_concat: /<>/bcftools concat -Ob -l --ligate-warn /tmp/zey1Mm0xMJ/concat.5.a.bcf /tmp/zey1Mm0xMJ/concat.5.b.bcf /tmp/zey1Mm0xMJ/concat.5.c.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -l --ligate-force /tmp/zey1Mm0xMJ/concat.5.a.bcf /tmp/zey1Mm0xMJ/concat.5.b.bcf /tmp/zey1Mm0xMJ/concat.5.c.bcf .. ok test_vcf_concat: /<>/bcftools concat -Ob -l --ligate-force /tmp/zey1Mm0xMJ/concat.5.a.bcf /tmp/zey1Mm0xMJ/concat.5.b.bcf /tmp/zey1Mm0xMJ/concat.5.c.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -G -a -D /tmp/zey1Mm0xMJ/concat.5.a.vcf.gz /tmp/zey1Mm0xMJ/concat.5.b.vcf.gz /tmp/zey1Mm0xMJ/concat.5.c.vcf.gz .. ok test_vcf_concat: /<>/bcftools concat -Ob -G -a -D /tmp/zey1Mm0xMJ/concat.5.a.vcf.gz /tmp/zey1Mm0xMJ/concat.5.b.vcf.gz /tmp/zey1Mm0xMJ/concat.5.c.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -G -a -D /tmp/zey1Mm0xMJ/concat.5.a.bcf /tmp/zey1Mm0xMJ/concat.5.b.bcf /tmp/zey1Mm0xMJ/concat.5.c.bcf .. ok test_vcf_concat: /<>/bcftools concat -Ob -G -a -D /tmp/zey1Mm0xMJ/concat.5.a.bcf /tmp/zey1Mm0xMJ/concat.5.b.bcf /tmp/zey1Mm0xMJ/concat.5.c.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/zey1Mm0xMJ/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/zey1Mm0xMJ/reheader.bcf | /<>/bcftools reheader -h /<>/test/reheader.hdr | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -h /<>/test/reheader.hdr /tmp/zey1Mm0xMJ/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/zey1Mm0xMJ/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples /tmp/zey1Mm0xMJ/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/zey1Mm0xMJ/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples2 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples2 /tmp/zey1Mm0xMJ/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/zey1Mm0xMJ/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples3 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples3 /tmp/zey1Mm0xMJ/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/zey1Mm0xMJ/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples4 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples4 /tmp/zey1Mm0xMJ/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/empty.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/empty.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/reheader.2.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -f /<>/test/reheader.fai /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/reheader.2.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -h /<>/test/reheader.2.hdr -f /<>/test/reheader.fai /tmp/zey1Mm0xMJ/reheader.2.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -f /<>/test/reheader.3.fai /<>/test/reheader.3.vcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -f /<>/test/reheader.3.fai /tmp/zey1Mm0xMJ/reheader.3.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -f /<>/test/reheader.3.fai /tmp/zey1Mm0xMJ/reheader.3.vcf.gz | /<>/bcftools view --no-version .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/zey1Mm0xMJ/rename.map -Ov /tmp/zey1Mm0xMJ/annotate.bcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/zey1Mm0xMJ/rename.map -Ob /tmp/zey1Mm0xMJ/annotate.bcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/zey1Mm0xMJ/rename.map -Ov /<>/test/annotate.vcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/zey1Mm0xMJ/rename.map -Ob /<>/test/annotate.vcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_vcf_convert: /<>/bcftools convert -g -,. /tmp/zey1Mm0xMJ/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/convert.vcf.gz | /<>/bcftools convert -g -,. .. ok test_vcf_convert: /<>/bcftools convert -g -,. --vcf-ids /tmp/zey1Mm0xMJ/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/convert.vcf.gz | /<>/bcftools convert -g -,. --vcf-ids .. ok test_vcf_convert: /<>/bcftools convert -g -,. --vcf-ids --3N6 /tmp/zey1Mm0xMJ/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/convert.vcf.gz | /<>/bcftools convert -g -,. --vcf-ids --3N6 .. ok test_vcf_convert: /<>/bcftools convert -g .,- /tmp/zey1Mm0xMJ/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/convert.vcf.gz | /<>/bcftools convert -g .,- .. ok test_vcf_convert_hs2vcf: /<>/bcftools convert --vcf-ids -G /<>/test/convert.gs.gt.ids.gen,/<>/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /<>/bcftools convert --vcf-ids -G /<>/test/convert.gs.gt.ids.gen,/<>/test/convert.gs.gt.samples -Ou | /<>/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /<>/bcftools convert -G /<>/test/convert.gs.gt.ids.gen,/<>/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /<>/bcftools convert -G /<>/test/convert.gs.gt.ids.gen,/<>/test/convert.gs.gt.samples -Ou | /<>/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /<>/bcftools convert --3N6 -G /<>/test/convert.gs.gt.ids.3N6.gen,/<>/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /<>/bcftools convert --3N6 -G /<>/test/convert.gs.gt.ids.3N6.gen,/<>/test/convert.gs.gt.samples -Ou | /<>/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /<>/bcftools convert --vcf-ids -G /<>/test/convert.gs.gt.ids.gen.rev,/<>/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /<>/bcftools convert --vcf-ids -G /<>/test/convert.gs.gt.ids.gen.rev,/<>/test/convert.gs.gt.samples -Ou | /<>/bcftools view | grep -v ^## .. ok test_vcf_convert_hs2vcf: /<>/bcftools convert -G /<>/test/convert.gs.gt.ids.gen.rev,/<>/test/convert.gs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /<>/bcftools convert -G /<>/test/convert.gs.gt.ids.gen.rev,/<>/test/convert.gs.gt.samples -Ou | /<>/bcftools view | grep -v ^## .. ok test_vcf_convert: /<>/bcftools convert -g -,. --tag PL /tmp/zey1Mm0xMJ/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/convert.vcf.gz | /<>/bcftools convert -g -,. --tag PL .. ok test_vcf_convert: /<>/bcftools convert -g .,- --tag PL /tmp/zey1Mm0xMJ/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/convert.vcf.gz | /<>/bcftools convert -g .,- --tag PL .. ok test_vcf_convert: /<>/bcftools convert -g -,. --vcf-ids /tmp/zey1Mm0xMJ/check.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/check.vcf.gz | /<>/bcftools convert -g -,. --vcf-ids .. ok test_vcf_convert: /<>/bcftools convert -g .,- --vcf-ids /tmp/zey1Mm0xMJ/check.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/check.vcf.gz | /<>/bcftools convert -g .,- --vcf-ids .. ok test_vcf_convert: /<>/bcftools convert -g -,. --3N6 /tmp/zey1Mm0xMJ/check.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/check.vcf.gz | /<>/bcftools convert -g -,. --3N6 .. ok test_vcf_convert: /<>/bcftools convert -g .,- --3N6 /tmp/zey1Mm0xMJ/check.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/check.vcf.gz | /<>/bcftools convert -g .,- --3N6 .. ok test_vcf_convert: /<>/bcftools convert -g -,. --3N6 --vcf-ids /tmp/zey1Mm0xMJ/check.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/check.vcf.gz | /<>/bcftools convert -g -,. --3N6 --vcf-ids .. ok test_vcf_convert: /<>/bcftools convert -g .,- --3N6 --vcf-ids /tmp/zey1Mm0xMJ/check.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/check.vcf.gz | /<>/bcftools convert -g .,- --3N6 --vcf-ids .. ok test_vcf_convert: /<>/bcftools convert -h -,.,. /tmp/zey1Mm0xMJ/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/convert.vcf.gz | /<>/bcftools convert -h -,.,. .. ok test_vcf_convert: /<>/bcftools convert -h .,-,. /tmp/zey1Mm0xMJ/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/convert.vcf.gz | /<>/bcftools convert -h .,-,. .. ok test_vcf_convert: /<>/bcftools convert -h .,-,. --vcf-ids /tmp/zey1Mm0xMJ/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/convert.vcf.gz | /<>/bcftools convert -h .,-,. --vcf-ids .. ok test_vcf_convert: /<>/bcftools convert -h .,.,- /tmp/zey1Mm0xMJ/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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: /<>/bcftools convert --haplegendsample -,.,. /tmp/zey1Mm0xMJ/convert.hap-missing.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/convert.hap-missing.vcf.gz | /<>/bcftools convert --haplegendsample -,.,. .. ok test_vcf_convert: /<>/bcftools convert --hapsample -,. /tmp/zey1Mm0xMJ/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/convert.vcf.gz | /<>/bcftools convert --hapsample -,. .. ok test_vcf_convert: /<>/bcftools convert --hapsample -,. --vcf-ids /tmp/zey1Mm0xMJ/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/convert.vcf.gz | /<>/bcftools convert --hapsample -,. --vcf-ids .. ok test_vcf_convert: /<>/bcftools convert --hapsample .,- /tmp/zey1Mm0xMJ/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/convert.vcf.gz | /<>/bcftools convert --hapsample .,- .. 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.ids.hap,/<>/test/convert.hs.gt.samples | grep -v ^## .. ok test_vcf_convert_hs2vcf: /<>/bcftools convert --vcf-ids --hapsample2vcf /<>/test/convert.hs.gt.ids.hap,/<>/test/convert.hs.gt.samples -Ou | /<>/bcftools view | grep -v ^## .. ok test_vcf_convert_gvcf: /<>/bcftools convert --no-version --gvcf2vcf -i'FILTER="PASS"' -f /<>/test/gvcf.fa /tmp/zey1Mm0xMJ/convert.gvcf.vcf.gz .. ok test_vcf_convert_gvcf: /<>/bcftools view -Ob /tmp/zey1Mm0xMJ/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_convert_tsv2vcf: /<>/bcftools convert --no-version -c -,CHROM,POS,REF,ALT -f /<>/test/23andme.fa --tsv2vcf /<>/test/convert.tsv .. ok test_vcf_convert_tsv2vcf: /<>/bcftools convert -Ou -c -,CHROM,POS,REF,ALT -f /<>/test/23andme.fa --tsv2vcf /<>/test/convert.tsv | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.vcf.gz -f /<>/test/consensus.fa -s - -m /<>/test/consensus.tab .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.bcf -f /<>/test/consensus.fa -s - -m /<>/test/consensus.tab .. ok test_vcf_consensus_chain: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.vcf.gz -f /<>/test/consensus.fa -s - -m /<>/test/consensus.tab -c /tmp/zey1Mm0xMJ/consensus.1.chain.new >/dev/null; cat /tmp/zey1Mm0xMJ/consensus.1.chain.new .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 -m /<>/test/consensus.tab .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.bcf -f /<>/test/consensus.fa -H 1 -m /<>/test/consensus.tab .. ok test_vcf_consensus_chain: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 -m /<>/test/consensus.tab -c /tmp/zey1Mm0xMJ/consensus.2.chain.new >/dev/null; cat /tmp/zey1Mm0xMJ/consensus.2.chain.new .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.vcf.gz -f /<>/test/consensus.fa -I -s - -m /<>/test/consensus.tab .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.bcf -f /<>/test/consensus.fa -I -s - -m /<>/test/consensus.tab .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.vcf.gz -f /<>/test/consensus.fa -s - -I -m /<>/test/consensus.tab --mask-with X -m /<>/test/consensus.tab --mask-with lc .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.bcf -f /<>/test/consensus.fa -s - -I -m /<>/test/consensus.tab --mask-with X -m /<>/test/consensus.tab --mask-with lc .. ok test_vcf_consensus_chain: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.vcf.gz -f /<>/test/consensus.fa -I -m /<>/test/consensus.tab -c /tmp/zey1Mm0xMJ/consensus.3.chain.new >/dev/null; cat /tmp/zey1Mm0xMJ/consensus.3.chain.new .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.bcf -f /<>/test/consensus.fa -H 1 .. ok test_vcf_consensus_chain: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 -c /tmp/zey1Mm0xMJ/consensus.4.chain.new >/dev/null; cat /tmp/zey1Mm0xMJ/consensus.4.chain.new .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus2.vcf.gz -f /<>/test/consensus2.fa -H 1 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus2.bcf -f /<>/test/consensus2.fa -H 1 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus2.vcf.gz -f /<>/test/consensus2.fa -H 2 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus2.bcf -f /<>/test/consensus2.fa -H 2 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/empty.vcf.gz -f /<>/test/consensus.fa -s - .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/empty.bcf -f /<>/test/consensus.fa -s - .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus3.vcf.gz -f /<>/test/consensus2.fa -H 2 -M "?" .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus3.bcf -f /<>/test/consensus2.fa -H 2 -M "?" .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus3.vcf.gz -f /<>/test/consensus2.fa -H 2 -M "?" -p xx_ .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus3.bcf -f /<>/test/consensus2.fa -H 2 -M "?" -p xx_ .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus4.vcf.gz -f /<>/test/consensus2.fa -s - .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus4.bcf -f /<>/test/consensus2.fa -s - .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus5.vcf.gz -f /<>/test/consensus5.fa --haplotype LA .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus5.bcf -f /<>/test/consensus5.fa --haplotype LA .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus6.vcf.gz -f /<>/test/consensus6.fa -s - .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus6.bcf -f /<>/test/consensus6.fa -s - .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus7.vcf.gz -f /<>/test/consensus7.fa -H 2 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus7.bcf -f /<>/test/consensus7.fa -H 2 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus7.vcf.gz -f /<>/test/consensus7.fa -H 4 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus7.bcf -f /<>/test/consensus7.fa -H 4 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus7.vcf.gz -f /<>/test/consensus7.fa -H 2pIu .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus7.bcf -f /<>/test/consensus7.fa -H 2pIu .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus7.vcf.gz -f /<>/test/consensus7.fa -H 4pIu .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus7.bcf -f /<>/test/consensus7.fa -H 4pIu .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus7.vcf.gz -f /<>/test/consensus7.fa -H 1 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus7.bcf -f /<>/test/consensus7.fa -H 1 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus7.vcf.gz -f /<>/test/consensus7.fa -H 3 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus7.bcf -f /<>/test/consensus7.fa -H 3 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus7.vcf.gz -f /<>/test/consensus7.fa -H 1pIu .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus7.bcf -f /<>/test/consensus7.fa -H 1pIu .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus7.vcf.gz -f /<>/test/consensus7.fa -H 3pIu .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus7.bcf -f /<>/test/consensus7.fa -H 3pIu .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus8.vcf.gz -f /<>/test/consensus.fa -s - .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus8.bcf -f /<>/test/consensus.fa -s - .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus8.vcf.gz -f /<>/test/consensus.fa -s - -a . .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus8.bcf -f /<>/test/consensus.fa -s - -a . .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus8.vcf.gz -f /<>/test/consensus.fa -s - -a . -i 'type="snp" || type="ref"' .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus8.bcf -f /<>/test/consensus.fa -s - -a . -i 'type="snp" || type="ref"' .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus8.vcf.gz -f /<>/test/consensus.fa -s - -a . -i 'ALT!=""' .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus8.bcf -f /<>/test/consensus.fa -s - -a . -i 'ALT!=""' .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus8.vcf.gz -f /<>/test/consensus.fa -s - -a . -e 'MinDP>15' .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus8.bcf -f /<>/test/consensus.fa -s - -a . -e 'MinDP>15' .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus8.vcf.gz -f /<>/test/consensus.fa -s - -a . -e 'MinDP<15' .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus8.bcf -f /<>/test/consensus.fa -s - -a . -e 'MinDP<15' .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.9.vcf.gz -f /<>/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.9.bcf -f /<>/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.9.vcf.gz -f /<>/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.9.bcf -f /<>/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.10.vcf.gz -f /<>/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.10.bcf -f /<>/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.10.vcf.gz -f /<>/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.10.bcf -f /<>/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.11.vcf.gz -f /<>/test/consensus.11.fa -s smpl .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.11.bcf -f /<>/test/consensus.11.fa -s smpl .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.11.vcf.gz -f /<>/test/consensus.11.fa -s smpl -a N .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.11.bcf -f /<>/test/consensus.11.fa -s smpl -a N .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.12.vcf.gz -f /<>/test/consensus.12.fa -s - .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.12.bcf -f /<>/test/consensus.12.fa -s - .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.13.vcf.gz -f /<>/test/consensus.13.fa -s - .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.13.bcf -f /<>/test/consensus.13.fa -s - .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.14.vcf.gz -f /<>/test/consensus.14.fa -s - .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.14.bcf -f /<>/test/consensus.14.fa -s - .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.12.vcf.gz -f /<>/test/consensus.12.fa -s - --mark-del - --mark-ins uc --mark-snv uc .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.12.bcf -f /<>/test/consensus.12.fa -s - --mark-del - --mark-ins uc --mark-snv uc .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.12.vcf.gz -f /<>/test/consensus.12.fa -s - --mark-del - --mark-ins + --mark-snv : .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.12.bcf -f /<>/test/consensus.12.fa -s - --mark-del - --mark-ins + --mark-snv : .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.15.vcf.gz -f /<>/test/consensus.15.fa -H I --mark-ins lc --mark-snv lc .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.15.bcf -f /<>/test/consensus.15.fa -H I --mark-ins lc --mark-snv lc .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.16.vcf.gz -f /<>/test/consensus.fa -s - -I .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.16.bcf -f /<>/test/consensus.fa -s - -I .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.16.vcf.gz -f /<>/test/consensus.fa -H I .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.16.bcf -f /<>/test/consensus.fa -H I .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.17.vcf.gz -f /<>/test/consensus2.fa -s - -M N -m /<>/test/consensus.17.bed .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.17.bcf -f /<>/test/consensus2.fa -s - -M N -m /<>/test/consensus.17.bed .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.18.vcf.gz -f /<>/test/consensus.18.fa -s - .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.18.bcf -f /<>/test/consensus.18.fa -s - .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.19.vcf.gz -f /<>/test/consensus.19.fa -s - .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.19.bcf -f /<>/test/consensus.19.fa -s - .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.20.vcf.gz -f /<>/test/consensus.20.fa -s - .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.20.bcf -f /<>/test/consensus.20.fa -s - .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.20.vcf.gz -f /<>/test/consensus.20.fa .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.20.bcf -f /<>/test/consensus.20.fa .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.20.vcf.gz -f /<>/test/consensus.20.fa -M . -s b .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.20.bcf -f /<>/test/consensus.20.fa -M . -s b .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.20.vcf.gz -f /<>/test/consensus.20.fa -M . -s a .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.20.bcf -f /<>/test/consensus.20.fa -M . -s a .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.21.vcf.gz -f /<>/test/consensus.21.fa .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.21.bcf -f /<>/test/consensus.21.fa .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.22.vcf.gz -f /<>/test/consensus.22.fa --regions-overlap 0 --mark-del . .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.22.bcf -f /<>/test/consensus.22.fa --regions-overlap 0 --mark-del . .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.22.vcf.gz -f /<>/test/consensus.22.fa --regions-overlap 1 --mark-del . .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.22.bcf -f /<>/test/consensus.22.fa --regions-overlap 1 --mark-del . .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.22.vcf.gz -f /<>/test/consensus.22.fa --regions-overlap 2 --mark-del . .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.22.bcf -f /<>/test/consensus.22.fa --regions-overlap 2 --mark-del . .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.22.vcf.gz -f /<>/test/consensus.22.fa --regions-overlap 0 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.22.bcf -f /<>/test/consensus.22.fa --regions-overlap 0 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.22.vcf.gz -f /<>/test/consensus.22.fa --regions-overlap 1 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.22.bcf -f /<>/test/consensus.22.fa --regions-overlap 1 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.22.vcf.gz -f /<>/test/consensus.22.fa --regions-overlap 2 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/zey1Mm0xMJ/consensus.22.bcf -f /<>/test/consensus.22.fa --regions-overlap 2 .. 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/zey1Mm0xMJ/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/zey1Mm0xMJ/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/zey1Mm0xMJ/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/zey1Mm0xMJ/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.sam /<>/test/mpileup/mpileup.2.sam /<>/test/mpileup/mpileup.3.sam | 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.sam /<>/test/mpileup/mpileup.2.sam /<>/test/mpileup/mpileup.3.sam | /<>/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.sam /<>/test/mpileup/mpileup.2.sam /<>/test/mpileup/mpileup.3.sam | 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.sam /<>/test/mpileup/mpileup.2.sam /<>/test/mpileup/mpileup.3.sam | /<>/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.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.3.sam | /<>/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.sam /<>/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -s HG00102 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.3.sam /<>/test/mpileup/mpileup.4.sam | /<>/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.sam /<>/test/mpileup/mpileup.4.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -s ^HG99999 -f /<>/test/mpileup/mpileup.ref.fa -Ob /<>/test/mpileup/mpileup.3.sam /<>/test/mpileup/mpileup.4.sam | /<>/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.sam /<>/test/mpileup/mpileup.4.sam | 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.sam /<>/test/mpileup/mpileup.4.sam | /<>/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.sam /<>/test/mpileup/mpileup.4.sam | 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.sam /<>/test/mpileup/mpileup.4.sam | /<>/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.sam | 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.sam | /<>/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 --indels-cns -f /<>/test/mpileup/indel-AD.1.fa /<>/test/mpileup/indel-AD.1.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a AD --indels-cns -f /<>/test/mpileup/indel-AD.1.fa -Ob /<>/test/mpileup/indel-AD.1.sam | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a AD --indels-cns -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 --indels-cns -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 --indels-cns -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 --indels-cns -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_mpileup: /<>/bcftools mpileup -t 1:100 --skip-all-set PAIRED,PROPER_PAIR,MREVERSE -f /<>/test/mpileup/mpileup-SCR.fa /<>/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -t 1:100 --skip-all-set PAIRED,PROPER_PAIR,MREVERSE -f /<>/test/mpileup/mpileup-SCR.fa -Ob /<>/test/mpileup/mpileup-filter.sam | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -t 1:100 --skip-any-set READ1 -f /<>/test/mpileup/mpileup-SCR.fa /<>/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -t 1:100 --skip-any-set READ1 -f /<>/test/mpileup/mpileup-SCR.fa -Ob /<>/test/mpileup/mpileup-filter.sam | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -t 1:100 --skip-all-unset READ1 -f /<>/test/mpileup/mpileup-SCR.fa /<>/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -t 1:100 --skip-all-unset READ1 -f /<>/test/mpileup/mpileup-SCR.fa -Ob /<>/test/mpileup/mpileup-filter.sam | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -t 1:100 --skip-any-unset READ1 -f /<>/test/mpileup/mpileup-SCR.fa /<>/test/mpileup/mpileup-filter.sam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -t 1:100 --skip-any-unset READ1 -f /<>/test/mpileup/mpileup-SCR.fa -Ob /<>/test/mpileup/mpileup-filter.sam | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a INFO/NMBZ -r chr19:69-99 -f /<>/test/mpileup/annot-NMBZ.1.fa /<>/test/mpileup/annot-NMBZ.1.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a INFO/NMBZ -r chr19:69-99 -f /<>/test/mpileup/annot-NMBZ.1.fa -Ob /<>/test/mpileup/annot-NMBZ.1.bam | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a INFO/NMBZ -r chr6:75 -f /<>/test/mpileup/annot-NMBZ.2.fa /<>/test/mpileup/annot-NMBZ.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a INFO/NMBZ -r chr6:75 -f /<>/test/mpileup/annot-NMBZ.2.fa -Ob /<>/test/mpileup/annot-NMBZ.2.bam | /<>/bcftools view | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a INFO/NMBZ -r chr16:75 -f /<>/test/mpileup/annot-NMBZ.3.fa /<>/test/mpileup/annot-NMBZ.3.1.bam /<>/test/mpileup/annot-NMBZ.3.2.bam | grep -v ^##bcftools | grep -v ^##reference .. ok test_mpileup: /<>/bcftools mpileup -a INFO/NMBZ -r chr16:75 -f /<>/test/mpileup/annot-NMBZ.3.fa -Ob /<>/test/mpileup/annot-NMBZ.3.1.bam /<>/test/mpileup/annot-NMBZ.3.2.bam | /<>/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: /<>/bcftools csq -f /<>/test/csq.nchr.fa -g /<>/test/csq.nchr.gff /<>/test/csq.nchr.vcf | /<>/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /<>/bcftools csq -f /<>/test/csq.ychr.fa -g /<>/test/csq.nchr.gff /<>/test/csq.nchr.vcf | /<>/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /<>/bcftools csq -f /<>/test/csq.nchr.fa -g /<>/test/csq.ychr.gff /<>/test/csq.nchr.vcf | /<>/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /<>/bcftools csq -f /<>/test/csq.ychr.fa -g /<>/test/csq.ychr.gff /<>/test/csq.nchr.vcf | /<>/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /<>/bcftools csq -f /<>/test/csq.ychr.fa -g /<>/test/csq.ychr.gff /<>/test/csq.ychr.vcf | /<>/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /<>/bcftools csq -f /<>/test/csq.ychr.fa -g /<>/test/csq.nchr.gff /<>/test/csq.ychr.vcf | /<>/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /<>/bcftools csq -f /<>/test/csq.nchr.fa -g /<>/test/csq.ychr.gff /<>/test/csq.ychr.vcf | /<>/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq: /<>/bcftools csq -f /<>/test/csq.nchr.fa -g /<>/test/csq.nchr.gff /<>/test/csq.ychr.vcf | /<>/bcftools query -f'[%TBCSQ\n]' | perl -pe 's/[\t,]/\n/g' | sort .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000373833/ENST00000373833.fa -g /<>/test/csq/ENST00000373833/ENST00000373833.gff /<>/test/csq/ENST00000373833/boundary-insertion.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000373833/ENST00000373833.fa -g /<>/test/csq/ENST00000373833/ENST00000373833.gff /<>/test/csq/ENST00000373833/boundary-insertion.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /<>/test/csq/ENST00000422159 && /<>/bcftools csq -f ENST00000422159.fa -g ENST00000422159.gff multiallelic.vcf | /<>/bcftools query -f'[%POS\t%REF\t%ALT\t%GT\t%TBCSQ\n]' | ../sort-csq -q ; echo ; /<>/bcftools csq -f ENST00000422159.fa -g short.gff multiallelic.vcf | /<>/bcftools query -f'[%POS\t%REF\t%ALT\t%GT\t%TBCSQ\n]' | ../sort-csq -q .. 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/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/ENST00000269081/ENST00000269081.fa -g /<>/test/csq/ENST00000269081/ENST00000269081.gff /<>/test/csq/ENST00000269081/stop-gained-not-inframe-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/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/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/ENST00000285021/ENST00000285021.fa -g /<>/test/csq/ENST00000285021/ENST00000285021.gff /<>/test/csq/ENST00000285021/stop-gained-inframe-indel.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: 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: 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 -b -f ENST00000410009.fa -g ENST00000410009.gff frameshift.vcf | ../sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000410009/ENST00000410009.fa -g /<>/test/csq/ENST00000410009/ENST00000410009.gff /<>/test/csq/ENST00000410009/frameshift.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: cd /<>/test/csq/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: 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/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/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: 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/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/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/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/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/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/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: cd /<>/test/csq/ENST00000379416 && /<>/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.del-snp.vcf | ../sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /<>/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-del.vcf | ../sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /<>/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-ins.vcf | ../sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /<>/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff compound.ins-snp.vcf | ../sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /<>/bcftools csq -B 3 -f ENST00000379416.fa -g ENST00000379416.gff single.vcf | ../sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\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/ENST00000624631/ENST00000624631.fa -g /<>/test/csq/ENST00000624631/ENST00000624631.gff /<>/test/csq/ENST00000624631/ambiguous.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/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/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/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/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/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/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/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-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-donor6.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor6.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-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/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/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/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-donor3.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-donor3.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000341065/ENST00000341065.fa -g /<>/test/csq/ENST00000341065/ENST00000341065.gff /<>/test/csq/ENST00000341065/splice-acceptor-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-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/ENST00000536784/ENST00000536784.fa -g /<>/test/csq/ENST00000536784/ENST00000536784.gff /<>/test/csq/ENST00000536784/not-a-start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -l -f /<>/test/csq/ENST00000536784/ENST00000536784.fa -g /<>/test/csq/ENST00000536784/ENST00000536784.gff /<>/test/csq/ENST00000536784/not-a-start-lost.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/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: cd /<>/test/csq/ENST00000000000 && /<>/bcftools csq -p a -f ENST00000000000.fa -g ENST00000000000.gff upstream-stop.vcf | /<>/bcftools query -f'[%POS\t%REF\t%ALT\t%SAMPLE\t%GT\t%TBCSQ\n]' | ../sort-csq -q .. 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: /<>/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/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: cd /<>/test/csq/ENST00000580206 && /<>/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.ins-snv.vcf | ../sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /<>/bcftools csq -f ENST00000580206.fa -g short.gff compound.ins-snv.vcf | ../sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /<>/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff single.ins-snv.vcf | ../sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /<>/bcftools csq -f ENST00000580206.fa -g short.gff single.ins-snv.vcf | ../sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /<>/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.del-snv.vcf | ../sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /<>/bcftools csq -f ENST00000580206.fa -g short.gff compound.del-snv.vcf | ../sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /<>/bcftools csq -f ENST00000580206.fa -g short.gff single.del-snv.vcf | ../sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /<>/bcftools csq -f ENST00000580206.fa -g ENST00000580206.gff compound.del-ins.vcf | ../sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /<>/bcftools csq -f ENST00000580206.fa -g short.gff compound.del-ins.vcf | ../sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' ; echo ; /<>/bcftools csq -f ENST00000580206.fa -g short.gff single.del-ins.vcf | ../sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/ENST00000520868/ENST00000520868.fa -g /<>/test/csq/ENST00000520868/ENST00000520868.gff /<>/test/csq/ENST00000520868/long-deletion.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/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/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/ENST00000571540/ENST00000571540.fa -g /<>/test/csq/ENST00000571540/ENST00000571540.gff /<>/test/csq/ENST00000571540/nmd.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/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/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/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/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/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/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/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/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/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/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/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/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/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/ENST00000357367/ENST00000357367.fa -g /<>/test/csq/ENST00000357367/ENST00000357367.gff /<>/test/csq/ENST00000357367/stop-retained.vcf | /<>/test/csq/sort-csq | /<>/bcftools query -f'%POS\t%REF\t%ALT\t%EXP\n%POS\t%REF\t%ALT\t%BCSQ\n\n' .. ok test_csq_real: /<>/bcftools csq -f /<>/test/csq/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/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/ENST00000360372/ENST00000360372.fa -g /<>/test/csq/ENST00000360372/ENST00000360372.gff /<>/test/csq/ENST00000360372/mnp.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/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/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_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/zey1Mm0xMJ/gtcheck.1.vcf.gz -g /tmp/zey1Mm0xMJ/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -u GT,GT /tmp/zey1Mm0xMJ/gtcheck.1.vcf.gz -g /tmp/zey1Mm0xMJ/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -u GT,PL /tmp/zey1Mm0xMJ/gtcheck.1.vcf.gz -g /tmp/zey1Mm0xMJ/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -u PL,GT /tmp/zey1Mm0xMJ/gtcheck.1.vcf.gz -g /tmp/zey1Mm0xMJ/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -u PL,PL /tmp/zey1Mm0xMJ/gtcheck.1.vcf.gz -g /tmp/zey1Mm0xMJ/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -p s1,s1 /tmp/zey1Mm0xMJ/gtcheck.1.vcf.gz -g /tmp/zey1Mm0xMJ/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 /tmp/zey1Mm0xMJ/gtcheck.2.vcf.gz -g /tmp/zey1Mm0xMJ/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -P /<>/test/gtcheck.3.pairs /tmp/zey1Mm0xMJ/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -u PL /tmp/zey1Mm0xMJ/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 --n-matches 4 /tmp/zey1Mm0xMJ/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO | sort .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -s qry:E,D,C /tmp/zey1Mm0xMJ/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -s qry:E,D,C -u PL /tmp/zey1Mm0xMJ/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -s qry:B -s gt:D /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -s qry:B -s gt:D,C /tmp/zey1Mm0xMJ/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -p B,C,B,D /tmp/zey1Mm0xMJ/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -u GT,GT -H /tmp/zey1Mm0xMJ/gtcheck.1.vcf.gz -g /tmp/zey1Mm0xMJ/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -u GT,PL -H /tmp/zey1Mm0xMJ/gtcheck.1.vcf.gz -g /tmp/zey1Mm0xMJ/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -u PL,GT -H /tmp/zey1Mm0xMJ/gtcheck.1.vcf.gz -g /tmp/zey1Mm0xMJ/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -u PL,PL -H /tmp/zey1Mm0xMJ/gtcheck.1.vcf.gz -g /tmp/zey1Mm0xMJ/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/zey1Mm0xMJ/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/zey1Mm0xMJ/gtcheck.4.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -u GT -e 30 /tmp/zey1Mm0xMJ/gtcheck.1.vcf.gz -g /tmp/zey1Mm0xMJ/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -u GT -e 30 -p s1,s1 /tmp/zey1Mm0xMJ/gtcheck.1.vcf.gz -g /tmp/zey1Mm0xMJ/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -u GT -e 300 /tmp/zey1Mm0xMJ/gtcheck.1.vcf.gz -g /tmp/zey1Mm0xMJ/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -u PL -e 30 /tmp/zey1Mm0xMJ/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck /tmp/zey1Mm0xMJ/gtcheck.ntop.vcf.gz -g /tmp/zey1Mm0xMJ/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck --n-matches 2 /tmp/zey1Mm0xMJ/gtcheck.ntop.vcf.gz -g /tmp/zey1Mm0xMJ/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck /tmp/zey1Mm0xMJ/gtcheck.5.vcf.gz -g /tmp/zey1Mm0xMJ/gtcheck.5.gts.vcf.gz | grep -v ^# | grep -v Time .. ok test_gtcheck: /<>/bcftools gtcheck -p A,B,B,C /tmp/zey1Mm0xMJ/gtcheck.6.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -t 11:33 -p A,D,A,E,D,E -u GT -e 10 /tmp/zey1Mm0xMJ/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok Number of tests: total .. 1745 passed .. 1745 failed .. 0 make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/bcftools/ make -j2 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/x86_64-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/x86_64-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 dh_installchangelogs debian/rules override_dh_installman make[1]: Entering directory '/<>' dh_installman --language=C make[1]: Leaving directory '/<>' dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dpkg-gencontrol: warning: package bcftools: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package bcftools: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'bcftools' in '../bcftools_1.20-1_amd64.deb'. dpkg-deb: building package 'bcftools-dbgsym' in '../bcftools-dbgsym_1.20-1_amd64.deb'. dpkg-genbuildinfo -O../bcftools_1.20-1_amd64.buildinfo dpkg-genchanges -O../bcftools_1.20-1_amd64.changes dpkg-genchanges: info: including full source code in upload dpkg-source -Zxz --after-build . dpkg-buildpackage: info: full upload (original source is included) -------------------------------------------------------------------------------- Build finished at 2024-06-02T23:53:46Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ bcftools_1.20-1_amd64.changes: ------------------------------ Format: 1.8 Date: Thu, 18 Apr 2024 17:14:39 +0200 Source: bcftools Binary: bcftools bcftools-dbgsym Architecture: source amd64 Version: 1.20-1 Distribution: perl-5.40-throwaway Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: bcftools - genomic variant calling and manipulation of VCF/BCF files Closes: 1069234 Changes: bcftools (1.20-1) unstable; urgency=medium . [ Charles Plessy ] * Team upload. * New upstream version . [ Andreas Tille ] * Add missing Depends Closes: #1069234 * Standards-Version: 4.7.0 (routine-update) Checksums-Sha1: 3a3b400a9285f872570c55b376b8048d8d7e691f 1242 bcftools_1.20-1.dsc a3505e61b1e5d646a0e221abe2698b8c42e71993 3621678 bcftools_1.20.orig.tar.gz 57185d0f9f03b467c1aed4d25e2b266bfa38f6bc 7796 bcftools_1.20-1.debian.tar.xz 0fd0f90bbc13f2a4279316f0f20c971bba372abc 2154880 bcftools-dbgsym_1.20-1_amd64.deb 2b567ad6f67da551b75bbdd0505b6fe13f9803fc 6268 bcftools_1.20-1_amd64.buildinfo f63999f440174ef93b2d3c25ea82aa6567be4752 760140 bcftools_1.20-1_amd64.deb Checksums-Sha256: 3c27d7970ae549a13ea4d2a533e693b76bcca837114c310b0a0c8b72e6357204 1242 bcftools_1.20-1.dsc 7f34abf9bc0ded947e1a1409b65eda4a00eb17e33b71ba92b883902709840fbc 3621678 bcftools_1.20.orig.tar.gz 22aa10ee052576b64dfd4cca6dde6a50fea352d222bb1518b453430448690274 7796 bcftools_1.20-1.debian.tar.xz b1415124898b50bcdf528601228c5f77f1b3869d10069760ac5eabb8c4cf3b8b 2154880 bcftools-dbgsym_1.20-1_amd64.deb bfe14d42abfe333c30157efab77745a0bcd60b3dfaec266a7ffdcd630e740e72 6268 bcftools_1.20-1_amd64.buildinfo 2f8136831a406af6beea6b7f9d372106bd2a754b2cd71bf7b9c1e24f68084140 760140 bcftools_1.20-1_amd64.deb Files: b373a74a258c648ed31cdf672c264a4f 1242 science optional bcftools_1.20-1.dsc c4b63687a028a08467f64f2a209c7dbd 3621678 science optional bcftools_1.20.orig.tar.gz 1beeb07d6acfb6e408c0d2633e68ee34 7796 science optional bcftools_1.20-1.debian.tar.xz af294c73c02bfb81fa00cc065ccf83ef 2154880 debug optional bcftools-dbgsym_1.20-1_amd64.deb 4b5eb0091cded7d0352f604850e51290 6268 science optional bcftools_1.20-1_amd64.buildinfo 61e6c6bd04578232955fec33b33c8cb4 760140 science optional bcftools_1.20-1_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: bcftools Binary: bcftools bcftools-dbgsym Architecture: amd64 source Version: 1.20-1 Checksums-Md5: b373a74a258c648ed31cdf672c264a4f 1242 bcftools_1.20-1.dsc af294c73c02bfb81fa00cc065ccf83ef 2154880 bcftools-dbgsym_1.20-1_amd64.deb 61e6c6bd04578232955fec33b33c8cb4 760140 bcftools_1.20-1_amd64.deb Checksums-Sha1: 3a3b400a9285f872570c55b376b8048d8d7e691f 1242 bcftools_1.20-1.dsc 0fd0f90bbc13f2a4279316f0f20c971bba372abc 2154880 bcftools-dbgsym_1.20-1_amd64.deb f63999f440174ef93b2d3c25ea82aa6567be4752 760140 bcftools_1.20-1_amd64.deb Checksums-Sha256: 3c27d7970ae549a13ea4d2a533e693b76bcca837114c310b0a0c8b72e6357204 1242 bcftools_1.20-1.dsc b1415124898b50bcdf528601228c5f77f1b3869d10069760ac5eabb8c4cf3b8b 2154880 bcftools-dbgsym_1.20-1_amd64.deb 2f8136831a406af6beea6b7f9d372106bd2a754b2cd71bf7b9c1e24f68084140 760140 bcftools_1.20-1_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Sun, 02 Jun 2024 23:53:45 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: autoconf (= 2.71-3), automake (= 1:1.16.5-1.3), autopoint (= 0.21-14), autotools-dev (= 20220109.1), base-files (= 13.2), base-passwd (= 3.6.3), bash (= 5.2.21-2+b1), binutils (= 2.42-4), binutils-common (= 2.42-4), binutils-x86-64-linux-gnu (= 2.42-4), bsdextrautils (= 2.40.1-7), bsdutils (= 1:2.40.1-7), build-essential (= 12.10), bzip2 (= 1.0.8-5.1), coreutils (= 9.4-3.1), cpp (= 4:13.2.0-7), cpp-13 (= 13.2.0-25), cpp-13-x86-64-linux-gnu (= 13.2.0-25), cpp-x86-64-linux-gnu (= 4:13.2.0-7), dash (= 0.5.12-8), debconf (= 1.5.86), debhelper (= 13.15.3), debianutils (= 5.17), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.14.0-1), diffutils (= 1:3.10-1), dpkg (= 1.22.6), dpkg-dev (= 1.22.6), dwz (= 0.15-1+b1), file (= 1:5.45-3), findutils (= 4.9.0-6), g++ (= 4:13.2.0-7), g++-13 (= 13.2.0-25), g++-13-x86-64-linux-gnu (= 13.2.0-25), g++-x86-64-linux-gnu (= 4:13.2.0-7), gcc (= 4:13.2.0-7), gcc-13 (= 13.2.0-25), gcc-13-base (= 13.2.0-25), gcc-13-x86-64-linux-gnu (= 13.2.0-25), gcc-14-base (= 14.1.0-1), gcc-x86-64-linux-gnu (= 4:13.2.0-7), gettext (= 0.21-14+b1), gettext-base (= 0.21-14+b1), grep (= 3.11-4), groff-base (= 1.23.0-4), gzip (= 1.12-1.1), hostname (= 3.23+nmu2), init-system-helpers (= 1.66), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.2-2), libarchive-zip-perl (= 1.68-1), libasan8 (= 14.1.0-1), libatomic1 (= 14.1.0-1), libattr1 (= 1:2.5.2-1), libaudit-common (= 1:3.1.2-2.1), libaudit1 (= 1:3.1.2-2.1), libbinutils (= 2.42-4), libblkid1 (= 2.40.1-7), libbrotli1 (= 1.1.0-2+b3), libbz2-1.0 (= 1.0.8-5.1), libbz2-dev (= 1.0.8-5.1), libc-bin (= 2.38-12), libc-dev-bin (= 2.38-12), libc6 (= 2.38-12), libc6-dev (= 2.38-12), libcap-ng0 (= 0.8.5-1), libcap2 (= 1:2.66-5), libcc1-0 (= 14.1.0-1), libcom-err2 (= 1.47.1-1), libcrypt-dev (= 1:4.4.36-4), libcrypt1 (= 1:4.4.36-4), libctf-nobfd0 (= 2.42-4), libctf0 (= 2.42-4), libcurl3t64-gnutls (= 8.8.0-1), libcurl4-gnutls-dev (= 8.8.0-1), libdb5.3t64 (= 5.3.28+dfsg2-7), libdebconfclient0 (= 0.272), libdebhelper-perl (= 13.15.3), libdeflate-dev (= 1.20-1), libdeflate0 (= 1.20-1), libdpkg-perl (= 1.22.6), libelf1t64 (= 0.191-1+b1), libffi8 (= 3.4.6-1), libfile-stripnondeterminism-perl (= 1.14.0-1), libgcc-13-dev (= 13.2.0-25), libgcc-s1 (= 14.1.0-1), libgdbm-compat4t64 (= 1.23-5.1+b1), libgdbm6t64 (= 1.23-5.1+b1), libgmp10 (= 2:6.3.0+dfsg-2+b1), libgnutls30t64 (= 3.8.5-4), libgomp1 (= 14.1.0-1), libgprofng0 (= 2.42-4), libgsl-dev (= 2.7.1+dfsg-6+b1), libgsl27 (= 2.7.1+dfsg-6+b1), libgslcblas0 (= 2.7.1+dfsg-6+b1), libgssapi-krb5-2 (= 1.20.1-6+b1), libhogweed6t64 (= 3.9.1-2.2), libhts-dev (= 1.20+ds-1), libhts3t64 (= 1.20+ds-1), libhtscodecs2 (= 1.6.0-1+b1), libhwasan0 (= 14.1.0-1), libicu72 (= 72.1-4+b1), libidn2-0 (= 2.3.7-2), libio-pty-perl (= 1:1.20-1+b2), libisl23 (= 0.26-3+b2), libitm1 (= 14.1.0-1), libjansson4 (= 2.14-2+b2), libk5crypto3 (= 1.20.1-6+b1), libkeyutils1 (= 1.6.3-3), libkrb5-3 (= 1.20.1-6+b1), libkrb5support0 (= 1.20.1-6+b1), libldap-2.5-0 (= 2.5.17+dfsg-1+b1), liblsan0 (= 14.1.0-1), liblzma-dev (= 5.6.1+really5.4.5-1), liblzma5 (= 5.6.1+really5.4.5-1), libmagic-mgc (= 1:5.45-3), libmagic1t64 (= 1:5.45-3), libmd0 (= 1.1.0-2), libmount1 (= 2.40.1-7), libmpc3 (= 1.3.1-1+b2), libmpfr6 (= 4.2.1-1+b1), libnettle8t64 (= 3.9.1-2.2), libnghttp2-14 (= 1.61.0-1+b1), libp11-kit0 (= 0.25.3-5), libpam-modules (= 1.5.3-7), libpam-modules-bin (= 1.5.3-7), libpam-runtime (= 1.5.3-7), libpam0g (= 1.5.3-7), libpcre2-8-0 (= 10.42-4+b1), libperl5.40 (= 5.40.0~rc1-1), libpipeline1 (= 1.5.7-2), libpsl5t64 (= 0.21.2-1.1), libquadmath0 (= 14.1.0-1), librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b4), libsasl2-2 (= 2.1.28+dfsg1-6), libsasl2-modules-db (= 2.1.28+dfsg1-6), libseccomp2 (= 2.5.5-1), libselinux1 (= 3.5-2+b2), libsframe1 (= 2.42-4), libsmartcols1 (= 2.40.1-7), libssh2-1t64 (= 1.11.0-5), libssl3t64 (= 3.2.1-3), libstdc++-13-dev (= 13.2.0-25), libstdc++6 (= 14.1.0-1), libsystemd0 (= 256~rc3-7), libtasn1-6 (= 4.19.0-3+b2), libtinfo6 (= 6.5-2), libtool (= 2.4.7-7), libtsan2 (= 14.1.0-1), libubsan1 (= 14.1.0-1), libuchardet0 (= 0.0.8-1+b1), libudev1 (= 256~rc3-7), libunistring5 (= 1.2-1), libuuid1 (= 2.40.1-7), libxml2 (= 2.12.7+dfsg-2), libzstd1 (= 1.5.5+dfsg2-2), linux-libc-dev (= 6.8.12-1), login (= 1:4.13+dfsg1-4), m4 (= 1.4.19-4), make (= 4.3-4.1), man-db (= 2.12.1-1), mawk (= 1.3.4.20240123-1), ncurses-base (= 6.5-2), ncurses-bin (= 6.5-2), patch (= 2.7.6-7), perl (= 5.40.0~rc1-1), perl-base (= 5.40.0~rc1-1), perl-modules-5.40 (= 5.40.0~rc1-1), po-debconf (= 1.0.21+nmu1), rpcsvc-proto (= 1.4.3-1), sed (= 4.9-2), sensible-utils (= 0.0.22), sysvinit-utils (= 3.09-1), tabix (= 1.20+ds-1), tar (= 1.35+dfsg-3), usr-is-merged (= 39), util-linux (= 2.40.1-7), xz-utils (= 5.6.1+really5.4.5-1), zlib1g (= 1:1.3.dfsg+really1.3.1-1), zlib1g-dev (= 1:1.3.dfsg+really1.3.1-1) Environment: DEB_BUILD_OPTIONS="parallel=2" LANG="en_GB.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" LD_LIBRARY_PATH="/usr/lib/libeatmydata" SOURCE_DATE_EPOCH="1713453279" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ bcftools-dbgsym_1.20-1_amd64.deb -------------------------------- new Debian package, version 2.0. size 2154880 bytes: control archive=2400 bytes. 1972 bytes, 12 lines control 4325 bytes, 41 lines md5sums Package: bcftools-dbgsym Source: bcftools Version: 1.20-1 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 2467 Depends: bcftools (= 1.20-1) Section: debug Priority: optional Description: debug symbols for bcftools Build-Ids: 0ecc40a92d9c3240ed8e604e931a9ce79778e47d 12ff705eff686623486108d8b25657ff1102c8db 19900fbebf68bbc76a6db887bb94a5544300486f 1e0bfad52cf38569b4971166554d5d2ae7694c1c 234ee360b3a7238df2c864c077b8d79f8a86314f 24d21d7152e7275b10bb076a9ea3f375f4c85697 2660b98fb0691249775f45929bf659f62c74f43c 46e950c6150ed89ea8980f069f793c74454358a7 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Depends: libc6 (>= 2.34), libhts3t64 (>= 1.17), python3-gffutils, python3-matplotlib Recommends: perl Suggests: python3, python3-numpy, texlive-latex-recommended Section: science Priority: optional Homepage: https://samtools.github.io/bcftools/ Description: genomic variant calling and manipulation of VCF/BCF files BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. 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+------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 51196 Build-Time: 163 Distribution: perl-5.40-throwaway Host Architecture: amd64 Install-Time: 11 Job: /srv/debomatic/incoming/bcftools_1.20-1.dsc Machine Architecture: amd64 Package: bcftools Package-Time: 181 Source-Version: 1.20-1 Space: 51196 Status: successful Version: 1.20-1 -------------------------------------------------------------------------------- Finished at 2024-06-02T23:53:46Z Build needed 00:03:01, 51196k disk space