sbuild (Debian sbuild) 0.85.9 (29 May 2024) on carme.larted.org.uk +==============================================================================+ | bcftools 1.20-2 (amd64) Tue, 25 Jun 2024 04:03:31 +0000 | +==============================================================================+ Package: bcftools Version: 1.20-2 Source Version: 1.20-2 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-1e26910d-e1ab-44c9-aec2-594dd0ffb962' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup bcftools_1.20-2 perl-5.40-throwaway amd64 ---------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup bcftools_1.20-2 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: NOTICE: Log filtering will replace 'build/bcftools-QGU687/resolver-q2lben' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.40 InRelease [3042 B] Hit:2 http://localhost:3142/debian sid InRelease Get:1 file:/srv/reprepro perl-5.40 InRelease [3042 B] Get:3 file:/srv/reprepro perl-5.40/main amd64 Packages [623 kB] Hit:4 http://deb.debian.org/debian unstable InRelease Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/bcftools_1.20-2.dsc exists in /srv/debomatic/incoming; copying to chroot I: NOTICE: Log filtering will replace 'build/bcftools-QGU687/bcftools-1.20' with '<>' I: NOTICE: Log filtering will replace 'build/bcftools-QGU687' 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 (97.6 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... 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 28.2 MB/28.2 MB of archives. After this operation, 106 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [936 B] Get:2 file:/srv/reprepro perl-5.40/main amd64 libio-pty-perl amd64 1:1.20-1+b2 [34.3 kB] Get:3 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3 [42.9 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.22.5-1 [199 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-4 [1180 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.1-9 [96.2 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get:12 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.12.1-2 [1411 kB] Get:13 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get:14 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.71-3 [332 kB] Get:15 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get:16 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get:17 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.22.5-1 [723 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.16 [88.6 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-7 [517 kB] Get:20 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get:21 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get:23 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get:24 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get:25 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get:26 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get:27 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg-3 [670 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.22.5-1 [1593 kB] Get:29 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:30 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:31 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.16 [891 kB] Get:32 http://deb.debian.org/debian unstable/main amd64 libfakeroot amd64 1.35.1-1 [28.6 kB] Get:33 http://deb.debian.org/debian unstable/main amd64 fakeroot amd64 1.35.1-1 [74.5 kB] Get:34 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get:35 http://deb.debian.org/debian unstable/main amd64 libbz2-dev amd64 1.0.8-5.1 [31.3 kB] Get:36 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.1-1 [22.9 kB] Get:37 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.2-1 [32.2 kB] Get:38 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.2-1 [80.0 kB] Get:39 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get:40 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.2-1 [324 kB] Get:41 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.2-1 [136 kB] Get:42 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.62.1-1 [75.5 kB] Get:43 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get:44 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get:45 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.0-5 [215 kB] Get:46 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.8.0-1 [434 kB] Get:47 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls-dev amd64 8.8.0-1 [540 kB] Get:48 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.20-1 [46.0 kB] Get:49 http://deb.debian.org/debian unstable/main amd64 libdeflate-dev amd64 1.20-1 [54.5 kB] Get:50 http://deb.debian.org/debian unstable/main amd64 libgslcblas0 amd64 2.7.1+dfsg-6+b1 [107 kB] Get:51 http://deb.debian.org/debian unstable/main amd64 libgsl27 amd64 2.7.1+dfsg-6+b1 [934 kB] Get:52 http://deb.debian.org/debian unstable/main amd64 libgsl-dev amd64 2.7.1+dfsg-6+b1 [1146 kB] Get:53 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.0-1+b1 [93.0 kB] Get:54 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.20+ds-1 [452 kB] Get:55 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.6.2-1 [299 kB] Get:56 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1 [919 kB] Get:57 http://deb.debian.org/debian unstable/main amd64 libhts-dev amd64 1.20+ds-1 [1684 kB] Get:58 http://deb.debian.org/debian unstable/main amd64 tabix amd64 1.20+ds-1 [483 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 28.2 MB in 0s (87.9 MB/s) Selecting previously unselected package sensible-utils. (Reading database ... 21757 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... 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_0.22.5-1_amd64.deb ... Unpacking gettext-base (0.22.5-1) ... 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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Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.16) ... 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 (1.62.1-1) ... Setting up libdeflate0:amd64 (1.20-1) ... Setting up gettext-base (0.22.5-1) ... 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 (1.35.1-1) ... Setting up libelf1t64:amd64 (0.191-1+b1) ... Setting up libkrb5support0:amd64 (1.21.2-1) ... Setting up fakeroot (1.35.1-1) ... 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 (0.22.5-1) ... Setting up libk5crypto3:amd64 (1.21.2-1) ... Setting up autoconf (2.71-3) ... Setting up liblzma-dev:amd64 (5.6.2-1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up libkrb5-3:amd64 (1.21.2-1) ... 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-3) ... 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 (0.22.5-1) ... 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 (1.21.2-1) ... 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 (2.12.1-2) ... 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 (13.16) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.38-13) ... +------------------------------------------------------------------------------+ | 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_2.42.50.20240618-1 dpkg-dev_1.22.6 g++-13_13.3.0-1 gcc-13_13.3.0-1 libc6-dev_2.38-13 libstdc++-13-dev_13.3.0-1 libstdc++6_14.1.0-2 linux-libc-dev_6.8.12-1 Package versions: adduser_3.137 apt_2.9.5 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.22.5-1 autotools-dev_20220109.1 base-files_13.3 base-passwd_3.6.3 bash_5.2.21-2.1 binutils_2.42.50.20240618-1 binutils-common_2.42.50.20240618-1 binutils-x86-64-linux-gnu_2.42.50.20240618-1 bsdextrautils_2.40.1-9 bsdutils_1:2.40.1-9 build-essential_12.10 bzip2_1.0.8-5.1 coreutils_9.4-3.1 cpp_4:13.2.0-7 cpp-13_13.3.0-1 cpp-13-x86-64-linux-gnu_13.3.0-1 cpp-x86-64-linux-gnu_4:13.2.0-7 dash_0.5.12-9 debconf_1.5.86 debhelper_13.16 debian-archive-keyring_2023.4 debianutils_5.19 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_1.35.1-1 file_1:5.45-3 findutils_4.10.0-2 g++_4:13.2.0-7 g++-13_13.3.0-1 g++-13-x86-64-linux-gnu_13.3.0-1 g++-x86-64-linux-gnu_4:13.2.0-7 gcc_4:13.2.0-7 gcc-13_13.3.0-1 gcc-13-base_13.3.0-1 gcc-13-x86-64-linux-gnu_13.3.0-1 gcc-14-base_14.1.0-2 gcc-x86-64-linux-gnu_4:13.2.0-7 gettext_0.22.5-1 gettext-base_0.22.5-1 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_2.9.5 libarchive-zip-perl_1.68-1 libasan8_14.1.0-2 libassuan0_2.5.6-1+b1 libatomic1_14.1.0-2 libattr1_1:2.5.2-1 libaudit-common_1:3.1.2-4 libaudit1_1:3.1.2-4 libbinutils_2.42.50.20240618-1 libblkid1_2.40.1-9 libbrotli1_1.1.0-2+b3 libbsd0_0.12.2-1 libbz2-1.0_1.0.8-5.1 libbz2-dev_1.0.8-5.1 libc-bin_2.38-13 libc-dev-bin_2.38-13 libc-l10n_2.38-13 libc6_2.38-13 libc6-dev_2.38-13 libcap-ng0_0.8.5-1 libcap2_1:2.66-5 libcc1-0_14.1.0-2 libcom-err2_1.47.1-1 libcrypt-dev_1:4.4.36-4 libcrypt1_1:4.4.36-4 libctf-nobfd0_2.42.50.20240618-1 libctf0_2.42.50.20240618-1 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_13.16 libdeflate-dev_1.20-1 libdeflate0_1.20-1 libdpkg-perl_1.22.6 libeatmydata1_131-2 libelf1t64_0.191-1+b1 libfakeroot_1.35.1-1 libffi8_3.4.6-1 libfile-stripnondeterminism-perl_1.14.0-1 libgcc-13-dev_13.3.0-1 libgcc-s1_14.1.0-2 libgcrypt20_1.10.3-3 libgdbm-compat4t64_1.23-6 libgdbm6t64_1.23-6 libgmp10_2:6.3.0+dfsg-2+b1 libgnutls30t64_3.8.5-4 libgomp1_14.1.0-2 libgpg-error0_1.49-2 libgprofng0_2.42.50.20240618-1 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_1.21.2-1 libhogweed6t64_3.10-1 libhts-dev_1.20+ds-1 libhts3t64_1.20+ds-1 libhtscodecs2_1.6.0-1+b1 libhwasan0_14.1.0-2 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_14.1.0-2 libjansson4_2.14-2+b2 libk5crypto3_1.21.2-1 libkeyutils1_1.6.3-3 libkrb5-3_1.21.2-1 libkrb5support0_1.21.2-1 libksba8_1.6.6-1 libldap-2.5-0_2.5.18+dfsg-1 liblsan0_14.1.0-2 liblz4-1_1.9.4-2 liblzma-dev_5.6.2-1 liblzma5_5.6.2-1 libmagic-mgc_1:5.45-3 libmagic1t64_1:5.45-3 libmd0_1.1.0-2 libmount1_2.40.1-9 libmpc3_1.3.1-1+b2 libmpfr6_4.2.1-1+b1 libncursesw6_6.5-2 libnettle8t64_3.10-1 libnghttp2-14_1.62.1-1 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_14.1.0-2 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_2.42.50.20240618-1 libsmartcols1_2.40.1-9 libsqlite3-0_3.46.0-1 libssh2-1t64_1.11.0-5 libssl3t64_3.2.2-1 libstdc++-13-dev_13.3.0-1 libstdc++6_14.1.0-2 libsystemd0_256.1-2 libtasn1-6_4.19.0-3+b2 libtinfo6_6.5-2 libtool_2.4.7-7 libtsan2_14.1.0-2 libubsan1_14.1.0-2 libuchardet0_0.0.8-1+b1 libudev1_256.1-2 libunistring5_1.2-1 libuuid1_2.40.1-9 libxml2_2.12.7+dfsg-3 libxxhash0_0.8.2-2+b1 libzstd1_1.5.6+dfsg-1 linux-libc-dev_6.8.12-1 locales-all_2.38-13 login_1:4.15.2-1 m4_1.4.19-4 make_4.3-4.1 man-db_2.12.1-2 mawk_1.3.4.20240123-1 ncurses-base_6.5-2 ncurses-bin_6.5-2 passwd_1:4.15.2-1 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_0.0.24 sysvinit-utils_3.09-2 tabix_1.20+ds-1 tar_1.35+dfsg-3 usr-is-merged_39 util-linux_2.40.1-9 xz-utils_5.6.2-1 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: 1.20-2 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 c925b1ca0077b9aec29892e70acf11022df0f057 7836 bcftools_1.20-2.debian.tar.xz Checksums-Sha256: 7f34abf9bc0ded947e1a1409b65eda4a00eb17e33b71ba92b883902709840fbc 3621678 bcftools_1.20.orig.tar.gz a1ff25568b1c641c9bf55dc5932efaa6e281c29efc6aff1c40cd2a2091585053 7836 bcftools_1.20-2.debian.tar.xz Files: c4b63687a028a08467f64f2a209c7dbd 3621678 bcftools_1.20.orig.tar.gz 321310607a83802b72a602acffcbb85e 7836 bcftools_1.20-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJGBAEBCgAwFiEEc0cUmcxg7Z7ugFlGxb1sjyKV1QIFAmZ6AxESHHBsZXNzeUBk ZWJpYW4ub3JnAAoJEMW9bI8ildUCBrUP/0k6uzsOVMPpplfMmD4pcPht+CJMphqj 6Pqnt18Ubp8RfOBn/bfXEj9kAiqLwgUZHUM05JdFlK7O+4Yv8kXli/aLJjRq6zg4 rswTDiIy8g19LZKeWcZQdaQBdoYRy4rq8QHRxruu3whFhqPKeQb8kS4ElW7Mv6oW h/Bnyu8O0Nh9aWCepAdNZMaVV/Kc/Ouq7fJ0KWOhB0Ijp9R4n/SJDkx7fsNOgNf+ bzAvaJS53wC+iSmw853NQhTNCTc0XvIO+uNsPrd3/t9BBjZBNVNIlngHgbUM4UjO SRn/MBJGiWL0tu6NOhDJB+FgCDlB6o3Ry3qSX+R2Jd1KdEZYYBx97+ldkSpG/qyu ST4nmmSEb1olNJomVERK2+bfEwHoAJqByqk7t5pImiTqqxE9rkuR3PcP+6kZTcC6 ifN82kEWHWQtkpsg469WUp+CoFi/7h8NXwhuJDQd3x63aIREqeJs9JqZvkyz0fyU bybYfMC0SVZYo5V6dO3/Zlu9LScZjFmX/hXdbrxCwDzL7OYeisE14S4n6nfZhk8R bAbZFL9zfviE8QkWuKCTGxMh+a/s6UBb3wa4CTatgRhtabKVM9HZXnk8KVVTO/5b IYB8aFd9Sa1Ui7kpxWktJyy2OzeNHtIQjUkJ1xc77pxNgQ5A5KiRT3+QpAGewanN KhKAWweySyYb =gI2+ -----END PGP SIGNATURE----- gpgv: Signature made Mon Jun 24 23:36:49 2024 UTC gpgv: using RSA key 73471499CC60ED9EEE805946C5BD6C8F2295D502 gpgv: issuer "plessy@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./bcftools_1.20-2.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_1.20-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying tests-pluginpath.patch dpkg-source: info: applying skip_new_test_failing_on_32bit.patch 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_1.20-2 perl-5.40-throwaway amd64 ---------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network bcftools_1.20-2 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-1e26910d-e1ab-44c9-aec2-594dd0ffb962 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 1.20-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Charles Plessy 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_1.20-2.debian.tar.xz dpkg-source: info: building bcftools in bcftools_1.20-2.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/77Ka2juTPq/merge.a.vcf.gz 2:3199812-3199812 .. ok test_tabix: /<>/bcftools view -H /tmp/77Ka2juTPq/merge.a.bcf 2:3199812-3199812 .. ok test_tabix: tabix /tmp/77Ka2juTPq/merge.a.vcf.gz 1:3000151-3000151 .. ok test_tabix: /<>/bcftools view -H /tmp/77Ka2juTPq/merge.a.bcf 1:3000151-3000151 .. ok test_index: /<>/bcftools view -H /tmp/77Ka2juTPq/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/77Ka2juTPq/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/77Ka2juTPq/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/77Ka2juTPq/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/77Ka2juTPq/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/77Ka2juTPq/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /<>/bcftools view -H /tmp/77Ka2juTPq/large_chrom_csi_limit.bcf chr20 .. ok test_index: /<>/bcftools view -H /tmp/77Ka2juTPq/large_chrom_csi_limit.bcf chr20 .. ok test_index: /<>/bcftools view -H /tmp/77Ka2juTPq/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /<>/bcftools view -H /tmp/77Ka2juTPq/large_chrom_csi_limit.bcf chr20 .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/77Ka2juTPq/idx.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/77Ka2juTPq/idx.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/77Ka2juTPq/idx.bcf .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/77Ka2juTPq/idx.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/77Ka2juTPq/idx.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/77Ka2juTPq/idx.vcf.gz.csi .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/77Ka2juTPq/idx.bcf .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/77Ka2juTPq/idx.bcf.csi .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/77Ka2juTPq/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/77Ka2juTPq/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/77Ka2juTPq/empty.bcf .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/77Ka2juTPq/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/77Ka2juTPq/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/77Ka2juTPq/empty.vcf.gz.csi .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/77Ka2juTPq/empty.bcf .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/77Ka2juTPq/empty.bcf.csi .. ok test_vcf_check: /<>/bcftools stats -s - /tmp/77Ka2juTPq/check.vcf.gz | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/check.1.chk /tmp/77Ka2juTPq/check.2.chk /tmp/77Ka2juTPq/check.3.chk /tmp/77Ka2juTPq/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/77Ka2juTPq/stats.a.vcf.gz /tmp/77Ka2juTPq/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /<>/bcftools stats -s B /tmp/77Ka2juTPq/stats.a.vcf.gz /tmp/77Ka2juTPq/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /<>/bcftools stats -s - /tmp/77Ka2juTPq/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /<>/bcftools stats -s - -i 'type="snp"' /tmp/77Ka2juTPq/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /<>/bcftools stats -s - /tmp/77Ka2juTPq/stats.vaf.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_isec: /<>/bcftools isec -n =2 /tmp/77Ka2juTPq/isec.a.vcf.gz /tmp/77Ka2juTPq/isec.b.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 /tmp/77Ka2juTPq/isec.a.vcf.gz /tmp/77Ka2juTPq/isec.b.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/77Ka2juTPq/isec.a.vcf.gz /tmp/77Ka2juTPq/isec.b.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 -i"STRLEN(REF)==2" /tmp/77Ka2juTPq/isec.a.vcf.gz /tmp/77Ka2juTPq/isec.b.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -n =2 -c both /tmp/77Ka2juTPq/isec.a.vcf.gz /tmp/77Ka2juTPq/isec.b.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 -c both /tmp/77Ka2juTPq/isec.a.vcf.gz /tmp/77Ka2juTPq/isec.b.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -n =2 -c any /tmp/77Ka2juTPq/isec.a.vcf.gz /tmp/77Ka2juTPq/isec.b.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 -c any /tmp/77Ka2juTPq/isec.a.vcf.gz /tmp/77Ka2juTPq/isec.b.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -C -c any /tmp/77Ka2juTPq/isec.a.vcf.gz /tmp/77Ka2juTPq/isec.b.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -Ob -C -c any /tmp/77Ka2juTPq/isec.a.vcf.gz /tmp/77Ka2juTPq/isec.b.vcf.gz .. ok test_vcf_isec2: /<>/bcftools isec --no-version -T /tmp/77Ka2juTPq/isec.tab.gz /tmp/77Ka2juTPq/isec.a.vcf.gz .. ok test_vcf_isec2: /<>/bcftools isec -Ob -T /tmp/77Ka2juTPq/isec.tab.gz /tmp/77Ka2juTPq/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/77Ka2juTPq/isec-miss.1.1.vcf.gz /tmp/77Ka2juTPq/isec-miss.1.2.vcf.gz /tmp/77Ka2juTPq/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/77Ka2juTPq/isec-miss.1.1.vcf.gz /tmp/77Ka2juTPq/isec-miss.1.2.vcf.gz /tmp/77Ka2juTPq/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -R /<>/test/isec-miss.1.regs.txt -n +1 /tmp/77Ka2juTPq/isec-miss.1.1.vcf.gz /tmp/77Ka2juTPq/isec-miss.1.2.vcf.gz /tmp/77Ka2juTPq/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -Ob -R /<>/test/isec-miss.1.regs.txt -n +1 /tmp/77Ka2juTPq/isec-miss.1.1.vcf.gz /tmp/77Ka2juTPq/isec-miss.1.2.vcf.gz /tmp/77Ka2juTPq/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/77Ka2juTPq/isec-miss.2.1.vcf.gz /tmp/77Ka2juTPq/isec-miss.2.2.vcf.gz /tmp/77Ka2juTPq/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/77Ka2juTPq/isec-miss.2.1.vcf.gz /tmp/77Ka2juTPq/isec-miss.2.2.vcf.gz /tmp/77Ka2juTPq/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -R /<>/test/isec-miss.1.regs.txt -n +1 /tmp/77Ka2juTPq/isec-miss.2.1.vcf.gz /tmp/77Ka2juTPq/isec-miss.2.2.vcf.gz /tmp/77Ka2juTPq/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -Ob -R /<>/test/isec-miss.1.regs.txt -n +1 /tmp/77Ka2juTPq/isec-miss.2.1.vcf.gz /tmp/77Ka2juTPq/isec-miss.2.2.vcf.gz /tmp/77Ka2juTPq/isec-miss.2.3.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -i AF:join /tmp/77Ka2juTPq/merge.join.a.vcf.gz /tmp/77Ka2juTPq/merge.join.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob -i AF:join /tmp/77Ka2juTPq/merge.join.a.vcf.gz /tmp/77Ka2juTPq/merge.join.b.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version -i AF:join /tmp/77Ka2juTPq/merge.join.a.bcf /tmp/77Ka2juTPq/merge.join.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob -i AF:join /tmp/77Ka2juTPq/merge.join.a.bcf /tmp/77Ka2juTPq/merge.join.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-single /tmp/77Ka2juTPq/merge.LPL.a.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-single /tmp/77Ka2juTPq/merge.LPL.a.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-single /tmp/77Ka2juTPq/merge.LPL.a.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-single /tmp/77Ka2juTPq/merge.LPL.a.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples /tmp/77Ka2juTPq/merge.LPL.a.vcf.gz /tmp/77Ka2juTPq/merge.LPL.b.vcf.gz /tmp/77Ka2juTPq/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples /tmp/77Ka2juTPq/merge.LPL.a.vcf.gz /tmp/77Ka2juTPq/merge.LPL.b.vcf.gz /tmp/77Ka2juTPq/merge.LPL.c.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples /tmp/77Ka2juTPq/merge.LPL.a.bcf /tmp/77Ka2juTPq/merge.LPL.b.bcf /tmp/77Ka2juTPq/merge.LPL.c.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples /tmp/77Ka2juTPq/merge.LPL.a.bcf /tmp/77Ka2juTPq/merge.LPL.b.bcf /tmp/77Ka2juTPq/merge.LPL.c.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -L 1 /tmp/77Ka2juTPq/merge.LPL.a.vcf.gz /tmp/77Ka2juTPq/merge.LPL.b.vcf.gz /tmp/77Ka2juTPq/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -L 1 /tmp/77Ka2juTPq/merge.LPL.a.vcf.gz /tmp/77Ka2juTPq/merge.LPL.b.vcf.gz /tmp/77Ka2juTPq/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/77Ka2juTPq/merge.LPL.a.bcf /tmp/77Ka2juTPq/merge.LPL.b.bcf /tmp/77Ka2juTPq/merge.LPL.c.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -L 1 /tmp/77Ka2juTPq/merge.LPL.a.bcf /tmp/77Ka2juTPq/merge.LPL.b.bcf /tmp/77Ka2juTPq/merge.LPL.c.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -L 2 /tmp/77Ka2juTPq/merge.LPL.a.vcf.gz /tmp/77Ka2juTPq/merge.LPL.b.vcf.gz /tmp/77Ka2juTPq/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -L 2 /tmp/77Ka2juTPq/merge.LPL.a.vcf.gz /tmp/77Ka2juTPq/merge.LPL.b.vcf.gz /tmp/77Ka2juTPq/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/77Ka2juTPq/merge.LPL.a.bcf /tmp/77Ka2juTPq/merge.LPL.b.bcf /tmp/77Ka2juTPq/merge.LPL.c.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -L 2 /tmp/77Ka2juTPq/merge.LPL.a.bcf /tmp/77Ka2juTPq/merge.LPL.b.bcf /tmp/77Ka2juTPq/merge.LPL.c.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -L 3 /tmp/77Ka2juTPq/merge.LPL.a.vcf.gz /tmp/77Ka2juTPq/merge.LPL.b.vcf.gz /tmp/77Ka2juTPq/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -L 3 /tmp/77Ka2juTPq/merge.LPL.a.vcf.gz /tmp/77Ka2juTPq/merge.LPL.b.vcf.gz /tmp/77Ka2juTPq/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/77Ka2juTPq/merge.LPL.a.bcf /tmp/77Ka2juTPq/merge.LPL.b.bcf /tmp/77Ka2juTPq/merge.LPL.c.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -L 3 /tmp/77Ka2juTPq/merge.LPL.a.bcf /tmp/77Ka2juTPq/merge.LPL.b.bcf /tmp/77Ka2juTPq/merge.LPL.c.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -L 4 /tmp/77Ka2juTPq/merge.LPL.a.vcf.gz /tmp/77Ka2juTPq/merge.LPL.b.vcf.gz /tmp/77Ka2juTPq/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -L 4 /tmp/77Ka2juTPq/merge.LPL.a.vcf.gz /tmp/77Ka2juTPq/merge.LPL.b.vcf.gz /tmp/77Ka2juTPq/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/77Ka2juTPq/merge.LPL.a.bcf /tmp/77Ka2juTPq/merge.LPL.b.bcf /tmp/77Ka2juTPq/merge.LPL.c.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -L 4 /tmp/77Ka2juTPq/merge.LPL.a.bcf /tmp/77Ka2juTPq/merge.LPL.b.bcf /tmp/77Ka2juTPq/merge.LPL.c.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -L 5 /tmp/77Ka2juTPq/merge.LPL.a.vcf.gz /tmp/77Ka2juTPq/merge.LPL.b.vcf.gz /tmp/77Ka2juTPq/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -L 5 /tmp/77Ka2juTPq/merge.LPL.a.vcf.gz /tmp/77Ka2juTPq/merge.LPL.b.vcf.gz /tmp/77Ka2juTPq/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/77Ka2juTPq/merge.LPL.a.bcf /tmp/77Ka2juTPq/merge.LPL.b.bcf /tmp/77Ka2juTPq/merge.LPL.c.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -L 5 /tmp/77Ka2juTPq/merge.LPL.a.bcf /tmp/77Ka2juTPq/merge.LPL.b.bcf /tmp/77Ka2juTPq/merge.LPL.c.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples /tmp/77Ka2juTPq/merge.a.vcf.gz /tmp/77Ka2juTPq/merge.b.vcf.gz /tmp/77Ka2juTPq/merge.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples /tmp/77Ka2juTPq/merge.a.vcf.gz /tmp/77Ka2juTPq/merge.b.vcf.gz /tmp/77Ka2juTPq/merge.c.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples /tmp/77Ka2juTPq/merge.a.bcf /tmp/77Ka2juTPq/merge.b.bcf /tmp/77Ka2juTPq/merge.c.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples /tmp/77Ka2juTPq/merge.a.bcf /tmp/77Ka2juTPq/merge.b.bcf /tmp/77Ka2juTPq/merge.c.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -Fx /tmp/77Ka2juTPq/merge.a.vcf.gz /tmp/77Ka2juTPq/merge.b.vcf.gz /tmp/77Ka2juTPq/merge.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -Fx /tmp/77Ka2juTPq/merge.a.vcf.gz /tmp/77Ka2juTPq/merge.b.vcf.gz /tmp/77Ka2juTPq/merge.c.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -Fx /tmp/77Ka2juTPq/merge.a.bcf /tmp/77Ka2juTPq/merge.b.bcf /tmp/77Ka2juTPq/merge.c.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -Fx /tmp/77Ka2juTPq/merge.a.bcf /tmp/77Ka2juTPq/merge.b.bcf /tmp/77Ka2juTPq/merge.c.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -0 /tmp/77Ka2juTPq/merge.a.vcf.gz /tmp/77Ka2juTPq/merge.b.vcf.gz /tmp/77Ka2juTPq/merge.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -0 /tmp/77Ka2juTPq/merge.a.vcf.gz /tmp/77Ka2juTPq/merge.b.vcf.gz /tmp/77Ka2juTPq/merge.c.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -0 /tmp/77Ka2juTPq/merge.a.bcf /tmp/77Ka2juTPq/merge.b.bcf /tmp/77Ka2juTPq/merge.c.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -0 /tmp/77Ka2juTPq/merge.a.bcf /tmp/77Ka2juTPq/merge.b.bcf /tmp/77Ka2juTPq/merge.c.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -m none /tmp/77Ka2juTPq/merge.2.a.vcf.gz /tmp/77Ka2juTPq/merge.2.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -m none /tmp/77Ka2juTPq/merge.2.a.vcf.gz /tmp/77Ka2juTPq/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/77Ka2juTPq/merge.2.a.bcf /tmp/77Ka2juTPq/merge.2.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -m none /tmp/77Ka2juTPq/merge.2.a.bcf /tmp/77Ka2juTPq/merge.2.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -m both /tmp/77Ka2juTPq/merge.2.a.vcf.gz /tmp/77Ka2juTPq/merge.2.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -m both /tmp/77Ka2juTPq/merge.2.a.vcf.gz /tmp/77Ka2juTPq/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/77Ka2juTPq/merge.2.a.bcf /tmp/77Ka2juTPq/merge.2.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -m both /tmp/77Ka2juTPq/merge.2.a.bcf /tmp/77Ka2juTPq/merge.2.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -m all /tmp/77Ka2juTPq/merge.2.a.vcf.gz /tmp/77Ka2juTPq/merge.2.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -m all /tmp/77Ka2juTPq/merge.2.a.vcf.gz /tmp/77Ka2juTPq/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/77Ka2juTPq/merge.2.a.bcf /tmp/77Ka2juTPq/merge.2.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -m all /tmp/77Ka2juTPq/merge.2.a.bcf /tmp/77Ka2juTPq/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/77Ka2juTPq/merge.3.a.vcf.gz /tmp/77Ka2juTPq/merge.3.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/77Ka2juTPq/merge.3.a.vcf.gz /tmp/77Ka2juTPq/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/77Ka2juTPq/merge.3.a.bcf /tmp/77Ka2juTPq/merge.3.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/77Ka2juTPq/merge.3.a.bcf /tmp/77Ka2juTPq/merge.3.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -m id /tmp/77Ka2juTPq/merge.4.a.vcf.gz /tmp/77Ka2juTPq/merge.4.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -m id /tmp/77Ka2juTPq/merge.4.a.vcf.gz /tmp/77Ka2juTPq/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/77Ka2juTPq/merge.4.a.bcf /tmp/77Ka2juTPq/merge.4.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -m id /tmp/77Ka2juTPq/merge.4.a.bcf /tmp/77Ka2juTPq/merge.4.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/77Ka2juTPq/gvcf.merge.1.vcf.gz /tmp/77Ka2juTPq/gvcf.merge.2.vcf.gz /tmp/77Ka2juTPq/gvcf.merge.3.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - /tmp/77Ka2juTPq/gvcf.merge.1.vcf.gz /tmp/77Ka2juTPq/gvcf.merge.2.vcf.gz /tmp/77Ka2juTPq/gvcf.merge.3.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/77Ka2juTPq/gvcf.merge.1.bcf /tmp/77Ka2juTPq/gvcf.merge.2.bcf /tmp/77Ka2juTPq/gvcf.merge.3.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - /tmp/77Ka2juTPq/gvcf.merge.1.bcf /tmp/77Ka2juTPq/gvcf.merge.2.bcf /tmp/77Ka2juTPq/gvcf.merge.3.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/77Ka2juTPq/merge.gvcf.2.a.vcf.gz /tmp/77Ka2juTPq/merge.gvcf.2.b.vcf.gz /tmp/77Ka2juTPq/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - /tmp/77Ka2juTPq/merge.gvcf.2.a.vcf.gz /tmp/77Ka2juTPq/merge.gvcf.2.b.vcf.gz /tmp/77Ka2juTPq/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/77Ka2juTPq/merge.gvcf.2.a.vcf.gz /tmp/77Ka2juTPq/merge.gvcf.2.b.vcf.gz /tmp/77Ka2juTPq/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - -m both,* /tmp/77Ka2juTPq/merge.gvcf.2.a.vcf.gz /tmp/77Ka2juTPq/merge.gvcf.2.b.vcf.gz /tmp/77Ka2juTPq/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/77Ka2juTPq/merge.gvcf.2.a.vcf.gz /tmp/77Ka2juTPq/merge.gvcf.2.b.vcf.gz /tmp/77Ka2juTPq/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - -m both,** /tmp/77Ka2juTPq/merge.gvcf.2.a.vcf.gz /tmp/77Ka2juTPq/merge.gvcf.2.b.vcf.gz /tmp/77Ka2juTPq/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/77Ka2juTPq/merge.gvcf.3.a.vcf.gz /tmp/77Ka2juTPq/merge.gvcf.3.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - -i SRC:join /tmp/77Ka2juTPq/merge.gvcf.3.a.vcf.gz /tmp/77Ka2juTPq/merge.gvcf.3.b.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/77Ka2juTPq/merge.gvcf.4.a.vcf.gz /tmp/77Ka2juTPq/merge.gvcf.4.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - /tmp/77Ka2juTPq/merge.gvcf.4.a.vcf.gz /tmp/77Ka2juTPq/merge.gvcf.4.b.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/77Ka2juTPq/merge.gvcf.4.a.bcf /tmp/77Ka2juTPq/merge.gvcf.4.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - /tmp/77Ka2juTPq/merge.gvcf.4.a.bcf /tmp/77Ka2juTPq/merge.gvcf.4.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version /tmp/77Ka2juTPq/merge.5.a.vcf.gz /tmp/77Ka2juTPq/merge.5.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob /tmp/77Ka2juTPq/merge.5.a.vcf.gz /tmp/77Ka2juTPq/merge.5.b.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version /tmp/77Ka2juTPq/merge.5.a.bcf /tmp/77Ka2juTPq/merge.5.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob /tmp/77Ka2juTPq/merge.5.a.bcf /tmp/77Ka2juTPq/merge.5.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version /tmp/77Ka2juTPq/merge.6.a.vcf.gz /tmp/77Ka2juTPq/merge.6.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob /tmp/77Ka2juTPq/merge.6.a.vcf.gz /tmp/77Ka2juTPq/merge.6.b.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version /tmp/77Ka2juTPq/merge.6.a.bcf /tmp/77Ka2juTPq/merge.6.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob /tmp/77Ka2juTPq/merge.6.a.bcf /tmp/77Ka2juTPq/merge.6.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/77Ka2juTPq/merge.gvcf.7.a.vcf.gz /tmp/77Ka2juTPq/merge.gvcf.7.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - /tmp/77Ka2juTPq/merge.gvcf.7.a.vcf.gz /tmp/77Ka2juTPq/merge.gvcf.7.b.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/77Ka2juTPq/merge.gvcf.7.a.bcf /tmp/77Ka2juTPq/merge.gvcf.7.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - /tmp/77Ka2juTPq/merge.gvcf.7.a.bcf /tmp/77Ka2juTPq/merge.gvcf.7.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/77Ka2juTPq/merge.gvcf.8.a.vcf.gz /tmp/77Ka2juTPq/merge.gvcf.8.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - /tmp/77Ka2juTPq/merge.gvcf.8.a.vcf.gz /tmp/77Ka2juTPq/merge.gvcf.8.b.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/77Ka2juTPq/merge.gvcf.8.a.bcf /tmp/77Ka2juTPq/merge.gvcf.8.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - /tmp/77Ka2juTPq/merge.gvcf.8.a.bcf /tmp/77Ka2juTPq/merge.gvcf.8.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples /tmp/77Ka2juTPq/merge.7.a.vcf.gz /tmp/77Ka2juTPq/merge.7.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples /tmp/77Ka2juTPq/merge.7.a.vcf.gz /tmp/77Ka2juTPq/merge.7.b.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples /tmp/77Ka2juTPq/merge.7.a.bcf /tmp/77Ka2juTPq/merge.7.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples /tmp/77Ka2juTPq/merge.7.a.bcf /tmp/77Ka2juTPq/merge.7.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf /<>/test/gvcf.fa /tmp/77Ka2juTPq/merge.gvcf.9a.vcf.gz /tmp/77Ka2juTPq/merge.gvcf.9b.vcf.gz /tmp/77Ka2juTPq/merge.gvcf.9c.vcf.gz /tmp/77Ka2juTPq/merge.gvcf.9d.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf /<>/test/gvcf.fa /tmp/77Ka2juTPq/merge.gvcf.9a.vcf.gz /tmp/77Ka2juTPq/merge.gvcf.9b.vcf.gz /tmp/77Ka2juTPq/merge.gvcf.9c.vcf.gz /tmp/77Ka2juTPq/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/77Ka2juTPq/merge.gvcf.9a.bcf /tmp/77Ka2juTPq/merge.gvcf.9b.bcf /tmp/77Ka2juTPq/merge.gvcf.9c.bcf /tmp/77Ka2juTPq/merge.gvcf.9d.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf /<>/test/gvcf.fa /tmp/77Ka2juTPq/merge.gvcf.9a.bcf /tmp/77Ka2juTPq/merge.gvcf.9b.bcf /tmp/77Ka2juTPq/merge.gvcf.9c.bcf /tmp/77Ka2juTPq/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/77Ka2juTPq/merge.gvcf.9a.vcf.gz /tmp/77Ka2juTPq/merge.gvcf.9b.vcf.gz /tmp/77Ka2juTPq/merge.gvcf.9c.vcf.gz /tmp/77Ka2juTPq/merge.gvcf.9d.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf /<>/test/gvcf.fa -r 22:21-23 /tmp/77Ka2juTPq/merge.gvcf.9a.vcf.gz /tmp/77Ka2juTPq/merge.gvcf.9b.vcf.gz /tmp/77Ka2juTPq/merge.gvcf.9c.vcf.gz /tmp/77Ka2juTPq/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/77Ka2juTPq/merge.gvcf.9a.bcf /tmp/77Ka2juTPq/merge.gvcf.9b.bcf /tmp/77Ka2juTPq/merge.gvcf.9c.bcf /tmp/77Ka2juTPq/merge.gvcf.9d.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf /<>/test/gvcf.fa -r 22:21-23 /tmp/77Ka2juTPq/merge.gvcf.9a.bcf /tmp/77Ka2juTPq/merge.gvcf.9b.bcf /tmp/77Ka2juTPq/merge.gvcf.9c.bcf /tmp/77Ka2juTPq/merge.gvcf.9d.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf /<>/test/gvcf.fa /tmp/77Ka2juTPq/merge.gvcf.9a.vcf.gz /tmp/77Ka2juTPq/merge.gvcf.9b.vcf.gz /tmp/77Ka2juTPq/merge.gvcf.9c.vcf.gz /tmp/77Ka2juTPq/merge.gvcf.9d.vcf.gz /tmp/77Ka2juTPq/merge.gvcf.9e.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf /<>/test/gvcf.fa /tmp/77Ka2juTPq/merge.gvcf.9a.vcf.gz /tmp/77Ka2juTPq/merge.gvcf.9b.vcf.gz /tmp/77Ka2juTPq/merge.gvcf.9c.vcf.gz /tmp/77Ka2juTPq/merge.gvcf.9d.vcf.gz /tmp/77Ka2juTPq/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/77Ka2juTPq/merge.gvcf.9a.bcf /tmp/77Ka2juTPq/merge.gvcf.9b.bcf /tmp/77Ka2juTPq/merge.gvcf.9c.bcf /tmp/77Ka2juTPq/merge.gvcf.9d.bcf /tmp/77Ka2juTPq/merge.gvcf.9e.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf /<>/test/gvcf.fa /tmp/77Ka2juTPq/merge.gvcf.9a.bcf /tmp/77Ka2juTPq/merge.gvcf.9b.bcf /tmp/77Ka2juTPq/merge.gvcf.9c.bcf /tmp/77Ka2juTPq/merge.gvcf.9d.bcf /tmp/77Ka2juTPq/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/77Ka2juTPq/merge.gvcf.9a.vcf.gz /tmp/77Ka2juTPq/merge.gvcf.9b.vcf.gz /tmp/77Ka2juTPq/merge.gvcf.9c.vcf.gz /tmp/77Ka2juTPq/merge.gvcf.9d.vcf.gz /tmp/77Ka2juTPq/merge.gvcf.9e.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf /<>/test/gvcf.fa -r 22:21-23 /tmp/77Ka2juTPq/merge.gvcf.9a.vcf.gz /tmp/77Ka2juTPq/merge.gvcf.9b.vcf.gz /tmp/77Ka2juTPq/merge.gvcf.9c.vcf.gz /tmp/77Ka2juTPq/merge.gvcf.9d.vcf.gz /tmp/77Ka2juTPq/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/77Ka2juTPq/merge.gvcf.9a.bcf /tmp/77Ka2juTPq/merge.gvcf.9b.bcf /tmp/77Ka2juTPq/merge.gvcf.9c.bcf /tmp/77Ka2juTPq/merge.gvcf.9d.bcf /tmp/77Ka2juTPq/merge.gvcf.9e.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf /<>/test/gvcf.fa -r 22:21-23 /tmp/77Ka2juTPq/merge.gvcf.9a.bcf /tmp/77Ka2juTPq/merge.gvcf.9b.bcf /tmp/77Ka2juTPq/merge.gvcf.9c.bcf /tmp/77Ka2juTPq/merge.gvcf.9d.bcf /tmp/77Ka2juTPq/merge.gvcf.9e.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version /tmp/77Ka2juTPq/merge.gvcf.10.a.vcf.gz /tmp/77Ka2juTPq/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob /tmp/77Ka2juTPq/merge.gvcf.10.a.vcf.gz /tmp/77Ka2juTPq/merge.gvcf.10.b.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version /tmp/77Ka2juTPq/merge.gvcf.10.a.bcf /tmp/77Ka2juTPq/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob /tmp/77Ka2juTPq/merge.gvcf.10.a.bcf /tmp/77Ka2juTPq/merge.gvcf.10.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version -m none /tmp/77Ka2juTPq/merge.gvcf.10.a.vcf.gz /tmp/77Ka2juTPq/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob -m none /tmp/77Ka2juTPq/merge.gvcf.10.a.vcf.gz /tmp/77Ka2juTPq/merge.gvcf.10.b.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version -m none /tmp/77Ka2juTPq/merge.gvcf.10.a.bcf /tmp/77Ka2juTPq/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob -m none /tmp/77Ka2juTPq/merge.gvcf.10.a.bcf /tmp/77Ka2juTPq/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/77Ka2juTPq/merge.gvcf.10.a.vcf.gz /tmp/77Ka2juTPq/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob -g /<>/test/merge.gvcf.10.fa /tmp/77Ka2juTPq/merge.gvcf.10.a.vcf.gz /tmp/77Ka2juTPq/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/77Ka2juTPq/merge.gvcf.10.a.bcf /tmp/77Ka2juTPq/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob -g /<>/test/merge.gvcf.10.fa /tmp/77Ka2juTPq/merge.gvcf.10.a.bcf /tmp/77Ka2juTPq/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/77Ka2juTPq/merge.gvcf.10.a.vcf.gz /tmp/77Ka2juTPq/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob -g /<>/test/merge.gvcf.10.fa -m none /tmp/77Ka2juTPq/merge.gvcf.10.a.vcf.gz /tmp/77Ka2juTPq/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/77Ka2juTPq/merge.gvcf.10.a.bcf /tmp/77Ka2juTPq/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob -g /<>/test/merge.gvcf.10.fa -m none /tmp/77Ka2juTPq/merge.gvcf.10.a.bcf /tmp/77Ka2juTPq/merge.gvcf.10.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version /tmp/77Ka2juTPq/merge.noidx.a.vcf.gz /tmp/77Ka2juTPq/merge.noidx.b.vcf.gz /tmp/77Ka2juTPq/merge.noidx.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob /tmp/77Ka2juTPq/merge.noidx.a.vcf.gz /tmp/77Ka2juTPq/merge.noidx.b.vcf.gz /tmp/77Ka2juTPq/merge.noidx.c.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version /tmp/77Ka2juTPq/merge.noidx.a.bcf /tmp/77Ka2juTPq/merge.noidx.b.bcf /tmp/77Ka2juTPq/merge.noidx.c.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob /tmp/77Ka2juTPq/merge.noidx.a.bcf /tmp/77Ka2juTPq/merge.noidx.b.bcf /tmp/77Ka2juTPq/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/77Ka2juTPq/merge.noidx.a.bcf /tmp/77Ka2juTPq/merge.noidx.b.bcf /tmp/77Ka2juTPq/merge.noidx.c.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --no-index /tmp/77Ka2juTPq/merge.noidx.a.bcf /tmp/77Ka2juTPq/merge.noidx.b.bcf /tmp/77Ka2juTPq/merge.noidx.c.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version /tmp/77Ka2juTPq/merge.8.a.vcf.gz /tmp/77Ka2juTPq/merge.8.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob /tmp/77Ka2juTPq/merge.8.a.vcf.gz /tmp/77Ka2juTPq/merge.8.b.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version /tmp/77Ka2juTPq/merge.8.a.bcf /tmp/77Ka2juTPq/merge.8.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob /tmp/77Ka2juTPq/merge.8.a.bcf /tmp/77Ka2juTPq/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/77Ka2juTPq/merge.8.a.vcf.gz /tmp/77Ka2juTPq/merge.8.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/77Ka2juTPq/merge.8.a.vcf.gz /tmp/77Ka2juTPq/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/77Ka2juTPq/merge.8.a.bcf /tmp/77Ka2juTPq/merge.8.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/77Ka2juTPq/merge.8.a.bcf /tmp/77Ka2juTPq/merge.8.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version /tmp/77Ka2juTPq/merge.9.a.vcf.gz /tmp/77Ka2juTPq/merge.9.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob /tmp/77Ka2juTPq/merge.9.a.vcf.gz /tmp/77Ka2juTPq/merge.9.b.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version /tmp/77Ka2juTPq/merge.9.a.bcf /tmp/77Ka2juTPq/merge.9.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob /tmp/77Ka2juTPq/merge.9.a.bcf /tmp/77Ka2juTPq/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/77Ka2juTPq/merge.9.a.vcf.gz /tmp/77Ka2juTPq/merge.9.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/77Ka2juTPq/merge.9.a.vcf.gz /tmp/77Ka2juTPq/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/77Ka2juTPq/merge.9.a.bcf /tmp/77Ka2juTPq/merge.9.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/77Ka2juTPq/merge.9.a.bcf /tmp/77Ka2juTPq/merge.9.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version -m none /tmp/77Ka2juTPq/merge.10.a.vcf.gz /tmp/77Ka2juTPq/merge.10.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob -m none /tmp/77Ka2juTPq/merge.10.a.vcf.gz /tmp/77Ka2juTPq/merge.10.b.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version -m none /tmp/77Ka2juTPq/merge.10.a.bcf /tmp/77Ka2juTPq/merge.10.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob -m none /tmp/77Ka2juTPq/merge.10.a.bcf /tmp/77Ka2juTPq/merge.10.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version -m both /tmp/77Ka2juTPq/merge.10.a.vcf.gz /tmp/77Ka2juTPq/merge.10.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob -m both /tmp/77Ka2juTPq/merge.10.a.vcf.gz /tmp/77Ka2juTPq/merge.10.b.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version -m both /tmp/77Ka2juTPq/merge.10.a.bcf /tmp/77Ka2juTPq/merge.10.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob -m both /tmp/77Ka2juTPq/merge.10.a.bcf /tmp/77Ka2juTPq/merge.10.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version -m snp-ins-del /tmp/77Ka2juTPq/merge.10.a.vcf.gz /tmp/77Ka2juTPq/merge.10.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob -m snp-ins-del /tmp/77Ka2juTPq/merge.10.a.vcf.gz /tmp/77Ka2juTPq/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/77Ka2juTPq/merge.10.a.bcf /tmp/77Ka2juTPq/merge.10.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob -m snp-ins-del /tmp/77Ka2juTPq/merge.10.a.bcf /tmp/77Ka2juTPq/merge.10.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/77Ka2juTPq/merge.mrules.1.a.vcf.gz /tmp/77Ka2juTPq/merge.mrules.1.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - /tmp/77Ka2juTPq/merge.mrules.1.a.vcf.gz /tmp/77Ka2juTPq/merge.mrules.1.b.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/77Ka2juTPq/merge.mrules.1.a.bcf /tmp/77Ka2juTPq/merge.mrules.1.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - /tmp/77Ka2juTPq/merge.mrules.1.a.bcf /tmp/77Ka2juTPq/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/77Ka2juTPq/merge.mrules.1.a.vcf.gz /tmp/77Ka2juTPq/merge.mrules.1.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - -M AD:.,PL:. /tmp/77Ka2juTPq/merge.mrules.1.a.vcf.gz /tmp/77Ka2juTPq/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/77Ka2juTPq/merge.mrules.1.a.bcf /tmp/77Ka2juTPq/merge.mrules.1.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - -M AD:.,PL:. /tmp/77Ka2juTPq/merge.mrules.1.a.bcf /tmp/77Ka2juTPq/merge.mrules.1.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/77Ka2juTPq/merge.gvcf.5.a.vcf.gz /tmp/77Ka2juTPq/merge.gvcf.5.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - /tmp/77Ka2juTPq/merge.gvcf.5.a.vcf.gz /tmp/77Ka2juTPq/merge.gvcf.5.b.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/77Ka2juTPq/merge.gvcf.5.a.bcf /tmp/77Ka2juTPq/merge.gvcf.5.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - /tmp/77Ka2juTPq/merge.gvcf.5.a.bcf /tmp/77Ka2juTPq/merge.gvcf.5.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - --merge none /tmp/77Ka2juTPq/merge.gvcf.5.a.vcf.gz /tmp/77Ka2juTPq/merge.gvcf.5.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - --merge none /tmp/77Ka2juTPq/merge.gvcf.5.a.vcf.gz /tmp/77Ka2juTPq/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/77Ka2juTPq/merge.gvcf.5.a.bcf /tmp/77Ka2juTPq/merge.gvcf.5.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - --merge none /tmp/77Ka2juTPq/merge.gvcf.5.a.bcf /tmp/77Ka2juTPq/merge.gvcf.5.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/77Ka2juTPq/merge.gvcf.11.a.vcf.gz /tmp/77Ka2juTPq/merge.gvcf.11.b.vcf.gz /tmp/77Ka2juTPq/merge.gvcf.11.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - /tmp/77Ka2juTPq/merge.gvcf.11.a.vcf.gz /tmp/77Ka2juTPq/merge.gvcf.11.b.vcf.gz /tmp/77Ka2juTPq/merge.gvcf.11.c.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/77Ka2juTPq/merge.gvcf.11.a.bcf /tmp/77Ka2juTPq/merge.gvcf.11.b.bcf /tmp/77Ka2juTPq/merge.gvcf.11.c.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - /tmp/77Ka2juTPq/merge.gvcf.11.a.bcf /tmp/77Ka2juTPq/merge.gvcf.11.b.bcf /tmp/77Ka2juTPq/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/77Ka2juTPq/query.string.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.string.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.string.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.string.2.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.string.2.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.variantkey.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/query.variantkey.vcf.gz | /<>/bcftools query -f '%RSX\t%VKX\n' .. ok test_vcf_query: /<>/bcftools query -f'%XRI\n' -i'XRI[*]>1111' /tmp/77Ka2juTPq/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/view.vectors.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.2.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/missing.vcf.gz | /<>/bcftools query -i'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /<>/bcftools query -i'IINT!="."' -f'%POS %IINT\n' /tmp/77Ka2juTPq/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/missing.vcf.gz | /<>/bcftools query -i'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /<>/bcftools query -e'IINT!="."' -f'%POS %IINT\n' /tmp/77Ka2juTPq/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/missing.vcf.gz | /<>/bcftools query -e'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /<>/bcftools query -e'IINT="."' -f'%POS %IINT\n' /tmp/77Ka2juTPq/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/missing.vcf.gz | /<>/bcftools query -e'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /<>/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' /tmp/77Ka2juTPq/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/missing.vcf.gz | /<>/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /<>/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' /tmp/77Ka2juTPq/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/missing.vcf.gz | /<>/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /<>/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' /tmp/77Ka2juTPq/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/missing.vcf.gz | /<>/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /<>/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' /tmp/77Ka2juTPq/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/missing.vcf.gz | /<>/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /<>/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' /tmp/77Ka2juTPq/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/missing.vcf.gz | /<>/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /<>/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' /tmp/77Ka2juTPq/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/missing.vcf.gz | /<>/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /<>/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' /tmp/77Ka2juTPq/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/missing.vcf.gz | /<>/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /<>/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' /tmp/77Ka2juTPq/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/filter.11.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/filter.11.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/filter.11.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/filter.11.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/filter.11.vcf.gz | /<>/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /<>/bcftools query -f'%LINE' /tmp/77Ka2juTPq/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/query.vcf.gz | /<>/bcftools query -f'%LINE' .. ok test_vcf_query: /<>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' /tmp/77Ka2juTPq/query.filter-type.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.filter-type.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.filter-type.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.filter-type.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.filter-type.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/filter-missing-floats.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/filter-missing-floats.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.filter.2.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/filter.5.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/filter.5.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.filter.3.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.filter.3.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.filter.3.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/filter.5.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.filter.4.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/view.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.filter.5.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.filter.5.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.filter.5.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.filter.5.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.filter.5.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.filter.5.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.gtidx.1.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.gtidx.1.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.gtidx.1.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.gtidx.1.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.gtidx.1.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.negative.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.negative.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.negative.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.negative.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.filter.11.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.filter.11.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.filter.11.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.filter.11.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.filter.6.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.filter.7.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.filter.7.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.filter.7.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.filter.7.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.filter.7.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.filter.7.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.filter.7.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.filter.7.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.filter.8.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.filter.8.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.filter.9.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.filter.9.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.filter.13.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.filter.10.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.filter.10.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.filter.12.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.filter.12.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.smpl.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.smpl.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.smpl.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.smpl.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.smpl.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.smpl.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.filter.id.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.filter.id.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/filter.12.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/filter.12.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/filter.12.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/filter.12.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/filter.12.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/filter.12.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/filter.10.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/filter.13.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.header.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.header.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.header.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.header.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.header.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.header.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.filter-or.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/query.filter-or.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/norm.vcf.gz -f /<>/test/norm.fa .. ok test_vcf_norm: /<>/bcftools norm --no-version -cx /tmp/77Ka2juTPq/norm.vcf.gz -f /<>/test/norm.fa -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- /tmp/77Ka2juTPq/norm.split.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- /tmp/77Ka2juTPq/norm.split.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- /tmp/77Ka2juTPq/norm.split.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- /tmp/77Ka2juTPq/norm.split.2.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- --force /tmp/77Ka2juTPq/norm.split.3.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- --force /tmp/77Ka2juTPq/norm.split.3.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- /tmp/77Ka2juTPq/norm.split.4.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- /tmp/77Ka2juTPq/norm.split.4.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- --keep-sum AD /tmp/77Ka2juTPq/norm.split.4.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- --keep-sum AD /tmp/77Ka2juTPq/norm.split.4.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- /tmp/77Ka2juTPq/norm.split.vcf.gz -f /<>/test/norm.fa .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- /tmp/77Ka2juTPq/norm.split.vcf.gz -f /<>/test/norm.fa -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m+ /tmp/77Ka2juTPq/norm.merge.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -m+ /tmp/77Ka2juTPq/norm.merge.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m+ /tmp/77Ka2juTPq/norm.merge.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -m+ /tmp/77Ka2juTPq/norm.merge.2.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m+ /tmp/77Ka2juTPq/norm.merge.3.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -m+ /tmp/77Ka2juTPq/norm.merge.3.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m+ -s /tmp/77Ka2juTPq/norm.merge.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -m+ -s /tmp/77Ka2juTPq/norm.merge.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -Nc s /tmp/77Ka2juTPq/norm.setref.vcf.gz -f /<>/test/norm.fa .. ok test_vcf_norm: /<>/bcftools norm --no-version -Nc s /tmp/77Ka2juTPq/norm.setref.vcf.gz -f /<>/test/norm.fa -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version /tmp/77Ka2juTPq/norm.telomere.vcf.gz -f /<>/test/norm.fa .. ok test_vcf_norm: /<>/bcftools norm --no-version /tmp/77Ka2juTPq/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/77Ka2juTPq/norm.rmdup.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -d snps /tmp/77Ka2juTPq/norm.rmdup.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d indels /tmp/77Ka2juTPq/norm.rmdup.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -d indels /tmp/77Ka2juTPq/norm.rmdup.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d both /tmp/77Ka2juTPq/norm.rmdup.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -d both /tmp/77Ka2juTPq/norm.rmdup.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d all /tmp/77Ka2juTPq/norm.rmdup.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -d all /tmp/77Ka2juTPq/norm.rmdup.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d none /tmp/77Ka2juTPq/norm.rmdup.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -d none /tmp/77Ka2juTPq/norm.rmdup.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d exact /tmp/77Ka2juTPq/norm.rmdup.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -d exact /tmp/77Ka2juTPq/norm.rmdup.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d none /tmp/77Ka2juTPq/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -d none /tmp/77Ka2juTPq/norm.rmdup.2.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d exact /tmp/77Ka2juTPq/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -d exact /tmp/77Ka2juTPq/norm.rmdup.2.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d indels /tmp/77Ka2juTPq/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -d indels /tmp/77Ka2juTPq/norm.rmdup.2.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d any /tmp/77Ka2juTPq/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -d any /tmp/77Ka2juTPq/norm.rmdup.2.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d both /tmp/77Ka2juTPq/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -d both /tmp/77Ka2juTPq/norm.rmdup.2.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d snps /tmp/77Ka2juTPq/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -d snps /tmp/77Ka2juTPq/norm.rmdup.2.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -c s -a /tmp/77Ka2juTPq/norm.2.vcf.gz -f /<>/test/norm.2.fa .. ok test_vcf_norm: /<>/bcftools norm --no-version -c s -a /tmp/77Ka2juTPq/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/77Ka2juTPq/norm.iupac.vcf.gz -f /<>/test/norm.iupac.fa .. ok test_vcf_norm: /<>/bcftools norm --no-version -c s /tmp/77Ka2juTPq/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/77Ka2juTPq/norm.3.vcf.gz -f /<>/test/norm.3.fa .. ok test_vcf_norm: /<>/bcftools norm --no-version -c s /tmp/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/atomize.split.1.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -m -any --old-rec-tag OLD_REC --force -a /tmp/77Ka2juTPq/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/77Ka2juTPq/atomize.split.1.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/77Ka2juTPq/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/77Ka2juTPq/atomize.split.1.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/77Ka2juTPq/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/77Ka2juTPq/atomize.split.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/77Ka2juTPq/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/77Ka2juTPq/atomize.split.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/77Ka2juTPq/atomize.split.2.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version --atomize --atom-overlaps . /tmp/77Ka2juTPq/atomize.split.3.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version --atomize --atom-overlaps . /tmp/77Ka2juTPq/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/77Ka2juTPq/atomize.split.4.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/77Ka2juTPq/atomize.split.4.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m +both /tmp/77Ka2juTPq/norm.4.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -m +both /tmp/77Ka2juTPq/norm.4.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m +any /tmp/77Ka2juTPq/norm.4.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -m +any /tmp/77Ka2juTPq/norm.4.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m - --multi-overlaps 0 /tmp/77Ka2juTPq/norm.5.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -m - --multi-overlaps 0 /tmp/77Ka2juTPq/norm.5.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m - --multi-overlaps . /tmp/77Ka2juTPq/norm.5.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -m - --multi-overlaps . /tmp/77Ka2juTPq/norm.5.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m -any /tmp/77Ka2juTPq/norm.m-any.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -m -any /tmp/77Ka2juTPq/norm.m-any.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m -any /tmp/77Ka2juTPq/norm.phased-split.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -m -any /tmp/77Ka2juTPq/norm.phased-split.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m +any /tmp/77Ka2juTPq/norm.phased-join.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -m +any /tmp/77Ka2juTPq/norm.phased-join.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version --old-rec-tag ORI /tmp/77Ka2juTPq/norm.symbolic.vcf.gz -f /<>/test/norm.symbolic.fa .. ok test_vcf_norm: /<>/bcftools norm --no-version --old-rec-tag ORI /tmp/77Ka2juTPq/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/77Ka2juTPq/norm.symbolic.2.vcf.gz -f /<>/test/norm.symbolic.fa .. ok test_vcf_norm: /<>/bcftools norm --no-version --old-rec-tag ORI /tmp/77Ka2juTPq/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/77Ka2juTPq/norm.right-align.vcf.gz -f /<>/test/norm.right-align.fa .. ok test_vcf_norm: /<>/bcftools norm --no-version --old-rec-tag ORI /tmp/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/norm.string-tags.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -m -any /tmp/77Ka2juTPq/norm.string-tags.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m - /tmp/77Ka2juTPq/norm.split.merge.vcf.gz | /<>/bcftools norm --no-version -m +both .. ok test_vcf_norm: /<>/bcftools norm --no-version -m - /tmp/77Ka2juTPq/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/77Ka2juTPq/norm.split.merge.vcf.gz | /<>/bcftools norm --no-version -m +indels .. ok test_vcf_norm: /<>/bcftools norm --no-version -m - /tmp/77Ka2juTPq/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/77Ka2juTPq/norm.split.merge.vcf.gz | /<>/bcftools norm --no-version -m +snps .. ok test_vcf_norm: /<>/bcftools norm --no-version -m - /tmp/77Ka2juTPq/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/77Ka2juTPq/norm.split.merge.vcf.gz | /<>/bcftools norm --no-version -m +any .. ok test_vcf_norm: /<>/bcftools norm --no-version -m - /tmp/77Ka2juTPq/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/77Ka2juTPq/norm.merge.4.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -m +any /tmp/77Ka2juTPq/norm.merge.4.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m +both /tmp/77Ka2juTPq/norm.merge.4.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -m +both /tmp/77Ka2juTPq/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/77Ka2juTPq/filter.string.1.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -i 'INFO/TAG=@/<>/test/filter.string.1.txt' /tmp/77Ka2juTPq/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/77Ka2juTPq/filter.string.1.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -i 'FMT/TAG=@/<>/test/filter.string.1.txt' /tmp/77Ka2juTPq/filter.string.1.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -HA /tmp/77Ka2juTPq/merge.gvcf.2.a.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -HAA /tmp/77Ka2juTPq/merge.gvcf.2.a.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version /tmp/77Ka2juTPq/weird-chr-names.vcf.gz -r 1 .. ok test_vcf_view: /<>/bcftools view -Ob /tmp/77Ka2juTPq/weird-chr-names.vcf.gz -r 1 | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version /tmp/77Ka2juTPq/weird-chr-names.vcf.gz -r 1:1-2 .. ok test_vcf_view: /<>/bcftools view -Ob /tmp/77Ka2juTPq/weird-chr-names.vcf.gz -r 1:1-2 | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version /tmp/77Ka2juTPq/weird-chr-names.vcf.gz -r 1:1,1:2 .. ok test_vcf_view: /<>/bcftools view -Ob /tmp/77Ka2juTPq/weird-chr-names.vcf.gz -r 1:1,1:2 | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version /tmp/77Ka2juTPq/weird-chr-names.vcf.gz -r 1:1-1 .. ok test_vcf_view: /<>/bcftools view -Ob /tmp/77Ka2juTPq/weird-chr-names.vcf.gz -r 1:1-1 | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version /tmp/77Ka2juTPq/weird-chr-names.vcf.gz -r {1:1} .. ok test_vcf_view: /<>/bcftools view -Ob /tmp/77Ka2juTPq/weird-chr-names.vcf.gz -r {1:1} | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version /tmp/77Ka2juTPq/weird-chr-names.vcf.gz -r {1:1}:1-2 .. ok test_vcf_view: /<>/bcftools view -Ob /tmp/77Ka2juTPq/weird-chr-names.vcf.gz -r {1:1}:1-2 | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version /tmp/77Ka2juTPq/weird-chr-names.vcf.gz -r {1:1}:1,{1:1}:2 .. ok test_vcf_view: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/weird-chr-names.vcf.gz -r {1:1}:1-1 .. ok test_vcf_view: /<>/bcftools view -Ob /tmp/77Ka2juTPq/weird-chr-names.vcf.gz -r {1:1}:1-1 | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version /tmp/77Ka2juTPq/weird-chr-names.vcf.gz -r {1:1-1} .. ok test_vcf_view: /<>/bcftools view -Ob /tmp/77Ka2juTPq/weird-chr-names.vcf.gz -r {1:1-1} | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version /tmp/77Ka2juTPq/weird-chr-names.vcf.gz -r {1:1-1}:1-2 .. ok test_vcf_view: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/weird-chr-names.vcf.gz -r {1:1-1}:1,{1:1-1}:2 .. ok test_vcf_view: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/weird-chr-names.vcf.gz -r {1:1-1}:1-1 .. ok test_vcf_view: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/weird-chr-names.vcf.gz -r {1:1-1}-2 .. ok, expected non-zero status test_vcf_view: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/77Ka2juTPq/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -f PASS -Xks NA00003 /tmp/77Ka2juTPq/view.vcf.gz -r20,Y .. ok test_vcf_view: /<>/bcftools view -Ob -f PASS -Xks NA00003 /tmp/77Ka2juTPq/view.vcf.gz -r20,Y | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -xs NA00003 /tmp/77Ka2juTPq/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -xs NA00003 /tmp/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -p /tmp/77Ka2juTPq/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -p /tmp/77Ka2juTPq/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -P /tmp/77Ka2juTPq/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -P /tmp/77Ka2juTPq/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -hm2 -M2 -q0.3 -Q0.7 /tmp/77Ka2juTPq/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/77Ka2juTPq/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -Hu /tmp/77Ka2juTPq/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -GVsnps /tmp/77Ka2juTPq/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -GVsnps /tmp/77Ka2juTPq/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -ne 'INDEL=1 || PV4[0]<0.006' /tmp/77Ka2juTPq/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/77Ka2juTPq/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -s ^NA00003 /tmp/77Ka2juTPq/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -s ^NA00003 /tmp/77Ka2juTPq/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version /tmp/77Ka2juTPq/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob /tmp/77Ka2juTPq/view.omitgenotypes.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -G /tmp/77Ka2juTPq/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -G /tmp/77Ka2juTPq/view.omitgenotypes.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -HG /tmp/77Ka2juTPq/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -a /tmp/77Ka2juTPq/many.alleles.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -a /tmp/77Ka2juTPq/many.alleles.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -asA /tmp/77Ka2juTPq/view.vectors.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -asA /tmp/77Ka2juTPq/view.vectors.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -asB /tmp/77Ka2juTPq/view.vectors.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -asB /tmp/77Ka2juTPq/view.vectors.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -asA /tmp/77Ka2juTPq/view.vectors.2.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -asA /tmp/77Ka2juTPq/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/77Ka2juTPq/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'FMT/FGS[*:2]="C"' /tmp/77Ka2juTPq/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'FMT/FGS[*:4]="EE"' /tmp/77Ka2juTPq/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'FMT/FRS[*:1]="BB"' /tmp/77Ka2juTPq/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'TXT0="text"' /tmp/77Ka2juTPq/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -T /<>/test/view.chrs.tab /tmp/77Ka2juTPq/view.chrs.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -T /<>/test/view.chrs.tab /tmp/77Ka2juTPq/view.chrs.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -i 'POS>=3062917' /tmp/77Ka2juTPq/filter.2.vcf.gz 1:3062917-3157410 .. ok test_vcf_view: /<>/bcftools view -Ob -i 'POS>=3062917' /tmp/77Ka2juTPq/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/77Ka2juTPq/idx.1.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -r 1:1172777-1172804,1:1172806-1172808 /tmp/77Ka2juTPq/idx.2.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -R /<>/test/idx.2.bed /tmp/77Ka2juTPq/idx.2.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -R /<>/test/idx.3.bed /tmp/77Ka2juTPq/idx.3.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -R /<>/test/idx.4.bed /tmp/77Ka2juTPq/idx.4.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -Ht 2 /tmp/77Ka2juTPq/view-t.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -Ht 3 /tmp/77Ka2juTPq/view-t.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 0 /tmp/77Ka2juTPq/overlap.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 1 /tmp/77Ka2juTPq/overlap.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 2 /tmp/77Ka2juTPq/overlap.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 0 /tmp/77Ka2juTPq/overlap.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 1 /tmp/77Ka2juTPq/overlap.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 2 /tmp/77Ka2juTPq/overlap.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 0 /tmp/77Ka2juTPq/overlap.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 1 /tmp/77Ka2juTPq/overlap.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 2 /tmp/77Ka2juTPq/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/77Ka2juTPq/view.minmaxac.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -c6:nonmajor /tmp/77Ka2juTPq/view.minmaxac.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -q0.3:major /tmp/77Ka2juTPq/view.minmaxac.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/77Ka2juTPq/view.filter.annovar.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i 'Gene.refGene~"NOD"' /tmp/77Ka2juTPq/view.filter.annovar.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i 'LJB2_MutationTaster=="0.291000"' /tmp/77Ka2juTPq/view.filter.annovar.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -a /tmp/77Ka2juTPq/view-a.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -T /<>/test/view.sites.txt /tmp/77Ka2juTPq/view.sites.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -T /<>/test/view.sites.txt /tmp/77Ka2juTPq/view.sites.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -T /<>/test/view.sites.txt.gz /tmp/77Ka2juTPq/view.sites.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -T /<>/test/view.sites.txt.gz /tmp/77Ka2juTPq/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/77Ka2juTPq/mpileup.2.vcf.gz .. ok test_vcf_head2: /<>/bcftools view --no-version -Ob /tmp/77Ka2juTPq/mpileup.2.vcf.gz | /<>/bcftools head -s0 .. ok test_vcf_head2: /<>/bcftools head -s1 /tmp/77Ka2juTPq/mpileup.2.vcf.gz .. ok test_vcf_head2: /<>/bcftools view --no-version -Ob /tmp/77Ka2juTPq/mpileup.2.vcf.gz | /<>/bcftools head -s1 .. ok test_vcf_head2: /<>/bcftools head -s2 -h2 /tmp/77Ka2juTPq/mpileup.2.vcf.gz .. ok test_vcf_head2: /<>/bcftools view --no-version -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/mpileup.tab.gz /<>/test/mpileup.vcf .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/77Ka2juTPq/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/77Ka2juTPq/mpileup.2.tab.gz /<>/test/mpileup.2.vcf .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/77Ka2juTPq/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/77Ka2juTPq/mpileup.3.tab.gz -i /<>/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/77Ka2juTPq/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/77Ka2juTPq/mpileup.4.tab.gz -i /<>/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/77Ka2juTPq/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/77Ka2juTPq/mpileup.5.tab.gz -i /<>/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/77Ka2juTPq/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/77Ka2juTPq/mpileup.6.tab.gz -i /<>/test/mpileup.4.vcf .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/77Ka2juTPq/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/77Ka2juTPq/mpileup.7.tab.gz -i /<>/test/mpileup.5.vcf .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/77Ka2juTPq/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/77Ka2juTPq/mpileup.cals.1.tab.gz /<>/test/mpileup.cals.1.vcf .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/77Ka2juTPq/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/77Ka2juTPq/mpileup.cals.2.tab.gz /<>/test/mpileup.cals.2.vcf .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/77Ka2juTPq/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/77Ka2juTPq/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/77Ka2juTPq/regions.tab.gz /tmp/77Ka2juTPq/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/77Ka2juTPq/regions.vcf.gz | /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/77Ka2juTPq/regions.tab.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/77Ka2juTPq/regions.tab.gz /tmp/77Ka2juTPq/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/77Ka2juTPq/regions.bed /tmp/77Ka2juTPq/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/77Ka2juTPq/regions.vcf.gz | /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/77Ka2juTPq/regions.bed .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/77Ka2juTPq/regions.bed /tmp/77Ka2juTPq/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/77Ka2juTPq/regions.bed.gz /tmp/77Ka2juTPq/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/77Ka2juTPq/regions.vcf.gz | /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/77Ka2juTPq/regions.bed.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/77Ka2juTPq/regions.bed.gz /tmp/77Ka2juTPq/regions.vcf.gz .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/77Ka2juTPq/annotate.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/77Ka2juTPq/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/77Ka2juTPq/annotate.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/77Ka2juTPq/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/77Ka2juTPq/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/77Ka2juTPq/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/77Ka2juTPq/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/77Ka2juTPq/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/77Ka2juTPq/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/77Ka2juTPq/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/77Ka2juTPq/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/77Ka2juTPq/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/77Ka2juTPq/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/77Ka2juTPq/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/77Ka2juTPq/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/77Ka2juTPq/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/77Ka2juTPq/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/77Ka2juTPq/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/77Ka2juTPq/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/77Ka2juTPq/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/77Ka2juTPq/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/77Ka2juTPq/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/77Ka2juTPq/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/77Ka2juTPq/annots4.vcf.gz -c +INFO /tmp/77Ka2juTPq/annotate4.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/77Ka2juTPq/annots4.vcf.gz -c +INFO /tmp/77Ka2juTPq/annotate4.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/77Ka2juTPq/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/77Ka2juTPq/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/77Ka2juTPq/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/77Ka2juTPq/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/77Ka2juTPq/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/77Ka2juTPq/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/77Ka2juTPq/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/77Ka2juTPq/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/77Ka2juTPq/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/77Ka2juTPq/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/77Ka2juTPq/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/77Ka2juTPq/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/77Ka2juTPq/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/77Ka2juTPq/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/77Ka2juTPq/annots11.vcf.gz -c FMT /tmp/77Ka2juTPq/annotate11.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/77Ka2juTPq/annots11.vcf.gz -c FMT /tmp/77Ka2juTPq/annotate11.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/77Ka2juTPq/annots2.vcf.gz -c FMT/newGT:=GT /tmp/77Ka2juTPq/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/77Ka2juTPq/annots2.vcf.gz -c FMT/newGT:=GT /tmp/77Ka2juTPq/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/77Ka2juTPq/annots12.vcf.gz -c FMT/GT:=newGT /tmp/77Ka2juTPq/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/77Ka2juTPq/annots12.vcf.gz -c FMT/GT:=newGT /tmp/77Ka2juTPq/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/77Ka2juTPq/annotate19.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/77Ka2juTPq/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/77Ka2juTPq/annotate19.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/77Ka2juTPq/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/77Ka2juTPq/annotate19.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/77Ka2juTPq/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/77Ka2juTPq/annotate19.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/77Ka2juTPq/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/77Ka2juTPq/annotate19.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/77Ka2juTPq/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/77Ka2juTPq/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/77Ka2juTPq/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER /tmp/77Ka2juTPq/annotate19.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/77Ka2juTPq/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER /tmp/77Ka2juTPq/annotate19.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/77Ka2juTPq/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER /tmp/77Ka2juTPq/annotate19.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/77Ka2juTPq/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER /tmp/77Ka2juTPq/annotate19.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/77Ka2juTPq/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER,FILTER /tmp/77Ka2juTPq/annotate19.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/77Ka2juTPq/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER,FILTER /tmp/77Ka2juTPq/annotate19.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/77Ka2juTPq/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=./FILTER /tmp/77Ka2juTPq/annotate19.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/77Ka2juTPq/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=./FILTER /tmp/77Ka2juTPq/annotate19.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/77Ka2juTPq/annotate20.src.vcf.gz -c FMT/GT /tmp/77Ka2juTPq/annotate20.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/77Ka2juTPq/annotate20.src.vcf.gz -c FMT/GT /tmp/77Ka2juTPq/annotate20.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/77Ka2juTPq/annotate20.src.vcf.gz -c +FMT/GT /tmp/77Ka2juTPq/annotate20.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/77Ka2juTPq/annotate20.src.vcf.gz -c +FMT/GT /tmp/77Ka2juTPq/annotate20.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/77Ka2juTPq/annotate20.src.vcf.gz -c -FMT/GT /tmp/77Ka2juTPq/annotate20.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/77Ka2juTPq/annotate20.src.vcf.gz -c -FMT/GT /tmp/77Ka2juTPq/annotate20.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/77Ka2juTPq/annotate22.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/77Ka2juTPq/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/77Ka2juTPq/annotate22.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/annotate24.src.vcf.gz -c XX /tmp/77Ka2juTPq/annotate24.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/77Ka2juTPq/annotate24.src.vcf.gz -c XX /tmp/77Ka2juTPq/annotate24.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/annotate26.tab.gz -c CHROM,POS,~POS /<>/test/annotate26.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/77Ka2juTPq/annotate26.tab.gz -c CHROM,POS,~POS /<>/test/annotate26.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/annots.id.vcf.gz -c ALT /tmp/77Ka2juTPq/annotate.id.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/77Ka2juTPq/annots.id.vcf.gz -c ALT /tmp/77Ka2juTPq/annotate.id.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/77Ka2juTPq/annots.id.vcf.gz -c +ALT /tmp/77Ka2juTPq/annotate.id.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/77Ka2juTPq/annots.id.vcf.gz -c +ALT /tmp/77Ka2juTPq/annotate.id.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/77Ka2juTPq/annots.id.2.vcf.gz --pair-logic some -c +ID /tmp/77Ka2juTPq/annotate.id.2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/77Ka2juTPq/annots.id.2.vcf.gz --pair-logic some -c +ID /tmp/77Ka2juTPq/annotate.id.2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/77Ka2juTPq/annots.id.2.vcf.gz --pair-logic any -c +ID /tmp/77Ka2juTPq/annotate.id.2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/77Ka2juTPq/annots.id.2.vcf.gz --pair-logic any -c +ID /tmp/77Ka2juTPq/annotate.id.2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/concat.1.a.vcf.gz /tmp/77Ka2juTPq/concat.1.b.vcf.gz .. ok test_vcf_concat: /<>/bcftools concat -Ob /tmp/77Ka2juTPq/concat.1.a.vcf.gz /tmp/77Ka2juTPq/concat.1.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version /tmp/77Ka2juTPq/concat.1.a.bcf /tmp/77Ka2juTPq/concat.1.b.bcf .. ok test_vcf_concat: /<>/bcftools concat -Ob /tmp/77Ka2juTPq/concat.1.a.bcf /tmp/77Ka2juTPq/concat.1.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -a /tmp/77Ka2juTPq/concat.2.a.vcf.gz /tmp/77Ka2juTPq/concat.2.b.vcf.gz .. ok test_vcf_concat: /<>/bcftools concat -Ob -a /tmp/77Ka2juTPq/concat.2.a.vcf.gz /tmp/77Ka2juTPq/concat.2.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -a /tmp/77Ka2juTPq/concat.2.a.bcf /tmp/77Ka2juTPq/concat.2.b.bcf .. ok test_vcf_concat: /<>/bcftools concat -Ob -a /tmp/77Ka2juTPq/concat.2.a.bcf /tmp/77Ka2juTPq/concat.2.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -aD /tmp/77Ka2juTPq/concat.2.a.vcf.gz /tmp/77Ka2juTPq/concat.2.b.vcf.gz .. ok test_vcf_concat: /<>/bcftools concat -Ob -aD /tmp/77Ka2juTPq/concat.2.a.vcf.gz /tmp/77Ka2juTPq/concat.2.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -aD /tmp/77Ka2juTPq/concat.2.a.bcf /tmp/77Ka2juTPq/concat.2.b.bcf .. ok test_vcf_concat: /<>/bcftools concat -Ob -aD /tmp/77Ka2juTPq/concat.2.a.bcf /tmp/77Ka2juTPq/concat.2.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -l --ligate-warn /tmp/77Ka2juTPq/concat.3.a.vcf.gz /tmp/77Ka2juTPq/concat.3.b.vcf.gz /tmp/77Ka2juTPq/concat.3.0.vcf.gz /tmp/77Ka2juTPq/concat.3.c.vcf.gz /tmp/77Ka2juTPq/concat.3.d.vcf.gz /tmp/77Ka2juTPq/concat.3.e.vcf.gz /tmp/77Ka2juTPq/concat.3.f.vcf.gz .. ok test_vcf_concat: /<>/bcftools concat -Ob -l --ligate-warn /tmp/77Ka2juTPq/concat.3.a.vcf.gz /tmp/77Ka2juTPq/concat.3.b.vcf.gz /tmp/77Ka2juTPq/concat.3.0.vcf.gz /tmp/77Ka2juTPq/concat.3.c.vcf.gz /tmp/77Ka2juTPq/concat.3.d.vcf.gz /tmp/77Ka2juTPq/concat.3.e.vcf.gz /tmp/77Ka2juTPq/concat.3.f.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -l --ligate-warn /tmp/77Ka2juTPq/concat.3.a.bcf /tmp/77Ka2juTPq/concat.3.b.bcf /tmp/77Ka2juTPq/concat.3.0.bcf /tmp/77Ka2juTPq/concat.3.c.bcf /tmp/77Ka2juTPq/concat.3.d.bcf /tmp/77Ka2juTPq/concat.3.e.bcf /tmp/77Ka2juTPq/concat.3.f.bcf .. ok test_vcf_concat: /<>/bcftools concat -Ob -l --ligate-warn /tmp/77Ka2juTPq/concat.3.a.bcf /tmp/77Ka2juTPq/concat.3.b.bcf /tmp/77Ka2juTPq/concat.3.0.bcf /tmp/77Ka2juTPq/concat.3.c.bcf /tmp/77Ka2juTPq/concat.3.d.bcf /tmp/77Ka2juTPq/concat.3.e.bcf /tmp/77Ka2juTPq/concat.3.f.bcf | /<>/bcftools view | grep -v ^##bcftools_ Random seed for test_naive_concat: 35209252 .. ok test_naive_concat: /<>/bcftools concat --naive-force /tmp/77Ka2juTPq/naive_concat.0.bcf /tmp/77Ka2juTPq/naive_concat.1.bcf /tmp/77Ka2juTPq/naive_concat.2.bcf /tmp/77Ka2juTPq/naive_concat.3.bcf /tmp/77Ka2juTPq/naive_concat.4.bcf /tmp/77Ka2juTPq/naive_concat.5.bcf /tmp/77Ka2juTPq/naive_concat.6.bcf /tmp/77Ka2juTPq/naive_concat.7.bcf /tmp/77Ka2juTPq/naive_concat.8.bcf /tmp/77Ka2juTPq/naive_concat.9.bcf | /<>/bcftools view -H .. ok test_naive_concat: /<>/bcftools concat --naive /tmp/77Ka2juTPq/naive_concat.0.vcf.gz /tmp/77Ka2juTPq/naive_concat.1.vcf.gz /tmp/77Ka2juTPq/naive_concat.2.vcf.gz /tmp/77Ka2juTPq/naive_concat.3.vcf.gz /tmp/77Ka2juTPq/naive_concat.4.vcf.gz /tmp/77Ka2juTPq/naive_concat.5.vcf.gz /tmp/77Ka2juTPq/naive_concat.6.vcf.gz /tmp/77Ka2juTPq/naive_concat.7.vcf.gz /tmp/77Ka2juTPq/naive_concat.8.vcf.gz /tmp/77Ka2juTPq/naive_concat.9.vcf.gz | /<>/bcftools view -H .. ok test_vcf_concat: /<>/bcftools concat --no-version -l /tmp/77Ka2juTPq/concat.4.a.vcf.gz /tmp/77Ka2juTPq/concat.4.b.vcf.gz .. ok test_vcf_concat: /<>/bcftools concat -Ob -l /tmp/77Ka2juTPq/concat.4.a.vcf.gz /tmp/77Ka2juTPq/concat.4.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -l /tmp/77Ka2juTPq/concat.4.a.bcf /tmp/77Ka2juTPq/concat.4.b.bcf .. ok test_vcf_concat: /<>/bcftools concat -Ob -l /tmp/77Ka2juTPq/concat.4.a.bcf /tmp/77Ka2juTPq/concat.4.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -l --ligate-warn /tmp/77Ka2juTPq/concat.5.a.vcf.gz /tmp/77Ka2juTPq/concat.5.b.vcf.gz /tmp/77Ka2juTPq/concat.5.c.vcf.gz .. ok test_vcf_concat: /<>/bcftools concat -Ob -l --ligate-warn /tmp/77Ka2juTPq/concat.5.a.vcf.gz /tmp/77Ka2juTPq/concat.5.b.vcf.gz /tmp/77Ka2juTPq/concat.5.c.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -l --ligate-warn /tmp/77Ka2juTPq/concat.5.a.bcf /tmp/77Ka2juTPq/concat.5.b.bcf /tmp/77Ka2juTPq/concat.5.c.bcf .. ok test_vcf_concat: /<>/bcftools concat -Ob -l --ligate-warn /tmp/77Ka2juTPq/concat.5.a.bcf /tmp/77Ka2juTPq/concat.5.b.bcf /tmp/77Ka2juTPq/concat.5.c.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -l --ligate-force /tmp/77Ka2juTPq/concat.5.a.bcf /tmp/77Ka2juTPq/concat.5.b.bcf /tmp/77Ka2juTPq/concat.5.c.bcf .. ok test_vcf_concat: /<>/bcftools concat -Ob -l --ligate-force /tmp/77Ka2juTPq/concat.5.a.bcf /tmp/77Ka2juTPq/concat.5.b.bcf /tmp/77Ka2juTPq/concat.5.c.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -G -a -D /tmp/77Ka2juTPq/concat.5.a.vcf.gz /tmp/77Ka2juTPq/concat.5.b.vcf.gz /tmp/77Ka2juTPq/concat.5.c.vcf.gz .. ok test_vcf_concat: /<>/bcftools concat -Ob -G -a -D /tmp/77Ka2juTPq/concat.5.a.vcf.gz /tmp/77Ka2juTPq/concat.5.b.vcf.gz /tmp/77Ka2juTPq/concat.5.c.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -G -a -D /tmp/77Ka2juTPq/concat.5.a.bcf /tmp/77Ka2juTPq/concat.5.b.bcf /tmp/77Ka2juTPq/concat.5.c.bcf .. ok test_vcf_concat: /<>/bcftools concat -Ob -G -a -D /tmp/77Ka2juTPq/concat.5.a.bcf /tmp/77Ka2juTPq/concat.5.b.bcf /tmp/77Ka2juTPq/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/77Ka2juTPq/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/77Ka2juTPq/reheader.bcf | /<>/bcftools reheader -h /<>/test/reheader.hdr | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -h /<>/test/reheader.hdr /tmp/77Ka2juTPq/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/77Ka2juTPq/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/77Ka2juTPq/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/77Ka2juTPq/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples /tmp/77Ka2juTPq/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/77Ka2juTPq/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/77Ka2juTPq/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/77Ka2juTPq/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples2 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples2 /tmp/77Ka2juTPq/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/77Ka2juTPq/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/77Ka2juTPq/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/77Ka2juTPq/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples3 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples3 /tmp/77Ka2juTPq/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/77Ka2juTPq/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/77Ka2juTPq/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/77Ka2juTPq/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples4 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples4 /tmp/77Ka2juTPq/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/77Ka2juTPq/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/77Ka2juTPq/empty.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/77Ka2juTPq/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/77Ka2juTPq/empty.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/77Ka2juTPq/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/77Ka2juTPq/reheader.2.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -f /<>/test/reheader.fai /tmp/77Ka2juTPq/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/77Ka2juTPq/reheader.2.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -h /<>/test/reheader.2.hdr -f /<>/test/reheader.fai /tmp/77Ka2juTPq/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/77Ka2juTPq/reheader.3.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -f /<>/test/reheader.3.fai /tmp/77Ka2juTPq/reheader.3.vcf.gz | /<>/bcftools view --no-version .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/77Ka2juTPq/rename.map -Ov /tmp/77Ka2juTPq/annotate.bcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/77Ka2juTPq/rename.map -Ob /tmp/77Ka2juTPq/annotate.bcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/77Ka2juTPq/rename.map -Ov /<>/test/annotate.vcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/77Ka2juTPq/rename.map -Ob /<>/test/annotate.vcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_vcf_convert: /<>/bcftools convert -g -,. /tmp/77Ka2juTPq/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/77Ka2juTPq/convert.vcf.gz | /<>/bcftools convert -g -,. .. ok test_vcf_convert: /<>/bcftools convert -g -,. --vcf-ids /tmp/77Ka2juTPq/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/77Ka2juTPq/convert.vcf.gz | /<>/bcftools convert -g -,. --vcf-ids .. ok test_vcf_convert: /<>/bcftools convert -g -,. --vcf-ids --3N6 /tmp/77Ka2juTPq/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/77Ka2juTPq/convert.vcf.gz | /<>/bcftools convert -g -,. --vcf-ids --3N6 .. ok test_vcf_convert: /<>/bcftools convert -g .,- /tmp/77Ka2juTPq/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/77Ka2juTPq/convert.vcf.gz | /<>/bcftools convert -g -,. --tag PL .. ok test_vcf_convert: /<>/bcftools convert -g .,- --tag PL /tmp/77Ka2juTPq/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/77Ka2juTPq/convert.vcf.gz | /<>/bcftools convert -g .,- --tag PL .. ok test_vcf_convert: /<>/bcftools convert -g -,. --vcf-ids /tmp/77Ka2juTPq/check.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/77Ka2juTPq/check.vcf.gz | /<>/bcftools convert -g -,. --vcf-ids .. ok test_vcf_convert: /<>/bcftools convert -g .,- --vcf-ids /tmp/77Ka2juTPq/check.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/77Ka2juTPq/check.vcf.gz | /<>/bcftools convert -g .,- --vcf-ids .. ok test_vcf_convert: /<>/bcftools convert -g -,. --3N6 /tmp/77Ka2juTPq/check.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/77Ka2juTPq/check.vcf.gz | /<>/bcftools convert -g -,. --3N6 .. ok test_vcf_convert: /<>/bcftools convert -g .,- --3N6 /tmp/77Ka2juTPq/check.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/77Ka2juTPq/check.vcf.gz | /<>/bcftools convert -g .,- --3N6 .. ok test_vcf_convert: /<>/bcftools convert -g -,. --3N6 --vcf-ids /tmp/77Ka2juTPq/check.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/77Ka2juTPq/check.vcf.gz | /<>/bcftools convert -g -,. --3N6 --vcf-ids .. ok test_vcf_convert: /<>/bcftools convert -g .,- --3N6 --vcf-ids /tmp/77Ka2juTPq/check.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/77Ka2juTPq/check.vcf.gz | /<>/bcftools convert -g .,- --3N6 --vcf-ids .. ok test_vcf_convert: /<>/bcftools convert -h -,.,. /tmp/77Ka2juTPq/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/77Ka2juTPq/convert.vcf.gz | /<>/bcftools convert -h -,.,. .. ok test_vcf_convert: /<>/bcftools convert -h .,-,. /tmp/77Ka2juTPq/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/77Ka2juTPq/convert.vcf.gz | /<>/bcftools convert -h .,-,. .. ok test_vcf_convert: /<>/bcftools convert -h .,-,. --vcf-ids /tmp/77Ka2juTPq/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/77Ka2juTPq/convert.vcf.gz | /<>/bcftools convert -h .,-,. --vcf-ids .. ok test_vcf_convert: /<>/bcftools convert -h .,.,- /tmp/77Ka2juTPq/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/convert.hap-missing.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/77Ka2juTPq/convert.hap-missing.vcf.gz | /<>/bcftools convert --haplegendsample -,.,. .. ok test_vcf_convert: /<>/bcftools convert --hapsample -,. /tmp/77Ka2juTPq/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/77Ka2juTPq/convert.vcf.gz | /<>/bcftools convert --hapsample -,. .. ok test_vcf_convert: /<>/bcftools convert --hapsample -,. --vcf-ids /tmp/77Ka2juTPq/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/77Ka2juTPq/convert.vcf.gz | /<>/bcftools convert --hapsample -,. --vcf-ids .. ok test_vcf_convert: /<>/bcftools convert --hapsample .,- /tmp/77Ka2juTPq/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/convert.gvcf.vcf.gz .. ok test_vcf_convert_gvcf: /<>/bcftools view -Ob /tmp/77Ka2juTPq/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/77Ka2juTPq/consensus.vcf.gz -f /<>/test/consensus.fa -s - -m /<>/test/consensus.tab .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus.bcf -f /<>/test/consensus.fa -s - -m /<>/test/consensus.tab .. ok test_vcf_consensus_chain: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus.vcf.gz -f /<>/test/consensus.fa -s - -m /<>/test/consensus.tab -c /tmp/77Ka2juTPq/consensus.1.chain.new >/dev/null; cat /tmp/77Ka2juTPq/consensus.1.chain.new .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 -m /<>/test/consensus.tab .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus.bcf -f /<>/test/consensus.fa -H 1 -m /<>/test/consensus.tab .. ok test_vcf_consensus_chain: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 -m /<>/test/consensus.tab -c /tmp/77Ka2juTPq/consensus.2.chain.new >/dev/null; cat /tmp/77Ka2juTPq/consensus.2.chain.new .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus.vcf.gz -f /<>/test/consensus.fa -I -s - -m /<>/test/consensus.tab .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus.bcf -f /<>/test/consensus.fa -I -s - -m /<>/test/consensus.tab .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/consensus.vcf.gz -f /<>/test/consensus.fa -I -m /<>/test/consensus.tab -c /tmp/77Ka2juTPq/consensus.3.chain.new >/dev/null; cat /tmp/77Ka2juTPq/consensus.3.chain.new .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus.bcf -f /<>/test/consensus.fa -H 1 .. ok test_vcf_consensus_chain: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 -c /tmp/77Ka2juTPq/consensus.4.chain.new >/dev/null; cat /tmp/77Ka2juTPq/consensus.4.chain.new .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus2.vcf.gz -f /<>/test/consensus2.fa -H 1 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus2.bcf -f /<>/test/consensus2.fa -H 1 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus2.vcf.gz -f /<>/test/consensus2.fa -H 2 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus2.bcf -f /<>/test/consensus2.fa -H 2 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/empty.vcf.gz -f /<>/test/consensus.fa -s - .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/empty.bcf -f /<>/test/consensus.fa -s - .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus3.vcf.gz -f /<>/test/consensus2.fa -H 2 -M "?" .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus3.bcf -f /<>/test/consensus2.fa -H 2 -M "?" .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus3.vcf.gz -f /<>/test/consensus2.fa -H 2 -M "?" -p xx_ .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus3.bcf -f /<>/test/consensus2.fa -H 2 -M "?" -p xx_ .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus4.vcf.gz -f /<>/test/consensus2.fa -s - .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus4.bcf -f /<>/test/consensus2.fa -s - .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus5.vcf.gz -f /<>/test/consensus5.fa --haplotype LA .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus5.bcf -f /<>/test/consensus5.fa --haplotype LA .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus6.vcf.gz -f /<>/test/consensus6.fa -s - .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus6.bcf -f /<>/test/consensus6.fa -s - .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus7.vcf.gz -f /<>/test/consensus7.fa -H 2 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus7.bcf -f /<>/test/consensus7.fa -H 2 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus7.vcf.gz -f /<>/test/consensus7.fa -H 4 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus7.bcf -f /<>/test/consensus7.fa -H 4 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus7.vcf.gz -f /<>/test/consensus7.fa -H 2pIu .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus7.bcf -f /<>/test/consensus7.fa -H 2pIu .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus7.vcf.gz -f /<>/test/consensus7.fa -H 4pIu .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus7.bcf -f /<>/test/consensus7.fa -H 4pIu .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus7.vcf.gz -f /<>/test/consensus7.fa -H 1 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus7.bcf -f /<>/test/consensus7.fa -H 1 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus7.vcf.gz -f /<>/test/consensus7.fa -H 3 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus7.bcf -f /<>/test/consensus7.fa -H 3 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus7.vcf.gz -f /<>/test/consensus7.fa -H 1pIu .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus7.bcf -f /<>/test/consensus7.fa -H 1pIu .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus7.vcf.gz -f /<>/test/consensus7.fa -H 3pIu .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus7.bcf -f /<>/test/consensus7.fa -H 3pIu .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus8.vcf.gz -f /<>/test/consensus.fa -s - .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus8.bcf -f /<>/test/consensus.fa -s - .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus8.vcf.gz -f /<>/test/consensus.fa -s - -a . .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus8.bcf -f /<>/test/consensus.fa -s - -a . .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus8.vcf.gz -f /<>/test/consensus.fa -s - -a . -i 'type="snp" || type="ref"' .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus8.bcf -f /<>/test/consensus.fa -s - -a . -i 'type="snp" || type="ref"' .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus8.vcf.gz -f /<>/test/consensus.fa -s - -a . -i 'ALT!=""' .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus8.bcf -f /<>/test/consensus.fa -s - -a . -i 'ALT!=""' .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus8.vcf.gz -f /<>/test/consensus.fa -s - -a . -e 'MinDP>15' .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus8.bcf -f /<>/test/consensus.fa -s - -a . -e 'MinDP>15' .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus8.vcf.gz -f /<>/test/consensus.fa -s - -a . -e 'MinDP<15' .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus8.bcf -f /<>/test/consensus.fa -s - -a . -e 'MinDP<15' .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus.9.vcf.gz -f /<>/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus.9.bcf -f /<>/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus.9.vcf.gz -f /<>/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus.9.bcf -f /<>/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus.10.vcf.gz -f /<>/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus.10.bcf -f /<>/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus.10.vcf.gz -f /<>/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus.10.bcf -f /<>/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus.11.vcf.gz -f /<>/test/consensus.11.fa -s smpl .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus.11.bcf -f /<>/test/consensus.11.fa -s smpl .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus.11.vcf.gz -f /<>/test/consensus.11.fa -s smpl -a N .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus.11.bcf -f /<>/test/consensus.11.fa -s smpl -a N .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus.12.vcf.gz -f /<>/test/consensus.12.fa -s - .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus.12.bcf -f /<>/test/consensus.12.fa -s - .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus.13.vcf.gz -f /<>/test/consensus.13.fa -s - .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus.13.bcf -f /<>/test/consensus.13.fa -s - .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus.14.vcf.gz -f /<>/test/consensus.14.fa -s - .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus.14.bcf -f /<>/test/consensus.14.fa -s - .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/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/77Ka2juTPq/consensus.12.bcf -f /<>/test/consensus.12.fa -s - --mark-del - --mark-ins uc --mark-snv uc .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus.12.vcf.gz -f /<>/test/consensus.12.fa -s - --mark-del - --mark-ins + --mark-snv : .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus.12.bcf -f /<>/test/consensus.12.fa -s - --mark-del - --mark-ins + --mark-snv : .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus.15.vcf.gz -f /<>/test/consensus.15.fa -H I --mark-ins lc --mark-snv lc .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus.15.bcf -f /<>/test/consensus.15.fa -H I --mark-ins lc --mark-snv lc .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus.16.vcf.gz -f /<>/test/consensus.fa -s - -I .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus.16.bcf -f /<>/test/consensus.fa -s - -I .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus.16.vcf.gz -f /<>/test/consensus.fa -H I .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus.16.bcf -f /<>/test/consensus.fa -H I .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus.17.vcf.gz -f /<>/test/consensus2.fa -s - -M N -m /<>/test/consensus.17.bed .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus.17.bcf -f /<>/test/consensus2.fa -s - -M N -m /<>/test/consensus.17.bed .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus.18.vcf.gz -f /<>/test/consensus.18.fa -s - .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus.18.bcf -f /<>/test/consensus.18.fa -s - .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus.19.vcf.gz -f /<>/test/consensus.19.fa -s - .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus.19.bcf -f /<>/test/consensus.19.fa -s - .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus.20.vcf.gz -f /<>/test/consensus.20.fa -s - .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus.20.bcf -f /<>/test/consensus.20.fa -s - .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus.20.vcf.gz -f /<>/test/consensus.20.fa .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus.20.bcf -f /<>/test/consensus.20.fa .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus.20.vcf.gz -f /<>/test/consensus.20.fa -M . -s b .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus.20.bcf -f /<>/test/consensus.20.fa -M . -s b .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus.20.vcf.gz -f /<>/test/consensus.20.fa -M . -s a .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus.20.bcf -f /<>/test/consensus.20.fa -M . -s a .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus.21.vcf.gz -f /<>/test/consensus.21.fa .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus.21.bcf -f /<>/test/consensus.21.fa .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus.22.vcf.gz -f /<>/test/consensus.22.fa --regions-overlap 0 --mark-del . .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus.22.bcf -f /<>/test/consensus.22.fa --regions-overlap 0 --mark-del . .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus.22.vcf.gz -f /<>/test/consensus.22.fa --regions-overlap 1 --mark-del . .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus.22.bcf -f /<>/test/consensus.22.fa --regions-overlap 1 --mark-del . .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus.22.vcf.gz -f /<>/test/consensus.22.fa --regions-overlap 2 --mark-del . .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus.22.bcf -f /<>/test/consensus.22.fa --regions-overlap 2 --mark-del . .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus.22.vcf.gz -f /<>/test/consensus.22.fa --regions-overlap 0 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus.22.bcf -f /<>/test/consensus.22.fa --regions-overlap 0 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus.22.vcf.gz -f /<>/test/consensus.22.fa --regions-overlap 1 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus.22.bcf -f /<>/test/consensus.22.fa --regions-overlap 1 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/consensus.22.vcf.gz -f /<>/test/consensus.22.fa --regions-overlap 2 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/gtcheck.1.vcf.gz -g /tmp/77Ka2juTPq/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -u GT,GT /tmp/77Ka2juTPq/gtcheck.1.vcf.gz -g /tmp/77Ka2juTPq/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -u GT,PL /tmp/77Ka2juTPq/gtcheck.1.vcf.gz -g /tmp/77Ka2juTPq/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -u PL,GT /tmp/77Ka2juTPq/gtcheck.1.vcf.gz -g /tmp/77Ka2juTPq/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -u PL,PL /tmp/77Ka2juTPq/gtcheck.1.vcf.gz -g /tmp/77Ka2juTPq/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -p s1,s1 /tmp/77Ka2juTPq/gtcheck.1.vcf.gz -g /tmp/77Ka2juTPq/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 /tmp/77Ka2juTPq/gtcheck.2.vcf.gz -g /tmp/77Ka2juTPq/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 /tmp/77Ka2juTPq/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/77Ka2juTPq/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -P /<>/test/gtcheck.3.pairs /tmp/77Ka2juTPq/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -u PL /tmp/77Ka2juTPq/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 --n-matches 4 /tmp/77Ka2juTPq/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO | sort .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -s qry:E,D,C /tmp/77Ka2juTPq/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -s qry:E,D,C -u PL /tmp/77Ka2juTPq/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -s qry:B -s gt:D /tmp/77Ka2juTPq/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/77Ka2juTPq/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -s qry:B -s gt:D,C /tmp/77Ka2juTPq/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -p B,C,B,D /tmp/77Ka2juTPq/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -u GT,GT -H /tmp/77Ka2juTPq/gtcheck.1.vcf.gz -g /tmp/77Ka2juTPq/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -u GT,PL -H /tmp/77Ka2juTPq/gtcheck.1.vcf.gz -g /tmp/77Ka2juTPq/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -u PL,GT -H /tmp/77Ka2juTPq/gtcheck.1.vcf.gz -g /tmp/77Ka2juTPq/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -u PL,PL -H /tmp/77Ka2juTPq/gtcheck.1.vcf.gz -g /tmp/77Ka2juTPq/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/77Ka2juTPq/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/77Ka2juTPq/gtcheck.4.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -u GT -e 30 /tmp/77Ka2juTPq/gtcheck.1.vcf.gz -g /tmp/77Ka2juTPq/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -u GT -e 30 -p s1,s1 /tmp/77Ka2juTPq/gtcheck.1.vcf.gz -g /tmp/77Ka2juTPq/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -u GT -e 300 /tmp/77Ka2juTPq/gtcheck.1.vcf.gz -g /tmp/77Ka2juTPq/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -u PL -e 30 /tmp/77Ka2juTPq/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck /tmp/77Ka2juTPq/gtcheck.ntop.vcf.gz -g /tmp/77Ka2juTPq/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck --n-matches 2 /tmp/77Ka2juTPq/gtcheck.ntop.vcf.gz -g /tmp/77Ka2juTPq/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck /tmp/77Ka2juTPq/gtcheck.5.vcf.gz -g /tmp/77Ka2juTPq/gtcheck.5.gts.vcf.gz | grep -v ^# | grep -v Time .. ok test_gtcheck: /<>/bcftools gtcheck -p A,B,B,C /tmp/77Ka2juTPq/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/77Ka2juTPq/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-dbgsym' in '../bcftools-dbgsym_1.20-2_amd64.deb'. dpkg-deb: building package 'bcftools' in '../bcftools_1.20-2_amd64.deb'. dpkg-genbuildinfo -O../bcftools_1.20-2_amd64.buildinfo dpkg-genchanges -O../bcftools_1.20-2_amd64.changes dpkg-genchanges: info: not including original source code in upload dpkg-source -Zxz --after-build . dpkg-buildpackage: info: binary and diff upload (original source NOT included) -------------------------------------------------------------------------------- Build finished at 2024-06-25T04:06:40Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ bcftools_1.20-2_amd64.changes: ------------------------------ Format: 1.8 Date: Tue, 25 Jun 2024 08:34:02 +0900 Source: bcftools Binary: bcftools bcftools-dbgsym Architecture: source amd64 Version: 1.20-2 Distribution: perl-5.40-throwaway Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Charles Plessy Description: bcftools - genomic variant calling and manipulation of VCF/BCF files Changes: bcftools (1.20-2) unstable; urgency=medium . * Team upload * Only recommend python-matplotlib and python3-gffutils Checksums-Sha1: d99fa10b3f137f6f409988e976a7acbadce46afe 1242 bcftools_1.20-2.dsc c925b1ca0077b9aec29892e70acf11022df0f057 7836 bcftools_1.20-2.debian.tar.xz 50148fc0328cb98303f288506465acd208d68b97 2154528 bcftools-dbgsym_1.20-2_amd64.deb 27fc7b802a71ee95f12952a5aa98dc63a61ff19d 6242 bcftools_1.20-2_amd64.buildinfo cce4ce705139d4fba02e704539044a18ad865a89 759896 bcftools_1.20-2_amd64.deb Checksums-Sha256: f120db3675c35efa78799c8d651d70f2b7f3c755e26344f15b446de68d7b6168 1242 bcftools_1.20-2.dsc a1ff25568b1c641c9bf55dc5932efaa6e281c29efc6aff1c40cd2a2091585053 7836 bcftools_1.20-2.debian.tar.xz 3585ed5471703f3c3df535b15c1bf83eadb116d6f1dc83253795feb757dd8962 2154528 bcftools-dbgsym_1.20-2_amd64.deb 013593670cff07d1554a6c386fa9993a9472802d65237041703fbca265214465 6242 bcftools_1.20-2_amd64.buildinfo 658e0180f887b96d804c0ad6085c66eac4179cef1c2f34d59b15775bae432e10 759896 bcftools_1.20-2_amd64.deb Files: 5995df7007f8a4a295134567d3e965f2 1242 science optional bcftools_1.20-2.dsc 321310607a83802b72a602acffcbb85e 7836 science optional bcftools_1.20-2.debian.tar.xz 30a7c00e805d59600b07c35d65b37dfc 2154528 debug optional bcftools-dbgsym_1.20-2_amd64.deb f79fc50c285381e5dac469e9e90365e5 6242 science optional bcftools_1.20-2_amd64.buildinfo 14597867585ebfaef7dece9365afe806 759896 science optional bcftools_1.20-2_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: bcftools Binary: bcftools bcftools-dbgsym Architecture: amd64 source Version: 1.20-2 Checksums-Md5: 5995df7007f8a4a295134567d3e965f2 1242 bcftools_1.20-2.dsc 30a7c00e805d59600b07c35d65b37dfc 2154528 bcftools-dbgsym_1.20-2_amd64.deb 14597867585ebfaef7dece9365afe806 759896 bcftools_1.20-2_amd64.deb Checksums-Sha1: d99fa10b3f137f6f409988e976a7acbadce46afe 1242 bcftools_1.20-2.dsc 50148fc0328cb98303f288506465acd208d68b97 2154528 bcftools-dbgsym_1.20-2_amd64.deb cce4ce705139d4fba02e704539044a18ad865a89 759896 bcftools_1.20-2_amd64.deb Checksums-Sha256: f120db3675c35efa78799c8d651d70f2b7f3c755e26344f15b446de68d7b6168 1242 bcftools_1.20-2.dsc 3585ed5471703f3c3df535b15c1bf83eadb116d6f1dc83253795feb757dd8962 2154528 bcftools-dbgsym_1.20-2_amd64.deb 658e0180f887b96d804c0ad6085c66eac4179cef1c2f34d59b15775bae432e10 759896 bcftools_1.20-2_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Tue, 25 Jun 2024 04:06:39 +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 (= 0.22.5-1), autotools-dev (= 20220109.1), base-files (= 13.3), base-passwd (= 3.6.3), bash (= 5.2.21-2.1), binutils (= 2.42.50.20240618-1), binutils-common (= 2.42.50.20240618-1), binutils-x86-64-linux-gnu (= 2.42.50.20240618-1), bsdextrautils (= 2.40.1-9), bsdutils (= 1:2.40.1-9), build-essential (= 12.10), bzip2 (= 1.0.8-5.1), coreutils (= 9.4-3.1), cpp (= 4:13.2.0-7), cpp-13 (= 13.3.0-1), cpp-13-x86-64-linux-gnu (= 13.3.0-1), cpp-x86-64-linux-gnu (= 4:13.2.0-7), dash (= 0.5.12-9), debconf (= 1.5.86), debhelper (= 13.16), debianutils (= 5.19), 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 (= 4.10.0-2), g++ (= 4:13.2.0-7), g++-13 (= 13.3.0-1), g++-13-x86-64-linux-gnu (= 13.3.0-1), g++-x86-64-linux-gnu (= 4:13.2.0-7), gcc (= 4:13.2.0-7), gcc-13 (= 13.3.0-1), gcc-13-base (= 13.3.0-1), gcc-13-x86-64-linux-gnu (= 13.3.0-1), gcc-14-base (= 14.1.0-2), gcc-x86-64-linux-gnu (= 4:13.2.0-7), gettext (= 0.22.5-1), gettext-base (= 0.22.5-1), 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 (= 14.1.0-2), libatomic1 (= 14.1.0-2), libattr1 (= 1:2.5.2-1), libaudit-common (= 1:3.1.2-4), libaudit1 (= 1:3.1.2-4), libbinutils (= 2.42.50.20240618-1), libblkid1 (= 2.40.1-9), libbrotli1 (= 1.1.0-2+b3), libbz2-1.0 (= 1.0.8-5.1), libbz2-dev (= 1.0.8-5.1), libc-bin (= 2.38-13), libc-dev-bin (= 2.38-13), libc6 (= 2.38-13), libc6-dev (= 2.38-13), libcap-ng0 (= 0.8.5-1), libcap2 (= 1:2.66-5), libcc1-0 (= 14.1.0-2), libcom-err2 (= 1.47.1-1), libcrypt-dev (= 1:4.4.36-4), libcrypt1 (= 1:4.4.36-4), libctf-nobfd0 (= 2.42.50.20240618-1), libctf0 (= 2.42.50.20240618-1), 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 (= 13.16), 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 (= 13.3.0-1), libgcc-s1 (= 14.1.0-2), libgdbm-compat4t64 (= 1.23-6), libgdbm6t64 (= 1.23-6), libgmp10 (= 2:6.3.0+dfsg-2+b1), libgnutls30t64 (= 3.8.5-4), libgomp1 (= 14.1.0-2), libgprofng0 (= 2.42.50.20240618-1), 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 (= 1.21.2-1), libhogweed6t64 (= 3.10-1), libhts-dev (= 1.20+ds-1), libhts3t64 (= 1.20+ds-1), libhtscodecs2 (= 1.6.0-1+b1), libhwasan0 (= 14.1.0-2), 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 (= 14.1.0-2), libjansson4 (= 2.14-2+b2), libk5crypto3 (= 1.21.2-1), libkeyutils1 (= 1.6.3-3), libkrb5-3 (= 1.21.2-1), libkrb5support0 (= 1.21.2-1), libldap-2.5-0 (= 2.5.18+dfsg-1), liblsan0 (= 14.1.0-2), liblzma-dev (= 5.6.2-1), liblzma5 (= 5.6.2-1), libmagic-mgc (= 1:5.45-3), libmagic1t64 (= 1:5.45-3), libmd0 (= 1.1.0-2), libmount1 (= 2.40.1-9), libmpc3 (= 1.3.1-1+b2), libmpfr6 (= 4.2.1-1+b1), libnettle8t64 (= 3.10-1), libnghttp2-14 (= 1.62.1-1), 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), libperl5.40 (= 5.40.0~rc1-1), libpipeline1 (= 1.5.7-2), libpsl5t64 (= 0.21.2-1.1), libquadmath0 (= 14.1.0-2), 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 (= 2.42.50.20240618-1), libsmartcols1 (= 2.40.1-9), libssh2-1t64 (= 1.11.0-5), libssl3t64 (= 3.2.2-1), libstdc++-13-dev (= 13.3.0-1), libstdc++6 (= 14.1.0-2), libsystemd0 (= 256.1-2), libtasn1-6 (= 4.19.0-3+b2), libtinfo6 (= 6.5-2), libtool (= 2.4.7-7), libtsan2 (= 14.1.0-2), libubsan1 (= 14.1.0-2), libuchardet0 (= 0.0.8-1+b1), libudev1 (= 256.1-2), libunistring5 (= 1.2-1), libuuid1 (= 2.40.1-9), libxml2 (= 2.12.7+dfsg-3), libzstd1 (= 1.5.6+dfsg-1), linux-libc-dev (= 6.8.12-1), m4 (= 1.4.19-4), make (= 4.3-4.1), man-db (= 2.12.1-2), mawk (= 1.3.4.20240123-1), ncurses-base (= 6.5-2), ncurses-bin 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lrwxrwxrwx root/root 0 2024-06-24 23:34 ./usr/share/doc/bcftools-dbgsym -> bcftools bcftools_1.20-2_amd64.deb ------------------------- new Debian package, version 2.0. size 759896 bytes: control archive=2264 bytes. 701 bytes, 15 lines control 4183 bytes, 55 lines md5sums Package: bcftools Version: 1.20-2 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 2632 Depends: libc6 (>= 2.34), libhts3t64 (>= 1.17) Recommends: perl, python3-gffutils, python3-matplotlib Suggests: python3, python3-numpy, texlive-latex-recommended Section: science Priority: optional Homepage: https://samtools.github.io/bcftools/ Description: genomic variant calling and manipulation of VCF/BCF files BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. drwxr-xr-x root/root 0 2024-06-24 23:34 ./ drwxr-xr-x root/root 0 2024-06-24 23:34 ./usr/ drwxr-xr-x root/root 0 2024-06-24 23:34 ./usr/bin/ -rwxr-xr-x root/root 1189072 2024-06-24 23:34 ./usr/bin/bcftools -rwxr-xr-x root/root 16949 2024-06-24 23:34 ./usr/bin/color-chrs.pl -rwxr-xr-x root/root 7404 2024-04-15 14:10 ./usr/bin/gff2gff.py -rwxr-xr-x root/root 4325 2024-06-24 23:34 ./usr/bin/guess-ploidy.py -rwxr-xr-x root/root 15632 2024-04-15 14:10 ./usr/bin/plot-roh.py -rwxr-xr-x root/root 90225 2024-06-24 23:34 ./usr/bin/plot-vcfstats -rwxr-xr-x root/root 13936 2024-06-24 23:34 ./usr/bin/run-roh.pl -rwxr-xr-x root/root 18202 2024-06-24 23:34 ./usr/bin/vcfutils.pl drwxr-xr-x root/root 0 2024-06-24 23:34 ./usr/lib/ drwxr-xr-x root/root 0 2024-06-24 23:34 ./usr/lib/x86_64-linux-gnu/ drwxr-xr-x root/root 0 2024-06-24 23:34 ./usr/lib/x86_64-linux-gnu/bcftools/ -rw-r--r-- root/root 27192 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+------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 47648 Build-Time: 167 Distribution: perl-5.40-throwaway Host Architecture: amd64 Install-Time: 11 Job: /srv/debomatic/incoming/bcftools_1.20-2.dsc Machine Architecture: amd64 Package: bcftools Package-Time: 189 Source-Version: 1.20-2 Space: 47648 Status: successful Version: 1.20-2 -------------------------------------------------------------------------------- Finished at 2024-06-25T04:06:40Z Build needed 00:03:09, 47648k disk space