sbuild (Debian sbuild) 0.85.10 (30 May 2024) on carme.larted.org.uk +==============================================================================+ | bcftools 1.20-2 (amd64) Sat, 14 Sep 2024 22:42:30 +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-3ce48c2a-ec26-4164-b7de-c15562d45cf7' 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-CWYtof/resolver-SetVZA' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.40 InRelease [3042 B] Get:1 file:/srv/reprepro perl-5.40 InRelease [3042 B] Get:2 http://deb.debian.org/debian unstable InRelease [202 kB] Get:3 http://deb.debian.org/debian unstable/main amd64 Packages.diff/Index [63.6 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 Packages T-2024-09-14-2006.11-F-2024-09-14-2006.11.pdiff [17.4 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 Packages T-2024-09-14-2006.11-F-2024-09-14-2006.11.pdiff [17.4 kB] Get:5 http://localhost:3142/debian sid InRelease [202 kB] Get:6 http://localhost:3142/debian sid/main Sources.diff/Index [63.6 kB] Get:7 http://localhost:3142/debian sid/main Sources T-2024-09-14-2006.11-F-2024-09-14-2006.11.pdiff [21.2 kB] Get:7 http://localhost:3142/debian sid/main Sources T-2024-09-14-2006.11-F-2024-09-14-2006.11.pdiff [21.2 kB] Fetched 570 kB in 6s (88.5 kB/s) 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-CWYtof/bcftools-1.20' with '<>' I: NOTICE: Log filtering will replace 'build/bcftools-CWYtof' 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 (102 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 libbrotli-dev libbrotli1 libbz2-dev libcom-err2 libcurl3t64-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libelf1t64 libevent-2.1-7t64 libfakeroot libfile-stripnondeterminism-perl libgmp-dev libgmpxx4ldbl libgnutls-dane0t64 libgnutls-openssl27t64 libgnutls28-dev libgsl-dev libgsl28 libgslcblas0 libgssapi-krb5-2 libhts-dev libhts3t64 libhtscodecs2 libicu72 libidn2-dev libio-pty-perl libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblzma-dev libmagic-mgc libmagic1t64 libnghttp2-14 libnghttp2-dev libnghttp3-9 libnghttp3-dev libngtcp2-16 libngtcp2-crypto-gnutls-dev libngtcp2-crypto-gnutls8 libngtcp2-dev libp11-kit-dev libpipeline1 libpkgconf3 libpsl-dev libpsl5t64 librtmp-dev librtmp1 libssh2-1-dev libssh2-1t64 libssl-dev libtasn1-6-dev libtool libuchardet0 libunbound8 libxml2 libzstd-dev m4 man-db nettle-dev pkgconf pkgconf-bin po-debconf sensible-utils tabix zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libcurl4-doc libidn-dev libkrb5-dev libldap2-dev gmp-doc libgmp10-doc libmpfr-dev dns-root-data gnutls-bin gnutls-doc gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html krb5-doc krb5-user liblzma-doc libnghttp2-doc p11-kit-doc libssl-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 libtasn1-doc 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 libbrotli-dev libbrotli1 libbz2-dev libcom-err2 libcurl3t64-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libelf1t64 libevent-2.1-7t64 libfakeroot libfile-stripnondeterminism-perl libgmp-dev libgmpxx4ldbl libgnutls-dane0t64 libgnutls-openssl27t64 libgnutls28-dev libgsl-dev libgsl28 libgslcblas0 libgssapi-krb5-2 libhts-dev libhts3t64 libhtscodecs2 libicu72 libidn2-dev libio-pty-perl libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblzma-dev libmagic-mgc libmagic1t64 libnghttp2-14 libnghttp2-dev libnghttp3-9 libnghttp3-dev libngtcp2-16 libngtcp2-crypto-gnutls-dev libngtcp2-crypto-gnutls8 libngtcp2-dev libp11-kit-dev libpipeline1 libpkgconf3 libpsl-dev libpsl5t64 librtmp-dev librtmp1 libssh2-1-dev libssh2-1t64 libssl-dev libtasn1-6-dev libtool libuchardet0 libunbound8 libxml2 libzstd-dev m4 man-db nettle-dev pkgconf pkgconf-bin po-debconf sbuild-build-depends-main-dummy sensible-utils tabix zlib1g-dev 0 upgraded, 85 newly installed, 0 to remove and 0 not upgraded. Need to get 38.8 MB/38.8 MB of archives. After this operation, 144 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [932 B] Get:2 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 0.22.5-2 [200 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 1.23.0-5 [1181 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.2-8 [97.3 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get:12 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 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 2.72-3 [493 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 0.22.5-2 [723 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.20 [89.7 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 0.191-2 [188 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 72.1-5 [9396 kB] Get:27 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg-3+b1 [671 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.22.5-2 [1601 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 13.20 [915 kB] Get:32 http://deb.debian.org/debian unstable/main amd64 libfakeroot amd64 1.36-1 [29.1 kB] Get:33 http://deb.debian.org/debian unstable/main amd64 fakeroot amd64 1.36-1 [75.1 kB] Get:34 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b4 [300 kB] Get:35 http://deb.debian.org/debian unstable/main amd64 libbrotli-dev amd64 1.1.0-2+b4 [313 kB] Get:36 http://deb.debian.org/debian unstable/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Get:37 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.1-1 [22.9 kB] Get:38 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get:39 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get:40 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get:41 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get:42 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get:43 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.63.0-1 [74.8 kB] Get:44 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.4.0-1 [63.1 kB] Get:45 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.6.0-1 [122 kB] Get:46 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.6.0-1 [19.6 kB] Get:47 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get:48 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get:49 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.0-7 [216 kB] Get:50 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.10.0-2 [359 kB] Get:51 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10 [181 kB] Get:52 http://deb.debian.org/debian unstable/main amd64 libunbound8 amd64 1.20.0-1+b1 [583 kB] Get:53 http://deb.debian.org/debian unstable/main amd64 libgnutls-dane0t64 amd64 3.8.6-2 [439 kB] Get:54 http://deb.debian.org/debian unstable/main amd64 libgnutls-openssl27t64 amd64 3.8.6-2 [439 kB] Get:55 http://deb.debian.org/debian unstable/main amd64 libidn2-dev amd64 2.3.7-2 [123 kB] Get:56 http://deb.debian.org/debian unstable/main amd64 libp11-kit-dev amd64 0.25.5-2 [208 kB] Get:57 http://deb.debian.org/debian unstable/main amd64 libtasn1-6-dev amd64 4.19.0-3+b2 [98.0 kB] Get:58 http://deb.debian.org/debian unstable/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-2+b1 [329 kB] Get:59 http://deb.debian.org/debian unstable/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-2+b1 [640 kB] Get:60 http://deb.debian.org/debian unstable/main amd64 nettle-dev amd64 3.10-1 [1316 kB] Get:61 http://deb.debian.org/debian unstable/main amd64 libgnutls28-dev amd64 3.8.6-2 [1381 kB] Get:62 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-3 [36.2 kB] Get:63 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-3 [29.9 kB] Get:64 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-3 [26.1 kB] Get:65 http://deb.debian.org/debian unstable/main amd64 libnghttp2-dev amd64 1.63.0-1 [115 kB] Get:66 http://deb.debian.org/debian unstable/main amd64 libnghttp3-dev amd64 1.4.0-1 [86.5 kB] Get:67 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.6.0-1 [23.8 kB] Get:68 http://deb.debian.org/debian unstable/main amd64 libngtcp2-dev amd64 1.6.0-1 [170 kB] Get:69 http://deb.debian.org/debian unstable/main amd64 libpsl-dev amd64 0.21.2-1.1 [77.4 kB] Get:70 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1 [919 kB] Get:71 http://deb.debian.org/debian unstable/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-2+b4 [67.7 kB] Get:72 http://deb.debian.org/debian unstable/main amd64 libssl-dev amd64 3.3.2-1 [2742 kB] Get:73 http://deb.debian.org/debian unstable/main amd64 libssh2-1-dev amd64 1.11.0-7 [357 kB] Get:74 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.6+dfsg-1 [368 kB] Get:75 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls-dev amd64 8.10.0-2 [471 kB] Get:76 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.21-1 [47.3 kB] Get:77 http://deb.debian.org/debian unstable/main amd64 libdeflate-dev amd64 1.21-1 [55.8 kB] Get:78 http://deb.debian.org/debian unstable/main amd64 libgslcblas0 amd64 2.8+dfsg-3 [116 kB] Get:79 http://deb.debian.org/debian unstable/main amd64 libgsl28 amd64 2.8+dfsg-3 [994 kB] Get:80 http://deb.debian.org/debian unstable/main amd64 libgsl-dev amd64 2.8+dfsg-3 [1223 kB] Get:81 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.1-1 [95.6 kB] Get:82 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.20+ds-1 [452 kB] Get:83 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.6.2-2 [299 kB] Get:84 http://deb.debian.org/debian unstable/main amd64 libhts-dev amd64 1.20+ds-1 [1684 kB] Get:85 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 38.8 MB in 0s (117 MB/s) Selecting previously unselected package sensible-utils. (Reading database ... 22986 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_0.22.5-2_amd64.deb ... Unpacking gettext-base (0.22.5-2) ... 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 libpkgconf3:amd64 (1.8.1-3) ... Setting up libgmpxx4ldbl:amd64 (2:6.3.0+dfsg-2+b1) ... Setting up libgnutls-dane0t64:amd64 (3.8.6-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up libssl-dev:amd64 (3.3.2-1) ... Setting up autopoint (0.22.5-2) ... Setting up pkgconf-bin (1.8.1-3) ... Setting up libk5crypto3:amd64 (1.21.3-3) ... Setting up libidn2-dev:amd64 (2.3.7-2) ... Setting up autoconf (2.72-3) ... Setting up libnghttp3-9:amd64 (1.4.0-1) ... Setting up libnghttp3-dev:amd64 (1.4.0-1) ... Setting up liblzma-dev:amd64 (5.6.2-2) ... 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 libngtcp2-16:amd64 (1.6.0-1) ... Setting up libkrb5-3:amd64 (1.21.3-3) ... Setting up libssh2-1t64:amd64 (1.11.0-7) ... Setting up libgsl28:amd64 (2.8+dfsg-3) ... Setting up libtasn1-6-dev:amd64 (4.19.0-3+b2) ... Setting up libdeflate-dev:amd64 (1.21-1) ... Setting up tabix (1.20+ds-1) ... Setting up libxml2:amd64 (2.12.7+dfsg-3+b1) ... Setting up libbrotli-dev:amd64 (1.1.0-2+b4) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.6.0-1) ... Setting up libp11-kit-dev:amd64 (0.25.5-2) ... Setting up libbz2-dev:amd64 (1.0.8-6) ... 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 (0.22.5-2) ... Setting up libgsl-dev (2.8+dfsg-3) ... Setting up libgmp-dev:amd64 (2:6.3.0+dfsg-2+b1) ... Setting up nettle-dev:amd64 (3.10-1) ... Setting up libtool (2.4.7-7) ... Setting up libngtcp2-crypto-gnutls-dev:amd64 (1.6.0-1) ... Setting up libngtcp2-dev:amd64 (1.6.0-1) ... Setting up pkgconf:amd64 (1.8.1-3) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up libssh2-1-dev:amd64 (1.11.0-7) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up libgnutls28-dev:amd64 (3.8.6-2) ... Setting up libnghttp2-dev:amd64 (1.63.0-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3t64-gnutls:amd64 (8.10.0-2) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up librtmp-dev:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up libhts3t64:amd64 (1.20+ds-1) ... Setting up debhelper (13.20) ... Setting up libcurl4-gnutls-dev:amd64 (8.10.0-2) ... Setting up libhts-dev:amd64 (1.20+ds-1) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.40-2) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 6.9.7-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.9.7-1 (2024-06-27) amd64 (x86_64) Toolchain package versions: binutils_2.43.1-4 dpkg-dev_1.22.11 g++-13_13.3.0-6 g++-14_14.2.0-4 gcc-13_13.3.0-6 gcc-14_14.2.0-4 libc6-dev_2.40-2 libstdc++-13-dev_13.3.0-6 libstdc++-14-dev_14.2.0-4 libstdc++6_14.2.0-4 linux-libc-dev_6.10.9-1 Package versions: adduser_3.137 apt_2.9.8 autoconf_2.72-3 automake_1:1.16.5-1.3 autopoint_0.22.5-2 autotools-dev_20220109.1 base-files_13.5 base-passwd_3.6.4 bash_5.2.32-1+b1 binutils_2.43.1-4 binutils-common_2.43.1-4 binutils-x86-64-linux-gnu_2.43.1-4 bsdextrautils_2.40.2-8 bsdutils_1:2.40.2-8 build-essential_12.10 bzip2_1.0.8-6 coreutils_9.4-3.1 cpp_4:14.1.0-2 cpp-13_13.3.0-6 cpp-13-x86-64-linux-gnu_13.3.0-6 cpp-14_14.2.0-4 cpp-14-x86-64-linux-gnu_14.2.0-4 cpp-x86-64-linux-gnu_4:14.1.0-2 dash_0.5.12-9 debconf_1.5.87 debhelper_13.20 debian-archive-keyring_2023.4 debianutils_5.20 dh-autoreconf_20 dh-strip-nondeterminism_1.14.0-1 diffutils_1:3.10-1 dirmngr_2.2.43-8+b1 dpkg_1.22.11 dpkg-dev_1.22.11 dwz_0.15-1+b1 eatmydata_131-2 fakeroot_1.36-1 file_1:5.45-3 findutils_4.10.0-3 g++_4:14.1.0-2 g++-13_13.3.0-6 g++-13-x86-64-linux-gnu_13.3.0-6 g++-14_14.2.0-4 g++-14-x86-64-linux-gnu_14.2.0-4 g++-x86-64-linux-gnu_4:14.1.0-2 gcc_4:14.1.0-2 gcc-13_13.3.0-6 gcc-13-base_13.3.0-6 gcc-13-x86-64-linux-gnu_13.3.0-6 gcc-14_14.2.0-4 gcc-14-base_14.2.0-4 gcc-14-x86-64-linux-gnu_14.2.0-4 gcc-x86-64-linux-gnu_4:14.1.0-2 gettext_0.22.5-2 gettext-base_0.22.5-2 gnupg_2.2.43-8 gnupg-l10n_2.2.43-8 gnupg-utils_2.2.43-8+b1 gpg_2.2.43-8+b1 gpg-agent_2.2.43-8+b1 gpg-wks-client_2.2.43-8+b1 gpgconf_2.2.43-8+b1 gpgsm_2.2.43-8+b1 gpgv_2.2.43-8+b1 grep_3.11-4 groff-base_1.23.0-5 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_2.9.8 libarchive-zip-perl_1.68-1 libasan8_14.2.0-4 libassuan0_2.5.6-1+b1 libassuan9_3.0.1-2 libatomic1_14.2.0-4 libattr1_1:2.5.2-1 libaudit-common_1:4.0.1-1 libaudit1_1:4.0.1-1 libbinutils_2.43.1-4 libblkid1_2.40.2-8 libbrotli-dev_1.1.0-2+b4 libbrotli1_1.1.0-2+b4 libbsd0_0.12.2-1 libbz2-1.0_1.0.8-6 libbz2-dev_1.0.8-6 libc-bin_2.40-2 libc-dev-bin_2.40-2 libc-l10n_2.40-2 libc6_2.40-2 libc6-dev_2.40-2 libcap-ng0_0.8.5-2 libcap2_1:2.66-5 libcc1-0_14.2.0-4 libcom-err2_1.47.1-1 libcrypt-dev_1:4.4.36-5 libcrypt1_1:4.4.36-5 libctf-nobfd0_2.43.1-4 libctf0_2.43.1-4 libcurl3t64-gnutls_8.10.0-2 libcurl4-gnutls-dev_8.10.0-2 libdb5.3t64_5.3.28+dfsg2-7 libdebconfclient0_0.272 libdebhelper-perl_13.20 libdeflate-dev_1.21-1 libdeflate0_1.21-1 libdpkg-perl_1.22.11 libeatmydata1_131-2 libelf1t64_0.191-2 libevent-2.1-7t64_2.1.12-stable-10 libfakeroot_1.36-1 libffi8_3.4.6-1 libfile-stripnondeterminism-perl_1.14.0-1 libgcc-13-dev_13.3.0-6 libgcc-14-dev_14.2.0-4 libgcc-s1_14.2.0-4 libgcrypt20_1.11.0-6 libgdbm-compat4t64_1.24-2 libgdbm6t64_1.24-2 libgmp-dev_2:6.3.0+dfsg-2+b1 libgmp10_2:6.3.0+dfsg-2+b1 libgmpxx4ldbl_2:6.3.0+dfsg-2+b1 libgnutls-dane0t64_3.8.6-2 libgnutls-openssl27t64_3.8.6-2 libgnutls28-dev_3.8.6-2 libgnutls30t64_3.8.6-2 libgomp1_14.2.0-4 libgpg-error0_1.50-3 libgprofng0_2.43.1-4 libgsl-dev_2.8+dfsg-3 libgsl28_2.8+dfsg-3 libgslcblas0_2.8+dfsg-3 libgssapi-krb5-2_1.21.3-3 libhogweed6t64_3.10-1 libhts-dev_1.20+ds-1 libhts3t64_1.20+ds-1 libhtscodecs2_1.6.1-1 libhwasan0_14.2.0-4 libicu72_72.1-5 libidn2-0_2.3.7-2 libidn2-dev_2.3.7-2 libio-pty-perl_1:1.20-1+b2 libisl23_0.27-1 libitm1_14.2.0-4 libjansson4_2.14-2+b2 libk5crypto3_1.21.3-3 libkeyutils1_1.6.3-3 libkrb5-3_1.21.3-3 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libsasl2-modules-db_2.1.28+dfsg1-8 libseccomp2_2.5.5-1+b1 libselinux1_3.7-3 libsemanage-common_3.7-2 libsemanage2_3.7-2 libsepol2_3.7-1 libsframe1_2.43.1-4 libsmartcols1_2.40.2-8 libsqlite3-0_3.46.1-1 libssh2-1-dev_1.11.0-7 libssh2-1t64_1.11.0-7 libssl-dev_3.3.2-1 libssl3t64_3.3.2-1 libstdc++-13-dev_13.3.0-6 libstdc++-14-dev_14.2.0-4 libstdc++6_14.2.0-4 libsystemd0_256.6-1 libtasn1-6_4.19.0-3+b2 libtasn1-6-dev_4.19.0-3+b2 libtinfo6_6.5-2 libtool_2.4.7-7 libtsan2_14.2.0-4 libubsan1_14.2.0-4 libuchardet0_0.0.8-1+b1 libudev1_256.6-1 libunbound8_1.20.0-1+b1 libunistring5_1.2-1 libuuid1_2.40.2-8 libxml2_2.12.7+dfsg-3+b1 libxxhash0_0.8.2-2+b1 libzstd-dev_1.5.6+dfsg-1 libzstd1_1.5.6+dfsg-1 linux-libc-dev_6.10.9-1 locales-all_2.40-2 login_1:4.16.0-2+really2.40.2-8 login.defs_1:4.16.0-4 m4_1.4.19-4 make_4.3-4.1 man-db_2.13.0-1 mawk_1.3.4.20240905-1 ncurses-base_6.5-2 ncurses-bin_6.5-2 nettle-dev_3.10-1 openssl-provider-legacy_3.3.2-1 passwd_1:4.16.0-4 patch_2.7.6-7 perl_5.40.0-5 perl-base_5.40.0-5 perl-modules-5.38_5.38.2-5 perl-modules-5.40_5.40.0-5 pinentry-curses_1.2.1-4+b1 pkgconf_1.8.1-3 pkgconf-bin_1.8.1-3 po-debconf_1.0.21+nmu1 readline-common_8.2-5 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_3.10-2 tabix_1.20+ds-1 tar_1.35+dfsg-3 usr-is-merged_39 util-linux_2.40.2-8 xz-utils_5.6.2-2 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-3ce48c2a-ec26-4164-b7de-c15562d45cf7 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 gcc option to enable large file support... none needed checking for htslib/sam.h... yes checking for hts_version in -lhts... yes checking shared library type... plain .so checking for library containing dlopen... none required checking if the compiler accepts -rdynamic... yes checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing regcomp... none required configure: creating ./config.status config.status: creating config.mk config.status: creating config.h make[1]: Leaving directory '/<>' 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 -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 vcfconcat.o vcfconcat.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 vcfcall.o vcfcall.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 mcall.o mcall.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 vcmp.o vcmp.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 gvcf.o gvcf.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 reheader.o reheader.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 convert.o convert.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 vcfconvert.o vcfconvert.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 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/ZSh03_bFL4/merge.a.vcf.gz 2:3199812-3199812 .. ok test_tabix: /<>/bcftools view -H /tmp/ZSh03_bFL4/merge.a.bcf 2:3199812-3199812 .. ok test_tabix: tabix /tmp/ZSh03_bFL4/merge.a.vcf.gz 1:3000151-3000151 .. ok test_tabix: /<>/bcftools view -H /tmp/ZSh03_bFL4/merge.a.bcf 1:3000151-3000151 .. ok test_index: /<>/bcftools view -H /tmp/ZSh03_bFL4/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/ZSh03_bFL4/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/ZSh03_bFL4/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/ZSh03_bFL4/large_chrom_csi_limit.vcf.gz chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/ZSh03_bFL4/large_chrom_csi_limit.bcf chr20:1-2147483647 .. ok test_index: /<>/bcftools view -H /tmp/ZSh03_bFL4/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /<>/bcftools view -H /tmp/ZSh03_bFL4/large_chrom_csi_limit.bcf chr20 .. ok test_index: /<>/bcftools view -H /tmp/ZSh03_bFL4/large_chrom_csi_limit.bcf chr20 .. ok test_index: /<>/bcftools view -H /tmp/ZSh03_bFL4/large_chrom_csi_limit.vcf.gz chr20 .. ok test_index: /<>/bcftools view -H /tmp/ZSh03_bFL4/large_chrom_csi_limit.bcf chr20 .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/ZSh03_bFL4/idx.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/ZSh03_bFL4/idx.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/ZSh03_bFL4/idx.bcf .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/ZSh03_bFL4/idx.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/ZSh03_bFL4/idx.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/ZSh03_bFL4/idx.vcf.gz.csi .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/ZSh03_bFL4/idx.bcf .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/ZSh03_bFL4/idx.bcf.csi .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/ZSh03_bFL4/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/ZSh03_bFL4/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -s /tmp/ZSh03_bFL4/empty.bcf .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/ZSh03_bFL4/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/ZSh03_bFL4/empty.vcf.gz .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/ZSh03_bFL4/empty.vcf.gz.csi .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/ZSh03_bFL4/empty.bcf .. ok test_vcf_idxstats: /<>/bcftools index -n /tmp/ZSh03_bFL4/empty.bcf.csi .. ok test_vcf_check: /<>/bcftools stats -s - /tmp/ZSh03_bFL4/check.vcf.gz | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID ' .. ok test_vcf_check: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/check.1.chk /tmp/ZSh03_bFL4/check.2.chk /tmp/ZSh03_bFL4/check.3.chk /tmp/ZSh03_bFL4/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/ZSh03_bFL4/stats.a.vcf.gz /tmp/ZSh03_bFL4/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /<>/bcftools stats -s B /tmp/ZSh03_bFL4/stats.a.vcf.gz /tmp/ZSh03_bFL4/stats.b.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /<>/bcftools stats -s - /tmp/ZSh03_bFL4/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /<>/bcftools stats -s - -i 'type="snp"' /tmp/ZSh03_bFL4/stats.counts.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_stats: /<>/bcftools stats -s - /tmp/ZSh03_bFL4/stats.vaf.vcf.gz | grep -v '^#' | grep -v '^ID ' .. ok test_vcf_isec: /<>/bcftools isec -n =2 /tmp/ZSh03_bFL4/isec.a.vcf.gz /tmp/ZSh03_bFL4/isec.b.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 /tmp/ZSh03_bFL4/isec.a.vcf.gz /tmp/ZSh03_bFL4/isec.b.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -n =2 -i"STRLEN(REF)==2" /tmp/ZSh03_bFL4/isec.a.vcf.gz /tmp/ZSh03_bFL4/isec.b.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 -i"STRLEN(REF)==2" /tmp/ZSh03_bFL4/isec.a.vcf.gz /tmp/ZSh03_bFL4/isec.b.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -n =2 -c both /tmp/ZSh03_bFL4/isec.a.vcf.gz /tmp/ZSh03_bFL4/isec.b.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 -c both /tmp/ZSh03_bFL4/isec.a.vcf.gz /tmp/ZSh03_bFL4/isec.b.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -n =2 -c any /tmp/ZSh03_bFL4/isec.a.vcf.gz /tmp/ZSh03_bFL4/isec.b.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -Ob -n =2 -c any /tmp/ZSh03_bFL4/isec.a.vcf.gz /tmp/ZSh03_bFL4/isec.b.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -C -c any /tmp/ZSh03_bFL4/isec.a.vcf.gz /tmp/ZSh03_bFL4/isec.b.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -Ob -C -c any /tmp/ZSh03_bFL4/isec.a.vcf.gz /tmp/ZSh03_bFL4/isec.b.vcf.gz .. ok test_vcf_isec2: /<>/bcftools isec --no-version -T /tmp/ZSh03_bFL4/isec.tab.gz /tmp/ZSh03_bFL4/isec.a.vcf.gz .. ok test_vcf_isec2: /<>/bcftools isec -Ob -T /tmp/ZSh03_bFL4/isec.tab.gz /tmp/ZSh03_bFL4/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/ZSh03_bFL4/isec-miss.1.1.vcf.gz /tmp/ZSh03_bFL4/isec-miss.1.2.vcf.gz /tmp/ZSh03_bFL4/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/ZSh03_bFL4/isec-miss.1.1.vcf.gz /tmp/ZSh03_bFL4/isec-miss.1.2.vcf.gz /tmp/ZSh03_bFL4/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -R /<>/test/isec-miss.1.regs.txt -n +1 /tmp/ZSh03_bFL4/isec-miss.1.1.vcf.gz /tmp/ZSh03_bFL4/isec-miss.1.2.vcf.gz /tmp/ZSh03_bFL4/isec-miss.1.3.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -Ob -R /<>/test/isec-miss.1.regs.txt -n +1 /tmp/ZSh03_bFL4/isec-miss.1.1.vcf.gz /tmp/ZSh03_bFL4/isec-miss.1.2.vcf.gz /tmp/ZSh03_bFL4/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/ZSh03_bFL4/isec-miss.2.1.vcf.gz /tmp/ZSh03_bFL4/isec-miss.2.2.vcf.gz /tmp/ZSh03_bFL4/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/ZSh03_bFL4/isec-miss.2.1.vcf.gz /tmp/ZSh03_bFL4/isec-miss.2.2.vcf.gz /tmp/ZSh03_bFL4/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -R /<>/test/isec-miss.1.regs.txt -n +1 /tmp/ZSh03_bFL4/isec-miss.2.1.vcf.gz /tmp/ZSh03_bFL4/isec-miss.2.2.vcf.gz /tmp/ZSh03_bFL4/isec-miss.2.3.vcf.gz .. ok test_vcf_isec: /<>/bcftools isec -Ob -R /<>/test/isec-miss.1.regs.txt -n +1 /tmp/ZSh03_bFL4/isec-miss.2.1.vcf.gz /tmp/ZSh03_bFL4/isec-miss.2.2.vcf.gz /tmp/ZSh03_bFL4/isec-miss.2.3.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -i AF:join /tmp/ZSh03_bFL4/merge.join.a.vcf.gz /tmp/ZSh03_bFL4/merge.join.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob -i AF:join /tmp/ZSh03_bFL4/merge.join.a.vcf.gz /tmp/ZSh03_bFL4/merge.join.b.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version -i AF:join /tmp/ZSh03_bFL4/merge.join.a.bcf /tmp/ZSh03_bFL4/merge.join.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob -i AF:join /tmp/ZSh03_bFL4/merge.join.a.bcf /tmp/ZSh03_bFL4/merge.join.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-single /tmp/ZSh03_bFL4/merge.LPL.a.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-single /tmp/ZSh03_bFL4/merge.LPL.a.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-single /tmp/ZSh03_bFL4/merge.LPL.a.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-single /tmp/ZSh03_bFL4/merge.LPL.a.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples /tmp/ZSh03_bFL4/merge.LPL.a.vcf.gz /tmp/ZSh03_bFL4/merge.LPL.b.vcf.gz /tmp/ZSh03_bFL4/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples /tmp/ZSh03_bFL4/merge.LPL.a.vcf.gz /tmp/ZSh03_bFL4/merge.LPL.b.vcf.gz /tmp/ZSh03_bFL4/merge.LPL.c.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples /tmp/ZSh03_bFL4/merge.LPL.a.bcf /tmp/ZSh03_bFL4/merge.LPL.b.bcf /tmp/ZSh03_bFL4/merge.LPL.c.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples /tmp/ZSh03_bFL4/merge.LPL.a.bcf /tmp/ZSh03_bFL4/merge.LPL.b.bcf /tmp/ZSh03_bFL4/merge.LPL.c.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -L 1 /tmp/ZSh03_bFL4/merge.LPL.a.vcf.gz /tmp/ZSh03_bFL4/merge.LPL.b.vcf.gz /tmp/ZSh03_bFL4/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -L 1 /tmp/ZSh03_bFL4/merge.LPL.a.vcf.gz /tmp/ZSh03_bFL4/merge.LPL.b.vcf.gz /tmp/ZSh03_bFL4/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/ZSh03_bFL4/merge.LPL.a.bcf /tmp/ZSh03_bFL4/merge.LPL.b.bcf /tmp/ZSh03_bFL4/merge.LPL.c.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -L 1 /tmp/ZSh03_bFL4/merge.LPL.a.bcf /tmp/ZSh03_bFL4/merge.LPL.b.bcf /tmp/ZSh03_bFL4/merge.LPL.c.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -L 2 /tmp/ZSh03_bFL4/merge.LPL.a.vcf.gz /tmp/ZSh03_bFL4/merge.LPL.b.vcf.gz /tmp/ZSh03_bFL4/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -L 2 /tmp/ZSh03_bFL4/merge.LPL.a.vcf.gz /tmp/ZSh03_bFL4/merge.LPL.b.vcf.gz /tmp/ZSh03_bFL4/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/ZSh03_bFL4/merge.LPL.a.bcf /tmp/ZSh03_bFL4/merge.LPL.b.bcf /tmp/ZSh03_bFL4/merge.LPL.c.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -L 2 /tmp/ZSh03_bFL4/merge.LPL.a.bcf /tmp/ZSh03_bFL4/merge.LPL.b.bcf /tmp/ZSh03_bFL4/merge.LPL.c.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -L 3 /tmp/ZSh03_bFL4/merge.LPL.a.vcf.gz /tmp/ZSh03_bFL4/merge.LPL.b.vcf.gz /tmp/ZSh03_bFL4/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -L 3 /tmp/ZSh03_bFL4/merge.LPL.a.vcf.gz /tmp/ZSh03_bFL4/merge.LPL.b.vcf.gz /tmp/ZSh03_bFL4/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/ZSh03_bFL4/merge.LPL.a.bcf /tmp/ZSh03_bFL4/merge.LPL.b.bcf /tmp/ZSh03_bFL4/merge.LPL.c.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -L 3 /tmp/ZSh03_bFL4/merge.LPL.a.bcf /tmp/ZSh03_bFL4/merge.LPL.b.bcf /tmp/ZSh03_bFL4/merge.LPL.c.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -L 4 /tmp/ZSh03_bFL4/merge.LPL.a.vcf.gz /tmp/ZSh03_bFL4/merge.LPL.b.vcf.gz /tmp/ZSh03_bFL4/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -L 4 /tmp/ZSh03_bFL4/merge.LPL.a.vcf.gz /tmp/ZSh03_bFL4/merge.LPL.b.vcf.gz /tmp/ZSh03_bFL4/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/ZSh03_bFL4/merge.LPL.a.bcf /tmp/ZSh03_bFL4/merge.LPL.b.bcf /tmp/ZSh03_bFL4/merge.LPL.c.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -L 4 /tmp/ZSh03_bFL4/merge.LPL.a.bcf /tmp/ZSh03_bFL4/merge.LPL.b.bcf /tmp/ZSh03_bFL4/merge.LPL.c.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -L 5 /tmp/ZSh03_bFL4/merge.LPL.a.vcf.gz /tmp/ZSh03_bFL4/merge.LPL.b.vcf.gz /tmp/ZSh03_bFL4/merge.LPL.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -L 5 /tmp/ZSh03_bFL4/merge.LPL.a.vcf.gz /tmp/ZSh03_bFL4/merge.LPL.b.vcf.gz /tmp/ZSh03_bFL4/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/ZSh03_bFL4/merge.LPL.a.bcf /tmp/ZSh03_bFL4/merge.LPL.b.bcf /tmp/ZSh03_bFL4/merge.LPL.c.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -L 5 /tmp/ZSh03_bFL4/merge.LPL.a.bcf /tmp/ZSh03_bFL4/merge.LPL.b.bcf /tmp/ZSh03_bFL4/merge.LPL.c.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples /tmp/ZSh03_bFL4/merge.a.vcf.gz /tmp/ZSh03_bFL4/merge.b.vcf.gz /tmp/ZSh03_bFL4/merge.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples /tmp/ZSh03_bFL4/merge.a.vcf.gz /tmp/ZSh03_bFL4/merge.b.vcf.gz /tmp/ZSh03_bFL4/merge.c.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples /tmp/ZSh03_bFL4/merge.a.bcf /tmp/ZSh03_bFL4/merge.b.bcf /tmp/ZSh03_bFL4/merge.c.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples /tmp/ZSh03_bFL4/merge.a.bcf /tmp/ZSh03_bFL4/merge.b.bcf /tmp/ZSh03_bFL4/merge.c.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -Fx /tmp/ZSh03_bFL4/merge.a.vcf.gz /tmp/ZSh03_bFL4/merge.b.vcf.gz /tmp/ZSh03_bFL4/merge.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -Fx /tmp/ZSh03_bFL4/merge.a.vcf.gz /tmp/ZSh03_bFL4/merge.b.vcf.gz /tmp/ZSh03_bFL4/merge.c.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -Fx /tmp/ZSh03_bFL4/merge.a.bcf /tmp/ZSh03_bFL4/merge.b.bcf /tmp/ZSh03_bFL4/merge.c.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -Fx /tmp/ZSh03_bFL4/merge.a.bcf /tmp/ZSh03_bFL4/merge.b.bcf /tmp/ZSh03_bFL4/merge.c.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -0 /tmp/ZSh03_bFL4/merge.a.vcf.gz /tmp/ZSh03_bFL4/merge.b.vcf.gz /tmp/ZSh03_bFL4/merge.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -0 /tmp/ZSh03_bFL4/merge.a.vcf.gz /tmp/ZSh03_bFL4/merge.b.vcf.gz /tmp/ZSh03_bFL4/merge.c.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -0 /tmp/ZSh03_bFL4/merge.a.bcf /tmp/ZSh03_bFL4/merge.b.bcf /tmp/ZSh03_bFL4/merge.c.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -0 /tmp/ZSh03_bFL4/merge.a.bcf /tmp/ZSh03_bFL4/merge.b.bcf /tmp/ZSh03_bFL4/merge.c.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -m none /tmp/ZSh03_bFL4/merge.2.a.vcf.gz /tmp/ZSh03_bFL4/merge.2.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -m none /tmp/ZSh03_bFL4/merge.2.a.vcf.gz /tmp/ZSh03_bFL4/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/ZSh03_bFL4/merge.2.a.bcf /tmp/ZSh03_bFL4/merge.2.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -m none /tmp/ZSh03_bFL4/merge.2.a.bcf /tmp/ZSh03_bFL4/merge.2.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -m both /tmp/ZSh03_bFL4/merge.2.a.vcf.gz /tmp/ZSh03_bFL4/merge.2.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -m both /tmp/ZSh03_bFL4/merge.2.a.vcf.gz /tmp/ZSh03_bFL4/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/ZSh03_bFL4/merge.2.a.bcf /tmp/ZSh03_bFL4/merge.2.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -m both /tmp/ZSh03_bFL4/merge.2.a.bcf /tmp/ZSh03_bFL4/merge.2.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -m all /tmp/ZSh03_bFL4/merge.2.a.vcf.gz /tmp/ZSh03_bFL4/merge.2.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -m all /tmp/ZSh03_bFL4/merge.2.a.vcf.gz /tmp/ZSh03_bFL4/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/ZSh03_bFL4/merge.2.a.bcf /tmp/ZSh03_bFL4/merge.2.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -m all /tmp/ZSh03_bFL4/merge.2.a.bcf /tmp/ZSh03_bFL4/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/ZSh03_bFL4/merge.3.a.vcf.gz /tmp/ZSh03_bFL4/merge.3.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/ZSh03_bFL4/merge.3.a.vcf.gz /tmp/ZSh03_bFL4/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/ZSh03_bFL4/merge.3.a.bcf /tmp/ZSh03_bFL4/merge.3.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -i TR:sum,TA:sum,TG:sum /tmp/ZSh03_bFL4/merge.3.a.bcf /tmp/ZSh03_bFL4/merge.3.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples -m id /tmp/ZSh03_bFL4/merge.4.a.vcf.gz /tmp/ZSh03_bFL4/merge.4.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -m id /tmp/ZSh03_bFL4/merge.4.a.vcf.gz /tmp/ZSh03_bFL4/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/ZSh03_bFL4/merge.4.a.bcf /tmp/ZSh03_bFL4/merge.4.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples -m id /tmp/ZSh03_bFL4/merge.4.a.bcf /tmp/ZSh03_bFL4/merge.4.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/ZSh03_bFL4/gvcf.merge.1.vcf.gz /tmp/ZSh03_bFL4/gvcf.merge.2.vcf.gz /tmp/ZSh03_bFL4/gvcf.merge.3.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - /tmp/ZSh03_bFL4/gvcf.merge.1.vcf.gz /tmp/ZSh03_bFL4/gvcf.merge.2.vcf.gz /tmp/ZSh03_bFL4/gvcf.merge.3.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/ZSh03_bFL4/gvcf.merge.1.bcf /tmp/ZSh03_bFL4/gvcf.merge.2.bcf /tmp/ZSh03_bFL4/gvcf.merge.3.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - /tmp/ZSh03_bFL4/gvcf.merge.1.bcf /tmp/ZSh03_bFL4/gvcf.merge.2.bcf /tmp/ZSh03_bFL4/gvcf.merge.3.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/ZSh03_bFL4/merge.gvcf.2.a.vcf.gz /tmp/ZSh03_bFL4/merge.gvcf.2.b.vcf.gz /tmp/ZSh03_bFL4/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - /tmp/ZSh03_bFL4/merge.gvcf.2.a.vcf.gz /tmp/ZSh03_bFL4/merge.gvcf.2.b.vcf.gz /tmp/ZSh03_bFL4/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/ZSh03_bFL4/merge.gvcf.2.a.vcf.gz /tmp/ZSh03_bFL4/merge.gvcf.2.b.vcf.gz /tmp/ZSh03_bFL4/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - -m both,* /tmp/ZSh03_bFL4/merge.gvcf.2.a.vcf.gz /tmp/ZSh03_bFL4/merge.gvcf.2.b.vcf.gz /tmp/ZSh03_bFL4/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/ZSh03_bFL4/merge.gvcf.2.a.vcf.gz /tmp/ZSh03_bFL4/merge.gvcf.2.b.vcf.gz /tmp/ZSh03_bFL4/merge.gvcf.2.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - -m both,** /tmp/ZSh03_bFL4/merge.gvcf.2.a.vcf.gz /tmp/ZSh03_bFL4/merge.gvcf.2.b.vcf.gz /tmp/ZSh03_bFL4/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/ZSh03_bFL4/merge.gvcf.3.a.vcf.gz /tmp/ZSh03_bFL4/merge.gvcf.3.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - -i SRC:join /tmp/ZSh03_bFL4/merge.gvcf.3.a.vcf.gz /tmp/ZSh03_bFL4/merge.gvcf.3.b.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/ZSh03_bFL4/merge.gvcf.4.a.vcf.gz /tmp/ZSh03_bFL4/merge.gvcf.4.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - /tmp/ZSh03_bFL4/merge.gvcf.4.a.vcf.gz /tmp/ZSh03_bFL4/merge.gvcf.4.b.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/ZSh03_bFL4/merge.gvcf.4.a.bcf /tmp/ZSh03_bFL4/merge.gvcf.4.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - /tmp/ZSh03_bFL4/merge.gvcf.4.a.bcf /tmp/ZSh03_bFL4/merge.gvcf.4.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version /tmp/ZSh03_bFL4/merge.5.a.vcf.gz /tmp/ZSh03_bFL4/merge.5.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob /tmp/ZSh03_bFL4/merge.5.a.vcf.gz /tmp/ZSh03_bFL4/merge.5.b.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version /tmp/ZSh03_bFL4/merge.5.a.bcf /tmp/ZSh03_bFL4/merge.5.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob /tmp/ZSh03_bFL4/merge.5.a.bcf /tmp/ZSh03_bFL4/merge.5.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version /tmp/ZSh03_bFL4/merge.6.a.vcf.gz /tmp/ZSh03_bFL4/merge.6.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob /tmp/ZSh03_bFL4/merge.6.a.vcf.gz /tmp/ZSh03_bFL4/merge.6.b.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version /tmp/ZSh03_bFL4/merge.6.a.bcf /tmp/ZSh03_bFL4/merge.6.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob /tmp/ZSh03_bFL4/merge.6.a.bcf /tmp/ZSh03_bFL4/merge.6.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/ZSh03_bFL4/merge.gvcf.7.a.vcf.gz /tmp/ZSh03_bFL4/merge.gvcf.7.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - /tmp/ZSh03_bFL4/merge.gvcf.7.a.vcf.gz /tmp/ZSh03_bFL4/merge.gvcf.7.b.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/ZSh03_bFL4/merge.gvcf.7.a.bcf /tmp/ZSh03_bFL4/merge.gvcf.7.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - /tmp/ZSh03_bFL4/merge.gvcf.7.a.bcf /tmp/ZSh03_bFL4/merge.gvcf.7.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/ZSh03_bFL4/merge.gvcf.8.a.vcf.gz /tmp/ZSh03_bFL4/merge.gvcf.8.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - /tmp/ZSh03_bFL4/merge.gvcf.8.a.vcf.gz /tmp/ZSh03_bFL4/merge.gvcf.8.b.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/ZSh03_bFL4/merge.gvcf.8.a.bcf /tmp/ZSh03_bFL4/merge.gvcf.8.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - /tmp/ZSh03_bFL4/merge.gvcf.8.a.bcf /tmp/ZSh03_bFL4/merge.gvcf.8.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples /tmp/ZSh03_bFL4/merge.7.a.vcf.gz /tmp/ZSh03_bFL4/merge.7.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples /tmp/ZSh03_bFL4/merge.7.a.vcf.gz /tmp/ZSh03_bFL4/merge.7.b.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --force-samples /tmp/ZSh03_bFL4/merge.7.a.bcf /tmp/ZSh03_bFL4/merge.7.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --force-samples /tmp/ZSh03_bFL4/merge.7.a.bcf /tmp/ZSh03_bFL4/merge.7.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf /<>/test/gvcf.fa /tmp/ZSh03_bFL4/merge.gvcf.9a.vcf.gz /tmp/ZSh03_bFL4/merge.gvcf.9b.vcf.gz /tmp/ZSh03_bFL4/merge.gvcf.9c.vcf.gz /tmp/ZSh03_bFL4/merge.gvcf.9d.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf /<>/test/gvcf.fa /tmp/ZSh03_bFL4/merge.gvcf.9a.vcf.gz /tmp/ZSh03_bFL4/merge.gvcf.9b.vcf.gz /tmp/ZSh03_bFL4/merge.gvcf.9c.vcf.gz /tmp/ZSh03_bFL4/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/ZSh03_bFL4/merge.gvcf.9a.bcf /tmp/ZSh03_bFL4/merge.gvcf.9b.bcf /tmp/ZSh03_bFL4/merge.gvcf.9c.bcf /tmp/ZSh03_bFL4/merge.gvcf.9d.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf /<>/test/gvcf.fa /tmp/ZSh03_bFL4/merge.gvcf.9a.bcf /tmp/ZSh03_bFL4/merge.gvcf.9b.bcf /tmp/ZSh03_bFL4/merge.gvcf.9c.bcf /tmp/ZSh03_bFL4/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/ZSh03_bFL4/merge.gvcf.9a.vcf.gz /tmp/ZSh03_bFL4/merge.gvcf.9b.vcf.gz /tmp/ZSh03_bFL4/merge.gvcf.9c.vcf.gz /tmp/ZSh03_bFL4/merge.gvcf.9d.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf /<>/test/gvcf.fa -r 22:21-23 /tmp/ZSh03_bFL4/merge.gvcf.9a.vcf.gz /tmp/ZSh03_bFL4/merge.gvcf.9b.vcf.gz /tmp/ZSh03_bFL4/merge.gvcf.9c.vcf.gz /tmp/ZSh03_bFL4/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/ZSh03_bFL4/merge.gvcf.9a.bcf /tmp/ZSh03_bFL4/merge.gvcf.9b.bcf /tmp/ZSh03_bFL4/merge.gvcf.9c.bcf /tmp/ZSh03_bFL4/merge.gvcf.9d.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf /<>/test/gvcf.fa -r 22:21-23 /tmp/ZSh03_bFL4/merge.gvcf.9a.bcf /tmp/ZSh03_bFL4/merge.gvcf.9b.bcf /tmp/ZSh03_bFL4/merge.gvcf.9c.bcf /tmp/ZSh03_bFL4/merge.gvcf.9d.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf /<>/test/gvcf.fa /tmp/ZSh03_bFL4/merge.gvcf.9a.vcf.gz /tmp/ZSh03_bFL4/merge.gvcf.9b.vcf.gz /tmp/ZSh03_bFL4/merge.gvcf.9c.vcf.gz /tmp/ZSh03_bFL4/merge.gvcf.9d.vcf.gz /tmp/ZSh03_bFL4/merge.gvcf.9e.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf /<>/test/gvcf.fa /tmp/ZSh03_bFL4/merge.gvcf.9a.vcf.gz /tmp/ZSh03_bFL4/merge.gvcf.9b.vcf.gz /tmp/ZSh03_bFL4/merge.gvcf.9c.vcf.gz /tmp/ZSh03_bFL4/merge.gvcf.9d.vcf.gz /tmp/ZSh03_bFL4/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/ZSh03_bFL4/merge.gvcf.9a.bcf /tmp/ZSh03_bFL4/merge.gvcf.9b.bcf /tmp/ZSh03_bFL4/merge.gvcf.9c.bcf /tmp/ZSh03_bFL4/merge.gvcf.9d.bcf /tmp/ZSh03_bFL4/merge.gvcf.9e.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf /<>/test/gvcf.fa /tmp/ZSh03_bFL4/merge.gvcf.9a.bcf /tmp/ZSh03_bFL4/merge.gvcf.9b.bcf /tmp/ZSh03_bFL4/merge.gvcf.9c.bcf /tmp/ZSh03_bFL4/merge.gvcf.9d.bcf /tmp/ZSh03_bFL4/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/ZSh03_bFL4/merge.gvcf.9a.vcf.gz /tmp/ZSh03_bFL4/merge.gvcf.9b.vcf.gz /tmp/ZSh03_bFL4/merge.gvcf.9c.vcf.gz /tmp/ZSh03_bFL4/merge.gvcf.9d.vcf.gz /tmp/ZSh03_bFL4/merge.gvcf.9e.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf /<>/test/gvcf.fa -r 22:21-23 /tmp/ZSh03_bFL4/merge.gvcf.9a.vcf.gz /tmp/ZSh03_bFL4/merge.gvcf.9b.vcf.gz /tmp/ZSh03_bFL4/merge.gvcf.9c.vcf.gz /tmp/ZSh03_bFL4/merge.gvcf.9d.vcf.gz /tmp/ZSh03_bFL4/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/ZSh03_bFL4/merge.gvcf.9a.bcf /tmp/ZSh03_bFL4/merge.gvcf.9b.bcf /tmp/ZSh03_bFL4/merge.gvcf.9c.bcf /tmp/ZSh03_bFL4/merge.gvcf.9d.bcf /tmp/ZSh03_bFL4/merge.gvcf.9e.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf /<>/test/gvcf.fa -r 22:21-23 /tmp/ZSh03_bFL4/merge.gvcf.9a.bcf /tmp/ZSh03_bFL4/merge.gvcf.9b.bcf /tmp/ZSh03_bFL4/merge.gvcf.9c.bcf /tmp/ZSh03_bFL4/merge.gvcf.9d.bcf /tmp/ZSh03_bFL4/merge.gvcf.9e.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version /tmp/ZSh03_bFL4/merge.gvcf.10.a.vcf.gz /tmp/ZSh03_bFL4/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob /tmp/ZSh03_bFL4/merge.gvcf.10.a.vcf.gz /tmp/ZSh03_bFL4/merge.gvcf.10.b.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version /tmp/ZSh03_bFL4/merge.gvcf.10.a.bcf /tmp/ZSh03_bFL4/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob /tmp/ZSh03_bFL4/merge.gvcf.10.a.bcf /tmp/ZSh03_bFL4/merge.gvcf.10.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version -m none /tmp/ZSh03_bFL4/merge.gvcf.10.a.vcf.gz /tmp/ZSh03_bFL4/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob -m none /tmp/ZSh03_bFL4/merge.gvcf.10.a.vcf.gz /tmp/ZSh03_bFL4/merge.gvcf.10.b.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version -m none /tmp/ZSh03_bFL4/merge.gvcf.10.a.bcf /tmp/ZSh03_bFL4/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob -m none /tmp/ZSh03_bFL4/merge.gvcf.10.a.bcf /tmp/ZSh03_bFL4/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/ZSh03_bFL4/merge.gvcf.10.a.vcf.gz /tmp/ZSh03_bFL4/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob -g /<>/test/merge.gvcf.10.fa /tmp/ZSh03_bFL4/merge.gvcf.10.a.vcf.gz /tmp/ZSh03_bFL4/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/ZSh03_bFL4/merge.gvcf.10.a.bcf /tmp/ZSh03_bFL4/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob -g /<>/test/merge.gvcf.10.fa /tmp/ZSh03_bFL4/merge.gvcf.10.a.bcf /tmp/ZSh03_bFL4/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/ZSh03_bFL4/merge.gvcf.10.a.vcf.gz /tmp/ZSh03_bFL4/merge.gvcf.10.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob -g /<>/test/merge.gvcf.10.fa -m none /tmp/ZSh03_bFL4/merge.gvcf.10.a.vcf.gz /tmp/ZSh03_bFL4/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/ZSh03_bFL4/merge.gvcf.10.a.bcf /tmp/ZSh03_bFL4/merge.gvcf.10.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob -g /<>/test/merge.gvcf.10.fa -m none /tmp/ZSh03_bFL4/merge.gvcf.10.a.bcf /tmp/ZSh03_bFL4/merge.gvcf.10.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version /tmp/ZSh03_bFL4/merge.noidx.a.vcf.gz /tmp/ZSh03_bFL4/merge.noidx.b.vcf.gz /tmp/ZSh03_bFL4/merge.noidx.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob /tmp/ZSh03_bFL4/merge.noidx.a.vcf.gz /tmp/ZSh03_bFL4/merge.noidx.b.vcf.gz /tmp/ZSh03_bFL4/merge.noidx.c.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version /tmp/ZSh03_bFL4/merge.noidx.a.bcf /tmp/ZSh03_bFL4/merge.noidx.b.bcf /tmp/ZSh03_bFL4/merge.noidx.c.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob /tmp/ZSh03_bFL4/merge.noidx.a.bcf /tmp/ZSh03_bFL4/merge.noidx.b.bcf /tmp/ZSh03_bFL4/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/ZSh03_bFL4/merge.noidx.a.bcf /tmp/ZSh03_bFL4/merge.noidx.b.bcf /tmp/ZSh03_bFL4/merge.noidx.c.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --no-index /tmp/ZSh03_bFL4/merge.noidx.a.bcf /tmp/ZSh03_bFL4/merge.noidx.b.bcf /tmp/ZSh03_bFL4/merge.noidx.c.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version /tmp/ZSh03_bFL4/merge.8.a.vcf.gz /tmp/ZSh03_bFL4/merge.8.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob /tmp/ZSh03_bFL4/merge.8.a.vcf.gz /tmp/ZSh03_bFL4/merge.8.b.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version /tmp/ZSh03_bFL4/merge.8.a.bcf /tmp/ZSh03_bFL4/merge.8.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob /tmp/ZSh03_bFL4/merge.8.a.bcf /tmp/ZSh03_bFL4/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/ZSh03_bFL4/merge.8.a.vcf.gz /tmp/ZSh03_bFL4/merge.8.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/ZSh03_bFL4/merge.8.a.vcf.gz /tmp/ZSh03_bFL4/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/ZSh03_bFL4/merge.8.a.bcf /tmp/ZSh03_bFL4/merge.8.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/ZSh03_bFL4/merge.8.a.bcf /tmp/ZSh03_bFL4/merge.8.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version /tmp/ZSh03_bFL4/merge.9.a.vcf.gz /tmp/ZSh03_bFL4/merge.9.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob /tmp/ZSh03_bFL4/merge.9.a.vcf.gz /tmp/ZSh03_bFL4/merge.9.b.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version /tmp/ZSh03_bFL4/merge.9.a.bcf /tmp/ZSh03_bFL4/merge.9.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob /tmp/ZSh03_bFL4/merge.9.a.bcf /tmp/ZSh03_bFL4/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/ZSh03_bFL4/merge.9.a.vcf.gz /tmp/ZSh03_bFL4/merge.9.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/ZSh03_bFL4/merge.9.a.vcf.gz /tmp/ZSh03_bFL4/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/ZSh03_bFL4/merge.9.a.bcf /tmp/ZSh03_bFL4/merge.9.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob -i AN:sum,AC:sum /tmp/ZSh03_bFL4/merge.9.a.bcf /tmp/ZSh03_bFL4/merge.9.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version -m none /tmp/ZSh03_bFL4/merge.10.a.vcf.gz /tmp/ZSh03_bFL4/merge.10.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob -m none /tmp/ZSh03_bFL4/merge.10.a.vcf.gz /tmp/ZSh03_bFL4/merge.10.b.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version -m none /tmp/ZSh03_bFL4/merge.10.a.bcf /tmp/ZSh03_bFL4/merge.10.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob -m none /tmp/ZSh03_bFL4/merge.10.a.bcf /tmp/ZSh03_bFL4/merge.10.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version -m both /tmp/ZSh03_bFL4/merge.10.a.vcf.gz /tmp/ZSh03_bFL4/merge.10.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob -m both /tmp/ZSh03_bFL4/merge.10.a.vcf.gz /tmp/ZSh03_bFL4/merge.10.b.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version -m both /tmp/ZSh03_bFL4/merge.10.a.bcf /tmp/ZSh03_bFL4/merge.10.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob -m both /tmp/ZSh03_bFL4/merge.10.a.bcf /tmp/ZSh03_bFL4/merge.10.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version -m snp-ins-del /tmp/ZSh03_bFL4/merge.10.a.vcf.gz /tmp/ZSh03_bFL4/merge.10.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob -m snp-ins-del /tmp/ZSh03_bFL4/merge.10.a.vcf.gz /tmp/ZSh03_bFL4/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/ZSh03_bFL4/merge.10.a.bcf /tmp/ZSh03_bFL4/merge.10.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob -m snp-ins-del /tmp/ZSh03_bFL4/merge.10.a.bcf /tmp/ZSh03_bFL4/merge.10.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/ZSh03_bFL4/merge.mrules.1.a.vcf.gz /tmp/ZSh03_bFL4/merge.mrules.1.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - /tmp/ZSh03_bFL4/merge.mrules.1.a.vcf.gz /tmp/ZSh03_bFL4/merge.mrules.1.b.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/ZSh03_bFL4/merge.mrules.1.a.bcf /tmp/ZSh03_bFL4/merge.mrules.1.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - /tmp/ZSh03_bFL4/merge.mrules.1.a.bcf /tmp/ZSh03_bFL4/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/ZSh03_bFL4/merge.mrules.1.a.vcf.gz /tmp/ZSh03_bFL4/merge.mrules.1.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - -M AD:.,PL:. /tmp/ZSh03_bFL4/merge.mrules.1.a.vcf.gz /tmp/ZSh03_bFL4/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/ZSh03_bFL4/merge.mrules.1.a.bcf /tmp/ZSh03_bFL4/merge.mrules.1.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - -M AD:.,PL:. /tmp/ZSh03_bFL4/merge.mrules.1.a.bcf /tmp/ZSh03_bFL4/merge.mrules.1.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/ZSh03_bFL4/merge.gvcf.5.a.vcf.gz /tmp/ZSh03_bFL4/merge.gvcf.5.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - /tmp/ZSh03_bFL4/merge.gvcf.5.a.vcf.gz /tmp/ZSh03_bFL4/merge.gvcf.5.b.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/ZSh03_bFL4/merge.gvcf.5.a.bcf /tmp/ZSh03_bFL4/merge.gvcf.5.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - /tmp/ZSh03_bFL4/merge.gvcf.5.a.bcf /tmp/ZSh03_bFL4/merge.gvcf.5.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - --merge none /tmp/ZSh03_bFL4/merge.gvcf.5.a.vcf.gz /tmp/ZSh03_bFL4/merge.gvcf.5.b.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - --merge none /tmp/ZSh03_bFL4/merge.gvcf.5.a.vcf.gz /tmp/ZSh03_bFL4/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/ZSh03_bFL4/merge.gvcf.5.a.bcf /tmp/ZSh03_bFL4/merge.gvcf.5.b.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - --merge none /tmp/ZSh03_bFL4/merge.gvcf.5.a.bcf /tmp/ZSh03_bFL4/merge.gvcf.5.b.bcf | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/ZSh03_bFL4/merge.gvcf.11.a.vcf.gz /tmp/ZSh03_bFL4/merge.gvcf.11.b.vcf.gz /tmp/ZSh03_bFL4/merge.gvcf.11.c.vcf.gz .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - /tmp/ZSh03_bFL4/merge.gvcf.11.a.vcf.gz /tmp/ZSh03_bFL4/merge.gvcf.11.b.vcf.gz /tmp/ZSh03_bFL4/merge.gvcf.11.c.vcf.gz | /<>/bcftools view --no-version | grep -v ^##bcftools_ .. ok test_vcf_merge: /<>/bcftools merge --no-version --gvcf - /tmp/ZSh03_bFL4/merge.gvcf.11.a.bcf /tmp/ZSh03_bFL4/merge.gvcf.11.b.bcf /tmp/ZSh03_bFL4/merge.gvcf.11.c.bcf .. ok test_vcf_merge: /<>/bcftools merge --no-version -Ob --gvcf - /tmp/ZSh03_bFL4/merge.gvcf.11.a.bcf /tmp/ZSh03_bFL4/merge.gvcf.11.b.bcf /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.string.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.string.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.string.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.string.2.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.string.2.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.variantkey.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/query.variantkey.vcf.gz | /<>/bcftools query -f '%RSX\t%VKX\n' .. ok test_vcf_query: /<>/bcftools query -f'%XRI\n' -i'XRI[*]>1111' /tmp/ZSh03_bFL4/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/view.vectors.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.2.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/missing.vcf.gz | /<>/bcftools query -i'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /<>/bcftools query -i'IINT!="."' -f'%POS %IINT\n' /tmp/ZSh03_bFL4/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/missing.vcf.gz | /<>/bcftools query -i'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /<>/bcftools query -e'IINT!="."' -f'%POS %IINT\n' /tmp/ZSh03_bFL4/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/missing.vcf.gz | /<>/bcftools query -e'IINT!="."' -f'%POS %IINT\n' .. ok test_vcf_query: /<>/bcftools query -e'IINT="."' -f'%POS %IINT\n' /tmp/ZSh03_bFL4/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/missing.vcf.gz | /<>/bcftools query -e'IINT="."' -f'%POS %IINT\n' .. ok test_vcf_query: /<>/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' /tmp/ZSh03_bFL4/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/missing.vcf.gz | /<>/bcftools query -i'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /<>/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' /tmp/ZSh03_bFL4/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/missing.vcf.gz | /<>/bcftools query -i'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /<>/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' /tmp/ZSh03_bFL4/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/missing.vcf.gz | /<>/bcftools query -e'IFLT!="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /<>/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' /tmp/ZSh03_bFL4/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/missing.vcf.gz | /<>/bcftools query -e'IFLT="."' -f'%POS %IFLT\n' .. ok test_vcf_query: /<>/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' /tmp/ZSh03_bFL4/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/missing.vcf.gz | /<>/bcftools query -i'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /<>/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' /tmp/ZSh03_bFL4/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/missing.vcf.gz | /<>/bcftools query -i'ISTR!="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /<>/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' /tmp/ZSh03_bFL4/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/missing.vcf.gz | /<>/bcftools query -e'ISTR="."' -f'%POS %ISTR\n' .. ok test_vcf_query: /<>/bcftools query -e'ISTR!="."' -f'%POS %ISTR\n' /tmp/ZSh03_bFL4/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/filter.11.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/filter.11.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/filter.11.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/filter.11.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/filter.11.vcf.gz | /<>/bcftools query -i'FILTER!~"A"' -f'%POS %FILTER\n' .. ok test_vcf_query: /<>/bcftools query -f'%LINE' /tmp/ZSh03_bFL4/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/query.vcf.gz | /<>/bcftools query -f'%LINE' .. ok test_vcf_query: /<>/bcftools query -f'%POS\t%REF\t%ALT\n' -i'type="snp"' /tmp/ZSh03_bFL4/query.filter-type.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.filter-type.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.filter-type.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.filter-type.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.filter-type.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/filter-missing-floats.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/filter-missing-floats.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/missing.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.filter.2.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/filter.5.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/filter.5.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/view.filter.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.filter.3.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.filter.3.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.filter.3.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/filter.5.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.filter.4.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/view.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.filter.5.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.filter.5.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.filter.5.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.filter.5.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.filter.5.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.filter.5.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.gtidx.1.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.gtidx.1.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.gtidx.1.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.gtidx.1.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.gtidx.1.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.negative.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.negative.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.negative.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.negative.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.filter.11.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.filter.11.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.filter.11.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.filter.11.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.filter.6.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.filter.7.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.filter.7.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.filter.7.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.filter.7.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.filter.7.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.filter.7.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.filter.7.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.filter.7.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.filter.8.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.filter.8.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.filter.9.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.filter.9.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.filter.13.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.filter.10.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.filter.10.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.filter.12.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.filter.12.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.smpl.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.smpl.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.smpl.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.smpl.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.smpl.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.smpl.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.filter.id.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.filter.id.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/filter.12.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/filter.12.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/filter.12.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/filter.12.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/filter.12.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/filter.12.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/filter.10.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/filter.13.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.header.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.header.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.header.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.header.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.header.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.header.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.filter-or.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/query.filter-or.vcf.gz .. ok test_vcf_query: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/norm.vcf.gz -f /<>/test/norm.fa .. ok test_vcf_norm: /<>/bcftools norm --no-version -cx /tmp/ZSh03_bFL4/norm.vcf.gz -f /<>/test/norm.fa -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- /tmp/ZSh03_bFL4/norm.split.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- /tmp/ZSh03_bFL4/norm.split.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- /tmp/ZSh03_bFL4/norm.split.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- /tmp/ZSh03_bFL4/norm.split.2.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- --force /tmp/ZSh03_bFL4/norm.split.3.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- --force /tmp/ZSh03_bFL4/norm.split.3.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- /tmp/ZSh03_bFL4/norm.split.4.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- /tmp/ZSh03_bFL4/norm.split.4.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- --keep-sum AD /tmp/ZSh03_bFL4/norm.split.4.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- --keep-sum AD /tmp/ZSh03_bFL4/norm.split.4.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- /tmp/ZSh03_bFL4/norm.split.vcf.gz -f /<>/test/norm.fa .. ok test_vcf_norm: /<>/bcftools norm --no-version -m- /tmp/ZSh03_bFL4/norm.split.vcf.gz -f /<>/test/norm.fa -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m+ /tmp/ZSh03_bFL4/norm.merge.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -m+ /tmp/ZSh03_bFL4/norm.merge.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m+ /tmp/ZSh03_bFL4/norm.merge.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -m+ /tmp/ZSh03_bFL4/norm.merge.2.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m+ /tmp/ZSh03_bFL4/norm.merge.3.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -m+ /tmp/ZSh03_bFL4/norm.merge.3.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m+ -s /tmp/ZSh03_bFL4/norm.merge.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -m+ -s /tmp/ZSh03_bFL4/norm.merge.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -Nc s /tmp/ZSh03_bFL4/norm.setref.vcf.gz -f /<>/test/norm.fa .. ok test_vcf_norm: /<>/bcftools norm --no-version -Nc s /tmp/ZSh03_bFL4/norm.setref.vcf.gz -f /<>/test/norm.fa -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version /tmp/ZSh03_bFL4/norm.telomere.vcf.gz -f /<>/test/norm.fa .. ok test_vcf_norm: /<>/bcftools norm --no-version /tmp/ZSh03_bFL4/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/ZSh03_bFL4/norm.rmdup.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -d snps /tmp/ZSh03_bFL4/norm.rmdup.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d indels /tmp/ZSh03_bFL4/norm.rmdup.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -d indels /tmp/ZSh03_bFL4/norm.rmdup.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d both /tmp/ZSh03_bFL4/norm.rmdup.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -d both /tmp/ZSh03_bFL4/norm.rmdup.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d all /tmp/ZSh03_bFL4/norm.rmdup.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -d all /tmp/ZSh03_bFL4/norm.rmdup.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d none /tmp/ZSh03_bFL4/norm.rmdup.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -d none /tmp/ZSh03_bFL4/norm.rmdup.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d exact /tmp/ZSh03_bFL4/norm.rmdup.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -d exact /tmp/ZSh03_bFL4/norm.rmdup.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d none /tmp/ZSh03_bFL4/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -d none /tmp/ZSh03_bFL4/norm.rmdup.2.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d exact /tmp/ZSh03_bFL4/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -d exact /tmp/ZSh03_bFL4/norm.rmdup.2.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d indels /tmp/ZSh03_bFL4/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -d indels /tmp/ZSh03_bFL4/norm.rmdup.2.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d any /tmp/ZSh03_bFL4/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -d any /tmp/ZSh03_bFL4/norm.rmdup.2.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d both /tmp/ZSh03_bFL4/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -d both /tmp/ZSh03_bFL4/norm.rmdup.2.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -d snps /tmp/ZSh03_bFL4/norm.rmdup.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -d snps /tmp/ZSh03_bFL4/norm.rmdup.2.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -c s -a /tmp/ZSh03_bFL4/norm.2.vcf.gz -f /<>/test/norm.2.fa .. ok test_vcf_norm: /<>/bcftools norm --no-version -c s -a /tmp/ZSh03_bFL4/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/ZSh03_bFL4/norm.iupac.vcf.gz -f /<>/test/norm.iupac.fa .. ok test_vcf_norm: /<>/bcftools norm --no-version -c s /tmp/ZSh03_bFL4/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/ZSh03_bFL4/norm.3.vcf.gz -f /<>/test/norm.3.fa .. ok test_vcf_norm: /<>/bcftools norm --no-version -c s /tmp/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/atomize.split.1.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -m -any --old-rec-tag OLD_REC --force -a /tmp/ZSh03_bFL4/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/ZSh03_bFL4/atomize.split.1.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/ZSh03_bFL4/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/ZSh03_bFL4/atomize.split.1.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/ZSh03_bFL4/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/ZSh03_bFL4/atomize.split.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version --atomize --old-rec-tag OLD_REC /tmp/ZSh03_bFL4/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/ZSh03_bFL4/atomize.split.2.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/ZSh03_bFL4/atomize.split.2.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version --atomize --atom-overlaps . /tmp/ZSh03_bFL4/atomize.split.3.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version --atomize --atom-overlaps . /tmp/ZSh03_bFL4/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/ZSh03_bFL4/atomize.split.4.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version --atomize --atom-overlaps . --old-rec-tag OLD_REC /tmp/ZSh03_bFL4/atomize.split.4.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m +both /tmp/ZSh03_bFL4/norm.4.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -m +both /tmp/ZSh03_bFL4/norm.4.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m +any /tmp/ZSh03_bFL4/norm.4.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -m +any /tmp/ZSh03_bFL4/norm.4.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m - --multi-overlaps 0 /tmp/ZSh03_bFL4/norm.5.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -m - --multi-overlaps 0 /tmp/ZSh03_bFL4/norm.5.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m - --multi-overlaps . /tmp/ZSh03_bFL4/norm.5.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -m - --multi-overlaps . /tmp/ZSh03_bFL4/norm.5.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m -any /tmp/ZSh03_bFL4/norm.m-any.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -m -any /tmp/ZSh03_bFL4/norm.m-any.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m -any /tmp/ZSh03_bFL4/norm.phased-split.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -m -any /tmp/ZSh03_bFL4/norm.phased-split.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m +any /tmp/ZSh03_bFL4/norm.phased-join.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -m +any /tmp/ZSh03_bFL4/norm.phased-join.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version --old-rec-tag ORI /tmp/ZSh03_bFL4/norm.symbolic.vcf.gz -f /<>/test/norm.symbolic.fa .. ok test_vcf_norm: /<>/bcftools norm --no-version --old-rec-tag ORI /tmp/ZSh03_bFL4/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/ZSh03_bFL4/norm.symbolic.2.vcf.gz -f /<>/test/norm.symbolic.fa .. ok test_vcf_norm: /<>/bcftools norm --no-version --old-rec-tag ORI /tmp/ZSh03_bFL4/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/ZSh03_bFL4/norm.right-align.vcf.gz -f /<>/test/norm.right-align.fa .. ok test_vcf_norm: /<>/bcftools norm --no-version --old-rec-tag ORI /tmp/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/norm.string-tags.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -m -any /tmp/ZSh03_bFL4/norm.string-tags.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m - /tmp/ZSh03_bFL4/norm.split.merge.vcf.gz | /<>/bcftools norm --no-version -m +both .. ok test_vcf_norm: /<>/bcftools norm --no-version -m - /tmp/ZSh03_bFL4/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/ZSh03_bFL4/norm.split.merge.vcf.gz | /<>/bcftools norm --no-version -m +indels .. ok test_vcf_norm: /<>/bcftools norm --no-version -m - /tmp/ZSh03_bFL4/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/ZSh03_bFL4/norm.split.merge.vcf.gz | /<>/bcftools norm --no-version -m +snps .. ok test_vcf_norm: /<>/bcftools norm --no-version -m - /tmp/ZSh03_bFL4/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/ZSh03_bFL4/norm.split.merge.vcf.gz | /<>/bcftools norm --no-version -m +any .. ok test_vcf_norm: /<>/bcftools norm --no-version -m - /tmp/ZSh03_bFL4/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/ZSh03_bFL4/norm.merge.4.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -m +any /tmp/ZSh03_bFL4/norm.merge.4.vcf.gz -Ou | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_norm: /<>/bcftools norm --no-version -m +both /tmp/ZSh03_bFL4/norm.merge.4.vcf.gz .. ok test_vcf_norm: /<>/bcftools norm --no-version -m +both /tmp/ZSh03_bFL4/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/ZSh03_bFL4/filter.string.1.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -i 'INFO/TAG=@/<>/test/filter.string.1.txt' /tmp/ZSh03_bFL4/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/ZSh03_bFL4/filter.string.1.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -i 'FMT/TAG=@/<>/test/filter.string.1.txt' /tmp/ZSh03_bFL4/filter.string.1.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -HA /tmp/ZSh03_bFL4/merge.gvcf.2.a.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -HAA /tmp/ZSh03_bFL4/merge.gvcf.2.a.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version /tmp/ZSh03_bFL4/weird-chr-names.vcf.gz -r 1 .. ok test_vcf_view: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/weird-chr-names.vcf.gz -r 1 | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version /tmp/ZSh03_bFL4/weird-chr-names.vcf.gz -r 1:1-2 .. ok test_vcf_view: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/weird-chr-names.vcf.gz -r 1:1-2 | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version /tmp/ZSh03_bFL4/weird-chr-names.vcf.gz -r 1:1,1:2 .. ok test_vcf_view: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/weird-chr-names.vcf.gz -r 1:1,1:2 | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version /tmp/ZSh03_bFL4/weird-chr-names.vcf.gz -r 1:1-1 .. ok test_vcf_view: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/weird-chr-names.vcf.gz -r 1:1-1 | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version /tmp/ZSh03_bFL4/weird-chr-names.vcf.gz -r {1:1} .. ok test_vcf_view: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/weird-chr-names.vcf.gz -r {1:1} | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version /tmp/ZSh03_bFL4/weird-chr-names.vcf.gz -r {1:1}:1-2 .. ok test_vcf_view: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/weird-chr-names.vcf.gz -r {1:1}:1-2 | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version /tmp/ZSh03_bFL4/weird-chr-names.vcf.gz -r {1:1}:1,{1:1}:2 .. ok test_vcf_view: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/weird-chr-names.vcf.gz -r {1:1}:1-1 .. ok test_vcf_view: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/weird-chr-names.vcf.gz -r {1:1}:1-1 | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version /tmp/ZSh03_bFL4/weird-chr-names.vcf.gz -r {1:1-1} .. ok test_vcf_view: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/weird-chr-names.vcf.gz -r {1:1-1} | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version /tmp/ZSh03_bFL4/weird-chr-names.vcf.gz -r {1:1-1}:1-2 .. ok test_vcf_view: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/weird-chr-names.vcf.gz -r {1:1-1}:1,{1:1-1}:2 .. ok test_vcf_view: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/weird-chr-names.vcf.gz -r {1:1-1}:1-1 .. ok test_vcf_view: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/weird-chr-names.vcf.gz -r {1:1-1}-2 .. ok, expected non-zero status test_vcf_view: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -aUc1 -C1 -s NA00002 -v snps /tmp/ZSh03_bFL4/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -f PASS -Xks NA00003 /tmp/ZSh03_bFL4/view.vcf.gz -r20,Y .. ok test_vcf_view: /<>/bcftools view -Ob -f PASS -Xks NA00003 /tmp/ZSh03_bFL4/view.vcf.gz -r20,Y | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -xs NA00003 /tmp/ZSh03_bFL4/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -xs NA00003 /tmp/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -p /tmp/ZSh03_bFL4/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -p /tmp/ZSh03_bFL4/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -P /tmp/ZSh03_bFL4/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -P /tmp/ZSh03_bFL4/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -hm2 -M2 -q0.3 -Q0.7 /tmp/ZSh03_bFL4/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -hm2 -M2 -q0.3 -Q0.7 /tmp/ZSh03_bFL4/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -Hu /tmp/ZSh03_bFL4/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -GVsnps /tmp/ZSh03_bFL4/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -GVsnps /tmp/ZSh03_bFL4/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -ne 'INDEL=1 || PV4[0]<0.006' /tmp/ZSh03_bFL4/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -ne 'INDEL=1 || PV4[0]<0.006' /tmp/ZSh03_bFL4/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -s ^NA00003 /tmp/ZSh03_bFL4/view.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -s ^NA00003 /tmp/ZSh03_bFL4/view.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version /tmp/ZSh03_bFL4/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/view.omitgenotypes.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -G /tmp/ZSh03_bFL4/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -G /tmp/ZSh03_bFL4/view.omitgenotypes.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -HG /tmp/ZSh03_bFL4/view.omitgenotypes.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -a /tmp/ZSh03_bFL4/many.alleles.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -a /tmp/ZSh03_bFL4/many.alleles.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -asA /tmp/ZSh03_bFL4/view.vectors.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -asA /tmp/ZSh03_bFL4/view.vectors.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -asB /tmp/ZSh03_bFL4/view.vectors.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -asB /tmp/ZSh03_bFL4/view.vectors.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -asA /tmp/ZSh03_bFL4/view.vectors.2.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -asA /tmp/ZSh03_bFL4/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/ZSh03_bFL4/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'FMT/FGS[*:2]="C"' /tmp/ZSh03_bFL4/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'FMT/FGS[*:4]="EE"' /tmp/ZSh03_bFL4/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'FMT/FRS[*:1]="BB"' /tmp/ZSh03_bFL4/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i'TXT0="text"' /tmp/ZSh03_bFL4/view.filter.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -T /<>/test/view.chrs.tab /tmp/ZSh03_bFL4/view.chrs.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -T /<>/test/view.chrs.tab /tmp/ZSh03_bFL4/view.chrs.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -i 'POS>=3062917' /tmp/ZSh03_bFL4/filter.2.vcf.gz 1:3062917-3157410 .. ok test_vcf_view: /<>/bcftools view -Ob -i 'POS>=3062917' /tmp/ZSh03_bFL4/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/ZSh03_bFL4/idx.1.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -r 1:1172777-1172804,1:1172806-1172808 /tmp/ZSh03_bFL4/idx.2.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -R /<>/test/idx.2.bed /tmp/ZSh03_bFL4/idx.2.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -R /<>/test/idx.3.bed /tmp/ZSh03_bFL4/idx.3.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -R /<>/test/idx.4.bed /tmp/ZSh03_bFL4/idx.4.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -Ht 2 /tmp/ZSh03_bFL4/view-t.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -Ht 3 /tmp/ZSh03_bFL4/view-t.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 0 /tmp/ZSh03_bFL4/overlap.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 1 /tmp/ZSh03_bFL4/overlap.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -r chr1:100-200 --regions-overlap 2 /tmp/ZSh03_bFL4/overlap.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 0 /tmp/ZSh03_bFL4/overlap.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 1 /tmp/ZSh03_bFL4/overlap.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -t chr1:100-200 --targets-overlap 2 /tmp/ZSh03_bFL4/overlap.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 0 /tmp/ZSh03_bFL4/overlap.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 1 /tmp/ZSh03_bFL4/overlap.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -t ^chr1:100-200 --targets-overlap 2 /tmp/ZSh03_bFL4/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/ZSh03_bFL4/view.minmaxac.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -c6:nonmajor /tmp/ZSh03_bFL4/view.minmaxac.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -q0.3:major /tmp/ZSh03_bFL4/view.minmaxac.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i 'Gene.refGene=="RAD21L1"' /tmp/ZSh03_bFL4/view.filter.annovar.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i 'Gene.refGene~"NOD"' /tmp/ZSh03_bFL4/view.filter.annovar.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -i 'LJB2_MutationTaster=="0.291000"' /tmp/ZSh03_bFL4/view.filter.annovar.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -H -a /tmp/ZSh03_bFL4/view-a.vcf.gz .. ok test_vcf_view: /<>/bcftools view --no-version -T /<>/test/view.sites.txt /tmp/ZSh03_bFL4/view.sites.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -T /<>/test/view.sites.txt /tmp/ZSh03_bFL4/view.sites.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_view: /<>/bcftools view --no-version -T /<>/test/view.sites.txt.gz /tmp/ZSh03_bFL4/view.sites.vcf.gz .. ok test_vcf_view: /<>/bcftools view -Ob -T /<>/test/view.sites.txt.gz /tmp/ZSh03_bFL4/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/ZSh03_bFL4/mpileup.2.vcf.gz .. ok test_vcf_head2: /<>/bcftools view --no-version -Ob /tmp/ZSh03_bFL4/mpileup.2.vcf.gz | /<>/bcftools head -s0 .. ok test_vcf_head2: /<>/bcftools head -s1 /tmp/ZSh03_bFL4/mpileup.2.vcf.gz .. ok test_vcf_head2: /<>/bcftools view --no-version -Ob /tmp/ZSh03_bFL4/mpileup.2.vcf.gz | /<>/bcftools head -s1 .. ok test_vcf_head2: /<>/bcftools head -s2 -h2 /tmp/ZSh03_bFL4/mpileup.2.vcf.gz .. ok test_vcf_head2: /<>/bcftools view --no-version -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/mpileup.tab.gz /<>/test/mpileup.vcf .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/ZSh03_bFL4/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/ZSh03_bFL4/mpileup.2.tab.gz /<>/test/mpileup.2.vcf .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/ZSh03_bFL4/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/ZSh03_bFL4/mpileup.3.tab.gz -i /<>/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/ZSh03_bFL4/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/ZSh03_bFL4/mpileup.4.tab.gz -i /<>/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/ZSh03_bFL4/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/ZSh03_bFL4/mpileup.5.tab.gz -i /<>/test/mpileup.3.vcf .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/ZSh03_bFL4/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/ZSh03_bFL4/mpileup.6.tab.gz -i /<>/test/mpileup.4.vcf .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/ZSh03_bFL4/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/ZSh03_bFL4/mpileup.7.tab.gz -i /<>/test/mpileup.5.vcf .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/ZSh03_bFL4/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/ZSh03_bFL4/mpileup.cals.1.tab.gz /<>/test/mpileup.cals.1.vcf .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/ZSh03_bFL4/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/ZSh03_bFL4/mpileup.cals.2.tab.gz /<>/test/mpileup.cals.2.vcf .. ok test_vcf_call_cAls: /<>/bcftools call -Ob -mA -C alleles -T /tmp/ZSh03_bFL4/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/ZSh03_bFL4/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/ZSh03_bFL4/regions.tab.gz /tmp/ZSh03_bFL4/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/regions.vcf.gz | /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/ZSh03_bFL4/regions.tab.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/ZSh03_bFL4/regions.tab.gz /tmp/ZSh03_bFL4/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/ZSh03_bFL4/regions.bed /tmp/ZSh03_bFL4/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/regions.vcf.gz | /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/ZSh03_bFL4/regions.bed .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/ZSh03_bFL4/regions.bed /tmp/ZSh03_bFL4/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/ZSh03_bFL4/regions.bed.gz /tmp/ZSh03_bFL4/regions.vcf.gz .. ok test_vcf_regions: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/regions.vcf.gz | /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -T /tmp/ZSh03_bFL4/regions.bed.gz .. ok test_vcf_regions: /<>/bcftools query -f'%CHROM %POS %REF,%ALT\n' -R /tmp/ZSh03_bFL4/regions.bed.gz /tmp/ZSh03_bFL4/regions.vcf.gz .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/ZSh03_bFL4/annotate.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/ZSh03_bFL4/annots.vcf.gz -c STR,ID,QUAL,FILTER /tmp/ZSh03_bFL4/annotate.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/ZSh03_bFL4/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/ZSh03_bFL4/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/ZSh03_bFL4/annots2.vcf.gz -c ID,QUAL,FILTER,INFO,FMT /tmp/ZSh03_bFL4/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/ZSh03_bFL4/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/ZSh03_bFL4/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/ZSh03_bFL4/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s A /tmp/ZSh03_bFL4/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/ZSh03_bFL4/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/ZSh03_bFL4/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/ZSh03_bFL4/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A B" /tmp/ZSh03_bFL4/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/ZSh03_bFL4/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/ZSh03_bFL4/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/ZSh03_bFL4/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "A C" /tmp/ZSh03_bFL4/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/ZSh03_bFL4/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/ZSh03_bFL4/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/ZSh03_bFL4/annots2.vcf.gz -c ID,QUAL,+FILTER,+INFO,FMT/GT -s "B C" /tmp/ZSh03_bFL4/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/ZSh03_bFL4/annots4.vcf.gz -c +INFO /tmp/ZSh03_bFL4/annotate4.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/ZSh03_bFL4/annots4.vcf.gz -c +INFO /tmp/ZSh03_bFL4/annotate4.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/ZSh03_bFL4/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/ZSh03_bFL4/annots2.vcf.gz -c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR -s A /tmp/ZSh03_bFL4/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/ZSh03_bFL4/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/ZSh03_bFL4/annots2.vcf.gz -c AAA:=IINT,FMT/BBB:=FMT/FINT /tmp/ZSh03_bFL4/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/ZSh03_bFL4/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/ZSh03_bFL4/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/ZSh03_bFL4/annots2.vcf.gz -x INFO -c INFO/IINT /tmp/ZSh03_bFL4/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/ZSh03_bFL4/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/ZSh03_bFL4/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/ZSh03_bFL4/annots2.vcf.gz -x INFO -c INFO/IINT -e'POS=3000001' -k /tmp/ZSh03_bFL4/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/ZSh03_bFL4/annots11.vcf.gz -c FMT /tmp/ZSh03_bFL4/annotate11.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/ZSh03_bFL4/annots11.vcf.gz -c FMT /tmp/ZSh03_bFL4/annotate11.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/ZSh03_bFL4/annots2.vcf.gz -c FMT/newGT:=GT /tmp/ZSh03_bFL4/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/ZSh03_bFL4/annots2.vcf.gz -c FMT/newGT:=GT /tmp/ZSh03_bFL4/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/ZSh03_bFL4/annots12.vcf.gz -c FMT/GT:=newGT /tmp/ZSh03_bFL4/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/ZSh03_bFL4/annots12.vcf.gz -c FMT/GT:=newGT /tmp/ZSh03_bFL4/annotate2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/ZSh03_bFL4/annotate19.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/ZSh03_bFL4/annotate19.src.vcf.gz -c INFO/ID:=ID,INFO/INFO_ID:=INFO/ID,ID,=ID:=INFO/ID /tmp/ZSh03_bFL4/annotate19.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/ZSh03_bFL4/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/ZSh03_bFL4/annotate19.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/ZSh03_bFL4/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/ZSh03_bFL4/annotate19.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/ZSh03_bFL4/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/ZSh03_bFL4/annotate19.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/ZSh03_bFL4/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER,INFO/INFO_FILTER:=INFO/FILTER /tmp/ZSh03_bFL4/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/ZSh03_bFL4/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER /tmp/ZSh03_bFL4/annotate19.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/ZSh03_bFL4/annotate19.src.vcf.gz -c INFO/FILTER:=FILTER /tmp/ZSh03_bFL4/annotate19.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/ZSh03_bFL4/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER /tmp/ZSh03_bFL4/annotate19.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/ZSh03_bFL4/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER /tmp/ZSh03_bFL4/annotate19.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/ZSh03_bFL4/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER,FILTER /tmp/ZSh03_bFL4/annotate19.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/ZSh03_bFL4/annotate19.src.vcf.gz -c INFO/FILTER:=./FILTER,FILTER /tmp/ZSh03_bFL4/annotate19.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/ZSh03_bFL4/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=./FILTER /tmp/ZSh03_bFL4/annotate19.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/ZSh03_bFL4/annotate19.src.vcf.gz -c FILTER,INFO/FILTER:=./FILTER /tmp/ZSh03_bFL4/annotate19.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/ZSh03_bFL4/annotate20.src.vcf.gz -c FMT/GT /tmp/ZSh03_bFL4/annotate20.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/ZSh03_bFL4/annotate20.src.vcf.gz -c FMT/GT /tmp/ZSh03_bFL4/annotate20.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/ZSh03_bFL4/annotate20.src.vcf.gz -c +FMT/GT /tmp/ZSh03_bFL4/annotate20.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/ZSh03_bFL4/annotate20.src.vcf.gz -c +FMT/GT /tmp/ZSh03_bFL4/annotate20.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/ZSh03_bFL4/annotate20.src.vcf.gz -c -FMT/GT /tmp/ZSh03_bFL4/annotate20.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/ZSh03_bFL4/annotate20.src.vcf.gz -c -FMT/GT /tmp/ZSh03_bFL4/annotate20.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/ZSh03_bFL4/annotate22.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/ZSh03_bFL4/annotate22.vcf.gz -c FMT/XX,INFO/XX -x FMT/XX,INFO/XX /tmp/ZSh03_bFL4/annotate22.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/annotate24.src.vcf.gz -c XX /tmp/ZSh03_bFL4/annotate24.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/ZSh03_bFL4/annotate24.src.vcf.gz -c XX /tmp/ZSh03_bFL4/annotate24.dst.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/annotate26.tab.gz -c CHROM,POS,~POS /<>/test/annotate26.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/ZSh03_bFL4/annotate26.tab.gz -c CHROM,POS,~POS /<>/test/annotate26.vcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/annots.id.vcf.gz -c ALT /tmp/ZSh03_bFL4/annotate.id.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/ZSh03_bFL4/annots.id.vcf.gz -c ALT /tmp/ZSh03_bFL4/annotate.id.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/ZSh03_bFL4/annots.id.vcf.gz -c +ALT /tmp/ZSh03_bFL4/annotate.id.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/ZSh03_bFL4/annots.id.vcf.gz -c +ALT /tmp/ZSh03_bFL4/annotate.id.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/ZSh03_bFL4/annots.id.2.vcf.gz --pair-logic some -c +ID /tmp/ZSh03_bFL4/annotate.id.2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/ZSh03_bFL4/annots.id.2.vcf.gz --pair-logic some -c +ID /tmp/ZSh03_bFL4/annotate.id.2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/ZSh03_bFL4/annots.id.2.vcf.gz --pair-logic any -c +ID /tmp/ZSh03_bFL4/annotate.id.2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -Ob -a /tmp/ZSh03_bFL4/annots.id.2.vcf.gz --pair-logic any -c +ID /tmp/ZSh03_bFL4/annotate.id.2.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_annotate: /<>/bcftools annotate -a /tmp/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/concat.1.a.vcf.gz /tmp/ZSh03_bFL4/concat.1.b.vcf.gz .. ok test_vcf_concat: /<>/bcftools concat -Ob /tmp/ZSh03_bFL4/concat.1.a.vcf.gz /tmp/ZSh03_bFL4/concat.1.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version /tmp/ZSh03_bFL4/concat.1.a.bcf /tmp/ZSh03_bFL4/concat.1.b.bcf .. ok test_vcf_concat: /<>/bcftools concat -Ob /tmp/ZSh03_bFL4/concat.1.a.bcf /tmp/ZSh03_bFL4/concat.1.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -a /tmp/ZSh03_bFL4/concat.2.a.vcf.gz /tmp/ZSh03_bFL4/concat.2.b.vcf.gz .. ok test_vcf_concat: /<>/bcftools concat -Ob -a /tmp/ZSh03_bFL4/concat.2.a.vcf.gz /tmp/ZSh03_bFL4/concat.2.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -a /tmp/ZSh03_bFL4/concat.2.a.bcf /tmp/ZSh03_bFL4/concat.2.b.bcf .. ok test_vcf_concat: /<>/bcftools concat -Ob -a /tmp/ZSh03_bFL4/concat.2.a.bcf /tmp/ZSh03_bFL4/concat.2.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -aD /tmp/ZSh03_bFL4/concat.2.a.vcf.gz /tmp/ZSh03_bFL4/concat.2.b.vcf.gz .. ok test_vcf_concat: /<>/bcftools concat -Ob -aD /tmp/ZSh03_bFL4/concat.2.a.vcf.gz /tmp/ZSh03_bFL4/concat.2.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -aD /tmp/ZSh03_bFL4/concat.2.a.bcf /tmp/ZSh03_bFL4/concat.2.b.bcf .. ok test_vcf_concat: /<>/bcftools concat -Ob -aD /tmp/ZSh03_bFL4/concat.2.a.bcf /tmp/ZSh03_bFL4/concat.2.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -l --ligate-warn /tmp/ZSh03_bFL4/concat.3.a.vcf.gz /tmp/ZSh03_bFL4/concat.3.b.vcf.gz /tmp/ZSh03_bFL4/concat.3.0.vcf.gz /tmp/ZSh03_bFL4/concat.3.c.vcf.gz /tmp/ZSh03_bFL4/concat.3.d.vcf.gz /tmp/ZSh03_bFL4/concat.3.e.vcf.gz /tmp/ZSh03_bFL4/concat.3.f.vcf.gz .. ok test_vcf_concat: /<>/bcftools concat -Ob -l --ligate-warn /tmp/ZSh03_bFL4/concat.3.a.vcf.gz /tmp/ZSh03_bFL4/concat.3.b.vcf.gz /tmp/ZSh03_bFL4/concat.3.0.vcf.gz /tmp/ZSh03_bFL4/concat.3.c.vcf.gz /tmp/ZSh03_bFL4/concat.3.d.vcf.gz /tmp/ZSh03_bFL4/concat.3.e.vcf.gz /tmp/ZSh03_bFL4/concat.3.f.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -l --ligate-warn /tmp/ZSh03_bFL4/concat.3.a.bcf /tmp/ZSh03_bFL4/concat.3.b.bcf /tmp/ZSh03_bFL4/concat.3.0.bcf /tmp/ZSh03_bFL4/concat.3.c.bcf /tmp/ZSh03_bFL4/concat.3.d.bcf /tmp/ZSh03_bFL4/concat.3.e.bcf /tmp/ZSh03_bFL4/concat.3.f.bcf .. ok test_vcf_concat: /<>/bcftools concat -Ob -l --ligate-warn /tmp/ZSh03_bFL4/concat.3.a.bcf /tmp/ZSh03_bFL4/concat.3.b.bcf /tmp/ZSh03_bFL4/concat.3.0.bcf /tmp/ZSh03_bFL4/concat.3.c.bcf /tmp/ZSh03_bFL4/concat.3.d.bcf /tmp/ZSh03_bFL4/concat.3.e.bcf /tmp/ZSh03_bFL4/concat.3.f.bcf | /<>/bcftools view | grep -v ^##bcftools_ Random seed for test_naive_concat: 901813397 .. ok test_naive_concat: /<>/bcftools concat --naive-force /tmp/ZSh03_bFL4/naive_concat.0.bcf /tmp/ZSh03_bFL4/naive_concat.1.bcf /tmp/ZSh03_bFL4/naive_concat.2.bcf /tmp/ZSh03_bFL4/naive_concat.3.bcf /tmp/ZSh03_bFL4/naive_concat.4.bcf /tmp/ZSh03_bFL4/naive_concat.5.bcf /tmp/ZSh03_bFL4/naive_concat.6.bcf /tmp/ZSh03_bFL4/naive_concat.7.bcf /tmp/ZSh03_bFL4/naive_concat.8.bcf /tmp/ZSh03_bFL4/naive_concat.9.bcf | /<>/bcftools view -H .. ok test_naive_concat: /<>/bcftools concat --naive /tmp/ZSh03_bFL4/naive_concat.0.vcf.gz /tmp/ZSh03_bFL4/naive_concat.1.vcf.gz /tmp/ZSh03_bFL4/naive_concat.2.vcf.gz /tmp/ZSh03_bFL4/naive_concat.3.vcf.gz /tmp/ZSh03_bFL4/naive_concat.4.vcf.gz /tmp/ZSh03_bFL4/naive_concat.5.vcf.gz /tmp/ZSh03_bFL4/naive_concat.6.vcf.gz /tmp/ZSh03_bFL4/naive_concat.7.vcf.gz /tmp/ZSh03_bFL4/naive_concat.8.vcf.gz /tmp/ZSh03_bFL4/naive_concat.9.vcf.gz | /<>/bcftools view -H .. ok test_vcf_concat: /<>/bcftools concat --no-version -l /tmp/ZSh03_bFL4/concat.4.a.vcf.gz /tmp/ZSh03_bFL4/concat.4.b.vcf.gz .. ok test_vcf_concat: /<>/bcftools concat -Ob -l /tmp/ZSh03_bFL4/concat.4.a.vcf.gz /tmp/ZSh03_bFL4/concat.4.b.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -l /tmp/ZSh03_bFL4/concat.4.a.bcf /tmp/ZSh03_bFL4/concat.4.b.bcf .. ok test_vcf_concat: /<>/bcftools concat -Ob -l /tmp/ZSh03_bFL4/concat.4.a.bcf /tmp/ZSh03_bFL4/concat.4.b.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -l --ligate-warn /tmp/ZSh03_bFL4/concat.5.a.vcf.gz /tmp/ZSh03_bFL4/concat.5.b.vcf.gz /tmp/ZSh03_bFL4/concat.5.c.vcf.gz .. ok test_vcf_concat: /<>/bcftools concat -Ob -l --ligate-warn /tmp/ZSh03_bFL4/concat.5.a.vcf.gz /tmp/ZSh03_bFL4/concat.5.b.vcf.gz /tmp/ZSh03_bFL4/concat.5.c.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -l --ligate-warn /tmp/ZSh03_bFL4/concat.5.a.bcf /tmp/ZSh03_bFL4/concat.5.b.bcf /tmp/ZSh03_bFL4/concat.5.c.bcf .. ok test_vcf_concat: /<>/bcftools concat -Ob -l --ligate-warn /tmp/ZSh03_bFL4/concat.5.a.bcf /tmp/ZSh03_bFL4/concat.5.b.bcf /tmp/ZSh03_bFL4/concat.5.c.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -l --ligate-force /tmp/ZSh03_bFL4/concat.5.a.bcf /tmp/ZSh03_bFL4/concat.5.b.bcf /tmp/ZSh03_bFL4/concat.5.c.bcf .. ok test_vcf_concat: /<>/bcftools concat -Ob -l --ligate-force /tmp/ZSh03_bFL4/concat.5.a.bcf /tmp/ZSh03_bFL4/concat.5.b.bcf /tmp/ZSh03_bFL4/concat.5.c.bcf | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -G -a -D /tmp/ZSh03_bFL4/concat.5.a.vcf.gz /tmp/ZSh03_bFL4/concat.5.b.vcf.gz /tmp/ZSh03_bFL4/concat.5.c.vcf.gz .. ok test_vcf_concat: /<>/bcftools concat -Ob -G -a -D /tmp/ZSh03_bFL4/concat.5.a.vcf.gz /tmp/ZSh03_bFL4/concat.5.b.vcf.gz /tmp/ZSh03_bFL4/concat.5.c.vcf.gz | /<>/bcftools view | grep -v ^##bcftools_ .. ok test_vcf_concat: /<>/bcftools concat --no-version -G -a -D /tmp/ZSh03_bFL4/concat.5.a.bcf /tmp/ZSh03_bFL4/concat.5.b.bcf /tmp/ZSh03_bFL4/concat.5.c.bcf .. ok test_vcf_concat: /<>/bcftools concat -Ob -G -a -D /tmp/ZSh03_bFL4/concat.5.a.bcf /tmp/ZSh03_bFL4/concat.5.b.bcf /tmp/ZSh03_bFL4/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/ZSh03_bFL4/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/ZSh03_bFL4/reheader.bcf | /<>/bcftools reheader -h /<>/test/reheader.hdr | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -h /<>/test/reheader.hdr /tmp/ZSh03_bFL4/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/ZSh03_bFL4/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/ZSh03_bFL4/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/ZSh03_bFL4/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples /tmp/ZSh03_bFL4/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/ZSh03_bFL4/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/ZSh03_bFL4/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/ZSh03_bFL4/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples2 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples2 /tmp/ZSh03_bFL4/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/ZSh03_bFL4/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/ZSh03_bFL4/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/ZSh03_bFL4/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples3 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples3 /tmp/ZSh03_bFL4/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/ZSh03_bFL4/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/ZSh03_bFL4/reheader.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/ZSh03_bFL4/reheader.bcf | /<>/bcftools reheader -s /<>/test/reheader.samples4 | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -s /<>/test/reheader.samples4 /tmp/ZSh03_bFL4/reheader.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/ZSh03_bFL4/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/ZSh03_bFL4/empty.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/ZSh03_bFL4/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/ZSh03_bFL4/empty.vcf.gz | /<>/bcftools view --no-version .. ok test_vcf_reheader: cat /tmp/ZSh03_bFL4/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/ZSh03_bFL4/reheader.2.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -f /<>/test/reheader.fai /tmp/ZSh03_bFL4/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/ZSh03_bFL4/reheader.2.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -h /<>/test/reheader.2.hdr -f /<>/test/reheader.fai /tmp/ZSh03_bFL4/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/ZSh03_bFL4/reheader.3.bcf | /<>/bcftools view --no-version .. ok test_vcf_reheader: /<>/bcftools reheader -f /<>/test/reheader.3.fai /tmp/ZSh03_bFL4/reheader.3.vcf.gz | /<>/bcftools view --no-version .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/ZSh03_bFL4/rename.map -Ov /tmp/ZSh03_bFL4/annotate.bcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/ZSh03_bFL4/rename.map -Ob /tmp/ZSh03_bFL4/annotate.bcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/ZSh03_bFL4/rename.map -Ov /<>/test/annotate.vcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_rename_chrs: /<>/bcftools annotate --rename-chrs /tmp/ZSh03_bFL4/rename.map -Ob /<>/test/annotate.vcf | /<>/bcftools query -f'%CHROM\t%POS\n' .. ok test_vcf_convert: /<>/bcftools convert -g -,. /tmp/ZSh03_bFL4/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/convert.vcf.gz | /<>/bcftools convert -g -,. .. ok test_vcf_convert: /<>/bcftools convert -g -,. --vcf-ids /tmp/ZSh03_bFL4/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/convert.vcf.gz | /<>/bcftools convert -g -,. --vcf-ids .. ok test_vcf_convert: /<>/bcftools convert -g -,. --vcf-ids --3N6 /tmp/ZSh03_bFL4/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/convert.vcf.gz | /<>/bcftools convert -g -,. --vcf-ids --3N6 .. ok test_vcf_convert: /<>/bcftools convert -g .,- /tmp/ZSh03_bFL4/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/convert.vcf.gz | /<>/bcftools convert -g -,. --tag PL .. ok test_vcf_convert: /<>/bcftools convert -g .,- --tag PL /tmp/ZSh03_bFL4/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/convert.vcf.gz | /<>/bcftools convert -g .,- --tag PL .. ok test_vcf_convert: /<>/bcftools convert -g -,. --vcf-ids /tmp/ZSh03_bFL4/check.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/check.vcf.gz | /<>/bcftools convert -g -,. --vcf-ids .. ok test_vcf_convert: /<>/bcftools convert -g .,- --vcf-ids /tmp/ZSh03_bFL4/check.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/check.vcf.gz | /<>/bcftools convert -g .,- --vcf-ids .. ok test_vcf_convert: /<>/bcftools convert -g -,. --3N6 /tmp/ZSh03_bFL4/check.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/check.vcf.gz | /<>/bcftools convert -g -,. --3N6 .. ok test_vcf_convert: /<>/bcftools convert -g .,- --3N6 /tmp/ZSh03_bFL4/check.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/check.vcf.gz | /<>/bcftools convert -g .,- --3N6 .. ok test_vcf_convert: /<>/bcftools convert -g -,. --3N6 --vcf-ids /tmp/ZSh03_bFL4/check.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/check.vcf.gz | /<>/bcftools convert -g -,. --3N6 --vcf-ids .. ok test_vcf_convert: /<>/bcftools convert -g .,- --3N6 --vcf-ids /tmp/ZSh03_bFL4/check.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/check.vcf.gz | /<>/bcftools convert -g .,- --3N6 --vcf-ids .. ok test_vcf_convert: /<>/bcftools convert -h -,.,. /tmp/ZSh03_bFL4/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/convert.vcf.gz | /<>/bcftools convert -h -,.,. .. ok test_vcf_convert: /<>/bcftools convert -h .,-,. /tmp/ZSh03_bFL4/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/convert.vcf.gz | /<>/bcftools convert -h .,-,. .. ok test_vcf_convert: /<>/bcftools convert -h .,-,. --vcf-ids /tmp/ZSh03_bFL4/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/convert.vcf.gz | /<>/bcftools convert -h .,-,. --vcf-ids .. ok test_vcf_convert: /<>/bcftools convert -h .,.,- /tmp/ZSh03_bFL4/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/convert.hap-missing.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/convert.hap-missing.vcf.gz | /<>/bcftools convert --haplegendsample -,.,. .. ok test_vcf_convert: /<>/bcftools convert --hapsample -,. /tmp/ZSh03_bFL4/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/convert.vcf.gz | /<>/bcftools convert --hapsample -,. .. ok test_vcf_convert: /<>/bcftools convert --hapsample -,. --vcf-ids /tmp/ZSh03_bFL4/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/convert.vcf.gz | /<>/bcftools convert --hapsample -,. --vcf-ids .. ok test_vcf_convert: /<>/bcftools convert --hapsample .,- /tmp/ZSh03_bFL4/convert.vcf.gz .. ok test_vcf_convert: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/convert.gvcf.vcf.gz .. ok test_vcf_convert_gvcf: /<>/bcftools view -Ob /tmp/ZSh03_bFL4/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/ZSh03_bFL4/consensus.vcf.gz -f /<>/test/consensus.fa -s - -m /<>/test/consensus.tab .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus.bcf -f /<>/test/consensus.fa -s - -m /<>/test/consensus.tab .. ok test_vcf_consensus_chain: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus.vcf.gz -f /<>/test/consensus.fa -s - -m /<>/test/consensus.tab -c /tmp/ZSh03_bFL4/consensus.1.chain.new >/dev/null; cat /tmp/ZSh03_bFL4/consensus.1.chain.new .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 -m /<>/test/consensus.tab .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus.bcf -f /<>/test/consensus.fa -H 1 -m /<>/test/consensus.tab .. ok test_vcf_consensus_chain: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 -m /<>/test/consensus.tab -c /tmp/ZSh03_bFL4/consensus.2.chain.new >/dev/null; cat /tmp/ZSh03_bFL4/consensus.2.chain.new .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus.vcf.gz -f /<>/test/consensus.fa -I -s - -m /<>/test/consensus.tab .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus.bcf -f /<>/test/consensus.fa -I -s - -m /<>/test/consensus.tab .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/consensus.vcf.gz -f /<>/test/consensus.fa -I -m /<>/test/consensus.tab -c /tmp/ZSh03_bFL4/consensus.3.chain.new >/dev/null; cat /tmp/ZSh03_bFL4/consensus.3.chain.new .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus.bcf -f /<>/test/consensus.fa -H 1 .. ok test_vcf_consensus_chain: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus.vcf.gz -f /<>/test/consensus.fa -H 1 -c /tmp/ZSh03_bFL4/consensus.4.chain.new >/dev/null; cat /tmp/ZSh03_bFL4/consensus.4.chain.new .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus2.vcf.gz -f /<>/test/consensus2.fa -H 1 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus2.bcf -f /<>/test/consensus2.fa -H 1 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus2.vcf.gz -f /<>/test/consensus2.fa -H 2 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus2.bcf -f /<>/test/consensus2.fa -H 2 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/empty.vcf.gz -f /<>/test/consensus.fa -s - .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/empty.bcf -f /<>/test/consensus.fa -s - .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus3.vcf.gz -f /<>/test/consensus2.fa -H 2 -M "?" .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus3.bcf -f /<>/test/consensus2.fa -H 2 -M "?" .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus3.vcf.gz -f /<>/test/consensus2.fa -H 2 -M "?" -p xx_ .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus3.bcf -f /<>/test/consensus2.fa -H 2 -M "?" -p xx_ .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus4.vcf.gz -f /<>/test/consensus2.fa -s - .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus4.bcf -f /<>/test/consensus2.fa -s - .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus5.vcf.gz -f /<>/test/consensus5.fa --haplotype LA .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus5.bcf -f /<>/test/consensus5.fa --haplotype LA .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus6.vcf.gz -f /<>/test/consensus6.fa -s - .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus6.bcf -f /<>/test/consensus6.fa -s - .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus7.vcf.gz -f /<>/test/consensus7.fa -H 2 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus7.bcf -f /<>/test/consensus7.fa -H 2 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus7.vcf.gz -f /<>/test/consensus7.fa -H 4 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus7.bcf -f /<>/test/consensus7.fa -H 4 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus7.vcf.gz -f /<>/test/consensus7.fa -H 2pIu .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus7.bcf -f /<>/test/consensus7.fa -H 2pIu .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus7.vcf.gz -f /<>/test/consensus7.fa -H 4pIu .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus7.bcf -f /<>/test/consensus7.fa -H 4pIu .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus7.vcf.gz -f /<>/test/consensus7.fa -H 1 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus7.bcf -f /<>/test/consensus7.fa -H 1 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus7.vcf.gz -f /<>/test/consensus7.fa -H 3 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus7.bcf -f /<>/test/consensus7.fa -H 3 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus7.vcf.gz -f /<>/test/consensus7.fa -H 1pIu .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus7.bcf -f /<>/test/consensus7.fa -H 1pIu .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus7.vcf.gz -f /<>/test/consensus7.fa -H 3pIu .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus7.bcf -f /<>/test/consensus7.fa -H 3pIu .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus8.vcf.gz -f /<>/test/consensus.fa -s - .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus8.bcf -f /<>/test/consensus.fa -s - .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus8.vcf.gz -f /<>/test/consensus.fa -s - -a . .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus8.bcf -f /<>/test/consensus.fa -s - -a . .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus8.vcf.gz -f /<>/test/consensus.fa -s - -a . -i 'type="snp" || type="ref"' .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus8.bcf -f /<>/test/consensus.fa -s - -a . -i 'type="snp" || type="ref"' .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus8.vcf.gz -f /<>/test/consensus.fa -s - -a . -i 'ALT!=""' .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus8.bcf -f /<>/test/consensus.fa -s - -a . -i 'ALT!=""' .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus8.vcf.gz -f /<>/test/consensus.fa -s - -a . -e 'MinDP>15' .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus8.bcf -f /<>/test/consensus.fa -s - -a . -e 'MinDP>15' .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus8.vcf.gz -f /<>/test/consensus.fa -s - -a . -e 'MinDP<15' .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus8.bcf -f /<>/test/consensus.fa -s - -a . -e 'MinDP<15' .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus.9.vcf.gz -f /<>/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus.9.bcf -f /<>/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus.9.vcf.gz -f /<>/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus.9.bcf -f /<>/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus.10.vcf.gz -f /<>/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus.10.bcf -f /<>/test/consensus.9.1.fa -H A .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus.10.vcf.gz -f /<>/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus.10.bcf -f /<>/test/consensus.9.2.fa -H A .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus.11.vcf.gz -f /<>/test/consensus.11.fa -s smpl .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus.11.bcf -f /<>/test/consensus.11.fa -s smpl .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus.11.vcf.gz -f /<>/test/consensus.11.fa -s smpl -a N .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus.11.bcf -f /<>/test/consensus.11.fa -s smpl -a N .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus.12.vcf.gz -f /<>/test/consensus.12.fa -s - .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus.12.bcf -f /<>/test/consensus.12.fa -s - .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus.13.vcf.gz -f /<>/test/consensus.13.fa -s - .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus.13.bcf -f /<>/test/consensus.13.fa -s - .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus.14.vcf.gz -f /<>/test/consensus.14.fa -s - .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus.14.bcf -f /<>/test/consensus.14.fa -s - .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/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/ZSh03_bFL4/consensus.12.bcf -f /<>/test/consensus.12.fa -s - --mark-del - --mark-ins uc --mark-snv uc .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus.12.vcf.gz -f /<>/test/consensus.12.fa -s - --mark-del - --mark-ins + --mark-snv : .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus.12.bcf -f /<>/test/consensus.12.fa -s - --mark-del - --mark-ins + --mark-snv : .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus.15.vcf.gz -f /<>/test/consensus.15.fa -H I --mark-ins lc --mark-snv lc .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus.15.bcf -f /<>/test/consensus.15.fa -H I --mark-ins lc --mark-snv lc .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus.16.vcf.gz -f /<>/test/consensus.fa -s - -I .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus.16.bcf -f /<>/test/consensus.fa -s - -I .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus.16.vcf.gz -f /<>/test/consensus.fa -H I .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus.16.bcf -f /<>/test/consensus.fa -H I .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus.17.vcf.gz -f /<>/test/consensus2.fa -s - -M N -m /<>/test/consensus.17.bed .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus.17.bcf -f /<>/test/consensus2.fa -s - -M N -m /<>/test/consensus.17.bed .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus.18.vcf.gz -f /<>/test/consensus.18.fa -s - .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus.18.bcf -f /<>/test/consensus.18.fa -s - .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus.19.vcf.gz -f /<>/test/consensus.19.fa -s - .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus.19.bcf -f /<>/test/consensus.19.fa -s - .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus.20.vcf.gz -f /<>/test/consensus.20.fa -s - .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus.20.bcf -f /<>/test/consensus.20.fa -s - .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus.20.vcf.gz -f /<>/test/consensus.20.fa .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus.20.bcf -f /<>/test/consensus.20.fa .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus.20.vcf.gz -f /<>/test/consensus.20.fa -M . -s b .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus.20.bcf -f /<>/test/consensus.20.fa -M . -s b .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus.20.vcf.gz -f /<>/test/consensus.20.fa -M . -s a .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus.20.bcf -f /<>/test/consensus.20.fa -M . -s a .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus.21.vcf.gz -f /<>/test/consensus.21.fa .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus.21.bcf -f /<>/test/consensus.21.fa .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus.22.vcf.gz -f /<>/test/consensus.22.fa --regions-overlap 0 --mark-del . .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus.22.bcf -f /<>/test/consensus.22.fa --regions-overlap 0 --mark-del . .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus.22.vcf.gz -f /<>/test/consensus.22.fa --regions-overlap 1 --mark-del . .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus.22.bcf -f /<>/test/consensus.22.fa --regions-overlap 1 --mark-del . .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus.22.vcf.gz -f /<>/test/consensus.22.fa --regions-overlap 2 --mark-del . .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus.22.bcf -f /<>/test/consensus.22.fa --regions-overlap 2 --mark-del . .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus.22.vcf.gz -f /<>/test/consensus.22.fa --regions-overlap 0 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus.22.bcf -f /<>/test/consensus.22.fa --regions-overlap 0 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus.22.vcf.gz -f /<>/test/consensus.22.fa --regions-overlap 1 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus.22.bcf -f /<>/test/consensus.22.fa --regions-overlap 1 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/consensus.22.vcf.gz -f /<>/test/consensus.22.fa --regions-overlap 2 .. ok test_vcf_consensus: /<>/bcftools consensus /tmp/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/gtcheck.1.vcf.gz -g /tmp/ZSh03_bFL4/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -u GT,GT /tmp/ZSh03_bFL4/gtcheck.1.vcf.gz -g /tmp/ZSh03_bFL4/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -u GT,PL /tmp/ZSh03_bFL4/gtcheck.1.vcf.gz -g /tmp/ZSh03_bFL4/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -u PL,GT /tmp/ZSh03_bFL4/gtcheck.1.vcf.gz -g /tmp/ZSh03_bFL4/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -u PL,PL /tmp/ZSh03_bFL4/gtcheck.1.vcf.gz -g /tmp/ZSh03_bFL4/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -p s1,s1 /tmp/ZSh03_bFL4/gtcheck.1.vcf.gz -g /tmp/ZSh03_bFL4/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 /tmp/ZSh03_bFL4/gtcheck.2.vcf.gz -g /tmp/ZSh03_bFL4/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 /tmp/ZSh03_bFL4/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/ZSh03_bFL4/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -P /<>/test/gtcheck.3.pairs /tmp/ZSh03_bFL4/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -u PL /tmp/ZSh03_bFL4/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 --n-matches 4 /tmp/ZSh03_bFL4/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO | sort .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -s qry:E,D,C /tmp/ZSh03_bFL4/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -s qry:E,D,C -u PL /tmp/ZSh03_bFL4/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -s qry:B -s gt:D /tmp/ZSh03_bFL4/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/ZSh03_bFL4/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -s qry:B -s gt:D,C /tmp/ZSh03_bFL4/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -p B,C,B,D /tmp/ZSh03_bFL4/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -u GT,GT -H /tmp/ZSh03_bFL4/gtcheck.1.vcf.gz -g /tmp/ZSh03_bFL4/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -u GT,PL -H /tmp/ZSh03_bFL4/gtcheck.1.vcf.gz -g /tmp/ZSh03_bFL4/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -u PL,GT -H /tmp/ZSh03_bFL4/gtcheck.1.vcf.gz -g /tmp/ZSh03_bFL4/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -e 0 -u PL,PL -H /tmp/ZSh03_bFL4/gtcheck.1.vcf.gz -g /tmp/ZSh03_bFL4/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/ZSh03_bFL4/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/ZSh03_bFL4/gtcheck.4.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -u GT -e 30 /tmp/ZSh03_bFL4/gtcheck.1.vcf.gz -g /tmp/ZSh03_bFL4/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -u GT -e 30 -p s1,s1 /tmp/ZSh03_bFL4/gtcheck.1.vcf.gz -g /tmp/ZSh03_bFL4/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -u GT -e 300 /tmp/ZSh03_bFL4/gtcheck.1.vcf.gz -g /tmp/ZSh03_bFL4/gtcheck.1.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck -u PL -e 30 /tmp/ZSh03_bFL4/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck /tmp/ZSh03_bFL4/gtcheck.ntop.vcf.gz -g /tmp/ZSh03_bFL4/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck --n-matches 2 /tmp/ZSh03_bFL4/gtcheck.ntop.vcf.gz -g /tmp/ZSh03_bFL4/gtcheck.ntop.gts.vcf.gz | grep -v ^# | grep -v ^INFO .. ok test_gtcheck: /<>/bcftools gtcheck /tmp/ZSh03_bFL4/gtcheck.5.vcf.gz -g /tmp/ZSh03_bFL4/gtcheck.5.gts.vcf.gz | grep -v ^# | grep -v Time .. ok test_gtcheck: /<>/bcftools gtcheck -p A,B,B,C /tmp/ZSh03_bFL4/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/ZSh03_bFL4/gtcheck.3.vcf.gz | grep -v ^# | grep -v ^INFO .. ok Number of tests: total .. 1745 passed .. 1745 failed .. 0 make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/bcftools/ make -j2 install DESTDIR=/<>/debian/bcftools AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/<>' mkdir -p -m 755 /<>/debian/bcftools/usr/bin /<>/debian/bcftools/usr/share/man/man1 /<>/debian/bcftools/usr/lib/x86_64-linux-gnu/bcftools install -p bcftools /<>/debian/bcftools/usr/bin install -p misc/color-chrs.pl misc/gff2gff.py misc/guess-ploidy.py misc/plot-vcfstats misc/plot-roh.py misc/run-roh.pl misc/vcfutils.pl /<>/debian/bcftools/usr/bin install -p -m 644 doc/bcftools.1 /<>/debian/bcftools/usr/share/man/man1 install -p plugins/*.so /<>/debian/bcftools/usr/lib/x86_64-linux-gnu/bcftools make[1]: Leaving directory '/<>' debian/rules override_dh_install make[1]: Entering directory '/<>' dh_install # Fix Perl interpreter PATH for pscript in `grep -Rl '#!/usr/bin/env \+perl' debian/*` ; do \ sed -i '1s?#!/usr/bin/env \+perl?#!/usr/bin/perl?' ${pscript} ; \ done make[1]: Leaving directory '/<>' dh_installdocs dh_installchangelogs debian/rules override_dh_installman make[1]: Entering directory '/<>' dh_installman --language=C make[1]: Leaving directory '/<>' dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dpkg-gencontrol: warning: package bcftools: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package bcftools: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'bcftools' in '../bcftools_1.20-2_amd64.deb'. dpkg-deb: building package 'bcftools-dbgsym' in '../bcftools-dbgsym_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 2024-09-14T22:45:14Z 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: 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321310607a83802b72a602acffcbb85e 7836 science optional bcftools_1.20-2.debian.tar.xz cab4c79d08065360016d47f275afcdbe 2172760 debug optional bcftools-dbgsym_1.20-2_amd64.deb a966d35287f3e1a93a410d8b30617963 7154 science optional bcftools_1.20-2_amd64.buildinfo 361d64a088fbe8067dcd3033087973de 767412 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 cab4c79d08065360016d47f275afcdbe 2172760 bcftools-dbgsym_1.20-2_amd64.deb 361d64a088fbe8067dcd3033087973de 767412 bcftools_1.20-2_amd64.deb Checksums-Sha1: d99fa10b3f137f6f409988e976a7acbadce46afe 1242 bcftools_1.20-2.dsc 83660f94b62f5cfee7e3389042271414f195b5d5 2172760 bcftools-dbgsym_1.20-2_amd64.deb fd9e3fbb7d5df268c7b52a8deb3f42b3709fd219 767412 bcftools_1.20-2_amd64.deb Checksums-Sha256: f120db3675c35efa78799c8d651d70f2b7f3c755e26344f15b446de68d7b6168 1242 bcftools_1.20-2.dsc a2e35bbb30e9d180f8c3334f4b67d2d0b7b7b4480366228dae92a32108df326d 2172760 bcftools-dbgsym_1.20-2_amd64.deb 6cc650d6e0bb966dabcc59424747bcd954f1ba5bf977ee1bfce37051d2cf98f7 767412 bcftools_1.20-2_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Sat, 14 Sep 2024 22:45:13 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: autoconf (= 2.72-3), automake (= 1:1.16.5-1.3), autopoint (= 0.22.5-2), autotools-dev (= 20220109.1), base-files (= 13.5), base-passwd (= 3.6.4), bash (= 5.2.32-1+b1), binutils (= 2.43.1-4), binutils-common (= 2.43.1-4), binutils-x86-64-linux-gnu (= 2.43.1-4), bsdextrautils (= 2.40.2-8), bsdutils (= 1:2.40.2-8), build-essential (= 12.10), bzip2 (= 1.0.8-6), coreutils (= 9.4-3.1), cpp (= 4:14.1.0-2), cpp-13 (= 13.3.0-6), cpp-13-x86-64-linux-gnu (= 13.3.0-6), cpp-14 (= 14.2.0-4), cpp-14-x86-64-linux-gnu (= 14.2.0-4), cpp-x86-64-linux-gnu (= 4:14.1.0-2), dash (= 0.5.12-9), debconf (= 1.5.87), debhelper (= 13.20), debianutils (= 5.20), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.14.0-1), diffutils (= 1:3.10-1), dpkg (= 1.22.11), dpkg-dev (= 1.22.11), dwz (= 0.15-1+b1), file (= 1:5.45-3), findutils (= 4.10.0-3), g++ (= 4:14.1.0-2), g++-14 (= 14.2.0-4), g++-14-x86-64-linux-gnu (= 14.2.0-4), g++-x86-64-linux-gnu (= 4:14.1.0-2), gcc (= 4:14.1.0-2), gcc-13 (= 13.3.0-6), gcc-13-base (= 13.3.0-6), gcc-13-x86-64-linux-gnu (= 13.3.0-6), gcc-14 (= 14.2.0-4), gcc-14-base (= 14.2.0-4), gcc-14-x86-64-linux-gnu (= 14.2.0-4), gcc-x86-64-linux-gnu (= 4:14.1.0-2), gettext (= 0.22.5-2), gettext-base (= 0.22.5-2), grep (= 3.11-4), groff-base (= 1.23.0-5), 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 (= 14.2.0-4), libatomic1 (= 14.2.0-4), libattr1 (= 1:2.5.2-1), libaudit-common (= 1:4.0.1-1), libaudit1 (= 1:4.0.1-1), libbinutils (= 2.43.1-4), libblkid1 (= 2.40.2-8), libbrotli-dev (= 1.1.0-2+b4), libbrotli1 (= 1.1.0-2+b4), libbz2-1.0 (= 1.0.8-6), libbz2-dev (= 1.0.8-6), libc-bin (= 2.40-2), libc-dev-bin (= 2.40-2), libc6 (= 2.40-2), libc6-dev (= 2.40-2), libcap-ng0 (= 0.8.5-2), libcap2 (= 1:2.66-5), libcc1-0 (= 14.2.0-4), libcom-err2 (= 1.47.1-1), libcrypt-dev (= 1:4.4.36-5), libcrypt1 (= 1:4.4.36-5), libctf-nobfd0 (= 2.43.1-4), libctf0 (= 2.43.1-4), libcurl3t64-gnutls (= 8.10.0-2), libcurl4-gnutls-dev (= 8.10.0-2), libdb5.3t64 (= 5.3.28+dfsg2-7), libdebconfclient0 (= 0.272), libdebhelper-perl (= 13.20), libdeflate-dev (= 1.21-1), libdeflate0 (= 1.21-1), libdpkg-perl (= 1.22.11), libelf1t64 (= 0.191-2), libevent-2.1-7t64 (= 2.1.12-stable-10), libffi8 (= 3.4.6-1), libfile-stripnondeterminism-perl (= 1.14.0-1), libgcc-13-dev (= 13.3.0-6), libgcc-14-dev (= 14.2.0-4), libgcc-s1 (= 14.2.0-4), libgdbm-compat4t64 (= 1.24-2), libgdbm6t64 (= 1.24-2), libgmp-dev (= 2:6.3.0+dfsg-2+b1), libgmp10 (= 2:6.3.0+dfsg-2+b1), libgmpxx4ldbl (= 2:6.3.0+dfsg-2+b1), libgnutls-dane0t64 (= 3.8.6-2), libgnutls-openssl27t64 (= 3.8.6-2), libgnutls28-dev (= 3.8.6-2), libgnutls30t64 (= 3.8.6-2), libgomp1 (= 14.2.0-4), libgprofng0 (= 2.43.1-4), libgsl-dev (= 2.8+dfsg-3), libgsl28 (= 2.8+dfsg-3), libgslcblas0 (= 2.8+dfsg-3), libgssapi-krb5-2 (= 1.21.3-3), libhogweed6t64 (= 3.10-1), libhts-dev (= 1.20+ds-1), libhts3t64 (= 1.20+ds-1), libhtscodecs2 (= 1.6.1-1), libhwasan0 (= 14.2.0-4), libicu72 (= 72.1-5), libidn2-0 (= 2.3.7-2), libidn2-dev (= 2.3.7-2), libio-pty-perl (= 1:1.20-1+b2), libisl23 (= 0.27-1), libitm1 (= 14.2.0-4), libjansson4 (= 2.14-2+b2), libk5crypto3 (= 1.21.3-3), libkeyutils1 (= 1.6.3-3), libkrb5-3 (= 1.21.3-3), libkrb5support0 (= 1.21.3-3), libldap-2.5-0 (= 2.5.18+dfsg-3+b1), liblsan0 (= 14.2.0-4), liblzma-dev (= 5.6.2-2), liblzma5 (= 5.6.2-2), libmagic-mgc (= 1:5.45-3), libmagic1t64 (= 1:5.45-3), libmd0 (= 1.1.0-2), libmount1 (= 2.40.2-8), libmpc3 (= 1.3.1-1+b2), libmpfr6 (= 4.2.1-1+b1), libnettle8t64 (= 3.10-1), libnghttp2-14 (= 1.63.0-1), libnghttp2-dev (= 1.63.0-1), libnghttp3-9 (= 1.4.0-1), libnghttp3-dev (= 1.4.0-1), libngtcp2-16 (= 1.6.0-1), libngtcp2-crypto-gnutls-dev (= 1.6.0-1), libngtcp2-crypto-gnutls8 (= 1.6.0-1), libngtcp2-dev (= 1.6.0-1), libp11-kit-dev (= 0.25.5-2), libp11-kit0 (= 0.25.5-2), 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 (= 5.40.0-5), libpipeline1 (= 1.5.8-1), libpkgconf3 (= 1.8.1-3), libpsl-dev (= 0.21.2-1.1), libpsl5t64 (= 0.21.2-1.1), libquadmath0 (= 14.2.0-4), librtmp-dev (= 2.4+20151223.gitfa8646d.1-2+b4), librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b4), libsasl2-2 (= 2.1.28+dfsg1-8), libsasl2-modules-db (= 2.1.28+dfsg1-8), libseccomp2 (= 2.5.5-1+b1), libselinux1 (= 3.7-3), libsframe1 (= 2.43.1-4), libsmartcols1 (= 2.40.2-8), libssh2-1-dev (= 1.11.0-7), libssh2-1t64 (= 1.11.0-7), libssl-dev (= 3.3.2-1), libssl3t64 (= 3.3.2-1), libstdc++-14-dev (= 14.2.0-4), libstdc++6 (= 14.2.0-4), libsystemd0 (= 256.6-1), libtasn1-6 (= 4.19.0-3+b2), libtasn1-6-dev (= 4.19.0-3+b2), libtinfo6 (= 6.5-2), libtool (= 2.4.7-7), libtsan2 (= 14.2.0-4), libubsan1 (= 14.2.0-4), libuchardet0 (= 0.0.8-1+b1), libudev1 (= 256.6-1), libunbound8 (= 1.20.0-1+b1), libunistring5 (= 1.2-1), libuuid1 (= 2.40.2-8), libxml2 (= 2.12.7+dfsg-3+b1), libzstd-dev (= 1.5.6+dfsg-1), libzstd1 (= 1.5.6+dfsg-1), linux-libc-dev (= 6.10.9-1), m4 (= 1.4.19-4), make (= 4.3-4.1), man-db (= 2.13.0-1), mawk (= 1.3.4.20240905-1), ncurses-base (= 6.5-2), ncurses-bin (= 6.5-2), nettle-dev (= 3.10-1), openssl-provider-legacy (= 3.3.2-1), patch (= 2.7.6-7), perl (= 5.40.0-5), perl-base (= 5.40.0-5), perl-modules-5.40 (= 5.40.0-5), pkgconf (= 1.8.1-3), pkgconf-bin (= 1.8.1-3), 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2024-06-24 23:34 ./usr/lib/debug/.dwz/x86_64-linux-gnu/bcftools.debug drwxr-xr-x root/root 0 2024-06-24 23:34 ./usr/share/ drwxr-xr-x root/root 0 2024-06-24 23:34 ./usr/share/doc/ 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 767412 bytes: control archive=2256 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: 2664 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 1213648 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 2024-06-24 23:34 ./usr/lib/x86_64-linux-gnu/bcftools/GTisec.so -rw-r--r-- root/root 14776 2024-06-24 23:34 ./usr/lib/x86_64-linux-gnu/bcftools/GTsubset.so -rw-r--r-- root/root 72648 2024-06-24 23:34 ./usr/lib/x86_64-linux-gnu/bcftools/ad-bias.so -rw-r--r-- root/root 18696 2024-06-24 23:34 ./usr/lib/x86_64-linux-gnu/bcftools/add-variantkey.so -rw-r--r-- root/root 23128 2024-06-24 23:34 ./usr/lib/x86_64-linux-gnu/bcftools/af-dist.so -rw-r--r-- root/root 14592 2024-06-24 23:34 ./usr/lib/x86_64-linux-gnu/bcftools/allele-length.so -rw-r--r-- root/root 18840 2024-06-24 23:34 ./usr/lib/x86_64-linux-gnu/bcftools/check-ploidy.so -rw-r--r-- root/root 23192 2024-06-24 23:34 ./usr/lib/x86_64-linux-gnu/bcftools/check-sparsity.so -rw-r--r-- root/root 35416 2024-06-24 23:34 ./usr/lib/x86_64-linux-gnu/bcftools/color-chrs.so -rw-r--r-- root/root 31928 2024-06-24 23:34 ./usr/lib/x86_64-linux-gnu/bcftools/contrast.so -rw-r--r-- root/root 14584 2024-06-24 23:34 ./usr/lib/x86_64-linux-gnu/bcftools/counts.so -rw-r--r-- root/root 27064 2024-06-24 23:34 ./usr/lib/x86_64-linux-gnu/bcftools/dosage.so -rw-r--r-- root/root 14616 2024-06-24 23:34 ./usr/lib/x86_64-linux-gnu/bcftools/fill-AN-AC.so -rw-r--r-- root/root 117656 2024-06-24 23:34 ./usr/lib/x86_64-linux-gnu/bcftools/fill-from-fasta.so -rw-r--r-- root/root 51960 2024-06-24 23:34 ./usr/lib/x86_64-linux-gnu/bcftools/fill-tags.so -rw-r--r-- root/root 43736 2024-06-24 23:34 ./usr/lib/x86_64-linux-gnu/bcftools/fixploidy.so -rw-r--r-- root/root 31560 2024-06-24 23:34 ./usr/lib/x86_64-linux-gnu/bcftools/fixref.so -rw-r--r-- root/root 14744 2024-06-24 23:34 ./usr/lib/x86_64-linux-gnu/bcftools/frameshifts.so -rw-r--r-- root/root 31640 2024-06-24 23:34 ./usr/lib/x86_64-linux-gnu/bcftools/guess-ploidy.so -rw-r--r-- root/root 23416 2024-06-24 23:34 ./usr/lib/x86_64-linux-gnu/bcftools/gvcfz.so -rw-r--r-- root/root 14624 2024-06-24 23:34 ./usr/lib/x86_64-linux-gnu/bcftools/impute-info.so -rw-r--r-- root/root 31672 2024-06-24 23:34 ./usr/lib/x86_64-linux-gnu/bcftools/indel-stats.so -rw-r--r-- root/root 23288 2024-06-24 23:34 ./usr/lib/x86_64-linux-gnu/bcftools/isecGT.so -rw-r--r-- root/root 40224 2024-06-24 23:34 ./usr/lib/x86_64-linux-gnu/bcftools/mendelian2.so -rw-r--r-- root/root 14776 2024-06-24 23:34 ./usr/lib/x86_64-linux-gnu/bcftools/missing2ref.so -rw-r--r-- root/root 23288 2024-06-24 23:34 ./usr/lib/x86_64-linux-gnu/bcftools/parental-origin.so -rw-r--r-- root/root 31896 2024-06-24 23:34 ./usr/lib/x86_64-linux-gnu/bcftools/prune.so -rw-r--r-- root/root 23384 2024-06-24 23:34 ./usr/lib/x86_64-linux-gnu/bcftools/remove-overlaps.so -rw-r--r-- root/root 31992 2024-06-24 23:34 ./usr/lib/x86_64-linux-gnu/bcftools/scatter.so -rw-r--r-- root/root 31384 2024-06-24 23:34 ./usr/lib/x86_64-linux-gnu/bcftools/setGT.so -rw-r--r-- root/root 31448 2024-06-24 23:34 ./usr/lib/x86_64-linux-gnu/bcftools/smpl-stats.so -rw-r--r-- root/root 65240 2024-06-24 23:34 ./usr/lib/x86_64-linux-gnu/bcftools/split-vep.so -rw-r--r-- root/root 40088 2024-06-24 23:34 ./usr/lib/x86_64-linux-gnu/bcftools/split.so -rw-r--r-- root/root 31400 2024-06-24 23:34 ./usr/lib/x86_64-linux-gnu/bcftools/tag2tag.so -rw-r--r-- root/root 57048 2024-06-24 23:34 ./usr/lib/x86_64-linux-gnu/bcftools/trio-dnm2.so -rw-r--r-- root/root 35736 2024-06-24 23:34 ./usr/lib/x86_64-linux-gnu/bcftools/trio-stats.so -rw-r--r-- root/root 23000 2024-06-24 23:34 ./usr/lib/x86_64-linux-gnu/bcftools/trio-switch-rate.so -rw-r--r-- root/root 27608 2024-06-24 23:34 ./usr/lib/x86_64-linux-gnu/bcftools/variant-distance.so -rw-r--r-- root/root 18744 2024-06-24 23:34 ./usr/lib/x86_64-linux-gnu/bcftools/variantkey-hex.so drwxr-xr-x root/root 0 2024-06-24 23:34 ./usr/share/ drwxr-xr-x root/root 0 2024-06-24 23:34 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-06-24 23:34 ./usr/share/doc/bcftools/ -rw-r--r-- root/root 2192 2024-04-15 14:10 ./usr/share/doc/bcftools/README -rw-r--r-- root/root 1693 2024-06-24 23:34 ./usr/share/doc/bcftools/changelog.Debian.gz -rw-r--r-- root/root 2613 2024-06-21 00:16 ./usr/share/doc/bcftools/copyright drwxr-xr-x root/root 0 2024-06-24 23:34 ./usr/share/lintian/ drwxr-xr-x root/root 0 2024-06-24 23:34 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 119 2024-06-21 00:16 ./usr/share/lintian/overrides/bcftools drwxr-xr-x root/root 0 2024-06-24 23:34 ./usr/share/man/ drwxr-xr-x root/root 0 2024-06-24 23:34 ./usr/share/man/man1/ -rw-r--r-- root/root 49174 2024-06-24 23:34 ./usr/share/man/man1/bcftools.1.gz -rw-r--r-- root/root 253 2024-06-24 23:34 ./usr/share/man/man1/color-chrs.pl.1.gz -rw-r--r-- root/root 271 2024-06-24 23:34 ./usr/share/man/man1/plot-vcfstats.1.gz -rw-r--r-- root/root 208 2024-06-24 23:34 ./usr/share/man/man1/vcfutils.pl.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 47920 Build-Time: 140 Distribution: perl-5.40-throwaway Host Architecture: amd64 Install-Time: 12 Job: /srv/debomatic/incoming/bcftools_1.20-2.dsc Machine Architecture: amd64 Package: bcftools Package-Time: 164 Source-Version: 1.20-2 Space: 47920 Status: successful Version: 1.20-2 -------------------------------------------------------------------------------- Finished at 2024-09-14T22:45:14Z Build needed 00:02:44, 47920k disk space